Energetics of Biological Macromolecules Part B

583 Pages·1998·13.13 MB·English

by  Gary K. Ackers, Michael L. Johnson (Eds.)

Contributors to Volume 295
Article numbers are in parentheses following the names of contributors.
Affiliations listed are current.
GARY K. ACKERS (10, 22), Department of Bio- Einstein College of Medicine of Yeshiva
chemistry and Molecular Biophysics, Wash- ,ytisrevinU Bronx, New York 16401
ington University School of Medicine, .tS PAUL W. CnUN (12), Department of Biochem-
Louis, Missouri 01136 yrtsi and Molecular Biology, University of
NORMA M. ALLEWELL (3), Department of Florida College of Medicine, ,ellivseniaG
Biochemistry, University of Minnesota, .tS adirolF 5420-01623
Paul, Minnesota 80155 ERIC DEPREZ (15), Institute ed Bioiogie
BRIAN M. BAKER (14), Department of Bio- Physico Chimique, 50057 Paris, ecnarF
,yrtsimehc University of Iowa, Iowa ,ytiC CARMELO DI PRIMO (15), Institute ed Biologie
Iowa 24225 Physico Chimique, 50057 Paris, ecnarF
ROBERT L. BALDWIN (1), Department of Bio- MICHAEL L. DOYLE (5), Department of -curtS
chemistry, Stanford University, Stanford, tural Biology, SmithKline Beecham Phar-
ainrofilaC 9115-50349 ,slacituecam King of Prussia, Pennsylva-
DOROTHY BECKEaW (21), Department of ain 60491
Chemistry and Biochemistry, University of HARVEY F. FISHER (16, 17), Laboratory of
Maryland Baltimore County, Baltimore, Molecular Biochemistry, Veterans Affairs
Maryland 05212 Medical Center, Kansas City, Missouri
Louise BENAZZ1 (11), lstituto di eigolonceT 82146
Biomediche Avanzate led CNR, 20090 ERNESTO FREmE (6), Department of ,ygoloiB
,etargeS Italy ehT Johns Hopkins ,ytisrevinU ,eromitlaB
PAUL BEROZA (9), Department of Molecular Maryland 81212
Biology, ehT Scripps Research ,etutitsnI La YECATS A. GAVIGAN (20), Department of Mo-
,alloJ California 73029 ralucel Biology and Biochemistry, -revinU
VICTOR A. BLOOMFIELD (18), Department of sity of ,ainrofilaC Irvine, California 79629
Biochemistry, University of Minnesota, .tS PRESTON HENSLEY (5), Department of -curtS
Paul, Minnesota 80155 tural Biology, SmithKline Beecham Phar-
MICHAEL BRENOWITZ (19), Department of ,slacituecam King of Prussia, Pennsylva-
Biochemistry and Center for Synchrotron ain 60491
,secneicsoiB Albert Einstein College of KAUNA HmSTOVA (4), Department of Physi-
Medicine of Yeshiva University, Bronx, ology and Biophysics, ytisrevinU of -rofilaC
New York 16401 ,ain Irvine, California 79629
DAVID S. BURZ (22), Wadsworth ,retneC Divi- GASTON HuI BON HOA (15), Institute ed Bio-
sion of citeneG ,sredrosiD Axelrod ,etutitsnI logie Physico Chimique, 75005 Paris,
Albany, New York 80221 ecnarF
DAVID A. CASE (9), Department of raluceloM LAWRENCE INDYK (17), Laboratory of -celoM
Biology, ehT Scripps hcraeseR ,etutitsnI La ular ,yrtsimehcoiB snareteV Affairs lacideM
Jolla, California 73029 ,retneC Kansas City, Missouri 82146
MARK CHANCE (19), Departments of Physiol- NEVILLE R. KALLENBACH (2), Department of
ogy and Biophysics and Biochemistry and Chemistry, New York University, New
retneC for Synchrotron ,secneicsoiB Albert York, New York 30001
X CONTRIBUTORS TO VOLUME 295
ALEXANDRA L. KLINGER (10), Department of ,etutitsnI ytisrevinU of ,hatU Salt Lake ,ytiC
Biochembtry and Molecular Biophysics, hatU 0335-21148
Washington ytisrevinU School of ,enicideM LAURA T. PERINI (20), Department of -uceloM
.tS Louis, Missouri 01136 ral Biology and Biochemistry, ytisrevinU of
ALEXEY S. LADOKHIN (4), Department of ,ainrofilaC Irvine, California 79629
Physiology and Biophysics, University of MICHELE PERRELLA (11), Dipartimento id
,ainrofilaC Irvine, California 79629 ezneicS e Tecnologie Biomediche, Uni-
THOMAS M. LAUE (24), Department of Bio- dtisrev di Milano, 20090 ,etargeS Italy
chemistry and Molecular Biology, -revinU THERESA M. RIDGEWAY (24), Department of
sity of New Hampshire, Durham, New Biochemistry and Molecular Biology, -inU
Hampshire 42830 ytisrev of New Hampshire, Durham, New
VINCE J. LICATA (3), Department of -igoloiB Hampshire 42830
lac Sciences, Louisiana State ,ytisrevinU MARILENA RIPAMONTI (11), Istituto id Tec-
Baton Rouge, Louisiana 30807 nologie Biomediche Avanzate led CNR,
IRENE LUQUE (6), DepartmentofBiology, ehT 09002 ,etargeS Italy
Johns Hopkins University, Baltimore, CAROL A. ROHL (1), Department of
Maryland 81212 Biochemistry, University of ,notgnihsaW
JEFFREY T. MASON (23), Division of Biophys- ,elttaeS Washington 2477-59189
ics, Department of Cellular Pathology, IOULIA ROUZINA (18), Department of Bio-
Armed secroF Institute of ,ygolohtaP Wash- chemistry, University of Minnesota, .tS
,notgni DC 0006-60302 Paul, Minnesota 80155
MARK A. MCLEAN (15), Beckman Institute ROSAmA RUSSO (11), Dipartimento id Scienze
for Advanced ecneicS and Technology, -inU e Tecnologie Biomediche, tgtisrevinU id -iM
ytisrev of Illinois, ,anabrU Illinois 10816 ,onal 20090 ,etargeS Italy
EDDINE K. MERABET (22), Department of JEFFERY M. SCHWEHM (8), Department of
Biochemistry and Molecular Biophysics, yrtsimehC and Biochemistry, University of
Washington ytisrevinU School of ,enicideM Arkansas, Fayetteville, Arkansas -10727
.tS Louis, Missouri 01136 1021
ALLEN P. MINTON (7), Section on Physical BIANCA SCLAVI (19), Department of Physiol-
Biochemistry, Laboratory of Biochemistry ogy and Biophysics and retneC for Synchro-
and ,sciteneG National Institute of setebaiD tron ,secneicsoiB Albert Einstein egelloC of
and Digestive and Kidney Diseases, Medicine of Yeshiva University, Bronx,
National Institutes of Health, Bethesda, New York 16401
Maryland 0380-29802 DONALD F. SENEAR (20), Department of Mo-
THOMAS P. MOODY (24), Department of Bio- ralucel Biology and Biochemistry, -revinU
chemistry and Molecular Biology, -revinU sity of ,ainrofilaC Irvine, California 79629
sity of New Hampshire, Durham, New HARVEY K. SHEPARD (24), Department of
Hampshire 42830 Physics, University of New Hampshire,
THOMAS A. MORTON (13), Division of Bio- Durham, New Hampshire 42830
chemistry and Molecular Biology, John STEPHEN G. SLIGAR (15), Beckman Institute
nitruC School of lacideM ,hcraeseR Austra- for Advanced ecneicS and Technology, -inU
lian National University, Canberra, ACT ytisrev of Illinois, ,anabrU Illinois 10816
,0020 Australia ERIK J. SPEK (2), Department of ,yrtsimehC
KENNETH P. MURPHY (14), Department of New York University, New York, New
Biochemistry, University of Iowa, Iowa York 30001
,ytiC Iowa 24225 WESLEY E. STITES (8), Department of -simehC
DAVID G. MYSZKA (13), Department of -nO yrt and Biochemistry, ytisrevinU of Arkan-
cological Sciences, Huntsman Cancer ,sas ,elliveneyaF Arkansas 1021-10727
CONTRIBUTORS TO VOLUME 295 xi
MICHAEL SULLIVAN (19), Department of TIMOTHY J. WILSON (24), Department of Bio-
Physiology and Biophysics and Center for chemistry and Molecular Biology, Univer-
Synchrotron Biosciences, Albert Einstein sity of New Hampshire, Durham, New
College of Medicine of Yeshiva University, Hampshire 42830
Bronx, New York 16401
WILLIAM C. WIMLEY (4), Department of Phys-
JON TALLY (16), Laboratory of Molecular
iology and Biophysics, University of Cali-
Biochemistry, Veterans Affairs Medical
fornia, Irvine, California 92697
Center, Kansas City, Missouri 82146
NEHPETS H. WHITE (4), Department of Physi- SARAH WOODSON (19), Department of Chem-
ology and Biophysics, University of Califor- istry and Biochemistry, University of Mary-
nia, Irvine, California 92697 land, College Park, Maryland 1202-24702
Preface
It has been three years since "Energetics of Biological Macromole-
cules," Methods in Enzymology, Volume 952 was published. During this
time the demand for modern thermodynamic techniques and conceptualiza-
tions has continued to grow in parallel with ongoing discoveries and synthe-
ses (e.g., by recombinant methods) of previously unknown biological macro-
molecules and the increased efforts to understand their biological
significance at new levels of structural and energetic detail. These trends,
and the strongly favorable response to the earlier volume, have motivated
a second ensemble of biothermodynamic articles. We trust that this volume
will also be especially useful to researchers and students whose goal is to
connect the functional energetics of macromolecular structures with their
biological functions.
GARY K. ACKERS
MICHAEL L. NOSNHOJ
iiix
METHODS IN ENZYMOLOGY
EMULOV I. Preparation and Assay of Enzymes
Edited by SIDNEY P. COLOWICK AND NATHAN 0. KAPLAN
EMULOV II. Preparation and Assay of Enzymes
Edited yb SIDNEY P. COLOWICK AND NATHAN O. KAPLAN
EMULOV III. Preparation and Assay of Substrates
Edited by YENDIS .P KCIWOLOC DNA NAHTAN 0. NALPAK
EMULOV IV. Special Techniques for the Enzymologist
Edited by YEND1S .P KCIWOLOC DNA NAHTAN O. NALPAK
EMULOV V. Preparation and Assay of Enzymes
Edited by SIDNEY P. COLOWICK AND NATHAN 0. KAPLAN
EMULOV VI. Preparation and Assay of Enzymes (Continued)
Preparation and Assay of Substrates
Special Techniques
Edited by YENDIS P. KCIWOLOC DNA NAHTAN O. NALPAK
EMULOV VII. Cumulative Subject Index
Edited by SIDNEY P. COLOW1CK AND NATHAN 0. KAPLAN
EMULOV VIII. Complex Carbohydrates
Edited yb ELIZABETH F. NEUFELD AND VICTOR GINSBURG
EMULOV IX. Carbohydrate Metabolism
Edited by SILLIW A. DOOW
EMULOV X. Oxidation and Phosphorylation
Edited by DLANOR W. KOORBATSE DNA DRANYAM E. NAMLLUP
EMULOV XI. Enzyme 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 by J. .M NIETSNEWOL
EMULOV XIV. Lipids
Edited by J. .M NIETSNEWOL
EMULOV XV. Steroids and Terpenoids
Edited yb DNOMYAR B. NOTYALC
VOLUME XVl. Fast Reactions
Edited by HTENNEK NITSUK
VX
xvi METHODS IN ENZYMOLOGY
EMULOV XVII. Metabolism of Amino Acids dna Amines (Parts A dna B)
Edited by HERBERT TABOR DNA CELIA WHITE TABOR
EMULOV XVIII. Vitamins dna Coenzymes (Parts A, B, dna )C
Edited by DONALD B. McCORMICK DNA LEMUEL D. WRIGHT
VOLUME XlX. Proteolytic Enzymes
Edited by GERTRUDE E. PERLMANN AND LASZLO LORAND
EMULOV XX. Nucleic Acids dna Protein Synthesis (Part )C
Edited by KIVlE MOLDAVE DNA LAWRENCE NAMSSORG
EMULOV XXL Nucleic Acids (Part D)
Edited by LAWRENCE NAMSSORG DNA KIVIE EVADLOM
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 dna Nitrogen Fixation (Part B)
Edited by ANTHONY SAN PIETRO
EMULOV XXV. Enzyme Structure (Part B)
Edited by C. H. W. HIRS DNA SERGE N. TIMASHEFF
EMULOV XXVI. Enzyme Structure (Part C)
Edited by C. H. W. HIRS DNA SERGE N. FFEHSAMIT
EMULOV XXVII. Enzyme Structure (Part D)
Edited by C. H. W. HIRS DNA SERGE N. TIMASHEFF
EMULOV XXVIII. Complex Carbohydrates (Part B)
Edited by VICTOR GRUBSNIG
EMULOV XXIX. Nucleic Acids dna Protein Synthesis (Part E)
Edited by LAWRENCE NAMSSORG DNA KIVlE MOLDAVE
EMULOV XXX. Nucleic Acids dna Protein Synthesis (Part F)
Edited by KIVIE MOLDAVE DNA ECNERWAL 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 O. 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 NI ENZYMOLOGY xvii
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 BERT W. O'MALLEY DNA JOEL G. HARDMAN
EMULOV XXXVIII. Hormone Action (Part C: Cyclic Nucleotides)
Edited by JOEL G. HARDMAN DNA BERT W. O'MALLEY
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 JOHN H. HASH
EMULOV XLIV. Immobilized Enzymes
Edited by SUALK HCABSOM
EMULOV XLV. Proteolytic Enzymes (Part B)
Edited by OLZSAL DNAROL
EMULOV XLVI. Affinity Labeling
Edited by 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 by C. H. W. HIRS DNA EGRES N. FFEHSAMIT
EMULOV L. Complex Carbohydrates (Part C)
Edited by ROTCIV ORUBSNIG
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 FLEISCHER DNA LESTER PACKER
xviii METHODS IN ENZYMOLOGY
EMULOV LV. Biomembranes (Part F: Bioenergetics)
Edited by SIDNEY FLEISCHER AND LESTER PACKER
EMULOV LVI. Biomembranes (Part "G Bioenergetics)
Edited by YENDIS FLEISCHER AND LESTER PACKER
EMULOV LVII. Bioluminescence and Chemiluminescence
Edited by ENELRAM A. DELUCA
EMULOV LVIII. Cell Culture
Edited by WILLIAM B. YBOKAJ AND IRA PASTAN
EMULOV LIX. Nucleic Acids and Protein Synthesis (Part G)
Edited by KIVIE MOLDAVE AND LAWRENCE GROSSMAN
EMULOV LX. Nucleic Acids and Protein Synthesis (Part H)
Edited by KIVIE MOLDAVE AND LAWRENCE GROSSMAN
EMULOV .16 Enzyme Structure (Part H)
Edited by C. H. W. HIRS DNA EGRES N. EFEHSAMIT
EMULOV .26 Vitamins and Coenzymes (Part D)
Edited by DONALD B. McCoRMICK AND 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 by LAWRENCE GROSSMAN AND KIVIE MOLDAVE
EMULOV .66 Vitamins and Coenzymes (Part E)
Edited by DONALD B. McCoRMICK AND LEMUEL D. WRIGHT
EMULOV .76 Vitamins and Coenzymes (Part F)
Edited by DONALD B. McCoRMICK AND LEMUEL D. WRIGHT
EMULOV .86 Recombinant DNA
Edited by YAR Wu
EMULOV .96 Photosynthesis and Nitrogen Fixation (Part C)
Edited yb YNOHTNA NAS ORTEIP
EMULOV 70. Immunochemical Techniques (Part A)
Edited by HELEN VAN VUNAKIS AND JOHN J. LANGONE
EMULOV .17 Lipids (Part C)
Edited by JOHN M. NIETSNEWOL
EMULOV .27 Lipids (Part D)
Edited yb JOHN M. NIETSNEWOL
EMULOV .37 Immunochemical Techniques (Part B)
Edited by JOHN J. ENOGNAL DNA HELEN NAV SIKANUV
METHODSIN ENZYMOLOGY xix
EMULOV .47 Immunochemical Techniques (Part C)
Edited by NHOJ J. LANGONE AND HELEN VAN VUNAKIS
EMULOV .57 Cumulative Subject Index Volumes XXXI, XXXII, XXXIV-LX
Edited yb EDWARD A. DENNIS AND MARTHA G. DENNIS
EMULOV .67 Hemoglobins
Edited by ERALDO ANTONINI, LUIGI ROSSI-BERNARDI, AND EMILIA CHIANCONE
EMULOV .77 Detoxication and Drug Metabolism
Edited by MAILLIW B. YBOKAJ
EMULOV .87 Interferons (Part A)
Edited yb YENDIS AKTSEP
EMULOV .97 Interferons (Part B)
Edited by YENDIS AKTSEP
EMULOV .08 Proteolytic Enzymes (Part C)
Edited by OLZSAL DNAROL
EMULOV .18 Biomembranes (Part H: Visual Pigments and Purple Mem-
branes, I)
Edited by RETSEL REKCAP
EMULOV .28 Structural and Contractile Proteins (Part A: Extracellular Matrix)
Edited by LEON W, CUNNINGHAM AND DIXIE W. FREDERIKSEN
EMULOV .38 Complex Carbohydrates (Part D)
Edited by ROTCIV GRUBSNIG
EMULOV .48 Immunochemical Techniques (Part D: Selected Immunoassays)
Edited by JOHN J. LANGONE AND HELEN VAN VUNAKIS
EMULOV .58 Structural and Contractile Proteins (Part B: The Contractile Appara-
tus and the Cytoskeleton)
Edited by DIXIE W. FREDERIKSEN AND LEON W. CUNNINGHAM
EMULOV .68 Prostaglandins and Arachidonate Metabolites
Edited by WILLIAM E. M, LANDS AND WILLIAM L, SMITH
EMULOV .78 Enzyme Kinetics and Mechanism (Part C: Intermediates, Stereo-
chemistry, and Rate Studies)
Edited by LEINAD L. HCIRUP
EMULOV .88 Biomembranes (Part I: Visual Pigments and Purple Mem-
branes, II)
Edited by RETSEL REKCAP
EMULOV .98 Carbohydrate Metabolism (Part D)
Edited by SILLIW A. DOOW
EMULOV .09 Carbohydrate Metabolism (Part E)
Edited by SILLIW A. DOOW
EMULOV .19 Enzyme Structure (Part I)
Edited by .C H. W. HIRS DNA EGRES N. FFEHSAMIT
XX METHODS IN ENZYMOLOGY
EMULOV 92. Immunochemical Techniques (Part E: Monoclonal Antibodies and
General Immunoassay Methods)
Edited by JOHN J. LANGONE DNA HELEN VAN SIKANUV
EMULOV 93. Immunochemical Techniques (Part F: Conventional Antibodies, Fc
Receptors, and Cytotoxicity)
Edited by JOHN J. LANGONE DNA HELEN VAN SIKANUV
EMULOV 94. Polyamines
Edited yb HERBERT TABOR DNA CELIA WHITE TABOR
EMULOV 95. Cumulative Subject Index Volumes 61-74, 76-80
Edited yb EDWARD A. DENNIS DNA MARTHA G. DENNIS
EMULOV 96. Biomembranes Part J: Membrane Biogenesis: Assembly and Tar-
geting (General Methods; Eukaryotes)
Edited yb SIDNEY FLEISCHER DNA BECCA REHCSIELF
EMULOV 97. Biomembranes Part K: Membrane Biogenesis: Assembly and Tar-
geting (Prokaryotes, Mitochondria, and Chloroplasts)
Edited by SIDNEY FLEISCHER DNA BECCA REHCSIELF
EMULOV 98. Biomembranes (Part L: Membrane Biogenesis: Processing and Re-
cycling)
Edited by SIDNEY FLEISCHER AND BECCA FLEISCHER
EMULOV 99. Hormone Action (Part F: Protein Kinases)
Edited by JACKIE D. CORBIN DNA JOEL G. HARDMAN
EMULOV 100. Recombinant DNA (Part )B
Edited by RAY Wu, LAWRENCE ,NAMSSORG DNA KIVIE MOLDAVE
EMULOV 101. Recombinant DNA (Part C)
Edited by RAY Wu, LAWRENCE ,NAMSSORG DNA KIVIE EVADLOM
EMULOV 102. Hormone Action (Part G: Calmodulin and Calcium-Binding Pro-
teins)
Edited by ANTHONY R. MEANS AND BERT W. O'MALLEY
EMULOV 103. Hormone Action (Part H: Neuroendocrine Peptides)
Edited by P. MICHAEL NNOC
EMULOV 104. Enzyme Purification and Related Techniques (Part C)
Edited by WILLIAM B. YBOKAJ
EMULOV 105. Oxygen Radicals in Biological Systems
Edited by LESTER PACKER
EMULOV 106. Posttranslational Modifications (Part )A
Edited yb FINN WOLD DNA KIVIE EVADLOM
EMULOV 107. Posttranslational Modifications (Part )B
Edited by FINN WOLD DNA KIVlE EVADLOM