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Macromolecular Crystallography Part B PDF

696 Pages·1997·17.001 MB·English
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Contributors to Volume 277 elcitrA srebmun era ni sesehtnerap gniwollof the seman of .srotubirtnoc snoitailiffA listed era .tnerruc ENRIQUE E. ABOLA (29), Protein Data Bank, SEMAJ B. CLARAGE (21), Department of -DiB Department of Biology, Brookhaven -aN chemistry and Cell Biology, Institute of tional Laboratory, Upton, New York 37911 Biosciences and Bioengineering, Rice ,ytisrevinU Houston, Texas 50077 DAVID J. BACON (26), Department of Com- puter ,ecneicS New York ,ytisrevinU New I. J. CLIFTON (23), Laboratory of raluceloM York, New York 21001 Biophysics, Oxford University, Oxford OX1 3QU, United Kingdom JOHN BADGER (17), Molecular Simulations KEVIN NATWOC (4), Department of -simehC Inc., naS Diego, California 12129 try, University of York, Heslington, York HELEN M. BERMAN (30), Department of YO1 5DD, England ,yrtsimehC Rutgers ,ytisrevinU ,yawatacsiP ELEANOR J. DODSON (32), Department of New Jersey 55880 ,yrtsimehC ytisrevinU of York, ,notgnilseH PHILIP E. BOURNE (30), naS Diego Supercom- York YO1 5DD, United Kingdom puter Center, La Jolla, California ,73029 E. M. H. DUKE (23), CCLRC Daresbury Lab- and Department of ,ygolocamrahP -revinU oratory, Warrington WA4 4AD, United sity of ,ainrofilaC naS Diego, naS Diego, Kingdom ainrofilaC 39029 DAVID GREBNESIE (20), Laboratory of -curtS SEMAJ U. BOWIE (20), Department of -simehC tural Biology dna Molecular ,enicideM yrt and Biochemistry, ytisrevinU of -rofilaC Molecular Biology Institute, University of ,ain Los Angeles, Los Angeles, ainrofilaC ,ainrofilaC Los Angeles, Los Angeles, -ilaC 59009 fornia 59009 DRAR~IG BRICOGNE (2, 5), MRC Laboratory BARRY C. FINZEL (12), Pharmacia and -pU of Molecular Biology, Cambridge 2BC john, Kalamazoo, Michigan 70094 2QH, United Kingdom, and LURE, Uni- PAULA M. D. FITZGERALD (30), Merck -eR ~tisrev Paris-Sud, 91405 Orsay, ecnarF hcraes Laboratories, Rahway, New Jersey 56070 AXLE T. BRONGER (13, 19), Howard Hughes lacideM etutitsnI and Department of -celoM ENNAZUS FORTIER (8), Departments of -mehC ular Biophysics and Biochemistry, Yale istry and Computing and Information Sci- ,ytisrevinU New Haven, Connecticut 02560 ,ecne Queen's ,ytisrevinU Kingston, oiratnO K7L 3N6, adanaC MIKE NOSRAC (25), retneC for -ucelomorcaM WILLIAM F. FUREY (31), yhpargollatsyrcoiB ral ,yhpargollatsyrC ytisrevinU of Alabama ,yrotarobaL snareteV Administration -ideM at Birmingham, Birmingham, Alabama lac ,retneC ,hgrubsttiP Pennsylvania ,04251 49253 and Department of ,yhpargollatsyrC Uni- SELRAHC W. CARTER, JR. (6), Department of ytisrev of ,hgrubsttiP ,hgrubsttiP Pennsylva- Biochemistry and Biophysics, ytisrevinU of ain 06251 North aniloraC at Chapel Hill, Chapel ,lliH GARY L. GILLILAND (28), Center for Ad- North aniloraC 99572 vanced Research in Biotechnology of eht ANTONY CHIVERTON (8), Department of Maryland Biotechnology Institute and -aN ,yrtsimehC Queen's ,ytisrevinU Kingston, tional Institute of sdradnatS and Technol- oiratnO K7L 3N6, adanaC ogy, Rockville, Maryland 05802 ix X CONTRIBUTORS TO VOLUME 277 REHPOTSIRHC J. GILMORE (5), Department of KEITH MOFFAT (22), Department of Biochem- Chemistry, University of Glasgow, Glasgow istry and Molecular Biology, University of G12 8QQ, Scotland Chicago, Chicago, Illinois 60637 JANICE GLASGOW (8), Department of Com- GEORGE N. PHILLIPS, JR. (21), Keck Center puting and Information Science, Queen's for Computational Biology, Department of University, Kingston, Ontario K7L 3N6, Biochemistry and Cell Biology, Rice Uni- adanaC versity, Houston, Texas 50077 ROGER S. GOODY (24), Abteilung Physikal- JAIME PRILUSKY (29), Bioinformatics Unit, ische Biochemie, Max Planck Institut far Weizmann Institute of Science, Rehovot Molekulare Physiologie, 44 931 Dort- ,00167 Israel mund, Germany FLORANTE A. QUIOCHO (9), Howard Hughes HERBERT A. HAUPTMAN (1), Hauptman- Medical Institute, Baylor College of Medi- Woodward Medical Research Institute, Inc., cine, Houston, Texas 03077 Buffalo, New York 30241 LYLE H. JENSEN (18), Departments of Biologi- ADAM RALPH (32), CCLRC Daresbury Labo- cal Structure and Biochemistry, University ratory, Warrington WA4 4AD, United of Washington, Seattle, Washington 59189 Kingdom T. ALWYN JONES (10, 11, 27), Department of RANDY J. READ (3, 7), Department of Medical Molecular Biology, Biomedical Centre, -pU Microbiology and Immunology, University psala University, S-75124 Uppsala, Sweden of Alberta, Edmonton, Alberta T6G 2H7, M. KJELDGAARD (10), Department of Chemis- adanaC try, University of Aarhus, DK-8000 Aar- Z. REN (23), Department of Biochemistry and ,Nuh Denmark Molecular Biology, University of ,ogacihC GERARD J. KLEYWEGT (11, 27), Department ,ogacihC Illinois 60637 of Molecular Biology, Biomedical Centre, LUKE M. RICE (13), Department of Molecular Uppsala University, S-75124 Uppsala, Biophysics and Biochemistry, Yale Univer- Sweden sity, New Haven, Connecticut 02560 VICTOR S. LAMZIN (14), European Molecular JOHN S. SACK (9), Department of Macromo- Biology Laboratory (EMBL), DESY, lecular Crystallography, Bristol-Myers 22603 Hamburg, Germany Squibb Pharmaceutical Research Institute, LAURENCE LEHERTE (8), Laboratoire de Princeton, New Jersey 34580 Physico-Chimie Informatique, Facult~s Universitaires Notre-Dame de la Paix, Na- ILME GNITHCILHCS (24), Abteilung Physikal- tour, Belgium ische Biochemie, Max Planck Institut far Molekulare Physiologie, 44 139 Dort- ROLAND L13THY (20), Amgen, Thousand mund, Germany Oaks, California 02319 PETER MAIN (4), Department of Physics, Uni- THOMAS R. SCHNEIDER (16), Max Planck In- versity of York, Heslington, York YO1 stitut far Molekulare Physiologie, 44 931 5DD, England Dortmund, Germany NANCY O. MANNING (29), Protein Data Bank, GEORGE M. SHELDRICK (16), Institut far An- Department of Biology, Brookhaven Na- organische Chemie, GOttingen University, tional Laboratory, Upton, New York 37911 D37077 GOttingen, Germany BRIAN MCMAHON (30), International Union JOEL L. SUSSMAN (29), Department of Struc- of Crystallography, Chester CH1 2HU, tural Biology, Weizmann Institute of Sci- United Kingdom ence, Rehovot 76100, Israel, and Protein ETHAN A. MERRITT (26), Department of -DiB Data Bank, Department of Biology, Brook- logical Structure, University of Washington, haven National Laboratory, Upton, New Seattle, Washington 59189 York 37911 CONTRIBUTORS TO VOLUME 772 xi S. NAHTANIMAWS (31), Biocrystallography JOHN D. WESTBROOK (30), Department of Laboratory, snareteV Administration Medi- ,yrtsimehC Rutgers ,ytisrevinU ,yawatacsiP lac ,retneC Pittsburgh, Pennsylvania ,04251 New Jersey 55880 and Department of ,yhpargollatsyrC Uni- ytisrev of ,hgrubsttiP ,hgrubsttiP -avlysnneP KEITH S. WILSON (14), European raluceloM ain 06251 Biology Laboratory (EMBL), DESY, DALE E. TRONRUD (15), Howard Hughes 30622 Hamburg, Germany lacideM Institute and Institute of raluceloM Biology, ytisrevinU of ,nogerO Eugene, -rO MARTYN WINN (32), CCLRC Daresbury Lab- oratory, Warrington WA4 4AD, United egon 30479 Kingdom F. M. D. VELLIEUX (3), Institut ed Biologie ,elarutcurtS erreiP-naeJ Ebel CEA CNRS, SHIBIN XIANG (6), Department of -simehcoiB 72083 Grenoble Cedex ,10 ecnarF yrt and ,scisyhpoiB ytisrevinU of North -raC S. WAKATSUKI (23), European Synchrotron olina at Chapel Hill, Chapel Hill, North Radiation Facility, :-38043 Grenoble aniloraC 99572 ,xedeC ecnarF KEITH D. WATENPAUGH (30), Physical and KAM Y. J. ZHANG (4), Division of Basic -icS Analytical ,yrtsimehC Pharmacia and -pU ,secne Fred Hutchinson Cancer hcraeseR john, Kalamazoo, Michigan 10094 ,retneC ,elttaeS Washington 90189 Preface Macromolecular crystallography is an indispensable component of enzy- mology. Structural biology, with macromolecular crystallography as its cen- tral technique, makes fundamental contributions to enzymology: one can pose few enzymological questions without first checking to see what relevant structures may be in the Protein Data Bank. Only then can one go on to learn what it implies about the mechanism, what suggestions it makes for genetic variation, and so on. We present these volumes to provide both a reference for practitioners of macromolecular crystallography and as a portal to the field for those who want to learn. Methods in Enzymology Volumes 411 and 115, edited by Wyckoff, Hirs, and Timasheff, were timely. They provided the basic outlines and many details of macromolecular crystallography to several scientific generations of structural biologists, and many chapters remain primary resources. Since the publication of these volumes in 1985, macromolecular crystallography has evolved from an immature science, when practitioners needed to evalu- ate and possibly redesign each step in the process, to a set of procedures that are increasingly likely to succeed. This trend toward automation had characterized small molecule crystallography during the previous two de- cades, and had begun for macromolecular crystallography at the time of the publication of the two Wyckoff et al. volumes. The trend has accelerated and doubtless will spawn a growth industry in "service" macromolecular crystallography. This is evidenced by the growing population of prac- titioners whose primary interest rests not with structure determination itself, but with what can be derived from subsequent analysis. Systematic studies and comparison of mutants, ligand complexes, and different structural poly- morphs depend on the rapid determination of structures. At the same time, fundamental experimental, theoretical, and computa- tional underpinnings of the field have experienced a parallel explosion. These include improved crystal growth and handling to provide higher resolution data, synchrotron X-ray sources, better detectors, improved methods for solving the phase problem, fragment library-based algorithms for the interpretation of electron density maps, and new refinement methods that, on the one hand, increase the radius of convergence for marginal models and, on the other, provide sophisticated models to exploit high- resolution data. We are becoming more sensitive to the importance of avoiding errors in interpretation and in understanding the limitations placed on refined parameters by the data. iiix xiv ECAFERP A consequence of these changes is that our volumes differ from the preceding set not only in content that has arisen 01 years later, but also in emphasis. We perceive that the original practitioners of the crystallographic art were physicists, who handed the tool to chemists. Many of those now solving macromolecular crystal structures have biology as their primary training and interest. The core personnel responsible for the continued development of the field have been diluted both by the dispersion into a broad variety of departments, professional disciplines, and industrial labora- tories and by the increasing numbers of relatively naive "users." Moreover, the multitude of techniques available offer multiple solutions to most of the rate-limiting steps. Often the choice of which approach to take depends more on personal experience and taste than on respect for the underlying principles. Therefore, while emphasizing experimental methods, we have included many chapters that describe the fundamentals of recent advances that may spark further transformation of the field. The chapters in these volumes present expert witness to the state-of- the-art for many individual aspects of the field. The two volumes provide the logical train of objectives necessary to solve, refine, and analyze a macromolecular crystal structure. Although these volumes may not serve as a simple textbook to introduce the field, individual chapters should provide a comprehensive background for each topic. Students and teachers alike will benefit from a careful reading of each chapter as it becomes relevant in the course of research. Part A (Volume 276) deals with the three requisites for structure solu- tion: crystals, data, and phases. The first section covers aspects of the theory and practice of growing high-quality crystals. Since exploiting intrinsic infor- mation from a crystal to its full extent depends on measuring the highest quality data, the second section provides information about radiation sources, instrumentation for recording, and software for processing these data. Finding the phases represents the final rate-limiting step in the solving of a structure. Therefore the third section includes a penetrating analysis of the statistical foundations of the phase problem and covers a broad range of experimental sources of phase information and the techniques for using them effectively. It ends with several "horizon" methods that may help transform phase determination in the coming decade. Part B (Volume 277) continues the section on horizon methods for phase determination. It follows with various ways in which structures are built, refined, and analyzed. An important development since 1985 is in model-independent, real-space refinement. Construction of atomic models is the crucial step in converting electron density maps into structures. Chap- ters are included that present the increasing trend toward computer-assisted and/or automated map interpretation. Fragment libraries representing how ECAFERP VX proteins fold are already integral parts of some of the software described previously. Use of simulated annealing in model refinement has increased the radius of convergence; it has become integrated de facto into the process of solving structures. New tools for refinement of models to fit high-resolu- tion data, when they can be measured, now permit the exploration of more detailed models. Procedures for cross-verification and post hoc analysis provide tools to help avoid unnecessary errors and possibly incorrect struc- tures. A long-term goal in structural biology is "molecular cinematography." The molecules we study undergo some kind of internal motion in carrying out its function. Some of these motions can be inferred experimentally by the analysis of the static diffraction patterns. Others require the use of multiple diffraction patterns recorded as a function of time. These topics are covered in the next section on dynamic properties. The final sections sample widely used accessory software for manipulat- ing, archiving, analyzing, and presenting structures. Databases, with tools for accessing specific information contained therein, are essential resources for those who study macromolecular structures, and even for those involved in crystal growth. Finally, we have documented some of the integrated packages of software which contain most of the tools needed for struc- ture solution. The ferocious march of technology places burdens on everyone con- cerned with the production of such a collection, and we are sincerely grateful to the authors for their cooperation and patience. The staff of Academic Press provided continuous and valuable support, which we both appreciate. CHARLES W. CARTER, JR. ROBERT M. SWEET METHODS IN ENZYMOLOGY EMULOV I. Preparation and Assay of Enzymes Edited by SIDNEY P. KCIWOLOC DNA NATHAN O. KAPLAN EMULOV II. Preparation and Assay of Enzymes Edited by SIDNEY P. KCIWOLOC DNA NATHAN O. KAPLAN EMULOV III. Preparation and Assay of Substrates Edited by SIDNEY P. KCIWOLOC DNA NATHAN O. KAPLAN EMULOV IV. Special Techniques for the Enzymologist Edited by YENDIS P. KCIWOLOC DNA NATHAN O. KAPLAN EMULOV V. Preparation and Assay of Enzymes Edited yb SIDNEY P. KCIWOLOC DNA NATHAN O. KAPLAN EMULOV VI. Preparation and Assay of Enzymes (Continued) Preparation and Assay of Substrates Special Techniques Edited by SIDNEY P. KCIWOLOC DNA NATHAN O. KAPLAN EMULOV VII. Cumulative Subject Index by Edited SIDNEY P. KCIWOLOC DNA NATHAN O. KAPLAN EMULOV VIII. Complex Carbohydrates Edited by ELIZABETH F. NEUFELD DNA VICTOR GRUBSNIG EMULOV IX. Carbohydrate Metabolism Edited yb WILLIS A. WOOD EMULOV X. Oxidation and Phosphorylation by Edited RONALD W. KOORBATSE DNA MAYNARD E. NAMLLUP EMULOV XI. emyznE Structure Edited by C. H. W. HIRS EMULOV XII. Nucleic Acids (Parts A and B) Edited by ECNERWAL NAMSSORG DNA KIVIE EVADLOM EMULOV XIII. Citric Acid Cycle Edited yb J. M. NIETSNEWOL EMULOV XIV. Lipids Edited by J. M. NIETSNEWOL EMULOV XV. Steroids and Terpenoids Edited yb DNOMYAR B. NOTYALC EMULOV XVI. Fast Reactions Edited yb NITSUK HTENNEK xvii .°° XVlU METHODS IN ENZYMOLOGY EMULOV XVII. Metabolism of Amino Acids and Amines (Parts A and B) Edited by HERBERT TABOR DNA CELIA WHITE TABOR EMULOV XVIII. Vitamins and Coenzymes (Parts A, B, and C) Edited by DONALD B. McCoRMICK DNA LEMUEL D. WRIGHT EMULOV XIX. Proteolytic Enzymes Edited by GERTRUDE E. NNAMLREP DNA LASZLO LORAND EMULOV XX. Nucleic Acids and Protein Synthesis (Part C) Edited by KIVIE MOLDAVE DNA ECNERWAL NAMSSORG EMULOV XXI. Nucleic Acids (Part D) Edited by LAWRENCE NAMSSORG DNA KIVIE MOLDAVE EMULOV XXII. Enzyme Purification and Related Techniques Edited by WILLIAM B. YBOKAJ EMULOV XXIII. Photosynthesis (Part )A Edited by ANTHONY SAN PIETRO EMULOV XXIV. Photosynthesis and Nitrogen Fixation (Part B) Edited by ANTHONY SAN PIETRO EMULOV XXV. Enzyme Structure (Part B) Edited by C. H. W. HIRS DNA SERGE N. FFEHSAMIT EMULOV XXVI. Enzyme Structure (Part C) Edited by C. H. W. HIRS DNA SERGE N. TIMASHEFF EMULOV XXVII. Enzyme Structure (Part D) Edited by C. H. W. HIRS DNA SERGE N. FFEHSAMIT EMULOV XXVIII. Complex Carbohydrates (Part B) Edited by VICTOR GRUBSNIG EMULOV XXIX. Nucleic Acids and Protein Synthesis (Part E) Edited by LAWRENCE NAMSSORG DNA KIVIE MOLDAVE EMULOV XXX. Nucleic Acids and Protein Synthesis (Part F) Edited by KIVIE MOLDAVE DNA LAWRENCE NAMSSORG EMULOV XXXI. Biomembranes (Part A) Edited by SIDNEY FLEISCHER DNA LESTER PACKER EMULOV XXXII. Biomembranes (Part B) Edited by SIDNEY FLEISCHER DNA LESTER PACKER EMULOV XXXIII. Cumulative Subject Index Volumes I-XXX Edited by MARTHA G. DENNIS DNA EDWARD A. DENNIS EMULOV XXXIV. Affinity Techniques (Enzyme Purification: Part B) Edited by WILLIAM B. JAKOBY DNA MEIR WILCHEK EMULOV XXXV. Lipids (Part B) Edited by JOHN M. NIETSNEWOL METHODS IN ENZYMOLOGY xix EMULOV XXXVI. Hormone Action (Part A: Steroid Hormones) Edited by BERT W. O'MALLEY DNA JOEL G. HARDMAN EMULOV XXXVII. Hormone Action (Part B: Peptide Hormones) Edited by TREB W. O'MALLEY DNA JOEL G. NAMDRAH EMULOV XXXVIII. Hormone Action (Part C: Cyclic Nucleotides) Edited by JOEL G. NAMDRAH DNA TREB W. YELLAM'O EMULOV XXXIX. Hormone Action (Part D: Isolated Cells, Tissues, and Organ Systems) Edited by JOEL G. HARDMAN DNA BERT W. O'MALLEY EMULOV XL. Hormone Action (Part E: Nuclear Structure and Function) Edited by BERT W. O'MALLEY DNA JOEL G. HARDMAN EMULOV XLI. Carbohydrate Metabolism (Part B) Edited by W. A. DOOW EMULOV XLII. Carbohydrate Metabolism (Part C) Edited by W. A. DOOW EMULOV XLIII. Antibiotics Edited by NHOJ H. HSAH EMULOV XLIV. Immobilized Enzymes Edited by SUALK HCABSOM EMULOV XLV. Proteolytic Enzymes (Part B) Edited by OLZSAL DNAROL EMULOV XLVI. Affinity Labeling Edited yb WILLIAM B. JAKOBY DNA MEIR WILCHEK EMULOV XLVII. Enzyme Structure (Part E) Edited by .C H. W. HIRS DNA EGRES N. FFEHSAMIT EMULOV XLVIII. Enzyme Structure (Part F) Edited by C. H. W. HIRS DNA EGRES N. FFEHSAMIT EMULOV XLIX. Enzyme Structure (Part G) Edited yb .C H. W. HIRS DNA EGRES N. FFEHSAMIT EMULOV L. Complex Carbohydrates (Part C) Edited by ROTCIV GRUBSNIG EMULOV LI. Purine and Pyrimidine Nucleotide Metabolism Edited by PATRICIA A. HOFFEE DNA MARY ELLEN JONES EMULOV LII. Biomembranes (Part C: Biological Oxidations) Edited by SIDNEY FLEISCHER DNA LESTER PACKER EMULOV LIII. Biomembranes (Part "D Biological Oxidations) Edited by SIDNEY FLEISCHER DNA LESTER PACKER EMULOV LIV. Biomembranes (Part E: Biological Oxidations) Edited by SIDNEY FLE1SCHER DNA LESTER PACKER XX METHODS NI ENZYMOLOGY EMULOV LV. Biomembranes (Part F: Bioenergetics) Edited by SIDNEY FLEISCHER DNA LESTER PACKER EMULOV LVI. Biomembranes (Part G: Bioenergetics) Edited by SIDNEY FLEISCHER DNA LESTER PACKER EMULOV LVII. Bioluminescence and Chemiluminescence Edited by ENELRAM A. DELucA EMULOV LVIII. Cell Culture Edited by WILLIAM B. JAKOBY DNA IRA PASTAN EMULOV LIX. Nucleic Acids and Protein Synthesis (Part G) Edited by KIVIE MOLDAVE DNA LAWRENCE GROSSMAN EMULOV LX. Nucleic Acids and Protein Synthesis (Part H) Edited by KIVlE MOLDAVE DNA LAWRENCE GROSSMAN EMULOV .16 Enzyme Structure (Part H) Edited by C. H. W. HIRS DNA EGRES N. FFEHSAMIT EMULOV .26 Vitamins and Coenzymes (Part D) Edited by DONALD B. McCORMICK DNA LEMUEL D. WRIGHT EMULOV .36 Enzyme Kinetics and Mechanism (Part A: Initial Rate and Inhibitor Methods) Edited by DANIEL L. PURICH EMULOV .46 Enzyme Kinetics and Mechanism (Part B: Isotopic Probes and Com- plex Enzyme Systems) Edited by DANIEL L. PURICH EMULOV .56 Nucleic Acids (Part I) Edited yb LAWRENCE GROSSMAN DNA KIVIE MOLDAVE EMULOV .66 Vitamins and Coenzymes (Part E) Edited by DONALD B. McCoRMICK DNA LEMUEL D. WRIGHT EMULOV .76 Vitamins and Coenzymes (Part F) Edited by DONALD B. McCORMICK DNA LEMUEL D. WRIGHT VOLUME 68. Recombinant DNA Edited by YAR Wu EMULOV .96 Photosynthesis and Nitrogen Fixation (Part C) Edited yb ANTHONY SAN PIETRO EMULOV .07 Immunochemical Techniques (Part A) Edited by HELEN VAN VUNAKIS DNA JOHN J. LANGONE EMULOV .17 Lipids (Part C) Edited by JOHN M. NIETSNEWOL EMULOV .27 Lipids (Part D) Edited by JOHN M. NIETSNEWOL

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