Table Of Content

Author index Abe,Y . 743 Carr,F.J. 1501 Eaton,S.F. 1137 Gudkov,A.T. 1373 Abelson,J. 997 Carriére,F. 563 Edelmann,E. 663 Guild,B.C. 1261 Aimoto,S. 461 Chaga,G. 1115 Egmond,M.R. 559, 793 Gustchina,A. 309 Alberghina,L. 531 Chakrabarti,P. 471 Eijsink,V.G.H. 425 Alkorta,I. 1221, 1231 Chang,W. 1311 Elliot,G.S. 1395 Haas,M.J. 551 Almo,S.C. 405 Chap,R. 431 elMasry,N.F. 777 Hadwiger,M.A. 1283 Alting,A.C. 991 Chapman,D. 255 Eltis,L.D. 1145 Hagen,W.R. 801 Altschuh,D. 769 Chartier,M. 1495 Endicott,J.A. 243 Hakala,J.M.L. 1069 Andersson,L. 1115 Chatterjee,P. 145 Engel,P.C. 1013 Hales,C.N. 137 Andrews,J. 783 Chelvanayagam,G. 173 Engelborghs,Y. 125 Hamers,R. 1129 Andrews,L.C. 359 Chemeris,V.V. 1041 Eppink,M.H.M. 801 Handford,P.A. 1121 Antheunisse,W.P. 793 Chen,H.-C. 445 Erickson,J.W. 831 Hansen,S. 571 Anthonsen,T. 589 Chen,P.-Y. 941 Eshhar,Z. 431 Hansen,T.V. 589 Aqvist,J. 385 Chiche,L. 689, 1333 Exterkate,F.A. 991 Hardy,F. 425 Argos,P. 173, 185, 613 Chickos,J.S. 149 Haris,P.I. 255 Arnold,J.R.P. 783 Cho,Y. 263 Fedorov,A.N. 1041 Harris,G.W. 1267 Aszédi,A. 633 Chou,K.-C. 65, 319 Feeney,J. 783 Harris,L.J. 815 Atarhouch,T. 1129 Christensen,U. 911 Feige,U. 663 Harris,W.J. 1501 Attwood,T.K. 195, 841 Christianson,K. 509 Feng,S.-L. 1017 Harrison,R.W. 359, 1353 Austen,D.E.G. 1121 Ciardelli,T.L. 1137 Fersht,A.R. 103, 777, Harvey,T.S. 109 Clark,D.A. 1295 1089 Hassan,M. 1485 Cleasby,A. 559 Ferszt,A. 1395 Hatrick,K. 34] Bacon,D. 953 Bajorath,J. 815 Cohen,F.E. 1411 Fidelis,K. 953 Hearst,D.P. 1411 Cohen,M.A. 1323 Fiers,;W. 5 Heinz,D.W. 301 Baker,K.C. 1267 Collura,V.P. 221 Filpula,D. 1017 Hejtmancik,J.F. 445 Baker Libby,C. 1109 Colson,C. 523 Findlay,J.B.C. 195 Hempel,J.C. 1485 Bamborough,P. 1077 Connerton,I.F. 1267 Finkelstein,A.V. 1041 Henderson,I.M.J. 1267 Barbosa,J.A.R.G. 1129 Cooperman,B.S. 823 Fischer,D. 39 Henrissat,B. 1281 Barclay,A.N. 515 Cornett,C.A.G. 1109 Flores,T.P. 31 Hirai,T. 733 Bartels,H. 1035 Coutinho,P.M. 393, 749, Flory,N. 1005 Hodges,R.S. 1365 Basran,J. 783 1005, 1281 Flower,D.R. 1305 Hofmann,O.M. 281 Batt,C.A. 263 Cregut,D. 689, 1333 Fogh,R. 1449 Holm,C. 537 Baty,D. 1495 Crouch,R.J. 1103 Ford,C. 1005, 1109 Holm,L. 1449 Bayley,H. 91, 655 Crowther,N.J. 137 Forster,S.J. 1501 Honda,N. 1239 Bazer,F.W. 863 Cummings,N.J. 1267 Freedman,R.B. 1035 Hooykaas,P.J.J. 905 Beck,M.E. 841 Cunningham,A. 1379 French,D.C. 83 Hope,J.N. 445 Bedouelle,H. 271 Curto,E.V. 863 Frenken,L.G.J. 559 Hori,K. 1387 Belfrage,P. 537 Friedman,T. 985 Horimoto,K. 1433 Benhar,I. 1509 Dale,G.E. 925, 933 Frigerio,F. 425 Horwitz,A.H. 805 Benner,S.A. 1323 Danielson,U.H. 1115 Frémmel,C. 627 Hough,E. 571 Better.M. 805 Danishefsky,A.T. 405 Fujita,I. 1239 Howland,K. 985 Birdsall,B. 783 D’Arcy,A. 933 Fusetti,F. 531 Hsiao,K.-c. 815 Birdsell,D.C. 705, 715 Dartois,V. 523 Huang,J.-L. 705 Bjorkstén,J. 487 Davasse,V. 681 Gago,F. 1455 Huang,M. 705, 715 Blaauw,M. 523 Davis,R.C. 437 Gaillard,J. 681 Hubbard,S.J. 613 Blattler,.W.A. 1261 De,A. 1053 Gallo,R.C. 145 Hughes,P.E. 1121 Blundell,T.L. 645 De Filippis,V. 1203 Georgiou,G. 131 Boel,E. 563 de Haas,G.H. 579 Geourjon,C. 157 fitid,A. 1255 Boelens,R. 761, 1449 de Prat Gay,G. 103 Gerritse,G. 523 Ikehara,M. 735 Bohm,G. 213, 1471 de Vlieg,J. 793 Gershoni,J.M. 145 Ikura,M. 109 Borchert,T.V. 945 de Vos,W.M. 991 Gerstein,M. 461 Tlyin,V.A. 1189 Bottomley,S.P. 1463 Declerck,N. 997 Gilkes,N.R. 117 Imoto,T. 743, 1249 Boulain,J.-C. 917 Dekeyzer,N. 125 Glumoff,T. 823 Inoue,M. 743 Bourne,P.E. 1311 Deléage,G. 157 Godowski,P.J. 895 Isakari,Y. 743 Bradley,J.C. 859 Brady,J.W. 263 Dembowski,N.J. 673 Goldmacher,V.S. 1261 Ishino,S. 733 Demleitner,G. 579 Goldman,A. 823 Iwagami,S.G. 1145 Branner,S. 793 Derewenda,U. 551 Gomi,H. 435 Izard,J. 1495 Breddam,K. 911 Brégégére,F. 271 Derewenda,Z.S. 551 Gonnet,G.H. 1323 Desplancq,D. 1027 Goodenough,P.W. 1267 Jackson,R.M. 371 Brennan,C. 509 Dijkstra,B.W. 523 Goraj,K. 945 Jaeger,K.-E. 523 Brinkmann,U. 697 Dodson,G.G. 137, 543 Gore,M.G. 1463 Jaenicke,R. 213, 1471 Brittain,T. 281 Doesburg,P. 991 Gorman,M. 1005 Jager,J. 605 Brocca,S. 531 Dolgikh,D.A. 1041 Gétz,F. 579 Jansonius,J.N. 605 Brocklehurst,K. 291 Donnelly,D. 645 Grandi,G. 425 Jarpe,M.A. 863 Broger,C. 933 Douthart,R.J. 705 Gray,P.M.D. 1501 Jerala,R. 977 Brown,M.H. 515 Drijfhout,M.C. 801 Greaney,P.J. 221 Jernigam,R.L. 1209 Brownlee,G.G. 1121 Du,P. 1221, 1231 Green,B.N. 285 Joerger,R. 551 Bruinenberg,P.G. 991 Dube,D.K. 83 Green,B.S. 431 Johnson,C.M. , 1089 Brzozowski,A.M. 543 Ducancel,F. 917 Green,R. 551 Johnson,H.M. Bulsink,Y.B.M. 579 Duché,D. 1495 Grewal,N. 205 Johnson,K.W. Dufton,M.J. 1423 Gross,K.-H. 613 Johnson,L.N. 243, 559 Cachau,R.E. 831 Duncan,D. 1077 Griitter.M.G. 663 Johnson,M.S. 475 Campbell,R.L. 1379 Dunn,B.M. 495 Gryaznova,O.I. 1373 Jones,S.T. 1267 Cardle,L. 1423 Dunn,J.P. 131 Gu,W. 263 Jergensen,P.N. 137 Author index Joss,U. 663 Mao,B. 319 Popplewell,A.G. 1463 Singh,J. 849 Jung,S.-H. 697 Marcovina,S.M. 723 Porath,J. 1115 Slingsby,C. 1395 Martial,J.A. 945 Porumb,T. 109 Slotboom,A.J. 579 Kadono,S. 99 Matouschek,A. 1089 Potekhin,S.A. 1097 Smith,D.L. 405 Kallen,J. 597 Matthews,B.W. 301 Presta,L.G. 895 Smith,J.C. 917 Kalsheker,N.A. 869 Matthews,J.M. 1089 Prevost,M. 309 Smith,M. 1145 Kamath,R.S. 1261 May,A.C.W. 475 Priestle,J.P. 663 Smythe,J.A. 145 Kanaoka,M. 435 Medina,C. 385 Protasova,N.Yu. 1373 Soares,C.M. 487 Kankare,J. 823 Medvedkin,V.N. 1097 Przybycien,T.M. 131 Soares,S. 805 Kantrowitz,E.R. 673 Ménez,A. 917 Ptitsyn,O.B. 593, 1041 Srai,K.S. 255 Kaptein,R. 761, 1449 Mezei,M. 331 Pu,C. 1311 Sri Widada,J. 689 Kashmiri,S.V.S. 1401 Miki,T. 743 Srinivasan,N. 869 Kashparov,I.A. 1097 Mikol,V. 597 Quignard,J.-F. 689 Stahl,S.J. 1103 Kasianowicz,J. 655 Milfeld,K. 1345 Quinkal,I. 681 Stennicke,H.R. 911 Katsube,Y. 453 Miller,C. 503 Stern,P.S. 953 Kaufman,J.D. 1103 Miller,R.C.,J r 117 Ramesh,B. 255 Sternberg,M.J.E. 149, 165, Kawano,K. 743 Misset,O. 523 Ramesh,V. 1053 371, 1295 Kay,C.M. 1365 Miyazaki,K. 99, 401 Ransac,S. 523 Stieger,M. 925 Kelly,D.C. 1501 Miyazawa,S. 1209 Rao,A.G. 1485 Stirk,H.J. 47 Kemp,G.J.L. 1501 Moriyama,H. 99, 453 Ravestein,P. 793 Stocklin,R. 285 Kerr,I.D. 255 Mortensen,U.H. 911 Reasoner,J.L. 705 Stouten,P.F.W. 23 Kidokoro,S.-I. 969 Moss,D.S. 31 Reilly,P.J. 393, 749, 1005, Stiiber,D. 933 Kikuchi,M. 735 Motoki,K. 1387 1109, 1281 Studnicka,G.M. 805 Kilburn,D.G. 117 Mould,R.M. 281 Reiter,Y. 697 Sugihara,A. 585 Kim,T.-R. 263 Moulis,J.-M. 681 Remington,S.J. 911 Sugimoto,Y . 1387 Kimura,H. 969 Moult,J. 953 Rety,S. 543 Sumner,I.G. 1267 King,D.J. 1027 Mountain,A. 1027 Richards,W.G. 859, 1077 Sun,T. 503 King,R.D. 1295 Munir,K.M. 83 Richelle,J. 309 Sundell,S. 571 Kireeva,M.L. 1373 Murphy,G. 1035 Ringe,D. 405 Sung,W.L. 1379 Kirpichnikov,M.P. 1041 Murphy,J.R. 985 Roberts,G.C.K. 783 Suominen,I. 1255 Kirsch,J.F. 413 Murzin,A.G. 1373 Robson,B. 221 Surowy,T. 509 Kishan,R. 945 Murzina,N.V. 1373 Rodenburg,K.W. 905 Sutton,B.J. 1463 Knegtel,R.M.A. 761 Muyldermans,S. 1129 Rollence,M.L. 1017 Suzuki,M. 461 Kolchanov,N.A. 349 Rose,D.R. 961 Svensson,B. 1479 Kolmakova-Partensky,L. 503 Nadell,R. 805 Rose,K. 285 Swenson,L. 551 Komeiji,Y. 1239 Nagao,T. 585 Roy,G. 173 Swimmer,C. 1261 Korn,A.P. 961 Nagaraja,V. 1053 Ruan,K.-H. 1345 Swindells,M.B. 1 Koschinsky,M.L. 723 Nakamura,H. 969 Russell,R.B. 1407 Kourinov,I.V. 359 Nakamura,M. 585 Riiterjans,H. 1449 Takasaki,Y . 1387 Krishna,N.R. 963 Nakatani,T. 435 Rypniewski,W.R. 57 Takenaka,H. 733 Krishnasastry,M. 655 Nardelli,B. 145 Talwar,G.P. 205 Kroone,R.C. 1395 Neal,G.S. 823 Sakurai,M. 99, 453 Tamura,T. 743, 1239 Kulmacz,R.J. 1345 Neuhaus,D. 461 Saldanha,J. 1129 Tanaka,N. 99, 453 Kuroda,Y. 969 Nilsson,O. 487 Salminen,T. 823 Tanaka,T. 969 Kusakabe,T. 1387 Nishikawa,K. 733 Salunke,D.M. 205 Tapia,O. 487 Lahti,R. 823 Noble,M.E.M. 559, 945 Samuelsson,J.-E. 385 Tavernier,J. 5 Lambert,J.M. 1261 Noguchi,H. 435 Sana,T.R. 1137 Tawfik,D.S. 431 Langen,H. 925, 933 Norel,R. 39 Sander,C. 23, 349, 1203, 1449 Taylor,M.A.J. 1267 Langin,D. 537 Norioka,N. 733 Sangrar,W. 723 Taylor,W.R. 341, 633 Lathrop,R.H. 1059 Nurse,P. 243 Sansom,C. 309 Tempest,P.R. 1501 Laue,T.M. 1137 Nussinov,R. 39 Sansom,M.S.P. 255 Tessier,D.C. 769 Laughton,C.A. 235 Saqi,M.A.S. 165 Thim,L. 563 Lawson,A.D.G. 1027 Offord,R.E. 285 Sarai,A. 1083 Thirstrup,K. 563 Lawson,D.M. 543 Ohshima,K. 1433 Sato,M. 453 Thomas,A. 917 Lee,B. 697 Onodera,K. 453 Sauder,U. 605 Thomas,J.A. 783 Lee,S.-P. 263 Onuffer,J.J. 413 Sawyer,J.R. 1401 Thornton,J.M. 31, 47 Lehar,S.M. 1261 Ortiz,A.R. 1455 Scarborough,P.E. 495 Thorpe,C.J. 869 Lessel,U. 1175 Oshima,T. 99, 401, 453 Scawen,M. 1463 Titball,R.W. 1501 Lesuisse,E. 523 QMsterlund,T. 537 Schanck,K. 523 Tjeenk,M.L. 579 Liautard,J.-P. 689, 1333 Otsuka,J. 1433 Scheeren-Groot,E. 905 Tominaga,Y. 585 Lim,C. 75 Ot,T.L. 863 Schlom,J. 1401 Tomme,P. 117 Lionne,C. 689 Overington,J.P. 645, 869 Schmitz,A. 663. Tomschy,A. 1471 Loeb,L.A. 83 Schnarr,M. 1449 Topham,C.M. 869 Lohner,K. 977 Parker,M.W. 1495 Schoenmakers,J.G.G. 1395 Tramontano,A. 531 Lokker,N.A. 895 Partali,V. 589 Schomburg,D. 1175 Travé,G. 689 Lone, Y.-C. 435 Pascarella,S. 185 Schénfeld,H.-J. 925 Trumble,W.R. 705, 715 Longhi,S. 531 Pastan,I. 697, 1509 Schotz,M.C. 537 Tsutsui,M. 1239 Lotti,M. 531 Pauptit,R.A. 605 Schwartz,J. 271 Turk,V. 977 Lubsen,N.H. 1395 Pedersen,J.T. 1261 Seidler,A. 1277 Luo,X. 1441 Peltonen,T. 1255 Serrano,L. 1455 Ueda,T. 743, 1249 Luthardt,G. 627 Perrakis,A. 57 Seto,Y. 733 Uversky,V.N. 1041, 1373 Peters,H. 793 Shimada,Y. 585 Maeda,Y. 1249 Pickersgill,R.W. 1267 Shimony,E. 503 Valax,P. 131 Mainfroid,V. 945 Pillet,L. 917 Shindyalov,I.N. 349, 1311 van Bemmel,C.J. 793 Mandecki,W. 509 Pisabarro,M.T. 1455 Shirazi,J. 1295 van Berkel,W.J.H. 801 Mannervik,B. 1115 Pizzi,E. 531 Sierks,M.R. 1479 van der Bolt,F.J.T. 801 Mantsala,P. 1255 Pontzer,C.H. 863 Siezen,R.J. 991 van der Vinne,B. 425 1520 van Oostrum,J. 663 Van Ostade,X. 5 vanderSpek,J.C. 985 Venema,G. 425 Venyaminov,S.Yu. 1097 Verger,R. 563 Verheij,H.M. 579 Verma,C. 543 Vernet,T. 769 Viguera,A.R. 1455 Vihinen,M. 1069, 1255 Viki¢é-Topi¢,S. 1103 Villar,H.O. 831 Volckaert,G. 125 Vorgias,C.E. 57 Vosbeck,K. 663 Vriend,G. 23, 425, 905, 1203 Waagen,V. 589 Wakarchuk,W.W. 1379 Walker,B. 91, 655 Walkinshaw,M.D. 597 Wan,T. 1463 Wang,C.-L. 705, 715 Wang,J. 75 Wang,K.-T. 941 Wang,X.-G. 1013 Wang,Y. 1083 Warren,A.J. 117 Warwicker,J. 1267 Watkins,S. 263 Watson,D.C. 1379 Webber,K.O. 697 Weber,I.T. 309, 1353 Wei,Y. 551 Weinstein,H. 1441 Wesson,C.A.R. 715 West,J.W. 705 White,P. 1501 Whitlow,M. 1017 Widersten,M. 1115 Wierenga,R.K. 945 Wijdenes,J. 435 Williams,R.E. 805 Williamson,E.D. 1501 Williamson,R.A. 1035 Wilson,K.S. 57 Wingfield,P.T. 1103 Winkler,U. 523 Wlodawer,A. 309 Wodak,S.Y. 309 Wolfson,H.J. 39 Wood,J.F. 1017 Wu,K.K. 1345 Wu,S.-H. 941 Wu,Z. 1137 Xiang,Y.-F. 75 Xiao,B. 137 Yaguchi,M. 1379 Yamada,H. 743, 1249 Yamaguchi,S. 551 Yamakawa,J. 435 Yamamoto,H. 1433 Yamato,I. 1239 Yanagi,K. 1433 Yao,T. 733 Yau,P. 109 Zeelen,J.Ph. 945 Zehfus,M.H. 335 Zerovnik,E. 977 Zhang,C.-T. 65, 319 Zhang,D. 1441 Zhou,N.E. 1365 Zimmerman,K. 1197 Zinn-Justin,S. 917 Subject index Active site Bacillus subtilis human tumour necrosis factor, lymphotoxin, structureactivity studies 5 3-isopropylmalate dehydrogenase chimera, three-dimensional structure lysozyme, fluctuation of for enzyme activity 743 453 mutagenesis of cathepsin D, substrate specificity 495 lipases, struct—f uunrctieon relationships 523 mutants, glucoamylase, specificity, sequence analysis 1479 thermostability of neutral protease, surface loops 425 papain, catalytic triads 75 Bacteriophages papain, mutagenesis of residues remote from active site, role of two- overproduction of Mu C protein by removal of secondary structure at domain interface 769 translation initiation region 1053 thiolate—imidazolium ion pair, recombinant caricain, effect of charged 8-Barrels residues 1267 automation of identification and analysis, graph theory, unsupervised Affinity chromatography algorithm 1305 immobilized metal ion, protein engineering of human glutathione-S- BC loop transferase M1-1 1115 poliovirus coat protein VP1, insertions, chimeras 47 introduction of N-terminal histidine tail, protein expression in Binding activity Escherichia coli 1277 antibody, pH on—off dependency, chemical modification by Aggregation tetranitromethane 431 Escherichia coli colicin A mutants, inclusion body 1495 Binding affinity multivalent Fvs, characterization of single chain Fv oligomers 1017 interaction of polyproline-based peptides with Abl-SH3, DOCK 1455 soluble anti-tumor sFv, periplasmic localization, induction conditions for protein—DNA interaction, assessment of mutational effect 1083 production of in Escherichia coli 1401 Binding constants Agrobacterium free energy, endothiapepsin inhibitor binding 385 VirG structure modelling, signal transduction 905 Binding domain AIDS cellulose and chitin, xylanase—endoglucanase fusion protein 117 drugs, HIV-1 protease—inhibitor interaction 309 ricin B chain, mutational and structural analysis of lectin activity 1261 Aldolase Binding protein human, A and B chimeras 1387 calcium, Nereis diversicolor, chloramphenicol acetyltransferase fusion Algorithm protein 125 computer, protein function prediction, sequence motifs 165 Binding site genetic, least-squares minimization, protein structure comparisons 475 receptor binding site of interleukin-18, mutational mapping 663 protein topology cartoons, motifs 31 ‘Bio’ Champollion Alignment dynamic programming regularization of secondary structure prediction divergence, evolutionary conservation of trypsin 57 1197 Alkaline phosphatase Biosynthesis modulation enzyme activity of alkaline phosphatase—epitope hybrid 509 of artificial proteins in vitro, novel approach to protein design 1041 monodomain IgG Fc binding —alkaline phosphatase fusion protein, enzymatic activity 715 Calcitonin Amino acid composition gene-related peptide, molecular modelling of the protein structure 1069 globular proteins, protein folding classes 319 Calcium starch binding and catalytic domains of glucoamylase, structure —function binding properties, calmodulin target peptide hybrid, NMR 109 relationships 393 binding protein, Nereis diversicolor, cloning, expression and purification a-Amylase 125 Bacillus stearothermophilus, C-terminal protein truncation, substrate Calcium binding site recognition 1255 site-directed mutagenesis modifies properties of annexin I 689 Annexin I Calmodulin homology modelling, three-dimensional profile, solvation 1333 molecular similarity, connected graph 331 Antibodies target peptide hybrid, calcium binding properties 109 humanization, binding activity of mAbs, non-CDR complementarity Calorimetry modulating residues 805 cooperative deformation, 8-a-barrel, thermal transition, molten globule humanization of anti-IL-2R, CDR graft 435 969 humanization of mAb 60.3, L2 loop, CD18, antib—oa ndtiyge n protein folding of barnase and urea concentration 1089 interaction 815 Camelids multimerization of single chain Fv variants 1027 immunoglobulin V,, structure, molecular modelling 1129 reshaping human monoclonal antibody, CDR, toxins, peptides 1501 Cancer therapy single domain, camelid immunoglobulin Vj, structure, molecular B1 and BS Fv fragments, Pseudomonas exotoxin 1509 modelling 1129 Candida rugosa Antibody engineering variability of isozymes, substrate specificity 531 characterization of single chain Fv oligomers, linker design 1017 Carboxypeptidase chemical modification, pH on—off dependency of antibody binding three-dimensional structure, functional environs, contour maps 1423 activity 431 Carboxypeptidase Y Antigen binding introduction of acidic residues, protein stability, substrate specificity, pH bifunctional hybrids of MalE and Ig variable domains 271 dependence 911 Apolipoprotein (a) Caricain expression and characterization of kringle IV types 1, 2 and 10 723 recombinant, effect of charged residues, active site thiolate —imidazolium Arabinose binding protein ion pair 1267 novel substrate specificity, protein engineering, fluorescence titration 997 Catalytic activity Aspergillus awamori site-directed mutagenesis of glutamate dehydrogenase, reactive cysteine, amino acid deletions in glucoamylase, secretion, O-glycosylation 1109 DTNB 1013 glucoamylase thermosensitive mutants, structural characterization 1005 Catalytic mechanism phospholipase C in Bacillus cereus, distance geometry calculations 571 Bacillus cereus Catalytic triads phospholipase C catalytic mechanism, distance geometry calculations 571 papain active site 75 Bacillus circulans Cathepsin D site-directed mutagenesis of xylanase, thermostability 1379 substrate specificity, mutagenesis of active site, aspartic proteinase 495 1523 Subject index Cavities Database intramolecular cavities in globular proteins, packing 613 protein mutant, construction of 733 CD4 Deletions HIV gp120 binding domains, molecular decoys, gene therapy 145 Aspergillus awamori glucoamylase, O-glycosylation, secretion, Cell cycle thermostability 1109 cde2/CDC28, p34 protein kinase, molecular modelling 243 Denatured state Chaperonins protein stability, single substitution mutants, inter-residue contact GroES and GroEL, overproduction, increased solubility of dihydrofolate energies, hydrophobic energy 1209 reductase 925 Dihydrofolate reductase Chemical labelling Escherichia coli, circularly permuted, tertiary protein structure 1373 cysteine engineering of charybdotoxin 503 Halobacterium volcanii, homology modelling, structure prediction 213 Chemical modification improving solubility by mutagenesis, inclusion bodies 933 Staphylococcus hyicus lipases 579 increased solubility by overproduction of GroES and GroEL 925 tetranitromethane, nitrotyrosine residues, antibody binding activity 431 Dimerization Chemical synthesis B-crystallin assembly, role of sequence extensions 1395 y-echistatin analogues, platelet aggregation 941 Diphtheria toxin Chimeras transmembrane domain, amphipathic helix, hydrophobic face, fusion Bacillus subtilis and Thermus thermophilus 3-isopropylmalate toxin 985 dehydrogenase 453 Distance geometry calculations human aldolase A and B chimeras 1387 Bacillus cereus phospholipase C, DGEOM, GRID 571 poliovirus coat protein VP1 BC loop, foreign epitopes 47 secondary structure formation in model polypeptide chains 633 Chimeric proteins Disulphide bonds enzyme activity, alkaline phosphatase —epitope hybrid 509 cross-linking, rapid crystallization of T4 lysozyme 301 immunoglobulin and scavenger receptor superfamily domains with B-lactoglobulin thermostable variants 263 domains 3 and 4 of CD4 515 protein engineering interchain disulphide bonds, disulphide-stabilized Fv xyla—e nndoagluscanease , cellulose and chitin binding domain 117 fragments 697 Choriogonadotropin DNA flexibility hormone -—receptor recognition, computer modelling 205 protein-DNA docking, Monte Carlo simulation 761 Co-enzymes Docking specificity, 3-isopropylmalate dehydrogenase 401 protein—DNA, Monte Carlo simulation 761 Coiled-coil Domains molecular recognition, assembly of receptor ectodomains, interleukin-2, discontinuous, method for location, compactness 335 leucine zipper 1137 insertion, protein folding 1407 mutation in leucine zipper of GCN4 1097 Drosophila protein stability, interhelical ion pairs, leucine zipper 1365 K10 repeat, solution structure, NMR 461 Complementarity determining region Dynamic programming reshaping human monoclonal antibody, toxins, peptides 1501 regularization, ‘Bio’ Champollion secondary structure prediction 1197 Computer modelling humanization of anti-IL-2R, CDR graft 435 LH/CG receptor, hormone—receptor recognition 205 +-Echistatin Conformation solid-phase peptide synthesis of analogues, platelet aggregation 941 amphipathic, conservation, secondary structure prediction, protein Ectothiorhodospira halophila structural alignments 185 hyperexpression of gene encoding HiPIP, fusion protein 1145 ligand binding, protein torsion angle changes 961 Electrostatic interactions polypeptide backbone, constructing segments of protein structure 953 active site thiolate-—-imidazolium ion pair, recombinant caricain 1267 proteinase inhibitor TIMP, structural analysis, intrinsic fluorescence 1035 Electrostatic properties Conformational change engineering of surface charges in a subtilisin, electrophoresis, ion- Escherichia coli aspartate aminotransferase mutant with increased exchange 793 enzymic activity 605 interhelical ion pairs, protein stability, leucine zipper 1365 negative co-operativity of aspartate aminotransferase, site-directed Ellipsoid analysis mutagenesis 413 amino acid composition of globular proteins 319 Conservation Entropy proline residues, Clostridium pasteurianum 2[4Fe—4S] 681 conformation, fusion entropy of protein side chains 149 sequence, Ser/Thr and Tyr protein kinase family 849 Enzyme activity Cooperativity lysozyme, mutagenesis, active site 743 cooperative deformation de novo designed protein, B-c-barrel, thermal modulation, alkaline phosphatase —epitope hybrid 509 transition 969 papain, mutagenesis of residues remote from active site, role of two- Crystal structure domain interface 769 aspartate aminotransferase, wild type and mutant 405 Enzyme kinetics fungal lipases, implications for structure—function relationships 551 pH-dependent, overlapping ionizations, review 291 Humicola lanuginosa lipases, substrate binding models using X-ray Epitope mapping crystallography 543 protein engineering of snake toxin, antibody —antigen binding 917 molecular mechanics of HIV-1 protease—inhibitor interaction 309 Epitopes TIM barrel-barrel enzyme hybrid, modular mutagenesis 945 analysis, insulin, proinsulin 137 8-Crystallin Escherichia coli assembly, role of sequence extensions, dimerization 1395 aspartate aminotransferase, negative co-operativity 413 Crystallins aspartate aminotransferase, wild type and mutant substrate specificity, role of N-terminal arm in 8A3/A1-crystallin association 445 crystal structure 405 Crystallization aspartate aminotransferase mutant, three-dimensional structure 605 rapid, T4 lysozyme, disulphide cross-linking 301 induction conditions for production of soluble anti-tumour sFv, Cysteine proteinase periplasmic localization 1401 effect of electrostatic interactions, active site thiolate—imidazolium ion pyrophosphatase structure comparison, X-ray crystallography, sequence pair 1267 motif 823 Cytochrome c pyrophosphatase structure comparison, X-ray crystallography, sequence three-dimensional structure, functional environs, contour maps 1423 motif 1173 Cytokines regulatory chain of aspartate transcarbamoylase, alanine scanning interleukin-13, predictive modelling, structure prediction 1077 mutagenesis 673 1524 Subject ind< Evolution Haemoglobin divergence, evolutionary conservation of trypsin 57 recombinant, incorporation of sulphaem 281 homologous protein sequences, amino acid substitution, Dayhoff matrices Halophilic adaptation 1323 Halobacterium volcanii dihydrofolate reductase, homology modelling 213 Helix cap stability, mutagenesis of N-capping box 777 Factor IX Helix — loop — helix human, protein engineering of hydrophobic domain, clotting factors 1121 sequence motifs, Epstein—Barr virus 1433 Fe binding domain Helix —turn— helix gene synthesis and functional expression of recombinant monodomain LexA, PrfA and Fur, DNA recognition 1449 IgG Fc binding protein 705 Helix dipole monodomain IgG Fc binding —alkaline phosphatase fusion protein 715 effect of on protein structure, helix packing, ion binding 471 Ferredoxin Helix packing conservation of proline residues, Clostridium pasteurianum 2[4Fe—4S}, transmembrane helices, bacteriorhodopsin, structure prediction 1221 electron transfer 681 Hepatocyte growth factor hyperexpression of gene encoding HiPIP, fusion protein 1145 HGF/NK1 region, structure—function relationships 895 Fingerprinting Herpes simplex virus type-1 G protein-coupled receptors, sequence alignment 195 thymidine kinase, random mutagenesis 83 Fluorescence titration HIV novel substrate specificity of arabinose binding protein 997 construction of active RNase H domain of reverse transcriptase, hybrid Footprinting proteins 1103 Drosophila K10 repeat DNA —protein interactions 461 HIV-1 IIB gpi20 V3 loop, enzyme activity of alkaline Fourier transform phosphataseepitope hybrid 509 fast, Fourier—Green function, effects of solvation 359 molecular mechanics of HIV-1 prote—i anhsibieto r interaction, crystal Fungi structure 309 lipases, protein crystallography and implications for structure —function protease, molecular dynamics simulation, peptide substrate 1353 relationships 551 protease cleavage sites, 2—4—6 subsite coupled effect 65 Fusion protein Homology bifunctional hybrids of MalE and Ig variable domains, antigen binding families of proteins with similar total structure 1283 271 Homology modelling hyperexpression of gene encoding HiPIP 1145 cysteine proteinase inhibitor, structural thermodynamics 977 monodomain IgG Fe binding —alkaline phosphatase 715 dihydrofolate reductase, structure prediction 213 Nereis diversicolor calcium binding protein and chloramphenicol novel procedure for structure refinement, human class Mu glutathione-S- acetyltransferase 125 transferase 831 xyla—e nndoagluscanease , engineered bifunctional enzyme 117 structural conservation of protein structure 173 v fragments structure —function properties of a-hordothionin, crambin, high lysine cloning of B1 and B5 Fv fragments, immunotoxins, cancer therapy 1509 analogues 1485 interchain disulphide bonds, recombinant immunotoxins containing structure prediction, simulated annealing, side chain conformation 235 disulphide-stabilized Fv fragments 697 a-Hordothionin multimerization of single chain Fv variants 1027 homology modelling with crambin, structure —function properties, high multivalent Fvs, characterization of single chain Fv oligomers 1017 lysine analogues 1485 Human rhodopsin G-proteins structure prediction, seven-helix membrane proteins, bacteriorhodopsin fingerprinting G protein-coupled receptors, sequence alignment 195 1221 Gene therapy Humanization CD4, HIV gp120 binding domains, molecular decoys 145 binding activity of mAbs, non-CDR complementarity modulating Geotrichum candidum residues 805 positional and fatty acid specificity of lipases 585 mAb 60.3, L2 loop, CD18 815 Globular proteins Humicola lanuginosa intramolecular cavities, packing 613 lipases, substrate binding models using X-ray crystallography 543 local polarity analysis, determination of incorrect folding 627 Hydrophobic core Glucoamylase fungal microbial RNase, non-polar nuclei, protein stability 1189 amino acid deletions, Aspergillus awamori, O-glycosylation, Hydrophobic effect thermostability 1109 solute—solvent interaction, surface tension 371 reading-frame shift in Saccharomyces glucoamylase improves sequence alignment with other glucoamyl 1281 specificity, sequence analysis 1479 IgG starch binding and catalytic domains, structure—function relationships gene synthesis and functional expression of recombinant monodomain 393 IgG Fe binding protein 705 structural similarities, hydrophobic cluster analysis 749 monodomain IgG Fe binding —alkaline phosphatase fusion protein, thermosensitive mutants of Aspergillus awamori, structural binding activity 715 characterization 1005 Immunoassays Glutamate dehydrogenase insulin, proinsulin, epitope analysis 137 site-directed mutagenesis, catalytic activity, reactive cysteine, DTNB Immunoglobulin 1013 camelid immunoglobulin V,,; structure, single domain antibody 1129 Glutathione-S-transferase Immunotoxins human class Mu, structure refinement, homology modelling 831 a-haemolysin, protease-activated trigger, mutagenesis 91 protein engineering of human glutathione-S-transferase M1-1, metal Pseudomonas exotoxin, B1 and BS Fv fragments, cancer therapy 1509 binding site 1115 Inclusion bodies Glyceraldehyde 3-phosphate dehydrogenase B-lactamase, secondary structure, Raman spectroscopy 131 Thermotoga, thermostability, ion pairs 1471 Insertions Glycerol derivatives poliovirus coat protein VP1 BC loop, foreign epitopes 47 homochiral, lipase-catalysed racemate resolution 589 Insulin Glycosylation deuterated, mass spectrometry, semisynthesis, electrospray 285 glucoamylases, structural similarities, hydrophobic cluster analysis 749 proinsulin, epitope analysis, immunoassays 137 Grafting Interactions CDR, humanization of anti-IL-2R 435 DNA-protein, Drosophila K10 repeat 461 Subject index Interferon Modelling IFN7 structural motif, CD spectra 863 Agrobacterium VirG structure, signal transduction 905 Interleukin-18 annexin I three-dimensional profile, solvation, conformation 1333 receptor binding site, muteins, mutational mapping 663 comparative, major house dust mite allergen Der p I, protein structure Interleukin-2 validation 869 coiled-coil molecular recognition, assembly of receptor ectodomains 1137 predictive, interleukin-13, structure prediction 1077 Ion channels three-dimensional model of thromboxane A, synthase, cytochrome P450, pore-forming domain of voltage-gated potassit..n channel protein 255 prostaglandin 1345 potassium, cysteine engineering of charybdotoxin 503 Modification potassium, selectivity and structure prediction, ROMK1 pore, Shaker chemical, tyrosine residues, isopropylmalate dehydrogenase 99 859 homology modelling of a-hordothionin with crambin, structure —function Ion pairs properties, high lysine analogues 1485 thermostability of glyceraldehyde 3-phosphate dehydrogenase 1471 Molecular decoys 3-Isopropylmalate dehydrogenase CD4, HIV gp120 binding domains, gene therapy 145 co-enzyme specificity 401 Molecular docking es thermodynamic quantities, Fourier—Green function 359 human aldolase A and B chimeras 1387 Molecular dynamics simulation variability and substrate specificity of Candida rugosa lipases 531 binding constants, endothiapepsin inhibitor binding 385 HIV-1 protease, peptide substrate 1353 properties of Rhodobacter capsulatus L3 loop, porins 487 Kringles Molecular interactions apolipoprotein (a) kringle IV types 1, 2 and 10, expression and (MeBm,t)'-cyclosporin—cyclophilin A, immunosuppression 597 characterization 723 antib—oa ntdigyen , protein stability 371 Molecular modelling Lactobacillus casei camelid immunoglobulin Vj; structure 1129 dihydrofolate reductase, effects of amino acid substitution on structure dihydrofolate reductase, improving solubility by mutagenesis 933 and function 783 hepatocyte growth factor, HGF/NK1 region 895 Lactococcus lactis interaction of polyproline-based peptides with Abl-5H3 1455 cell envelope proteinase, protein engineering of catalytic domain 991 p34 protein kinase, cell cycle 243 B-Lactoglobulin pore-forming domain of voltage-gated potassium channel protein 255 thermostable variants, disulphide bonds 263 protein design, geometric recognition 1411 Lens proteins protein structure of calcitonin gene-related peptide 1069 B-crystallin assembly, role of sequence extensions 1395 Molecular similarity Leucine zipper calmodulin, connected graph 331 mutation of in GCN4 1097 Molecular surface recognition Ligand analysis receptor —ligand interaction, computer vision-based technique 39 Monte Carlo immunoglobulin and scavenger receptor superfamily domains, chimeric proteins with domains 3 and 4 of CD4 515 fusion entropy of protein side chains 149 Lipases sampling, 2—4—6 subsite coupled effect, protease cleavage sites 65 Monte Carlo simulation Candida rugosa, variability of isozymes, substrate specificity 531 protein—DNA docking, DNA flexibility 761 fungal, protein crystallography and implications for struc—tf uunrcteio n relationships 551 Motifs Geotrichum candidum, positional and fatty acid specificity 585 sequence, protein function prediction, computer algorithm 165 homochiral glycerol derivatives by lipase-catalysed racemate resolution Multimerization 589 single chain Fv variants 1027 hormone-sensitive, structure, function, evolution and expression, three- Mutagenesis dimensional structure 537 a-haemolysin protease-activated trigger, pore-forming protein 91 Humicola lanuginosa, substrate binding models using X-ray a-haemolysin, zinc-activated switch 655 crystallography 543 alanine scanning, role of regulatory chain of E.coli aspartate novel pancreatic lipases from guinea-pig and coypu, phospholipase transcarbamoylase 673 activity 563 cassette, trp repressor, protein—ligand interaction, free energy Pseudomonas aeruginosa and Bacillus subtilis, three-dimensional perturbation 1239 structure, crystallization 523 cathepsin D active site, substrate specificity 495 Pseudomonas glumae, protein structure, triacylglycerol acylhydrolase 559 chymotrypsin inhibitor-2, protein stability 103 Staphylococcus hyicus, inactivation of by chemical modification and cysteine engineering of charybdotoxin 503 mutagenesis, active site serine 579 IgG binding protein, fluorescence spectroscopy, protein stability 1463 Loops improving solubility of dihydrofolate reductase 933 HIV-1 IIB gpi20 V3 loop 509 in vitro, BA3/A\1-crystallin association 445 Rhodobacter capsulatus L3 loop, molecular dynamics simulation, porins Lactobacillus casei dihydrofolate reductase, effects of amino acid 487 substitution on structure and function 783 Lysozyme lysozyme, enzyme activity, active site 743 enzyme activity, active site, mutagenesis 743 modular, TIM barrel-barrel enzyme hybrid 945 human, function and genesis, engineering 735 N-capping box, helix cap stability, chymotrypsin inhibitor 2 777 role of net charge on renaturation, sulphydryl—disulphide interchange random, Herpes simplex virus type-1 thymidine kinase 83 1249 random, thermosensitive mutants of Aspergillus awamori glucoamylase 1005 residues remote from active site, papain 769 Machine learning site-directed calcium binding site, properties of annexin I 689 topological rules, packing of @-strands, modelling 1295 site-specific, Pseudomonas fluorescens p-hydroxybenzoate hydroxylase Major house dust mite allergen Der p I 801 protein structure validation, cysteine proteinases 869 Staphylococcus hyicus lipases 579 Mass spectrometry Mutational analysis deuterated insulin, semisynthesis, electrospray 285 hepatocyte growth factor, HGF/NK1 region 895 Membrane proteins Mutational effect sequence analysis, fingerprints, structural motif 841 assessment of, binding affinity of protein—DNA interaction 1083 Metal binding site human glutathione-S-transferase M1-1, immobilized metal ion affinity N-terminal arm chromatography 1115 role of in 8A3/A\1-crystallin association 445 1526 NMR prediction, sequence motifs, computer algorithm 165 Drosophila K10 repeat solution structure 461 Protein kinase NMR spectroscopy Ser/Thr and Tyr family, sequence conservation, modelling 849 dihydrofolate reductase, amino acid substitution 783 Protein—ligand interaction Papain cassette mutagenesis of trp repressor, free energy perturbation 1239 active site, catalytic triads 75 enzyme activity, mutagenesis of residues remote from active site 769 chymotrypsin inhibitor 2, mutagenesis of N-capping box, helix cap Peptide synthesis stability 777 leucine zipper of GCN4 1097 chymotrypsin inhibitor-2, reverse turns, salt bridges 103 Peptides coiled-coil, interhelical ion pairs, leucine zipper 1365 reshaping human monoclonal antibody, CDR, toxins 1501 Escherichia coli colicin A mutants, hydrophobic cavity 1495 Phospholipase activity fungal microbial RNase, non-polar nuclei, hydrophobic core 1189 novel pancreatic lipases from guinea-pig and coypu 563 fusion entropy of protein side chains 149 Phospholipase C hydrocarbon solubility, solute—solvent interaction 371 catalytic mechanism in Bacillus cereus, distance geometry calculations IgG binding protein, fluorescence spectroscopy 1463 571 introduction of acidic residues into carboxypeptidase Y 911 Point mutations single substitution mutants, denatured state, inter-residue contact energies local changes in protein structure, predictive rules 1203 1209 Polarity Protein structure local polarity analysis of globular proteins, determination of incorrect (MeBm,t)'-cyclosporin—cyclophilin A, molecular interactions 597 folding 627 adaptation, protein cores, structural conservation 173 Poliovirus Agrobacterium VirG 905 coat protein VP1 BC loop, insertions, chimeras 47 algorithm, protein topology cartoons, motifs 31 Pore 8-barrels, identification and analysis, graph theory, unsupervised a-haemolysin pore-forming protein, protease-activated trigger, algorithm 1305 mutagenesis 91 calcitonin gene-related peptide, molecular modelling 1069 pore-forming protein a-haemolysin has a zinc-activated switch 655 comparisons, genetic algorithm, dynamic programming, least-squares Porins minimization 475 Rhodobacter capsulatus L3 loop, molecular dynamics simulation 487 constructing segments, systematic search procedure 953 Positional specificity Drosophila K10 repeat solution structure 461 fatty acid specificity of Geotrichum candidum lipases 585 effect of helix dipole, hydrogen bonding, ion binding 471 Property profile matching Epstein —Barr virus basic helix—loop—helix sequence motifs 1433 sequence —structure relationships, protein databases 23 Escherichia coli pyrophosphatase, X-ray crystallography, structure Proteases comparison, sequence motif 1173 Bacillus subtilis neutral protease, surface loops 425 intramolecular cavities in globular proteins 613 cleavage sites, HIV, Monte Carlo sampling 65 local changes, predictive rules, point mutations 1203 Protein databases modelling, packing of 6-strands, machine learning 1295 sequence —structure relationships, property profile matching 23 molecular dynamics simulation of HIV-1 protease, peptide substrate 1353 Protein— DNA interaction novel approach to protein design, artificial proteins, biosynthesis in vitro binding affinity, assessment of mutational effect 1083 1041 Protein design pore-forming domain of voltage-gated potassium channel protein 255 B-a-barrel, cooperative deformation, thermal transition 969 protein folding, sequence alignment 1 calmodulin target peptide hybrid, calcium binding properties, NMR 109 Pseudomonas glumae lipases, conformational changes, hydrolase fold endothiapepsin, inhibitor binding, molecular dynamics simulation 385 559 novel approach to artificial proteins, biosynthesis in vitro 1041 pyrophosphatase, X-ray crystallography, structure comparison, sequence novel proteins, geometric recognition 1411 motif 823 Protein engineering reverse turns, salt bridges, chymotrypsin inhibitor-2 protein stability 103 domain insertion, protein folding 1407 self-optimized secondary structure prediction, amino acid sequences 157 Escherichia coli colicin A mutants, aggregation, hydrophobic cavity similarities, Ca distance comparison 1175 1495 structural similarities in glucoamylases, hydrophobic cluster analysis 749 glucoamylase, starch hydrolases 1479 tertiary, circularly permuted dihydrofolate reductase 1373 human glutathione-S-transferase M1-1, metal binding site 1115 tertiary, functional environs, carboxypeptidases A and B, cytochrome c hydrophobic domain of human factor IX, clotting factors 1121 1423 interchain disulphide bonds, disulphide-stabilized Fv fragments 697 tertiary structure, families of proteins with similar total structure, modular mutagenesis of TIM barrel-barrel enzyme hybrid, crystal statistical geometry 1283 structure 945 three-dimensional, glutathione-S-transferase, structure refinement 831 novel proteins, distance matrix, geometric recognition, GRAFTER 1411 validation, environmental amino acid propensity table 869 novel substrate specificity of arabinose binding protein 997 Protein threading recombinant monodomain IgG Fc binding protein 705 protein threading problem is NP-complete, sequence—structure alignment site-directed mutagenesis of snake toxin, antibody —antigen binding 917 1059 society of Japan, abstracts of 6th annual meeting 1151 Protein topology Protein expression cartoons, algorithm 31 secretory protein in Escherichia coli, N-terminal histidine tail 1277 Protein truncation Protein folding C-terminal, a-amylase, substrate recognition 1255 barnase, urea concentration, protein stability 1089 Proteinase classes, amino acid composition of globular proteins 319 cysteine proteinase inhibitor, stefins, homology modelling, structural determination of incorrect folding of globular proteins, local polarity thermodynamics 977 analysis 627 inhibitor, TIMP, conformational analysis, intrinsic fluorescence 1035 domain insertion, protein engineering 1407 Lactococcus lactis, protein engineering of catalytic domain, substrate IgG binding protein, fluorescence spectroscopy 1463 specificity, surface loop 991 kinetic and equilibrium intermediates, phase transitions 593 Pseudomonas aeruginosa secondary structure formation in model polypeptide chains, hydrophobic lipases, structure —function relationships 523 effect 633 Pseudomonas fluorescens sequence alignment 1 thiol reactivity of p-hydroxybenzoate hydroxylase 801 Protein function Pseudomonas glumae circularly permuted dihydrofolate reductase, tertiary protein structure lipases, protein structure, triacylglycerol acylhydrolase 559 1373 Pyrophosphatase genesis of proteins, human lysozyme 735 X-ray crystallography, structure comparison, sequence motif 823 1527 Subject index X-ray crystallography, structure comparison, sequence motif 1173 Sequence divergence analysis seven-helix membrane proteins, bacteriorhodopsin 1221 Query language structure prediction of seven-helix membrane proteins 1231 macromolecular, protein structure, pattern expression, protein data bank Sequence extensions 1311 role of in assembly of 6-crystallin 1395 Sequence motifs Racemate resolution basic/helix —loop—helix, principal component analysis 1433 lipase-catalysed, homochiral glycerol derivatives 589 Signal transduction Raman spectroscopy Agrobacterium VirG mutants, VirG structure modelling 905 B-lactamase inclusion bodies secondary structure 131 molecular dynamics, G protein-coupled receptors, serotonin 1441 Receptor Simulated annealing ectodomains, expression and structure, interleukin-2 1137 method for assessing solvent treatment, structure prediction 221 receptor binding site of interleukin-16, mutational mapping 663 structure prediction, homology modelling, side chain conformation 235 structure, G protein-coupled receptors, serotonin 1441 Single-chain antibodies Receptorligand interaction soluble anti-tumour sFv, aggregation, periplasmic localization 1401 computer vision-based technique 39 Site-directed annexin I Receptors mutagenesis of calcium binding site modifies properties 689 G protein-coupled, fingerprinting, sequence alignment 195 Site-directed mutagenesis LH/CG receptor, hormone—receptor recognition, computer modelling carboxypeptidase Y, introduction of acidic residues 911 205 glutamate dehydrogenase, catalytic activity, reactive cysteine, DTNB Recombinant proteins 1013 apolipoprotein (a) kringle IV types 1, 2 and 10, expression and humanization of anti-IL-2R, CDR graft 435 characterization 723 3-isopropylmalate dehydrogenase, co-enzyme specificity 401 Regulatory chain negative co-operativity of aspartate aminotransferase 413 E.coli aspartate transcarbamoylase, alanine scanning mutagenesis 673 snake toxin, three-dimensional structure 917 Renaturation T4 lysozyme crystallization, disulphide cross-linking 301 role of net charge, lysozyme, aggregation 1249 tyrosine residues, 3-isopropylmalate dehydrogenase 99 Reverse transcriptase xylanase, thermostability, introduction of disulphide bonds 1379 construction of active RNase H domain, hybrid proteins 1103 Solubility Rhodobacter capsulatus dihydrofolate reductase, increased solubility by overproduction of GroES properties of L3 loop, molecular dynamics simulation, porins 487 and GroEL 925 Ricin B chain dihydrofolate reductase, mutagenesis 933 binding domain, mutational and structural analysis of lectin activity 1261 Solvation mRNA effects, thermodynamic quantities of molecular docking, Fourier—Green secondary structure, overproduction of Mu C protein 1053 function 359 RNase homology modelling of annexin I, three-dimensional profile, fungal microbial, non-polar nuclei, protein stability 1189 conformation 1333 RNase H Solvent effect construction of active domain, HIV, reverse transcriptase, hybrid method for assessing solvent treatment, simulated annealing 221 proteins 1103 SOPM secondary structure prediction, amino acid sequences 157 Saccharomyces Staphylococcus hyicus reading-frame shift in glucoamylase improves sequence alignment with inactivation of lipases by chemical modification and mutagenesis, active other glucoamylases 1281 site serine 579 Secondary structure Stefins B-lactamase inclusion bodies, Raman spectroscopy 131 structural thermodynamics, homology modelling 977 formation in model polypeptide chains, distance geometry calculations Structural analysis 633 proteinase inhibitor TIMP, conformational analysis, intrinsic fluorescence overproduction of Mu C protein by removal of at translation initiation 1035 region 1053 Structural motif prediction, conservation of amphipathic conformations, protein structural IFNz, CD spectra 863 alignments 185 sequence analysis, pattern recognition, PRINTS database 841 structure prediction of a-helices, helix capping rules 645 Structure—activity studies Secretion human tumour necrosis factor, lymphotoxin 5 amino acid deletions in Aspergillus awamori glucoamylase, O- Structure—function relationships glycosylation 1109 fungal lipases, protein crystallography 551 Secretory protein glucoamylase, amino acid composition 393 Escherichia coli, protein expression, N-terminal histidine tail 1277 novel pancreatic lipases from guinea-pig and coypu 563 Sequence-—structure alignment Pseudomonas aeruginosa and Bacillus subtilis lipases 523 protein threading problem is NP-complete 1059 Structure prediction Sequence—structure relationships a-helices, Fourier transform, substitution tables 645 property profile matching, protein databases 23 ‘Bio’ Champollion, dynamic programming regularization 1197 Sequence alignment correlated mutations, residue contacts, distance geometry 349 fingerprinting G protein-coupled receptors 195 dihydrofolate reductase, homology modelling 213 homologous protein sequences, amino acid substitution, Dayhoff matrices human rhodopsin, seven-helix membrane proteins 1231 1323 IFN7 structural motif, CD spectra 863 multiple, compensating changes 341 interleukin-13, predictive modelling 1077 multiple, correlated mutations, structure prediction 349 local changes in protein structure, point mutations 1203 mutational and structural analysis of lectin activity in binding domain of modelling, packing of 6-strands, machine learning 1295 ricin B chain 1261 multiple sequence alignment, conservation 341 protein folding 1 protein—DNA docking, Monte Carlo simulation 761 reading-frame shift in Saccharomyces glucoamylase 1281 protein threading problem is NP-complete, sequence—structure alignment Ser/Thr and Tyr protein kinase family, sequence conservation, modelling 1059 849 selectivity, computer simulations, potassium ion channels, ROMK1 pore, Sequence analysis Shaker 859 fingerprints, pattern recognition, PRINTS database 841 self-optimized, amino acid sequences 157 Sequence comparison side chain conformation, simulated annealing, homology modelling 235 LexA repressor, CAP, iron uptake regulator 1449 solvent models, method for assessing solvent treatment 221 1528

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Protein Engineering 1994: Vol 7 Index PDF

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Preview Protein Engineering 1994: Vol 7 Index

Author index Abe,Y . 743 Carr,F.J. 1501 Eaton,S.F. 1137 Gudkov,A.T. 1373 Abelson,J. 997 Carriére,F. 563 Edelmann,E. 663 Guild,B.C. 1261 Aimoto,S. 461 Chaga,G. 1115 Egmond,M.R. 559, 793 Gustchina,A. 309 Alberghina,L. 531 Chakrabarti,P. 471 Eijsink,V.G.H. 425 Alkorta,I. 1221, 1231 Chang,W. 1311 Elliot,G.S. 1395 Haas,M.J. 551 Almo,S.C. 405 Chap,R. 431 elMasry,N.F. 777 Hadwiger,M.A. 1283 Alting,A.C. 991 Chapman,D. 255 Eltis,L.D. 1145 Hagen,W.R. 801 Altschuh,D. 769 Chartier,M. 1495 Endicott,J.A. 243 Hakala,J.M.L. 1069 Andersson,L. 1115 Chatterjee,P. 145 Engel,P.C. 1013 Hales,C.N. 137 Andrews,J. 783 Chelvanayagam,G. 173 Engelborghs,Y. 125 Hamers,R. 1129 Andrews,L.C. 359 Chemeris,V.V. 1041 Eppink,M.H.M. 801 Handford,P.A. 1121 Antheunisse,W.P. 793 Chen,H.-C. 445 Erickson,J.W. 831 Hansen,S. 571 Anthonsen,T. 589 Chen,P.-Y. 941 Eshhar,Z. 431 Hansen,T.V. 589 Aqvist,J. 385 Chiche,L. 689, 1333 Exterkate,F.A. 991 Hardy,F. 425 Argos,P. 173, 185, 613 Chickos,J.S. 149 Haris,P.I. 255 Arnold,J.R.P. 783 Cho,Y. 263 Fedorov,A.N. 1041 Harris,G.W. 1267 Aszédi,A. 633 Chou,K.-C. 65, 319 Feeney,J. 783 Harris,L.J. 815 Atarhouch,T. 1129 Christensen,U. 911 Feige,U. 663 Harris,W.J. 1501 Attwood,T.K. 195, 841 Christianson,K. 509 Feng,S.-L. 1017 Harrison,R.W. 359, 1353 Austen,D.E.G. 1121 Ciardelli,T.L. 1137 Fersht,A.R. 103, 777, Harvey,T.S. 109 Clark,D.A. 1295 1089 Hassan,M. 1485 Cleasby,A. 559 Ferszt,A. 1395 Hatrick,K. 34] Bacon,D. 953 Bajorath,J. 815 Cohen,F.E. 1411 Fidelis,K. 953 Hearst,D.P. 1411 Cohen,M.A. 1323 Fiers,;W. 5 Heinz,D.W. 301 Baker,K.C. 1267 Collura,V.P. 221 Filpula,D. 1017 Hejtmancik,J.F. 445 Baker Libby,C. 1109 Colson,C. 523 Findlay,J.B.C. 195 Hempel,J.C. 1485 Bamborough,P. 1077 Connerton,I.F. 1267 Finkelstein,A.V. 1041 Henderson,I.M.J. 1267 Barbosa,J.A.R.G. 1129 Cooperman,B.S. 823 Fischer,D. 39 Henrissat,B. 1281 Barclay,A.N. 515 Cornett,C.A.G. 1109 Flores,T.P. 31 Hirai,T. 733 Bartels,H. 1035 Coutinho,P.M. 393, 749, Flory,N. 1005 Hodges,R.S. 1365 Basran,J. 783 1005, 1281 Flower,D.R. 1305 Hofmann,O.M. 281 Batt,C.A. 263 Cregut,D. 689, 1333 Fogh,R. 1449 Holm,C. 537 Baty,D. 1495 Crouch,R.J. 1103 Ford,C. 1005, 1109 Holm,L. 1449 Bayley,H. 91, 655 Crowther,N.J. 137 Forster,S.J. 1501 Honda,N. 1239 Bazer,F.W. 863 Cummings,N.J. 1267 Freedman,R.B. 1035 Hooykaas,P.J.J. 905 Beck,M.E. 841 Cunningham,A. 1379 French,D.C. 83 Hope,J.N. 445 Bedouelle,H. 271 Curto,E.V. 863 Frenken,L.G.J. 559 Hori,K. 1387 Belfrage,P. 537 Friedman,T. 985 Horimoto,K. 1433 Benhar,I. 1509 Dale,G.E. 925, 933 Frigerio,F. 425 Horwitz,A.H. 805 Benner,S.A. 1323 Danielson,U.H. 1115 Frémmel,C. 627 Hough,E. 571 Better.M. 805 Danishefsky,A.T. 405 Fujita,I. 1239 Howland,K. 985 Birdsall,B. 783 D’Arcy,A. 933 Fusetti,F. 531 Hsiao,K.-c. 815 Birdsell,D.C. 705, 715 Dartois,V. 523 Huang,J.-L. 705 Bjorkstén,J. 487 Davasse,V. 681 Gago,F. 1455 Huang,M. 705, 715 Blaauw,M. 523 Davis,R.C. 437 Gaillard,J. 681 Hubbard,S.J. 613 Blattler,.W.A. 1261 De,A. 1053 Gallo,R.C. 145 Hughes,P.E. 1121 Blundell,T.L. 645 De Filippis,V. 1203 Georgiou,G. 131 Boel,E. 563 de Haas,G.H. 579 Geourjon,C. 157 fitid,A. 1255 Boelens,R. 761, 1449 de Prat Gay,G. 103 Gerritse,G. 523 Ikehara,M. 735 Bohm,G. 213, 1471 de Vlieg,J. 793 Gershoni,J.M. 145 Ikura,M. 109 Borchert,T.V. 945 de Vos,W.M. 991 Gerstein,M. 461 Tlyin,V.A. 1189 Bottomley,S.P. 1463 Declerck,N. 997 Gilkes,N.R. 117 Imoto,T. 743, 1249 Boulain,J.-C. 917 Dekeyzer,N. 125 Glumoff,T. 823 Inoue,M. 743 Bourne,P.E. 1311 Deléage,G. 157 Godowski,P.J. 895 Isakari,Y. 743 Bradley,J.C. 859 Brady,J.W. 263 Dembowski,N.J. 673 Goldmacher,V.S. 1261 Ishino,S. 733 Demleitner,G. 579 Goldman,A. 823 Iwagami,S.G. 1145 Branner,S. 793 Derewenda,U. 551 Gomi,H. 435 Izard,J. 1495 Breddam,K. 911 Brégégére,F. 271 Derewenda,Z.S. 551 Gonnet,G.H. 1323 Desplancq,D. 1027 Goodenough,P.W. 1267 Jackson,R.M. 371 Brennan,C. 509 Dijkstra,B.W. 523 Goraj,K. 945 Jaeger,K.-E. 523 Brinkmann,U. 697 Dodson,G.G. 137, 543 Gore,M.G. 1463 Jaenicke,R. 213, 1471 Brittain,T. 281 Doesburg,P. 991 Gorman,M. 1005 Jager,J. 605 Brocca,S. 531 Dolgikh,D.A. 1041 Gétz,F. 579 Jansonius,J.N. 605 Brocklehurst,K. 291 Donnelly,D. 645 Grandi,G. 425 Jarpe,M.A. 863 Broger,C. 933 Douthart,R.J. 705 Gray,P.M.D. 1501 Jerala,R. 977 Brown,M.H. 515 Drijfhout,M.C. 801 Greaney,P.J. 221 Jernigam,R.L. 1209 Brownlee,G.G. 1121 Du,P. 1221, 1231 Green,B.N. 285 Joerger,R. 551 Bruinenberg,P.G. 991 Dube,D.K. 83 Green,B.S. 431 Johnson,C.M. , 1089 Brzozowski,A.M. 543 Ducancel,F. 917 Green,R. 551 Johnson,H.M. Bulsink,Y.B.M. 579 Duché,D. 1495 Grewal,N. 205 Johnson,K.W. Dufton,M.J. 1423 Gross,K.-H. 613 Johnson,L.N. 243, 559 Cachau,R.E. 831 Duncan,D. 1077 Griitter.M.G. 663 Johnson,M.S. 475 Campbell,R.L. 1379 Dunn,B.M. 495 Gryaznova,O.I. 1373 Jones,S.T. 1267 Cardle,L. 1423 Dunn,J.P. 131 Gu,W. 263 Jergensen,P.N. 137 Author index Joss,U. 663 Mao,B. 319 Popplewell,A.G. 1463 Singh,J. 849 Jung,S.-H. 697 Marcovina,S.M. 723 Porath,J. 1115 Slingsby,C. 1395 Martial,J.A. 945 Porumb,T. 109 Slotboom,A.J. 579 Kadono,S. 99 Matouschek,A. 1089 Potekhin,S.A. 1097 Smith,D.L. 405 Kallen,J. 597 Matthews,B.W. 301 Presta,L.G. 895 Smith,J.C. 917 Kalsheker,N.A. 869 Matthews,J.M. 1089 Prevost,M. 309 Smith,M. 1145 Kamath,R.S. 1261 May,A.C.W. 475 Priestle,J.P. 663 Smythe,J.A. 145 Kanaoka,M. 435 Medina,C. 385 Protasova,N.Yu. 1373 Soares,C.M. 487 Kankare,J. 823 Medvedkin,V.N. 1097 Przybycien,T.M. 131 Soares,S. 805 Kantrowitz,E.R. 673 Ménez,A. 917 Ptitsyn,O.B. 593, 1041 Srai,K.S. 255 Kaptein,R. 761, 1449 Mezei,M. 331 Pu,C. 1311 Sri Widada,J. 689 Kashmiri,S.V.S. 1401 Miki,T. 743 Srinivasan,N. 869 Kashparov,I.A. 1097 Mikol,V. 597 Quignard,J.-F. 689 Stahl,S.J. 1103 Kasianowicz,J. 655 Milfeld,K. 1345 Quinkal,I. 681 Stennicke,H.R. 911 Katsube,Y. 453 Miller,C. 503 Stern,P.S. 953 Kaufman,J.D. 1103 Miller,R.C.,J r 117 Ramesh,B. 255 Sternberg,M.J.E. 149, 165, Kawano,K. 743 Misset,O. 523 Ramesh,V. 1053 371, 1295 Kay,C.M. 1365 Miyazaki,K. 99, 401 Ransac,S. 523 Stieger,M. 925 Kelly,D.C. 1501 Miyazawa,S. 1209 Rao,A.G. 1485 Stirk,H.J. 47 Kemp,G.J.L. 1501 Moriyama,H. 99, 453 Ravestein,P. 793 Stocklin,R. 285 Kerr,I.D. 255 Mortensen,U.H. 911 Reasoner,J.L. 705 Stouten,P.F.W. 23 Kidokoro,S.-I. 969 Moss,D.S. 31 Reilly,P.J. 393, 749, 1005, Stiiber,D. 933 Kikuchi,M. 735 Motoki,K. 1387 1109, 1281 Studnicka,G.M. 805 Kilburn,D.G. 117 Mould,R.M. 281 Reiter,Y. 697 Sugihara,A. 585 Kim,T.-R. 263 Moulis,J.-M. 681 Remington,S.J. 911 Sugimoto,Y . 1387 Kimura,H. 969 Moult,J. 953 Rety,S. 543 Sumner,I.G. 1267 King,D.J. 1027 Mountain,A. 1027 Richards,W.G. 859, 1077 Sun,T. 503 King,R.D. 1295 Munir,K.M. 83 Richelle,J. 309 Sundell,S. 571 Kireeva,M.L. 1373 Murphy,G. 1035 Ringe,D. 405 Sung,W.L. 1379 Kirpichnikov,M.P. 1041 Murphy,J.R. 985 Roberts,G.C.K. 783 Suominen,I. 1255 Kirsch,J.F. 413 Murzin,A.G. 1373 Robson,B. 221 Surowy,T. 509 Kishan,R. 945 Murzina,N.V. 1373 Rodenburg,K.W. 905 Sutton,B.J. 1463 Knegtel,R.M.A. 761 Muyldermans,S. 1129 Rollence,M.L. 1017 Suzuki,M. 461 Kolchanov,N.A. 349 Rose,D.R. 961 Svensson,B. 1479 Kolmakova-Partensky,L. 503 Nadell,R. 805 Rose,K. 285 Swenson,L. 551 Komeiji,Y. 1239 Nagao,T. 585 Roy,G. 173 Swimmer,C. 1261 Korn,A.P. 961 Nagaraja,V. 1053 Ruan,K.-H. 1345 Swindells,M.B. 1 Koschinsky,M.L. 723 Nakamura,H. 969 Russell,R.B. 1407 Kourinov,I.V. 359 Nakamura,M. 585 Riiterjans,H. 1449 Takasaki,Y . 1387 Krishna,N.R. 963 Nakatani,T. 435 Rypniewski,W.R. 57 Takenaka,H. 733 Krishnasastry,M. 655 Nardelli,B. 145 Talwar,G.P. 205 Kroone,R.C. 1395 Neal,G.S. 823 Sakurai,M. 99, 453 Tamura,T. 743, 1239 Kulmacz,R.J. 1345 Neuhaus,D. 461 Saldanha,J. 1129 Tanaka,N. 99, 453 Kuroda,Y. 969 Nilsson,O. 487 Salminen,T. 823 Tanaka,T. 969 Kusakabe,T. 1387 Nishikawa,K. 733 Salunke,D.M. 205 Tapia,O. 487 Lahti,R. 823 Noble,M.E.M. 559, 945 Samuelsson,J.-E. 385 Tavernier,J. 5 Lambert,J.M. 1261 Noguchi,H. 435 Sana,T.R. 1137 Tawfik,D.S. 431 Langen,H. 925, 933 Norel,R. 39 Sander,C. 23, 349, 1203, 1449 Taylor,M.A.J. 1267 Langin,D. 537 Norioka,N. 733 Sangrar,W. 723 Taylor,W.R. 341, 633 Lathrop,R.H. 1059 Nurse,P. 243 Sansom,C. 309 Tempest,P.R. 1501 Laue,T.M. 1137 Nussinov,R. 39 Sansom,M.S.P. 255 Tessier,D.C. 769 Laughton,C.A. 235 Saqi,M.A.S. 165 Thim,L. 563 Lawson,A.D.G. 1027 Offord,R.E. 285 Sarai,A. 1083 Thirstrup,K. 563 Lawson,D.M. 543 Ohshima,K. 1433 Sato,M. 453 Thomas,A. 917 Lee,B. 697 Onodera,K. 453 Sauder,U. 605 Thomas,J.A. 783 Lee,S.-P. 263 Onuffer,J.J. 413 Sawyer,J.R. 1401 Thornton,J.M. 31, 47 Lehar,S.M. 1261 Ortiz,A.R. 1455 Scarborough,P.E. 495 Thorpe,C.J. 869 Lessel,U. 1175 Oshima,T. 99, 401, 453 Scawen,M. 1463 Titball,R.W. 1501 Lesuisse,E. 523 QMsterlund,T. 537 Schanck,K. 523 Tjeenk,M.L. 579 Liautard,J.-P. 689, 1333 Otsuka,J. 1433 Scheeren-Groot,E. 905 Tominaga,Y. 585 Lim,C. 75 Ot,T.L. 863 Schlom,J. 1401 Tomme,P. 117 Lionne,C. 689 Overington,J.P. 645, 869 Schmitz,A. 663. Tomschy,A. 1471 Loeb,L.A. 83 Schnarr,M. 1449 Topham,C.M. 869 Lohner,K. 977 Parker,M.W. 1495 Schoenmakers,J.G.G. 1395 Tramontano,A. 531 Lokker,N.A. 895 Partali,V. 589 Schomburg,D. 1175 Travé,G. 689 Lone, Y.-C. 435 Pascarella,S. 185 Schénfeld,H.-J. 925 Trumble,W.R. 705, 715 Longhi,S. 531 Pastan,I. 697, 1509 Schotz,M.C. 537 Tsutsui,M. 1239 Lotti,M. 531 Pauptit,R.A. 605 Schwartz,J. 271 Turk,V. 977 Lubsen,N.H. 1395 Pedersen,J.T. 1261 Seidler,A. 1277 Luo,X. 1441 Peltonen,T. 1255 Serrano,L. 1455 Ueda,T. 743, 1249 Luthardt,G. 627 Perrakis,A. 57 Seto,Y. 733 Uversky,V.N. 1041, 1373 Peters,H. 793 Shimada,Y. 585 Maeda,Y. 1249 Pickersgill,R.W. 1267 Shimony,E. 503 Valax,P. 131 Mainfroid,V. 945 Pillet,L. 917 Shindyalov,I.N. 349, 1311 van Bemmel,C.J. 793 Mandecki,W. 509 Pisabarro,M.T. 1455 Shirazi,J. 1295 van Berkel,W.J.H. 801 Mannervik,B. 1115 Pizzi,E. 531 Sierks,M.R. 1479 van der Bolt,F.J.T. 801 Mantsala,P. 1255 Pontzer,C.H. 863 Siezen,R.J. 991 van der Vinne,B. 425 1520 van Oostrum,J. 663 Van Ostade,X. 5 vanderSpek,J.C. 985 Venema,G. 425 Venyaminov,S.Yu. 1097 Verger,R. 563 Verheij,H.M. 579 Verma,C. 543 Vernet,T. 769 Viguera,A.R. 1455 Vihinen,M. 1069, 1255 Viki¢é-Topi¢,S. 1103 Villar,H.O. 831 Volckaert,G. 125 Vorgias,C.E. 57 Vosbeck,K. 663 Vriend,G. 23, 425, 905, 1203 Waagen,V. 589 Wakarchuk,W.W. 1379 Walker,B. 91, 655 Walkinshaw,M.D. 597 Wan,T. 1463 Wang,C.-L. 705, 715 Wang,J. 75 Wang,K.-T. 941 Wang,X.-G. 1013 Wang,Y. 1083 Warren,A.J. 117 Warwicker,J. 1267 Watkins,S. 263 Watson,D.C. 1379 Webber,K.O. 697 Weber,I.T. 309, 1353 Wei,Y. 551 Weinstein,H. 1441 Wesson,C.A.R. 715 West,J.W. 705 White,P. 1501 Whitlow,M. 1017 Widersten,M. 1115 Wierenga,R.K. 945 Wijdenes,J. 435 Williams,R.E. 805 Williamson,E.D. 1501 Williamson,R.A. 1035 Wilson,K.S. 57 Wingfield,P.T. 1103 Winkler,U. 523 Wlodawer,A. 309 Wodak,S.Y. 309 Wolfson,H.J. 39 Wood,J.F. 1017 Wu,K.K. 1345 Wu,S.-H. 941 Wu,Z. 1137 Xiang,Y.-F. 75 Xiao,B. 137 Yaguchi,M. 1379 Yamada,H. 743, 1249 Yamaguchi,S. 551 Yamakawa,J. 435 Yamamoto,H. 1433 Yamato,I. 1239 Yanagi,K. 1433 Yao,T. 733 Yau,P. 109 Zeelen,J.Ph. 945 Zehfus,M.H. 335 Zerovnik,E. 977 Zhang,C.-T. 65, 319 Zhang,D. 1441 Zhou,N.E. 1365 Zimmerman,K. 1197 Zinn-Justin,S. 917 Subject index Active site Bacillus subtilis human tumour necrosis factor, lymphotoxin, structureactivity studies 5 3-isopropylmalate dehydrogenase chimera, three-dimensional structure lysozyme, fluctuation of for enzyme activity 743 453 mutagenesis of cathepsin D, substrate specificity 495 lipases, struct—f uunrctieon relationships 523 mutants, glucoamylase, specificity, sequence analysis 1479 thermostability of neutral protease, surface loops 425 papain, catalytic triads 75 Bacteriophages papain, mutagenesis of residues remote from active site, role of two- overproduction of Mu C protein by removal of secondary structure at domain interface 769 translation initiation region 1053 thiolate—imidazolium ion pair, recombinant caricain, effect of charged 8-Barrels residues 1267 automation of identification and analysis, graph theory, unsupervised Affinity chromatography algorithm 1305 immobilized metal ion, protein engineering of human glutathione-S- BC loop transferase M1-1 1115 poliovirus coat protein VP1, insertions, chimeras 47 introduction of N-terminal histidine tail, protein expression in Binding activity Escherichia coli 1277 antibody, pH on—off dependency, chemical modification by Aggregation tetranitromethane 431 Escherichia coli colicin A mutants, inclusion body 1495 Binding affinity multivalent Fvs, characterization of single chain Fv oligomers 1017 interaction of polyproline-based peptides with Abl-SH3, DOCK 1455 soluble anti-tumor sFv, periplasmic localization, induction conditions for protein—DNA interaction, assessment of mutational effect 1083 production of in Escherichia coli 1401 Binding constants Agrobacterium free energy, endothiapepsin inhibitor binding 385 VirG structure modelling, signal transduction 905 Binding domain AIDS cellulose and chitin, xylanase—endoglucanase fusion protein 117 drugs, HIV-1 protease—inhibitor interaction 309 ricin B chain, mutational and structural analysis of lectin activity 1261 Aldolase Binding protein human, A and B chimeras 1387 calcium, Nereis diversicolor, chloramphenicol acetyltransferase fusion Algorithm protein 125 computer, protein function prediction, sequence motifs 165 Binding site genetic, least-squares minimization, protein structure comparisons 475 receptor binding site of interleukin-18, mutational mapping 663 protein topology cartoons, motifs 31 ‘Bio’ Champollion Alignment dynamic programming regularization of secondary structure prediction divergence, evolutionary conservation of trypsin 57 1197 Alkaline phosphatase Biosynthesis modulation enzyme activity of alkaline phosphatase—epitope hybrid 509 of artificial proteins in vitro, novel approach to protein design 1041 monodomain IgG Fc binding —alkaline phosphatase fusion protein, enzymatic activity 715 Calcitonin Amino acid composition gene-related peptide, molecular modelling of the protein structure 1069 globular proteins, protein folding classes 319 Calcium starch binding and catalytic domains of glucoamylase, structure —function binding properties, calmodulin target peptide hybrid, NMR 109 relationships 393 binding protein, Nereis diversicolor, cloning, expression and purification a-Amylase 125 Bacillus stearothermophilus, C-terminal protein truncation, substrate Calcium binding site recognition 1255 site-directed mutagenesis modifies properties of annexin I 689 Annexin I Calmodulin homology modelling, three-dimensional profile, solvation 1333 molecular similarity, connected graph 331 Antibodies target peptide hybrid, calcium binding properties 109 humanization, binding activity of mAbs, non-CDR complementarity Calorimetry modulating residues 805 cooperative deformation, 8-a-barrel, thermal transition, molten globule humanization of anti-IL-2R, CDR graft 435 969 humanization of mAb 60.3, L2 loop, CD18, antib—oa ndtiyge n protein folding of barnase and urea concentration 1089 interaction 815 Camelids multimerization of single chain Fv variants 1027 immunoglobulin V,, structure, molecular modelling 1129 reshaping human monoclonal antibody, CDR, toxins, peptides 1501 Cancer therapy single domain, camelid immunoglobulin Vj, structure, molecular B1 and BS Fv fragments, Pseudomonas exotoxin 1509 modelling 1129 Candida rugosa Antibody engineering variability of isozymes, substrate specificity 531 characterization of single chain Fv oligomers, linker design 1017 Carboxypeptidase chemical modification, pH on—off dependency of antibody binding three-dimensional structure, functional environs, contour maps 1423 activity 431 Carboxypeptidase Y Antigen binding introduction of acidic residues, protein stability, substrate specificity, pH bifunctional hybrids of MalE and Ig variable domains 271 dependence 911 Apolipoprotein (a) Caricain expression and characterization of kringle IV types 1, 2 and 10 723 recombinant, effect of charged residues, active site thiolate —imidazolium Arabinose binding protein ion pair 1267 novel substrate specificity, protein engineering, fluorescence titration 997 Catalytic activity Aspergillus awamori site-directed mutagenesis of glutamate dehydrogenase, reactive cysteine, amino acid deletions in glucoamylase, secretion, O-glycosylation 1109 DTNB 1013 glucoamylase thermosensitive mutants, structural characterization 1005 Catalytic mechanism phospholipase C in Bacillus cereus, distance geometry calculations 571 Bacillus cereus Catalytic triads phospholipase C catalytic mechanism, distance geometry calculations 571 papain active site 75 Bacillus circulans Cathepsin D site-directed mutagenesis of xylanase, thermostability 1379 substrate specificity, mutagenesis of active site, aspartic proteinase 495 1523 Subject index Cavities Database intramolecular cavities in globular proteins, packing 613 protein mutant, construction of 733 CD4 Deletions HIV gp120 binding domains, molecular decoys, gene therapy 145 Aspergillus awamori glucoamylase, O-glycosylation, secretion, Cell cycle thermostability 1109 cde2/CDC28, p34 protein kinase, molecular modelling 243 Denatured state Chaperonins protein stability, single substitution mutants, inter-residue contact GroES and GroEL, overproduction, increased solubility of dihydrofolate energies, hydrophobic energy 1209 reductase 925 Dihydrofolate reductase Chemical labelling Escherichia coli, circularly permuted, tertiary protein structure 1373 cysteine engineering of charybdotoxin 503 Halobacterium volcanii, homology modelling, structure prediction 213 Chemical modification improving solubility by mutagenesis, inclusion bodies 933 Staphylococcus hyicus lipases 579 increased solubility by overproduction of GroES and GroEL 925 tetranitromethane, nitrotyrosine residues, antibody binding activity 431 Dimerization Chemical synthesis B-crystallin assembly, role of sequence extensions 1395 y-echistatin analogues, platelet aggregation 941 Diphtheria toxin Chimeras transmembrane domain, amphipathic helix, hydrophobic face, fusion Bacillus subtilis and Thermus thermophilus 3-isopropylmalate toxin 985 dehydrogenase 453 Distance geometry calculations human aldolase A and B chimeras 1387 Bacillus cereus phospholipase C, DGEOM, GRID 571 poliovirus coat protein VP1 BC loop, foreign epitopes 47 secondary structure formation in model polypeptide chains 633 Chimeric proteins Disulphide bonds enzyme activity, alkaline phosphatase —epitope hybrid 509 cross-linking, rapid crystallization of T4 lysozyme 301 immunoglobulin and scavenger receptor superfamily domains with B-lactoglobulin thermostable variants 263 domains 3 and 4 of CD4 515 protein engineering interchain disulphide bonds, disulphide-stabilized Fv xyla—e nndoagluscanease , cellulose and chitin binding domain 117 fragments 697 Choriogonadotropin DNA flexibility hormone -—receptor recognition, computer modelling 205 protein-DNA docking, Monte Carlo simulation 761 Co-enzymes Docking specificity, 3-isopropylmalate dehydrogenase 401 protein—DNA, Monte Carlo simulation 761 Coiled-coil Domains molecular recognition, assembly of receptor ectodomains, interleukin-2, discontinuous, method for location, compactness 335 leucine zipper 1137 insertion, protein folding 1407 mutation in leucine zipper of GCN4 1097 Drosophila protein stability, interhelical ion pairs, leucine zipper 1365 K10 repeat, solution structure, NMR 461 Complementarity determining region Dynamic programming reshaping human monoclonal antibody, toxins, peptides 1501 regularization, ‘Bio’ Champollion secondary structure prediction 1197 Computer modelling humanization of anti-IL-2R, CDR graft 435 LH/CG receptor, hormone—receptor recognition 205 +-Echistatin Conformation solid-phase peptide synthesis of analogues, platelet aggregation 941 amphipathic, conservation, secondary structure prediction, protein Ectothiorhodospira halophila structural alignments 185 hyperexpression of gene encoding HiPIP, fusion protein 1145 ligand binding, protein torsion angle changes 961 Electrostatic interactions polypeptide backbone, constructing segments of protein structure 953 active site thiolate-—-imidazolium ion pair, recombinant caricain 1267 proteinase inhibitor TIMP, structural analysis, intrinsic fluorescence 1035 Electrostatic properties Conformational change engineering of surface charges in a subtilisin, electrophoresis, ion- Escherichia coli aspartate aminotransferase mutant with increased exchange 793 enzymic activity 605 interhelical ion pairs, protein stability, leucine zipper 1365 negative co-operativity of aspartate aminotransferase, site-directed Ellipsoid analysis mutagenesis 413 amino acid composition of globular proteins 319 Conservation Entropy proline residues, Clostridium pasteurianum 2[4Fe—4S] 681 conformation, fusion entropy of protein side chains 149 sequence, Ser/Thr and Tyr protein kinase family 849 Enzyme activity Cooperativity lysozyme, mutagenesis, active site 743 cooperative deformation de novo designed protein, B-c-barrel, thermal modulation, alkaline phosphatase —epitope hybrid 509 transition 969 papain, mutagenesis of residues remote from active site, role of two- Crystal structure domain interface 769 aspartate aminotransferase, wild type and mutant 405 Enzyme kinetics fungal lipases, implications for structure—function relationships 551 pH-dependent, overlapping ionizations, review 291 Humicola lanuginosa lipases, substrate binding models using X-ray Epitope mapping crystallography 543 protein engineering of snake toxin, antibody —antigen binding 917 molecular mechanics of HIV-1 protease—inhibitor interaction 309 Epitopes TIM barrel-barrel enzyme hybrid, modular mutagenesis 945 analysis, insulin, proinsulin 137 8-Crystallin Escherichia coli assembly, role of sequence extensions, dimerization 1395 aspartate aminotransferase, negative co-operativity 413 Crystallins aspartate aminotransferase, wild type and mutant substrate specificity, role of N-terminal arm in 8A3/A1-crystallin association 445 crystal structure 405 Crystallization aspartate aminotransferase mutant, three-dimensional structure 605 rapid, T4 lysozyme, disulphide cross-linking 301 induction conditions for production of soluble anti-tumour sFv, Cysteine proteinase periplasmic localization 1401 effect of electrostatic interactions, active site thiolate—imidazolium ion pyrophosphatase structure comparison, X-ray crystallography, sequence pair 1267 motif 823 Cytochrome c pyrophosphatase structure comparison, X-ray crystallography, sequence three-dimensional structure, functional environs, contour maps 1423 motif 1173 Cytokines regulatory chain of aspartate transcarbamoylase, alanine scanning interleukin-13, predictive modelling, structure prediction 1077 mutagenesis 673 1524 Subject ind< Evolution Haemoglobin divergence, evolutionary conservation of trypsin 57 recombinant, incorporation of sulphaem 281 homologous protein sequences, amino acid substitution, Dayhoff matrices Halophilic adaptation 1323 Halobacterium volcanii dihydrofolate reductase, homology modelling 213 Helix cap stability, mutagenesis of N-capping box 777 Factor IX Helix — loop — helix human, protein engineering of hydrophobic domain, clotting factors 1121 sequence motifs, Epstein—Barr virus 1433 Fe binding domain Helix —turn— helix gene synthesis and functional expression of recombinant monodomain LexA, PrfA and Fur, DNA recognition 1449 IgG Fc binding protein 705 Helix dipole monodomain IgG Fc binding —alkaline phosphatase fusion protein 715 effect of on protein structure, helix packing, ion binding 471 Ferredoxin Helix packing conservation of proline residues, Clostridium pasteurianum 2[4Fe—4S}, transmembrane helices, bacteriorhodopsin, structure prediction 1221 electron transfer 681 Hepatocyte growth factor hyperexpression of gene encoding HiPIP, fusion protein 1145 HGF/NK1 region, structure—function relationships 895 Fingerprinting Herpes simplex virus type-1 G protein-coupled receptors, sequence alignment 195 thymidine kinase, random mutagenesis 83 Fluorescence titration HIV novel substrate specificity of arabinose binding protein 997 construction of active RNase H domain of reverse transcriptase, hybrid Footprinting proteins 1103 Drosophila K10 repeat DNA —protein interactions 461 HIV-1 IIB gpi20 V3 loop, enzyme activity of alkaline Fourier transform phosphataseepitope hybrid 509 fast, Fourier—Green function, effects of solvation 359 molecular mechanics of HIV-1 prote—i anhsibieto r interaction, crystal Fungi structure 309 lipases, protein crystallography and implications for structure —function protease, molecular dynamics simulation, peptide substrate 1353 relationships 551 protease cleavage sites, 2—4—6 subsite coupled effect 65 Fusion protein Homology bifunctional hybrids of MalE and Ig variable domains, antigen binding families of proteins with similar total structure 1283 271 Homology modelling hyperexpression of gene encoding HiPIP 1145 cysteine proteinase inhibitor, structural thermodynamics 977 monodomain IgG Fe binding —alkaline phosphatase 715 dihydrofolate reductase, structure prediction 213 Nereis diversicolor calcium binding protein and chloramphenicol novel procedure for structure refinement, human class Mu glutathione-S- acetyltransferase 125 transferase 831 xyla—e nndoagluscanease , engineered bifunctional enzyme 117 structural conservation of protein structure 173 v fragments structure —function properties of a-hordothionin, crambin, high lysine cloning of B1 and B5 Fv fragments, immunotoxins, cancer therapy 1509 analogues 1485 interchain disulphide bonds, recombinant immunotoxins containing structure prediction, simulated annealing, side chain conformation 235 disulphide-stabilized Fv fragments 697 a-Hordothionin multimerization of single chain Fv variants 1027 homology modelling with crambin, structure —function properties, high multivalent Fvs, characterization of single chain Fv oligomers 1017 lysine analogues 1485 Human rhodopsin G-proteins structure prediction, seven-helix membrane proteins, bacteriorhodopsin fingerprinting G protein-coupled receptors, sequence alignment 195 1221 Gene therapy Humanization CD4, HIV gp120 binding domains, molecular decoys 145 binding activity of mAbs, non-CDR complementarity modulating Geotrichum candidum residues 805 positional and fatty acid specificity of lipases 585 mAb 60.3, L2 loop, CD18 815 Globular proteins Humicola lanuginosa intramolecular cavities, packing 613 lipases, substrate binding models using X-ray crystallography 543 local polarity analysis, determination of incorrect folding 627 Hydrophobic core Glucoamylase fungal microbial RNase, non-polar nuclei, protein stability 1189 amino acid deletions, Aspergillus awamori, O-glycosylation, Hydrophobic effect thermostability 1109 solute—solvent interaction, surface tension 371 reading-frame shift in Saccharomyces glucoamylase improves sequence alignment with other glucoamyl 1281 specificity, sequence analysis 1479 IgG starch binding and catalytic domains, structure—function relationships gene synthesis and functional expression of recombinant monodomain 393 IgG Fe binding protein 705 structural similarities, hydrophobic cluster analysis 749 monodomain IgG Fe binding —alkaline phosphatase fusion protein, thermosensitive mutants of Aspergillus awamori, structural binding activity 715 characterization 1005 Immunoassays Glutamate dehydrogenase insulin, proinsulin, epitope analysis 137 site-directed mutagenesis, catalytic activity, reactive cysteine, DTNB Immunoglobulin 1013 camelid immunoglobulin V,,; structure, single domain antibody 1129 Glutathione-S-transferase Immunotoxins human class Mu, structure refinement, homology modelling 831 a-haemolysin, protease-activated trigger, mutagenesis 91 protein engineering of human glutathione-S-transferase M1-1, metal Pseudomonas exotoxin, B1 and BS Fv fragments, cancer therapy 1509 binding site 1115 Inclusion bodies Glyceraldehyde 3-phosphate dehydrogenase B-lactamase, secondary structure, Raman spectroscopy 131 Thermotoga, thermostability, ion pairs 1471 Insertions Glycerol derivatives poliovirus coat protein VP1 BC loop, foreign epitopes 47 homochiral, lipase-catalysed racemate resolution 589 Insulin Glycosylation deuterated, mass spectrometry, semisynthesis, electrospray 285 glucoamylases, structural similarities, hydrophobic cluster analysis 749 proinsulin, epitope analysis, immunoassays 137 Grafting Interactions CDR, humanization of anti-IL-2R 435 DNA-protein, Drosophila K10 repeat 461 Subject index Interferon Modelling IFN7 structural motif, CD spectra 863 Agrobacterium VirG structure, signal transduction 905 Interleukin-18 annexin I three-dimensional profile, solvation, conformation 1333 receptor binding site, muteins, mutational mapping 663 comparative, major house dust mite allergen Der p I, protein structure Interleukin-2 validation 869 coiled-coil molecular recognition, assembly of receptor ectodomains 1137 predictive, interleukin-13, structure prediction 1077 Ion channels three-dimensional model of thromboxane A, synthase, cytochrome P450, pore-forming domain of voltage-gated potassit..n channel protein 255 prostaglandin 1345 potassium, cysteine engineering of charybdotoxin 503 Modification potassium, selectivity and structure prediction, ROMK1 pore, Shaker chemical, tyrosine residues, isopropylmalate dehydrogenase 99 859 homology modelling of a-hordothionin with crambin, structure —function Ion pairs properties, high lysine analogues 1485 thermostability of glyceraldehyde 3-phosphate dehydrogenase 1471 Molecular decoys 3-Isopropylmalate dehydrogenase CD4, HIV gp120 binding domains, gene therapy 145 co-enzyme specificity 401 Molecular docking es thermodynamic quantities, Fourier—Green function 359 human aldolase A and B chimeras 1387 Molecular dynamics simulation variability and substrate specificity of Candida rugosa lipases 531 binding constants, endothiapepsin inhibitor binding 385 HIV-1 protease, peptide substrate 1353 properties of Rhodobacter capsulatus L3 loop, porins 487 Kringles Molecular interactions apolipoprotein (a) kringle IV types 1, 2 and 10, expression and (MeBm,t)'-cyclosporin—cyclophilin A, immunosuppression 597 characterization 723 antib—oa ntdigyen , protein stability 371 Molecular modelling Lactobacillus casei camelid immunoglobulin Vj; structure 1129 dihydrofolate reductase, effects of amino acid substitution on structure dihydrofolate reductase, improving solubility by mutagenesis 933 and function 783 hepatocyte growth factor, HGF/NK1 region 895 Lactococcus lactis interaction of polyproline-based peptides with Abl-5H3 1455 cell envelope proteinase, protein engineering of catalytic domain 991 p34 protein kinase, cell cycle 243 B-Lactoglobulin pore-forming domain of voltage-gated potassium channel protein 255 thermostable variants, disulphide bonds 263 protein design, geometric recognition 1411 Lens proteins protein structure of calcitonin gene-related peptide 1069 B-crystallin assembly, role of sequence extensions 1395 Molecular similarity Leucine zipper calmodulin, connected graph 331 mutation of in GCN4 1097 Molecular surface recognition Ligand analysis receptor —ligand interaction, computer vision-based technique 39 Monte Carlo immunoglobulin and scavenger receptor superfamily domains, chimeric proteins with domains 3 and 4 of CD4 515 fusion entropy of protein side chains 149 Lipases sampling, 2—4—6 subsite coupled effect, protease cleavage sites 65 Monte Carlo simulation Candida rugosa, variability of isozymes, substrate specificity 531 protein—DNA docking, DNA flexibility 761 fungal, protein crystallography and implications for struc—tf uunrcteio n relationships 551 Motifs Geotrichum candidum, positional and fatty acid specificity 585 sequence, protein function prediction, computer algorithm 165 homochiral glycerol derivatives by lipase-catalysed racemate resolution Multimerization 589 single chain Fv variants 1027 hormone-sensitive, structure, function, evolution and expression, three- Mutagenesis dimensional structure 537 a-haemolysin protease-activated trigger, pore-forming protein 91 Humicola lanuginosa, substrate binding models using X-ray a-haemolysin, zinc-activated switch 655 crystallography 543 alanine scanning, role of regulatory chain of E.coli aspartate novel pancreatic lipases from guinea-pig and coypu, phospholipase transcarbamoylase 673 activity 563 cassette, trp repressor, protein—ligand interaction, free energy Pseudomonas aeruginosa and Bacillus subtilis, three-dimensional perturbation 1239 structure, crystallization 523 cathepsin D active site, substrate specificity 495 Pseudomonas glumae, protein structure, triacylglycerol acylhydrolase 559 chymotrypsin inhibitor-2, protein stability 103 Staphylococcus hyicus, inactivation of by chemical modification and cysteine engineering of charybdotoxin 503 mutagenesis, active site serine 579 IgG binding protein, fluorescence spectroscopy, protein stability 1463 Loops improving solubility of dihydrofolate reductase 933 HIV-1 IIB gpi20 V3 loop 509 in vitro, BA3/A\1-crystallin association 445 Rhodobacter capsulatus L3 loop, molecular dynamics simulation, porins Lactobacillus casei dihydrofolate reductase, effects of amino acid 487 substitution on structure and function 783 Lysozyme lysozyme, enzyme activity, active site 743 enzyme activity, active site, mutagenesis 743 modular, TIM barrel-barrel enzyme hybrid 945 human, function and genesis, engineering 735 N-capping box, helix cap stability, chymotrypsin inhibitor 2 777 role of net charge on renaturation, sulphydryl—disulphide interchange random, Herpes simplex virus type-1 thymidine kinase 83 1249 random, thermosensitive mutants of Aspergillus awamori glucoamylase 1005 residues remote from active site, papain 769 Machine learning site-directed calcium binding site, properties of annexin I 689 topological rules, packing of @-strands, modelling 1295 site-specific, Pseudomonas fluorescens p-hydroxybenzoate hydroxylase Major house dust mite allergen Der p I 801 protein structure validation, cysteine proteinases 869 Staphylococcus hyicus lipases 579 Mass spectrometry Mutational analysis deuterated insulin, semisynthesis, electrospray 285 hepatocyte growth factor, HGF/NK1 region 895 Membrane proteins Mutational effect sequence analysis, fingerprints, structural motif 841 assessment of, binding affinity of protein—DNA interaction 1083 Metal binding site human glutathione-S-transferase M1-1, immobilized metal ion affinity N-terminal arm chromatography 1115 role of in 8A3/A\1-crystallin association 445 1526 NMR prediction, sequence motifs, computer algorithm 165 Drosophila K10 repeat solution structure 461 Protein kinase NMR spectroscopy Ser/Thr and Tyr family, sequence conservation, modelling 849 dihydrofolate reductase, amino acid substitution 783 Protein—ligand interaction Papain cassette mutagenesis of trp repressor, free energy perturbation 1239 active site, catalytic triads 75 enzyme activity, mutagenesis of residues remote from active site 769 chymotrypsin inhibitor 2, mutagenesis of N-capping box, helix cap Peptide synthesis stability 777 leucine zipper of GCN4 1097 chymotrypsin inhibitor-2, reverse turns, salt bridges 103 Peptides coiled-coil, interhelical ion pairs, leucine zipper 1365 reshaping human monoclonal antibody, CDR, toxins 1501 Escherichia coli colicin A mutants, hydrophobic cavity 1495 Phospholipase activity fungal microbial RNase, non-polar nuclei, hydrophobic core 1189 novel pancreatic lipases from guinea-pig and coypu 563 fusion entropy of protein side chains 149 Phospholipase C hydrocarbon solubility, solute—solvent interaction 371 catalytic mechanism in Bacillus cereus, distance geometry calculations IgG binding protein, fluorescence spectroscopy 1463 571 introduction of acidic residues into carboxypeptidase Y 911 Point mutations single substitution mutants, denatured state, inter-residue contact energies local changes in protein structure, predictive rules 1203 1209 Polarity Protein structure local polarity analysis of globular proteins, determination of incorrect (MeBm,t)'-cyclosporin—cyclophilin A, molecular interactions 597 folding 627 adaptation, protein cores, structural conservation 173 Poliovirus Agrobacterium VirG 905 coat protein VP1 BC loop, insertions, chimeras 47 algorithm, protein topology cartoons, motifs 31 Pore 8-barrels, identification and analysis, graph theory, unsupervised a-haemolysin pore-forming protein, protease-activated trigger, algorithm 1305 mutagenesis 91 calcitonin gene-related peptide, molecular modelling 1069 pore-forming protein a-haemolysin has a zinc-activated switch 655 comparisons, genetic algorithm, dynamic programming, least-squares Porins minimization 475 Rhodobacter capsulatus L3 loop, molecular dynamics simulation 487 constructing segments, systematic search procedure 953 Positional specificity Drosophila K10 repeat solution structure 461 fatty acid specificity of Geotrichum candidum lipases 585 effect of helix dipole, hydrogen bonding, ion binding 471 Property profile matching Epstein —Barr virus basic helix—loop—helix sequence motifs 1433 sequence —structure relationships, protein databases 23 Escherichia coli pyrophosphatase, X-ray crystallography, structure Proteases comparison, sequence motif 1173 Bacillus subtilis neutral protease, surface loops 425 intramolecular cavities in globular proteins 613 cleavage sites, HIV, Monte Carlo sampling 65 local changes, predictive rules, point mutations 1203 Protein databases modelling, packing of 6-strands, machine learning 1295 sequence —structure relationships, property profile matching 23 molecular dynamics simulation of HIV-1 protease, peptide substrate 1353 Protein— DNA interaction novel approach to protein design, artificial proteins, biosynthesis in vitro binding affinity, assessment of mutational effect 1083 1041 Protein design pore-forming domain of voltage-gated potassium channel protein 255 B-a-barrel, cooperative deformation, thermal transition 969 protein folding, sequence alignment 1 calmodulin target peptide hybrid, calcium binding properties, NMR 109 Pseudomonas glumae lipases, conformational changes, hydrolase fold endothiapepsin, inhibitor binding, molecular dynamics simulation 385 559 novel approach to artificial proteins, biosynthesis in vitro 1041 pyrophosphatase, X-ray crystallography, structure comparison, sequence novel proteins, geometric recognition 1411 motif 823 Protein engineering reverse turns, salt bridges, chymotrypsin inhibitor-2 protein stability 103 domain insertion, protein folding 1407 self-optimized secondary structure prediction, amino acid sequences 157 Escherichia coli colicin A mutants, aggregation, hydrophobic cavity similarities, Ca distance comparison 1175 1495 structural similarities in glucoamylases, hydrophobic cluster analysis 749 glucoamylase, starch hydrolases 1479 tertiary, circularly permuted dihydrofolate reductase 1373 human glutathione-S-transferase M1-1, metal binding site 1115 tertiary, functional environs, carboxypeptidases A and B, cytochrome c hydrophobic domain of human factor IX, clotting factors 1121 1423 interchain disulphide bonds, disulphide-stabilized Fv fragments 697 tertiary structure, families of proteins with similar total structure, modular mutagenesis of TIM barrel-barrel enzyme hybrid, crystal statistical geometry 1283 structure 945 three-dimensional, glutathione-S-transferase, structure refinement 831 novel proteins, distance matrix, geometric recognition, GRAFTER 1411 validation, environmental amino acid propensity table 869 novel substrate specificity of arabinose binding protein 997 Protein threading recombinant monodomain IgG Fc binding protein 705 protein threading problem is NP-complete, sequence—structure alignment site-directed mutagenesis of snake toxin, antibody —antigen binding 917 1059 society of Japan, abstracts of 6th annual meeting 1151 Protein topology Protein expression cartoons, algorithm 31 secretory protein in Escherichia coli, N-terminal histidine tail 1277 Protein truncation Protein folding C-terminal, a-amylase, substrate recognition 1255 barnase, urea concentration, protein stability 1089 Proteinase classes, amino acid composition of globular proteins 319 cysteine proteinase inhibitor, stefins, homology modelling, structural determination of incorrect folding of globular proteins, local polarity thermodynamics 977 analysis 627 inhibitor, TIMP, conformational analysis, intrinsic fluorescence 1035 domain insertion, protein engineering 1407 Lactococcus lactis, protein engineering of catalytic domain, substrate IgG binding protein, fluorescence spectroscopy 1463 specificity, surface loop 991 kinetic and equilibrium intermediates, phase transitions 593 Pseudomonas aeruginosa secondary structure formation in model polypeptide chains, hydrophobic lipases, structure —function relationships 523 effect 633 Pseudomonas fluorescens sequence alignment 1 thiol reactivity of p-hydroxybenzoate hydroxylase 801 Protein function Pseudomonas glumae circularly permuted dihydrofolate reductase, tertiary protein structure lipases, protein structure, triacylglycerol acylhydrolase 559 1373 Pyrophosphatase genesis of proteins, human lysozyme 735 X-ray crystallography, structure comparison, sequence motif 823 1527 Subject index X-ray crystallography, structure comparison, sequence motif 1173 Sequence divergence analysis seven-helix membrane proteins, bacteriorhodopsin 1221 Query language structure prediction of seven-helix membrane proteins 1231 macromolecular, protein structure, pattern expression, protein data bank Sequence extensions 1311 role of in assembly of 6-crystallin 1395 Sequence motifs Racemate resolution basic/helix —loop—helix, principal component analysis 1433 lipase-catalysed, homochiral glycerol derivatives 589 Signal transduction Raman spectroscopy Agrobacterium VirG mutants, VirG structure modelling 905 B-lactamase inclusion bodies secondary structure 131 molecular dynamics, G protein-coupled receptors, serotonin 1441 Receptor Simulated annealing ectodomains, expression and structure, interleukin-2 1137 method for assessing solvent treatment, structure prediction 221 receptor binding site of interleukin-16, mutational mapping 663 structure prediction, homology modelling, side chain conformation 235 structure, G protein-coupled receptors, serotonin 1441 Single-chain antibodies Receptorligand interaction soluble anti-tumour sFv, aggregation, periplasmic localization 1401 computer vision-based technique 39 Site-directed annexin I Receptors mutagenesis of calcium binding site modifies properties 689 G protein-coupled, fingerprinting, sequence alignment 195 Site-directed mutagenesis LH/CG receptor, hormone—receptor recognition, computer modelling carboxypeptidase Y, introduction of acidic residues 911 205 glutamate dehydrogenase, catalytic activity, reactive cysteine, DTNB Recombinant proteins 1013 apolipoprotein (a) kringle IV types 1, 2 and 10, expression and humanization of anti-IL-2R, CDR graft 435 characterization 723 3-isopropylmalate dehydrogenase, co-enzyme specificity 401 Regulatory chain negative co-operativity of aspartate aminotransferase 413 E.coli aspartate transcarbamoylase, alanine scanning mutagenesis 673 snake toxin, three-dimensional structure 917 Renaturation T4 lysozyme crystallization, disulphide cross-linking 301 role of net charge, lysozyme, aggregation 1249 tyrosine residues, 3-isopropylmalate dehydrogenase 99 Reverse transcriptase xylanase, thermostability, introduction of disulphide bonds 1379 construction of active RNase H domain, hybrid proteins 1103 Solubility Rhodobacter capsulatus dihydrofolate reductase, increased solubility by overproduction of GroES properties of L3 loop, molecular dynamics simulation, porins 487 and GroEL 925 Ricin B chain dihydrofolate reductase, mutagenesis 933 binding domain, mutational and structural analysis of lectin activity 1261 Solvation mRNA effects, thermodynamic quantities of molecular docking, Fourier—Green secondary structure, overproduction of Mu C protein 1053 function 359 RNase homology modelling of annexin I, three-dimensional profile, fungal microbial, non-polar nuclei, protein stability 1189 conformation 1333 RNase H Solvent effect construction of active domain, HIV, reverse transcriptase, hybrid method for assessing solvent treatment, simulated annealing 221 proteins 1103 SOPM secondary structure prediction, amino acid sequences 157 Saccharomyces Staphylococcus hyicus reading-frame shift in glucoamylase improves sequence alignment with inactivation of lipases by chemical modification and mutagenesis, active other glucoamylases 1281 site serine 579 Secondary structure Stefins B-lactamase inclusion bodies, Raman spectroscopy 131 structural thermodynamics, homology modelling 977 formation in model polypeptide chains, distance geometry calculations Structural analysis 633 proteinase inhibitor TIMP, conformational analysis, intrinsic fluorescence overproduction of Mu C protein by removal of at translation initiation 1035 region 1053 Structural motif prediction, conservation of amphipathic conformations, protein structural IFNz, CD spectra 863 alignments 185 sequence analysis, pattern recognition, PRINTS database 841 structure prediction of a-helices, helix capping rules 645 Structure—activity studies Secretion human tumour necrosis factor, lymphotoxin 5 amino acid deletions in Aspergillus awamori glucoamylase, O- Structure—function relationships glycosylation 1109 fungal lipases, protein crystallography 551 Secretory protein glucoamylase, amino acid composition 393 Escherichia coli, protein expression, N-terminal histidine tail 1277 novel pancreatic lipases from guinea-pig and coypu 563 Sequence-—structure alignment Pseudomonas aeruginosa and Bacillus subtilis lipases 523 protein threading problem is NP-complete 1059 Structure prediction Sequence—structure relationships a-helices, Fourier transform, substitution tables 645 property profile matching, protein databases 23 ‘Bio’ Champollion, dynamic programming regularization 1197 Sequence alignment correlated mutations, residue contacts, distance geometry 349 fingerprinting G protein-coupled receptors 195 dihydrofolate reductase, homology modelling 213 homologous protein sequences, amino acid substitution, Dayhoff matrices human rhodopsin, seven-helix membrane proteins 1231 1323 IFN7 structural motif, CD spectra 863 multiple, compensating changes 341 interleukin-13, predictive modelling 1077 multiple, correlated mutations, structure prediction 349 local changes in protein structure, point mutations 1203 mutational and structural analysis of lectin activity in binding domain of modelling, packing of 6-strands, machine learning 1295 ricin B chain 1261 multiple sequence alignment, conservation 341 protein folding 1 protein—DNA docking, Monte Carlo simulation 761 reading-frame shift in Saccharomyces glucoamylase 1281 protein threading problem is NP-complete, sequence—structure alignment Ser/Thr and Tyr protein kinase family, sequence conservation, modelling 1059 849 selectivity, computer simulations, potassium ion channels, ROMK1 pore, Sequence analysis Shaker 859 fingerprints, pattern recognition, PRINTS database 841 self-optimized, amino acid sequences 157 Sequence comparison side chain conformation, simulated annealing, homology modelling 235 LexA repressor, CAP, iron uptake regulator 1449 solvent models, method for assessing solvent treatment 221 1528

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