numerical computer methods, part d

Nucleic Acids and Protein Synthesis Part C Edited by Kivie Moldave and Lawrence Grossman Volume XXI.. Nucleic Acids and Protein Synthesis Part E Edited by Lawrence Grossman and Kivie Mol

DIVISION OF BIOLOGY CALIFORNIA INSTITUTE OF TECHNOLOGY

PASADENA, CALIFORNIA

FOUNDING EDITORS

Sidney P Colowick and Nathan O Kaplan

Article numbers are in parentheses and following the names of contributors.

Affiliations listed are current.

David Baker (4), Department of

Bio-chemistry and Howard Hughes

Medi-cal Institute, University of Washington,

Seattle, Washington 98195

Nathan A Baker (5), Department of

Biochemistry and Molecular Biophysics,

Washington University in St Louis,

St Louis, Missouri 63110

Emery N Brown (16), Department of

Anesthesia and Critical Care, Division

of Health Sciences and Technology,

Harvard Medical School and

Massachu-setts Institute Technology, Boston,

Massachusetts 02114

Joseph C Cappelleri (17), Global

Re-search and Development, Pfizer Inc.,

Groton, Connecticut 06340

Yong Choe (16), Max Planck Institute of

Neurobiology, Martinsried D-82152,

Germany

Adrian H Elcock (8), Department of

Biochemistry, University of Iowa, Iowa

City, Iowa 52242

Patrick J Fleming (3), Jenkins Department

of Biophysics, Johns Hopkins University,

Baltimore, Maryland 21218

Angel E Garci´a (6), Theoretical Biology

and Biophysics Group, Los Alamos

National Laboratory, Los Alamos, New

Mexico 87545

S Gnanakaran (6), Theoretical Biology

and Biophysics Group, Los Alamos

National Laboratory, Los Alamos, New

Mexico 87545

Norma Greenfield (12), Department

of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854

Craig Hill (15), Department of mology and High Throughput Screen- ing, Celera Genomics, San Francisco, California 94080

Enzy-Sven Hovmo¨ller (1), Structural istry, Stockholm University, Stockholm S-10691, Sweden

Chem-John H Ipsen (9), Physics Department, MEMPHYS Center for Biomem- brane Research, University of South- ern Denmark, Odense M DK-5230, Denmark

Roger E Ison (1), Manic Software, Loveland, Colorado 80537

James W Janc (15), Department of mology and High Throughput Screen- ing, Celera Genomics, San Francisco, California 94080

Enzy-Robert H Kretsinger (1), Department

of Biology, University of Virginia, Charlottesville, Virginia 22903

Petr Kuzmicˇ (15), Biokin Ltd., Pullman, Washington 99163

Joseph Lau (17), Institute for Clinical Research and Health Policy Studies, Tufts-New England Medical Center, Boston, Massachusetts 02111

vii

Ling Miao (9), Physics Department,

MEM-PHYS Center for Biomembrane

Re-search, University of Southern Denmark,

Odense M DK-5230, Denmark

Kira M S Misura (4), Department of

Biochemistry and Howard Hughes

Med-ical Institute, University of Washington,

Seattle, Washington 98195

Ole Mouritsen (9), Physics

Depart-ment, MEMPHYS Center for

Biomem-brane Research, University of Southern

Denmark, Odense M DK-5230, Denmark

Jay I Myung (14), Department of

Psychology, Ohio State University,

Columbus, Ohio 43210

Morten Nielsen (9), Biocentrum-DTU,

Technical University of Denmark,

Lyngby DK-2800, Denmark

Hugh Nymeyer (6), Theoretical Biology

and Biophysics Group, Los Alamos

National Laboratory, Los Alamos, New

Mexico 87545

Mark A Pitt (14), Department of

Psychology, Ohio State University,

Columbus, Ohio 43210

Douglas Poland (18), Department of

Chemistry, The Johns Hopkins

University, Baltimore, Maryland 21218

James Polson (9), Department of Physics,

University of Prince Edward Island,

Charllottetown, Prince Edward C1A

4P3, Canada

Carol Rohl (4), Department of

Biochem-istry and Howard Hughes Medical

Institute, University of Washington,

Seattle, Washington 98195

George D Rose (3), Jenkins

Depart-ment of Biophysics, Johns Hopkins

University, Baltimore, Maryland 21218

Robert Schleif (2), Biology Department,

Johns Hopkins University, Baltimore,

Maryland 21218

Christopher H Schmid (17), Institute for Clinical Research and Health Policy Studies, Tufts-New England Medical Center, Boston, Massachusetts 02111 Victor Solo (16), Department of Electri- cal Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan 48101

Narasihma Sreerama (13), Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523

Rajgopal Srinivasan (3), Jenkins ment of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218 Martin Straume (7), Department of Inter- nal Medicine, Division of Endocrinol- ogy and Metabolism, University of Virginia Health System, Charlottesville, Virginia 22904

Depart-Charlie E M Strauss (4), Biosciences Division, Los Alamos National Labora- tory, Los Alamos, New Mexico 87545 Joel Tellinghuisen (11), Department

of Chemistry, Vanderbilt University, Nashville, Tennessee 37235

Jenifer Thewalt (9), Department of sics, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada Antonius VanDongen (10), Department

Phy-of Pharmacology, Duke University, Durham, North Carolina 27710 Ilpo Vattulainen (9), Laboratory of Computational Engineering, Helsinki University of Technology, Espoo 02150, Finland

Robert W Woody (13), Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523

Zhenhua Zhang (16), Human Computer

Interaction Institute, Carnegie Melon

University, Pittsburgh, Pennsylvania

15213

Hong Zhu (9), Department of Physics,

McGill University, Montreal, Quebec

H3A 2T8, Canada

Martin Zuckerman (9), Department

of Physics, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada

The speed of laboratory computers doubles every year or two As a sequence, complex and time-consuming data analysis methods, that were pro-hibitively slow a few years ago, can now be routinely employed Examples ofsuch methods within this volume include wavelets, transfer functions, inverseconvolutions, robust fitting, moment analysis, maximum-entropy, and singularvalue decomposition There are also many new and exciting approaches formodeling and prediction of biologically relevant molecules such as proteins,lipid bilayers, and ion channels.

con-There is also an interesting trend in the educational background ofnew biomedical researchers over the last few years For example, three ofthe authors in this volume are Ph.D mathematicians who have facultyappointments in the School of Medicine at the University of Virginia

The combination of faster computers and more quantitatively oriented medical researchers has yielded new and more precise methods for the analysis

bio-of biomedical data These better analyses have enhanced the conclusions thatcan be drawn from biomedical data and they have changed the way that theexperiments are designed and performed This is our fourth ‘‘Numerical Com-puter Methods’’ volume for Methods in Enzymology The aim of volumes 210,

240, 321, and the present volume is to inform biomedical researchers aboutsome of these recent applications of modern data analysis and simulationmethods as applied to biomedical research

Ludwig BrandMichael L Johnson

xi

METHODS IN ENZYMOLOGY

Volume I Preparation and Assay of Enzymes

Edited by Sidney P Colowick and Nathan O Kaplan

Volume II Preparation and Assay of Enzymes

Edited by Sidney P Colowick and Nathan O Kaplan

Volume III Preparation and Assay of Substrates

Edited by Sidney P Colowick and Nathan O Kaplan

Volume IV Special Techniques for the Enzymologist

Edited by Sidney P Colowick and Nathan O Kaplan

Volume V Preparation and Assay of Enzymes

Edited by Sidney P Colowick and Nathan O Kaplan

Volume VI Preparation and Assay of Enzymes (Continued)

Preparation and Assay of Substrates

Special Techniques

Edited by Sidney P Colowick and Nathan O Kaplan

Volume VII Cumulative Subject Index

Edited by Sidney P Colowick and Nathan O Kaplan

Volume VIII Complex Carbohydrates

Edited by Elizabeth F Neufeld and Victor Ginsburg

Volume IX Carbohydrate Metabolism

Edited by Willis A Wood

Volume X Oxidation and Phosphorylation

Edited by Ronald W Estabrook and Maynard E Pullman

Volume XI Enzyme Structure

Edited by C H W Hirs

Volume XII Nucleic Acids (Parts A and B)

Edited by Lawrence Grossman and Kivie Moldave

Volume XIII Citric Acid Cycle

Edited by J M Lowenstein

Volume XIV Lipids

Edited by J M Lowenstein

Volume XV Steroids and Terpenoids

Edited by Raymond B Clayton

xiii

Volume XVI Fast Reactions

Edited by Kenneth Kustin

Volume XVII Metabolism of Amino Acids and Amines (Parts A and B)Edited by Herbert Tabor and Celia White Tabor

Volume XVIII Vitamins and Coenzymes (Parts A, B, and C)

Edited by Donald B McCormick and Lemuel D Wright

Volume XIX Proteolytic Enzymes

Edited by Gertrude E Perlmann and Laszlo Lorand

Volume XX Nucleic Acids and Protein Synthesis (Part C)

Edited by Kivie Moldave and Lawrence Grossman

Volume XXI Nucleic Acids (Part D)

Edited by Lawrence Grossman and Kivie Moldave

Volume XXII Enzyme Purification and Related Techniques

Edited by William B Jakoby

Volume XXIII Photosynthesis (Part A)

Edited by Anthony San Pietro

Volume XXIV Photosynthesis and Nitrogen Fixation (Part B)

Edited by Anthony San Pietro

Volume XXV Enzyme Structure (Part B)

Edited by C H W Hirs and Serge N Timasheff

Volume XXVI Enzyme Structure (Part C)

Edited by C H W Hirs and Serge N Timasheff

Volume XXVII Enzyme Structure (Part D)

Edited by C H W Hirs and Serge N Timasheff

Volume XXVIII Complex Carbohydrates (Part B)

Edited by Victor Ginsburg

Volume XXIX Nucleic Acids and Protein Synthesis (Part E)

Edited by Lawrence Grossman and Kivie Moldave

Volume XXX Nucleic Acids and Protein Synthesis (Part F)

Edited by Kivie Moldave and Lawrence Grossman

Volume XXXI Biomembranes (Part A)

Edited by Sidney Fleischer and Lester Packer

Volume XXXII Biomembranes (Part B)

Edited by Sidney Fleischer and Lester Packer

Volume XXXIII Cumulative Subject Index Volumes I-XXX

Edited by Martha G Dennis and Edward A Dennis

Volume XXXIV Affinity Techniques (Enzyme Purification: Part B)Edited by William B Jakoby and Meir Wilchek

Volume XXXV Lipids (Part B)

Edited by John M Lowenstein

Volume XXXVI Hormone Action (Part A: Steroid Hormones)

Edited by Bert W O’Malley and Joel G Hardman

Volume XXXVII Hormone Action (Part B: Peptide Hormones)

Edited by Bert W O’Malley and Joel G Hardman

Volume XXXVIII Hormone Action (Part C: Cyclic Nucleotides)

Edited by Joel G Hardman and Bert W O’Malley

Volume XXXIX Hormone Action (Part D: Isolated Cells, Tissues,

and Organ Systems)

Edited by Joel G Hardman and Bert W O’Malley

Volume XL Hormone Action (Part E: Nuclear Structure and Function)Edited by Bert W O’Malley and Joel G Hardman

Volume XLI Carbohydrate Metabolism (Part B)

Edited by W A Wood

Volume XLII Carbohydrate Metabolism (Part C)

Edited by W A Wood

Volume XLIII Antibiotics

Edited by John H Hash

Volume XLIV Immobilized Enzymes

Edited by Klaus Mosbach

Volume XLV Proteolytic Enzymes (Part B)

Edited by Laszlo Lorand

Volume XLVI Affinity Labeling

Edited by William B Jakoby and Meir Wilchek

Volume XLVII Enzyme Structure (Part E)

Edited by C H W Hirs and Serge N Timasheff

Volume XLVIII Enzyme Structure (Part F)

Edited by C H W Hirs and Serge N Timasheff

Volume XLIX Enzyme Structure (Part G)

Edited by C H W Hirs and Serge N Timasheff

Volume L Complex Carbohydrates (Part C)

Edited by Victor Ginsburg

Volume LI Purine and Pyrimidine Nucleotide Metabolism

Edited by Patricia A Hoffee and Mary Ellen Jones

Volume LII Biomembranes (Part C: Biological Oxidations)

Edited by Sidney Fleischer and Lester Packer

Volume LIII Biomembranes (Part D: Biological Oxidations)

Edited by Sidney Fleischer and Lester Packer

Volume LIV Biomembranes (Part E: Biological Oxidations)

Edited by Sidney Fleischer and Lester Packer

Volume LV Biomembranes (Part F: Bioenergetics)

Edited by Sidney Fleischer and Lester Packer

Volume LVI Biomembranes (Part G: Bioenergetics)

Edited by Sidney Fleischer and Lester Packer

Volume LVII Bioluminescence and Chemiluminescence

Edited by Marlene A DeLuca

Volume LVIII Cell Culture

Edited by William B Jakoby and Ira Pastan

Volume LIX Nucleic Acids and Protein Synthesis (Part G)

Edited by Kivie Moldave and Lawrence Grossman

Volume LX Nucleic Acids and Protein Synthesis (Part H)

Edited by Kivie Moldave and Lawrence Grossman

Volume 61 Enzyme Structure (Part H)

Edited by C H W Hirs and Serge N Timasheff

Volume 62 Vitamins and Coenzymes (Part D)

Edited by Donald B McCormick and Lemuel D Wright

Volume 63 Enzyme Kinetics and Mechanism (Part A: Initial Rate andInhibitor Methods)

Edited by Daniel L Purich

Volume 64 Enzyme Kinetics and Mechanism (Part B: Isotopic Probes andComplex Enzyme Systems)

Edited by Daniel L Purich

Volume 65 Nucleic Acids (Part I)

Edited by Lawrence Grossman and Kivie Moldave

Volume 66 Vitamins and Coenzymes (Part E)

Edited by Donald B McCormick and Lemuel D Wright

Volume 67 Vitamins and Coenzymes (Part F)

Edited by Donald B McCormick and Lemuel D Wright

Volume 68 Recombinant DNA

Edited by Ray Wu

Volume 69 Photosynthesis and Nitrogen Fixation (Part C)

Edited by Anthony San Pietro

Volume 70 Immunochemical Techniques (Part A)

Edited by Helen Van Vunakis and John J Langone

Volume 71 Lipids (Part C)

Edited by John M Lowenstein

Volume 72 Lipids (Part D)

Edited by John M Lowenstein

Volume 73 Immunochemical Techniques (Part B)

Edited by John J Langone and Helen Van Vunakis

Volume 74 Immunochemical Techniques (Part C)

Edited by John J Langone and Helen Van Vunakis

Volume 75 Cumulative Subject Index Volumes XXXI, XXXII, XXXIV–LXEdited by Edward A Dennis and Martha G Dennis

Volume 76 Hemoglobins

Edited by Eraldo Antonini, Luigi Rossi-Bernardi, and Emilia ChianconeVolume 77 Detoxication and Drug Metabolism

Edited by William B Jakoby

Volume 78 Interferons (Part A)

Edited by Sidney Pestka

Volume 79 Interferons (Part B)

Edited by Sidney Pestka

Volume 80 Proteolytic Enzymes (Part C)

Edited by Laszlo Lorand

Volume 81 Biomembranes (Part H: Visual Pigments and Purple Membranes, I)Edited by Lester Packer

Volume 82 Structural and Contractile Proteins (Part A: Extracellular Matrix)Edited by Leon W Cunningham and Dixie W Frederiksen

Volume 83 Complex Carbohydrates (Part D)

Edited by Victor Ginsburg

Volume 84 Immunochemical Techniques (Part D: Selected Immunoassays)Edited by John J Langone and Helen Van Vunakis

Volume 85 Structural and Contractile Proteins (Part B: The ContractileApparatus and the Cytoskeleton)

Edited by Dixie W Frederiksen and Leon W Cunningham

Volume 86 Prostaglandins and Arachidonate Metabolites

Edited by William E M Lands and William L Smith

Volume 87 Enzyme Kinetics and Mechanism (Part C: Intermediates,

Stereo-chemistry, and Rate Studies)

Edited by Daniel L Purich

Volume 88 Biomembranes (Part I: Visual Pigments and Purple Membranes, II)Edited by Lester Packer

Volume 89 Carbohydrate Metabolism (Part D)

Edited by Willis A Wood

Volume 90 Carbohydrate Metabolism (Part E)

Edited by Willis A Wood

Volume 91 Enzyme Structure (Part I)

Edited by C H W Hirs and Serge N Timasheff

Volume 92 Immunochemical Techniques (Part E: Monoclonal Antibodies andGeneral Immunoassay Methods)

Edited by John J Langone and Helen Van Vunakis

Volume 93 Immunochemical Techniques (Part F: Conventional Antibodies,

Fc Receptors, and Cytotoxicity)

Edited by John J Langone and Helen Van Vunakis

Volume 94 Polyamines

Edited by Herbert Tabor and Celia White Tabor

Volume 95 Cumulative Subject Index Volumes 61–74, 76–80

Edited by Edward A Dennis and Martha G Dennis

Volume 96 Biomembranes [Part J: Membrane Biogenesis: Assembly andTargeting (General Methods; Eukaryotes)]

Edited by Sidney Fleischer and Becca Fleischer

Volume 97 Biomembranes [Part K: Membrane Biogenesis: Assembly andTargeting (Prokaryotes, Mitochondria, and Chloroplasts)]

Edited by Sidney Fleischer and Becca Fleischer

Volume 98 Biomembranes (Part L: Membrane Biogenesis: Processingand Recycling)

Edited by Sidney Fleischer and Becca Fleischer

Volume 99 Hormone Action (Part F: Protein Kinases)

Edited by Jackie D Corbin and Joel G Hardman

Volume 100 Recombinant DNA (Part B)

Edited by Ray Wu, Lawrence Grossman, and Kivie Moldave

Volume 101 Recombinant DNA (Part C)

Edited by Ray Wu, Lawrence Grossman, and Kivie Moldave

Volume 102 Hormone Action (Part G: Calmodulin and

Calcium-Binding Proteins)

Edited by Anthony R Means and Bert W O’Malley

Volume 103 Hormone Action (Part H: Neuroendocrine Peptides)

Edited by P Michael Conn

Volume 104 Enzyme Purification and Related Techniques (Part C)

Edited by William B Jakoby

Volume 105 Oxygen Radicals in Biological Systems

Edited by Lester Packer

Volume 106 Posttranslational Modifications (Part A)

Edited by Finn Wold and Kivie Moldave

Volume 107 Posttranslational Modifications (Part B)

Edited by Finn Wold and Kivie Moldave

Volume 108 Immunochemical Techniques (Part G: Separation and

Characterization of Lymphoid Cells)

Edited by Giovanni Di Sabato, John J Langone, and Helen Van VunakisVolume 109 Hormone Action (Part I: Peptide Hormones)

Edited by Lutz Birnbaumer and Bert W O’Malley

Volume 110 Steroids and Isoprenoids (Part A)

Edited by John H Law and Hans C Rilling

Volume 111 Steroids and Isoprenoids (Part B)

Edited by John H Law and Hans C Rilling

Volume 112 Drug and Enzyme Targeting (Part A)

Edited by Kenneth J Widder and Ralph Green

Volume 113 Glutamate, Glutamine, Glutathione, and Related CompoundsEdited by Alton Meister

Volume 114 Diffraction Methods for Biological Macromolecules (Part A)Edited by Harold W Wyckoff, C H W Hirs, and Serge N TimasheffVolume 115 Diffraction Methods for Biological Macromolecules (Part B)Edited by Harold W Wyckoff, C H W Hirs, and Serge N TimasheffVolume 116 Immunochemical Techniques (Part H: Effectors and Mediators ofLymphoid Cell Functions)

Edited by Giovanni Di Sabato, John J Langone, and Helen Van VunakisVolume 117 Enzyme Structure (Part J)

Edited by C H W Hirs and Serge N Timasheff

Volume 118 Plant Molecular Biology

Edited by Arthur Weissbach and Herbert Weissbach

Volume 119 Interferons (Part C)

Edited by Sidney Pestka

Volume 120 Cumulative Subject Index Volumes 81–94, 96–101

Volume 121 Immunochemical Techniques (Part I: Hybridoma Technologyand Monoclonal Antibodies)

Edited by John J Langone and Helen Van Vunakis

Volume 122 Vitamins and Coenzymes (Part G)

Edited by Frank Chytil and Donald B McCormick

Volume 123 Vitamins and Coenzymes (Part H)

Edited by Frank Chytil and Donald B McCormick

Volume 124 Hormone Action (Part J: Neuroendocrine Peptides)

Edited by P Michael Conn

Volume 125 Biomembranes (Part M: Transport in Bacteria, Mitochondria,and Chloroplasts: General Approaches and Transport Systems)

Edited by Sidney Fleischer and Becca Fleischer

Volume 126 Biomembranes (Part N: Transport in Bacteria, Mitochondria, andChloroplasts: Protonmotive Force)

Edited by Sidney Fleischer and Becca Fleischer

Volume 127 Biomembranes (Part O: Protons and Water: Structure

and Translocation)

Edited by Lester Packer

Volume 128 Plasma Lipoproteins (Part A: Preparation, Structure, andMolecular Biology)

Edited by Jere P Segrest and John J Albers

Volume 129 Plasma Lipoproteins (Part B: Characterization, Cell Biology,and Metabolism)

Edited by John J Albers and Jere P Segrest

Volume 130 Enzyme Structure (Part K)

Edited by C H W Hirs and Serge N Timasheff

Volume 131 Enzyme Structure (Part L)

Edited by C H W Hirs and Serge N Timasheff

Volume 132 Immunochemical Techniques (Part J: Phagocytosis and

Cell-Mediated Cytotoxicity)

Edited by Giovanni Di Sabato and Johannes Everse

Volume 133 Bioluminescence and Chemiluminescence (Part B)

Edited by Marlene DeLuca and William D McElroy

Volume 134 Structural and Contractile Proteins (Part C: The ContractileApparatus and the Cytoskeleton)

Edited by Richard B Vallee

Volume 135 Immobilized Enzymes and Cells (Part B)

Edited by Klaus Mosbach

Volume 136 Immobilized Enzymes and Cells (Part C)

Edited by Klaus Mosbach

Volume 137 Immobilized Enzymes and Cells (Part D)

Edited by Klaus Mosbach

Volume 138 Complex Carbohydrates (Part E)

Edited by Victor Ginsburg

Volume 139 Cellular Regulators (Part A: Calcium- and

Calmodulin-Binding Proteins)

Edited by Anthony R Means and P Michael Conn

Volume 140 Cumulative Subject Index Volumes 102–119, 121–134

Volume 141 Cellular Regulators (Part B: Calcium and Lipids)

Edited by P Michael Conn and Anthony R Means

Volume 142 Metabolism of Aromatic Amino Acids and Amines

Edited by Seymour Kaufman

Volume 143 Sulfur and Sulfur Amino Acids

Edited by William B Jakoby and Owen Griffith

Volume 144 Structural and Contractile Proteins (Part D: Extracellular Matrix)Edited by Leon W Cunningham

Volume 145 Structural and Contractile Proteins (Part E: Extracellular Matrix)Edited by Leon W Cunningham

Volume 146 Peptide Growth Factors (Part A)

Edited by David Barnes and David A Sirbasku

Volume 147 Peptide Growth Factors (Part B)

Edited by David Barnes and David A Sirbasku

Volume 148 Plant Cell Membranes

Edited by Lester Packer and Roland Douce

Volume 149 Drug and Enzyme Targeting (Part B)

Edited by Ralph Green and Kenneth J Widder

Volume 150 Immunochemical Techniques (Part K: In Vitro Models of B and TCell Functions and Lymphoid Cell Receptors)

Edited by Giovanni Di Sabato

Volume 151 Molecular Genetics of Mammalian Cells

Edited by Michael M Gottesman

Volume 152 Guide to Molecular Cloning Techniques

Edited by Shelby L Berger and Alan R Kimmel

Volume 153 Recombinant DNA (Part D)

Edited by Ray Wu and Lawrence Grossman

Volume 154 Recombinant DNA (Part E)

Edited by Ray Wu and Lawrence Grossman

Volume 155 Recombinant DNA (Part F)

Edited by Ray Wu

Volume 156 Biomembranes (Part P: ATP-Driven Pumps and RelatedTransport: The Na, K-Pump)

Edited by Sidney Fleischer and Becca Fleischer

Volume 157 Biomembranes (Part Q: ATP-Driven Pumps and RelatedTransport: Calcium, Proton, and Potassium Pumps)

Edited by Sidney Fleischer and Becca Fleischer

Volume 158 Metalloproteins (Part A)

Edited by James F Riordan and Bert L Vallee

Volume 159 Initiation and Termination of Cyclic Nucleotide ActionEdited by Jackie D Corbin and Roger A Johnson

Volume 160 Biomass (Part A: Cellulose and Hemicellulose)

Edited by Willis A Wood and Scott T Kellogg

Volume 161 Biomass (Part B: Lignin, Pectin, and Chitin)

Edited by Willis A Wood and Scott T Kellogg

Volume 162 Immunochemical Techniques (Part L: Chemotaxis

and Inflammation)

Edited by Giovanni Di Sabato

Volume 163 Immunochemical Techniques (Part M: Chemotaxis

and Inflammation)

Edited by Giovanni Di Sabato

Volume 164 Ribosomes

Edited by Harry F Noller, Jr and Kivie Moldave

Volume 165 Microbial Toxins: Tools for Enzymology

Edited by Sidney Harshman

Volume 166 Branched-Chain Amino Acids

Edited by Robert Harris and John R Sokatch

Volume 167 Cyanobacteria

Edited by Lester Packer and Alexander N Glazer

Volume 168 Hormone Action (Part K: Neuroendocrine Peptides)Edited by P Michael Conn

Volume 169 Platelets: Receptors, Adhesion, Secretion (Part A)

Edited by Jacek Hawiger

Volume 170 Nucleosomes

Edited by Paul M Wassarman and Roger D Kornberg

Volume 171 Biomembranes (Part R: Transport Theory: Cells and ModelMembranes)

Edited by Sidney Fleischer and Becca Fleischer

Volume 172 Biomembranes (Part S: Transport: Membrane Isolation andCharacterization)

Edited by Sidney Fleischer and Becca Fleischer

Volume 173 Biomembranes [Part T: Cellular and Subcellular Transport:Eukaryotic (Nonepithelial) Cells]

Edited by Sidney Fleischer and Becca Fleischer

Volume 174 Biomembranes [Part U: Cellular and Subcellular Transport:Eukaryotic (Nonepithelial) Cells]

Edited by Sidney Fleischer and Becca Fleischer

Volume 175 Cumulative Subject Index Volumes 135–139, 141–167

Volume 176 Nuclear Magnetic Resonance (Part A: Spectral Techniques andDynamics)

Edited by Norman J Oppenheimer and Thomas L James

Volume 177 Nuclear Magnetic Resonance (Part B: Structure and Mechanism)Edited by Norman J Oppenheimer and Thomas L James

Volume 178 Antibodies, Antigens, and Molecular Mimicry

Edited by John J Langone

Volume 179 Complex Carbohydrates (Part F)

Edited by Victor Ginsburg

Volume 180 RNA Processing (Part A: General Methods)

Edited by James E Dahlberg and John N Abelson

Volume 181 RNA Processing (Part B: Specific Methods)

Edited by James E Dahlberg and John N Abelson

Volume 182 Guide to Protein Purification

Edited by Murray P Deutscher

Volume 183 Molecular Evolution: Computer Analysis of Protein and NucleicAcid Sequences

Edited by Russell F Doolittle

Volume 184 Avidin-Biotin Technology

Edited by Meir Wilchek and Edward A Bayer

Volume 185 Gene Expression Technology

Edited by David V Goeddel

Volume 186 Oxygen Radicals in Biological Systems (Part B: Oxygen Radicalsand Antioxidants)

Edited by Lester Packer and Alexander N Glazer

Volume 187 Arachidonate Related Lipid Mediators

Edited by Robert C Murphy and Frank A Fitzpatrick

Volume 188 Hydrocarbons and Methylotrophy

Edited by Mary E Lidstrom

Volume 189 Retinoids (Part A: Molecular and Metabolic Aspects)

Edited by Lester Packer

Volume 190 Retinoids (Part B: Cell Differentiation and Clinical Applications)Edited by Lester Packer

Volume 191 Biomembranes (Part V: Cellular and Subcellular Transport:Epithelial Cells)

Edited by Sidney Fleischer and Becca Fleischer

Volume 192 Biomembranes (Part W: Cellular and Subcellular Transport:Epithelial Cells)

Edited by Sidney Fleischer and Becca Fleischer

Volume 193 Mass Spectrometry

Edited by James A McCloskey

Volume 194 Guide to Yeast Genetics and Molecular Biology

Edited by Christine Guthrie and Gerald R Fink

Volume 195 Adenylyl Cyclase, G Proteins, and Guanylyl CyclaseEdited by Roger A Johnson and Jackie D Corbin

Volume 196 Molecular Motors and the Cytoskeleton

Edited by Richard B Vallee

Volume 197 Phospholipases

Edited by Edward A Dennis

Volume 198 Peptide Growth Factors (Part C)

Edited by David Barnes, J P Mather, and Gordon H Sato

Volume 199 Cumulative Subject Index Volumes 168–174, 176–194Volume 200 Protein Phosphorylation (Part A: Protein Kinases: Assays,Purification, Antibodies, Functional Analysis, Cloning, and Expression)Edited by Tony Hunter and Bartholomew M Sefton

Volume 201 Protein Phosphorylation (Part B: Analysis of ProteinPhosphorylation, Protein Kinase Inhibitors, and Protein Phosphatases)Edited by Tony Hunter and Bartholomew M Sefton

Volume 202 Molecular Design and Modeling: Concepts and Applications(Part A: Proteins, Peptides, and Enzymes)

Edited by John J Langone

Volume 203 Molecular Design and Modeling: Concepts and Applications(Part B: Antibodies and Antigens, Nucleic Acids, Polysaccharides,and Drugs)

Edited by John J Langone

Volume 204 Bacterial Genetic Systems

Edited by Jeffrey H Miller

Volume 205 Metallobiochemistry (Part B: Metallothionein and

Related Molecules)

Edited by James F Riordan and Bert L Vallee

Volume 206 Cytochrome P450

Edited by Michael R Waterman and Eric F Johnson

Volume 207 Ion Channels

Edited by Bernardo Rudy and Linda E Iverson

Volume 208 Protein–DNA Interactions

Edited by Robert T Sauer

Volume 209 Phospholipid Biosynthesis

Edited by Edward A Dennis and Dennis E Vance

Volume 210 Numerical Computer Methods

Edited by Ludwig Brand and Michael L Johnson

Volume 211 DNA Structures (Part A: Synthesis and Physical Analysis

of DNA)

Edited by David M J Lilley and James E Dahlberg

Volume 212 DNA Structures (Part B: Chemical and Electrophoretic

Analysis of DNA)

Edited by David M J Lilley and James E Dahlberg

Volume 213 Carotenoids (Part A: Chemistry, Separation, Quantitation,and Antioxidation)

Edited by Lester Packer

Volume 214 Carotenoids (Part B: Metabolism, Genetics, and Biosynthesis)Edited by Lester Packer

Volume 215 Platelets: Receptors, Adhesion, Secretion (Part B)

Edited by Jacek J Hawiger

Volume 216 Recombinant DNA (Part G)

Volume 219 Reconstitution of Intracellular Transport

Edited by James E Rothman

Volume 220 Membrane Fusion Techniques (Part A)

Edited by Nejat Du¨zgu¨nes,

Volume 221 Membrane Fusion Techniques (Part B)

Edited by Nejat Du¨zgu¨nes,

Volume 222 Proteolytic Enzymes in Coagulation, Fibrinolysis, and

Complement Activation (Part A: Mammalian Blood Coagulation Factorsand Inhibitors)

Edited by Laszlo Lorand and Kenneth G Mann

Volume 223 Proteolytic Enzymes in Coagulation, Fibrinolysis, and

Complement Activation (Part B: Complement Activation, Fibrinolysis, andNonmammalian Blood Coagulation Factors)

Edited by Laszlo Lorand and Kenneth G Mann

Volume 224 Molecular Evolution: Producing the Biochemical Data

Edited by Elizabeth Anne Zimmer, Thomas J White, Rebecca L Cann,andAllan C Wilson

Volume 225 Guide to Techniques in Mouse Development

Edited by Paul M Wassarman and Melvin L DePamphilis

Volume 226 Metallobiochemistry (Part C: Spectroscopic and

Physical Methods for Probing Metal Ion Environments in Metalloenzymesand Metalloproteins)

Edited by James F Riordan and Bert L Vallee

Volume 227 Metallobiochemistry (Part D: Physical and SpectroscopicMethods for Probing Metal Ion Environments in Metalloproteins)

Edited by James F Riordan and Bert L Vallee

Volume 228 Aqueous Two-Phase Systems

Edited by Harry Walter and Go¨te Johansson

Volume 229 Cumulative Subject Index Volumes 195–198, 200–227

Volume 230 Guide to Techniques in Glycobiology

Edited by William J Lennarz and Gerald W Hart

Volume 231 Hemoglobins (Part B: Biochemical and Analytical Methods)Edited by Johannes Everse, Kim D Vandegriff, and Robert M WinslowVolume 232 Hemoglobins (Part C: Biophysical Methods)

Edited by Johannes Everse, Kim D Vandegriff, and Robert M WinslowVolume 233 Oxygen Radicals in Biological Systems (Part C)

Edited by Lester Packer

Volume 234 Oxygen Radicals in Biological Systems (Part D)

Edited by Lester Packer

Volume 235 Bacterial Pathogenesis (Part A: Identification and Regulation ofVirulence Factors)

Edited by Virginia L Clark and Patrik M Bavoil

Volume 236 Bacterial Pathogenesis (Part B: Integration of PathogenicBacteria with Host Cells)

Edited by Virginia L Clark and Patrik M Bavoil

Volume 237 Heterotrimeric G Proteins

Edited by Ravi Iyengar

Volume 238 Heterotrimeric G-Protein Effectors

Edited by Ravi Iyengar

Volume 239 Nuclear Magnetic Resonance (Part C)

Edited by Thomas L James and Norman J Oppenheimer

Volume 240 Numerical Computer Methods (Part B)

Edited by Michael L Johnson and Ludwig Brand

Volume 241 Retroviral Proteases

Edited by Lawrence C Kuo and Jules A Shafer

Volume 242 Neoglycoconjugates (Part A)

Edited by Y C Lee and Reiko T Lee

Volume 243 Inorganic Microbial Sulfur Metabolism

Edited by Harry D Peck, Jr and Jean LeGall

Volume 244 Proteolytic Enzymes: Serine and Cysteine Peptidases

Edited by Alan J Barrett

Volume 245 Extracellular Matrix Components

Edited by E Ruoslahti and E Engvall

Volume 246 Biochemical Spectroscopy

Edited by Kenneth Sauer

Volume 247 Neoglycoconjugates (Part B: Biomedical Applications)

Edited by Y C Lee and Reiko T Lee

Volume 248 Proteolytic Enzymes: Aspartic and Metallo Peptidases

Edited by Alan J Barrett

Volume 249 Enzyme Kinetics and Mechanism (Part D: Developments inEnzyme Dynamics)

Edited by Daniel L Purich

Volume 250 Lipid Modifications of Proteins

Edited by Patrick J Casey and Janice E Buss

Volume 251 Biothiols (Part A: Monothiols and Dithiols, Protein Thiols, andThiyl Radicals)

Edited by Lester Packer

Volume 252 Biothiols (Part B: Glutathione and Thioredoxin; Thiols in SignalTransduction and Gene Regulation)

Edited by Lester Packer

Volume 253 Adhesion of Microbial Pathogens

Edited by Ron J Doyle and Itzhak Ofek

Volume 254 Oncogene Techniques

Edited by Peter K Vogt and Inder M Verma

Volume 255 Small GTPases and Their Regulators (Part A: Ras Family)Edited by W E Balch, Channing J Der, and Alan Hall

Volume 256 Small GTPases and Their Regulators (Part B: Rho Family)Edited by W E Balch, Channing J Der, and Alan Hall

Volume 257 Small GTPases and Their Regulators (Part C: Proteins Involved

in Transport)

Edited by W E Balch, Channing J Der, and Alan Hall

Volume 258 Redox-Active Amino Acids in Biology

Edited by Judith P Klinman

Volume 259 Energetics of Biological Macromolecules

Edited by Michael L Johnson and Gary K Ackers

Volume 260 Mitochondrial Biogenesis and Genetics (Part A)

Edited by Giuseppe M Attardi and Anne Chomyn

Volume 261 Nuclear Magnetic Resonance and Nucleic Acids

Edited by Thomas L James

Volume 262 DNA Replication

Edited by Judith L Campbell

Volume 263 Plasma Lipoproteins (Part C: Quantitation)

Edited by William A Bradley, Sandra H Gianturco, and Jere P SegrestVolume 264 Mitochondrial Biogenesis and Genetics (Part B)

Edited by Giuseppe M Attardi and Anne Chomyn

Volume 265 Cumulative Subject Index Volumes 228, 230–262

Volume 266 Computer Methods for Macromolecular Sequence AnalysisEdited by Russell F Doolittle

Volume 267 Combinatorial Chemistry

Edited by John N Abelson

Volume 268 Nitric Oxide (Part A: Sources and Detection of NO; NOSynthase)

Edited by Lester Packer

Volume 269 Nitric Oxide (Part B: Physiological and Pathological Processes)Edited by Lester Packer

Volume 270 High Resolution Separation and Analysis of Biological

Macromolecules (Part A: Fundamentals)

Edited by Barry L Karger and William S Hancock

Volume 271 High Resolution Separation and Analysis of Biological

Macromolecules (Part B: Applications)

Edited by Barry L Karger and William S Hancock

Volume 272 Cytochrome P450 (Part B)

Edited by Eric F Johnson and Michael R Waterman

Volume 273 RNA Polymerase and Associated Factors (Part A)

Edited by Sankar Adhya

Volume 274 RNA Polymerase and Associated Factors (Part B)

Edited by Sankar Adhya

Volume 275 Viral Polymerases and Related Proteins

Edited by Lawrence C Kuo, David B Olsen, and Steven S CarrollVolume 276 Macromolecular Crystallography (Part A)

Edited by Charles W Carter, Jr and Robert M Sweet

Volume 277 Macromolecular Crystallography (Part B)

Edited by Charles W Carter, Jr and Robert M Sweet

Volume 278 Fluorescence Spectroscopy

Edited by Ludwig Brand and Michael L Johnson

Volume 279 Vitamins and Coenzymes (Part I)

Edited by Donald B McCormick, John W Suttie, and Conrad Wagner

Volume 280 Vitamins and Coenzymes (Part J)

Edited by Donald B McCormick, John W Suttie, and Conrad WagnerVolume 281 Vitamins and Coenzymes (Part K)

Edited by Donald B McCormick, John W Suttie, and Conrad WagnerVolume 282 Vitamins and Coenzymes (Part L)

Edited by Donald B McCormick, John W Suttie, and Conrad WagnerVolume 283 Cell Cycle Control

Edited by William G Dunphy

Volume 284 Lipases (Part A: Biotechnology)

Edited by Byron Rubin and Edward A Dennis

Volume 285 Cumulative Subject Index Volumes 263, 264, 266–284, 286–289Volume 286 Lipases (Part B: Enzyme Characterization and Utilization)Edited by Byron Rubin and Edward A Dennis

Volume 287 Chemokines

Edited by Richard Horuk

Volume 288 Chemokine Receptors

Edited by Richard Horuk

Volume 289 Solid Phase Peptide Synthesis

Edited by Gregg B Fields

Volume 290 Molecular Chaperones

Edited by George H Lorimer and Thomas Baldwin

Volume 291 Caged Compounds

Edited by Gerard Marriott

Volume 292 ABC Transporters: Biochemical, Cellular, and Molecular AspectsEdited by Suresh V Ambudkar and Michael M Gottesman

Volume 293 Ion Channels (Part B)

Edited by P Michael Conn

Volume 294 Ion Channels (Part C)

Edited by P Michael Conn

Volume 295 Energetics of Biological Macromolecules (Part B)

Edited by Gary K Ackers and Michael L Johnson

Volume 296 Neurotransmitter Transporters

Edited by Susan G Amara

Volume 297 Photosynthesis: Molecular Biology of Energy Capture

Edited by Lee McIntosh

Volume 298 Molecular Motors and the Cytoskeleton (Part B)

Edited by Richard B Vallee

Volume 299 Oxidants and Antioxidants (Part A)

Edited by Lester Packer

Volume 300 Oxidants and Antioxidants (Part B)

Edited by Lester Packer

Volume 301 Nitric Oxide: Biological and Antioxidant Activities (Part C)Edited by Lester Packer

Volume 302 Green Fluorescent Protein

Edited by P Michael Conn

Volume 303 cDNA Preparation and Display

Edited by Sherman M Weissman

Volume 304 Chromatin

Edited by Paul M Wassarman and Alan P Wolffe

Volume 305 Bioluminescence and Chemiluminescence (Part C)

Edited by Thomas O Baldwin and Miriam M Ziegler

Volume 306 Expression of Recombinant Genes in Eukaryotic SystemsEdited by Joseph C Glorioso and Martin C Schmidt

Volume 307 Confocal Microscopy

Edited by P Michael Conn

Volume 308 Enzyme Kinetics and Mechanism (Part E: Energetics ofEnzyme Catalysis)

Edited by Daniel L Purich and Vern L Schramm

Volume 309 Amyloid, Prions, and Other Protein Aggregates

Edited by Ronald Wetzel

Volume 310 Biofilms

Edited by Ron J Doyle

Volume 311 Sphingolipid Metabolism and Cell Signaling (Part A)

Edited by Alfred H Merrill, Jr and Yusuf A Hannun

Volume 312 Sphingolipid Metabolism and Cell Signaling (Part B)

Edited by Alfred H Merrill, Jr and Yusuf A Hannun

Volume 313 Antisense Technology (Part A: General Methods, Methods ofDelivery, and RNA Studies)

Edited by M Ian Phillips

Volume 314 Antisense Technology (Part B: Applications)

Edited by M Ian Phillips

Volume 315 Vertebrate Phototransduction and the Visual Cycle (Part A)Edited by Krzysztof Palczewski

Volume 316 Vertebrate Phototransduction and the Visual Cycle (Part B)Edited by Krzysztof Palczewski

Volume 317 RNA–Ligand Interactions (Part A: Structural Biology Methods)Edited by Daniel W Celander and John N Abelson

Volume 318 RNA–Ligand Interactions (Part B: Molecular Biology Methods)Edited by Daniel W Celander and John N Abelson

Volume 319 Singlet Oxygen, UV-A, and Ozone

Edited by Lester Packer and Helmut Sies

Volume 320 Cumulative Subject Index Volumes 290–319

Volume 321 Numerical Computer Methods (Part C)

Edited by Michael L Johnson and Ludwig Brand

Volume 322 Apoptosis

Edited by John C Reed

Volume 323 Energetics of Biological Macromolecules (Part C)

Edited by Michael L Johnson and Gary K Ackers

Volume 324 Branched-Chain Amino Acids (Part B)

Edited by Robert A Harris and John R Sokatch

Volume 325 Regulators and Effectors of Small GTPases (Part D: Rho Family)Edited by W E Balch, Channing J Der, and Alan Hall

Volume 326 Applications of Chimeric Genes and Hybrid Proteins (Part A:Gene Expression and Protein Purification)

Edited by Jeremy Thorner, Scott D Emr, and John N Abelson

Volume 327 Applications of Chimeric Genes and Hybrid Proteins (Part B:Cell Biology and Physiology)

Edited by Jeremy Thorner, Scott D Emr, and John N Abelson

Volume 328 Applications of Chimeric Genes and Hybrid Proteins (Part C:Protein–Protein Interactions and Genomics)

Edited by Jeremy Thorner, Scott D Emr, and John N Abelson

Volume 329 Regulators and Effectors of Small GTPases (Part E: GTPasesInvolved in Vesicular Traffic)

Edited by W E Balch, Channing J Der, and Alan Hall

Volume 330 Hyperthermophilic Enzymes (Part A)

Edited by Michael W W Adams and Robert M Kelly

Volume 331 Hyperthermophilic Enzymes (Part B)

Edited by Michael W W Adams and Robert M Kelly

Volume 332 Regulators and Effectors of Small GTPases (Part F: Ras Family I)Edited by W E Balch, Channing J Der, and Alan Hall

Volume 333 Regulators and Effectors of Small GTPases (Part G: Ras Family II)Edited by W E Balch, Channing J Der, and Alan Hall

Volume 334 Hyperthermophilic Enzymes (Part C)

Edited by Michael W W Adams and Robert M Kelly

Volume 335 Flavonoids and Other Polyphenols

Edited by Lester Packer

Volume 336 Microbial Growth in Biofilms (Part A: Developmental andMolecular Biological Aspects)

Edited by Ron J Doyle

Volume 337 Microbial Growth in Biofilms (Part B: Special Environments andPhysicochemical Aspects)

Edited by Ron J Doyle

Volume 338 Nuclear Magnetic Resonance of Biological

Macromolecules (Part A)

Edited by Thomas L James, Volker Do¨tsch, and Uli Schmitz

Volume 339 Nuclear Magnetic Resonance of Biological

Macromolecules (Part B)

Edited by Thomas L James, Volker Do¨tsch, and Uli Schmitz

Volume 340 Drug–Nucleic Acid Interactions

Edited by Jonathan B Chaires and Michael J Waring

Volume 341 Ribonucleases (Part A)

Edited by Allen W Nicholson

Volume 342 Ribonucleases (Part B)

Edited by Allen W Nicholson

Volume 343 G Protein Pathways (Part A: Receptors)

Edited by Ravi Iyengar and John D Hildebrandt

Volume 344 G Protein Pathways (Part B: G Proteins and Their Regulators)Edited by Ravi Iyengar and John D Hildebrandt

Volume 345 G Protein Pathways (Part C: Effector Mechanisms)

Edited by Ravi Iyengar and John D Hildebrandt

Volume 346 Gene Therapy Methods

Edited by M Ian Phillips

Volume 347 Protein Sensors and Reactive Oxygen Species (Part A:

Selenoproteins and Thioredoxin)

Edited by Helmut Sies and Lester Packer

Volume 348 Protein Sensors and Reactive Oxygen Species (Part B: ThiolEnzymes and Proteins)

Edited by Helmut Sies and Lester Packer

Volume 349 Superoxide Dismutase

Edited by Lester Packer

Volume 350 Guide to Yeast Genetics and Molecular and Cell Biology (Part B)Edited by Christine Guthrie and Gerald R Fink

Volume 351 Guide to Yeast Genetics and Molecular and Cell Biology (Part C)Edited by Christine Guthrie and Gerald R Fink

Volume 352 Redox Cell Biology and Genetics (Part A)

Edited by Chandan K Sen and Lester Packer

Volume 353 Redox Cell Biology and Genetics (Part B)

Edited by Chandan K Sen and Lester Packer

Volume 354 Enzyme Kinetics and Mechanisms (Part F: Detection andCharacterization of Enzyme Reaction Intermediates)

Edited by Daniel L Purich

Volume 355 Cumulative Subject Index Volumes 321–354

Volume 356 Laser Capture Microscopy and Microdissection

Edited by P Michael Conn

Volume 357 Cytochrome P450, Part C

Edited by Eric F Johnson and Michael R Waterman

Volume 358 Bacterial Pathogenesis (Part C: Identification, Regulation, andFunction of Virulence Factors)

Edited by Virginia L Clark and Patrik M Bavoil

Volume 359 Nitric Oxide (Part D)

Edited by Enrique Cadenas and Lester Packer

Volume 360 Biophotonics (Part A)

Edited by Gerard Marriott and Ian Parker

Volume 361 Biophotonics (Part B)

Edited by Gerard Marriott and Ian Parker

Volume 362 Recognition of Carbohydrates in Biological Systems (Part A)Edited by Yuan C Lee and Reiko T Lee

Volume 363 Recognition of Carbohydrates in Biological Systems (Part B)Edited by Yuan C Lee and Reiko T Lee

Volume 364 Nuclear Receptors

Edited by David W Russell and David J Mangelsdorf

Volume 365 Differentiation of Embryonic Stem Cells

Edited by Paul M Wassauman and Gordon M Keller

Volume 366 Protein Phosphatases

Edited by Susanne Klumpp and Josef Krieglstein

Volume 367 Liposomes (Part A)

Edited by Nejat Du¨zgu¨nes,

Volume 368 Macromolecular Crystallography (Part C)

Edited by Charles W Carter, Jr and Robert M Sweet

Volume 369 Combinational Chemistry (Part B)

Edited by Guillermo A Morales and Barry A Bunin

Volume 370 RNA Polymerases and Associated Factors (Part C)

Edited by Sankar L Adhya and Susan Garges

Volume 371 RNA Polymerases and Associated Factors (Part D)Edited by Sankar L Adhya and Susan Garges

Volume 372 Liposomes (Part B)

Edited by Negat Du¨zgu¨nes,

Volume 373 Liposomes (Part C)

Edited by Negat Du¨zgu¨nes,

Volume 374 Macromolecular Crystallography (Part D)

Edited by Charles W Carter, Jr and Robert W Sweet

Volume 375 Chromatin and Chromatin Remodeling Enzymes (Part A)Edited by C David Allis and Carl Wu

Volume 376 Chromatin and Chromatin Remodeling Enzymes (Part B)Edited by C David Allis and Carl Wu

Volume 377 Chromatin and Chromatin Remodeling Enzymes (Part C)Edited by C David Allis and Carl Wu

Volume 378 Quinones and Quinone Enzymes (Part A)

Edited by Helmut Sies and Lester Packer

Volume 379 Energetics of Biological Macromolecules (Part D)Edited by Jo M Holt, Michael L Johnson, and Gary K AckersVolume 380 Energetics of Biological Macromolecules (Part E)

Edited by Jo M Holt, Michael L Johnson, and Gary K AckersVolume 381 Oxygen Sensing

Edited by Chandan K Sen and Gregg L Semenza

Volume 382 Quinones and Quinone Enzymes (Part B)

Edited by Helmut Sies and Lester Packer

Volume 383 Numerical Computer Methods (Part D)

Edited by Ludwig Brand and Michael L Johnson

Volume 384 Numerical Computer Methods (Part E)

Edited by Michael L Johnson and Ludwig Brand

Volume 385 Imaging in Biological Research (Part A) (in preparation)Edited by P Michael Conn

Volume 386 Imaging in Biological Research (Part B) (in preparation)Edited by P Michael Conn

Volume 387 Liposomes (Part D) (in preparation)

Edited by Negat Du¨zgu¨nes,

[1] Prediction of Protein Structure

By Robert H Kretsinger, Roger E Ison, and Sven Hovmo¨ller

Overview and Perspective

Extraction of Structural Information from Protein Sequence

The determination of crystal and of solution structures has been greatlyrationalized over the past decade; however, it remains tedious, expensivework In contrast, thousands of protein-encoding genes are sequenced eachday The deduced sequences of proteins provide invaluable insights into thefunctions of those proteins and the evolution of the organisms producingthose proteins However, much more information would be forthcoming ifthe structures of those proteins accompanied their sequences This review

is intended for the biologist who has no special expertise and who is notinvolved in the determination of protein structure We have two goals:

1 To provide the generalist with enough background to understandthe concepts, opportunities, and difficulties of protein structure prediction

2 To outline a general strategy that should allow the extraction andinterpretion of structural information about a target sequence frompublicly available databases, servers, and programs

The (nearly) complete DNA sequences of 84 bacteria, 16 archaea, and

15 eukaryotes, including Anopheles gambiae, Arabidopsis thaliana, norhabditis elegans, Drosophila melanogaster, Encephalitozoon cuniculi,Guillardia theta, Saccharomyces cerevisiae, Plasmodium falciparum, andSchizosaccharomyces pombe, a total of 22 billion base pairs, were available

Cae-as of January 2003 from the National Institutes of Health (NIH, Bethesda,MD) or are described in the Genome News Network (Table I1–24)

1 J Westbrook, Z Feng, L Chen, H Yang, and H M Berman, Nucleic Acids Res 31, 489 (2003).

2 J.-F Gibrat, T Madej, and S H Bryant, Curr Opin Struct Biol 6, 377 (1996).

3 A G Murzin, S E Brenner, T Hubbard, and C Chothia, J Mol Biol 247, 536 (1995).

4 F M G Pearl, D Lee, J E Bray, I Sillitoe, A E Todd, A P Harrison, J M Thornton, and C A Orengo, Nucleic Acids Res 28, 277 (2000).

5 R L Tatusov, M Y Galperin, D A Natale, and E V Koonin, Nucleic Acids Res 28, 33 (2000).

6 K Mizuguchi, C M Deane, T L Blundell, and J P Overington, Protein Sci 7, 2469 (1998).

7 R Sowdhamini, D F Burke, J.-F Huang, K Mizuguchi, H A Nagarajaram, N Srinivasan,

R E Steward, and T L Blundell, Structure 6, 1087 (1998).

8 J Moult, K Fidelis, A Zemla, and T Hubbard, Proteins 5(Suppl.), 2 (2001).

Copyright 2004, Elsevier Inc All rights reserved.

TABLE I Databases, Servers, and Programs Referred to in Text

Description/URL Databases Entrez search NCBI combined site to search PubMed, various sequence and

Nonredundant PDB Selected highly dissimilar chains from the PDB, presumably

nonhomologous or only distantly related

http://www.ncbi.nlm.nih.gov/Structure/VAST/nrpdb.html

Select 25% Representative selections from the PDB, about 1/15 th of the full list,

suitable for investigations when the full PDB with its many redundant entries is not required

http://homepages.fh-giessen.de/~hg12640/pdbselect/recent.

pdb_select25 VAST Vector Alignment Search Tool, direct comparison of 3D structures,

PDB entries classified by similarity

TABLE I (continued) Description/URL Servers and Programs Homolog search and alignment

BLAST server Sequence search and alignment

BestFit server Optimal alignments are found by inserting gaps to maximize the

number of matches using the local homology algorithm of Smith and Waterman

http://www.biology.wustl.edu/gcg/bestfit.html http://www.infobiogen.fr/doc/GCGdoc/Program_Manual/ Comparison/bestfit.html

Secondary structure prediction

PSIPRED server With links to MEMSAT and GenThreader

SAM-T02 server Alignment to individual or family of proteins by HMM; protein

database query; secondary structure prediction; homology-based structure prediction

Modeling of target to homolog in 3D

3D-Jigsaw server Builds 3D models based on homologs

CODA server Predicts loops Runs two programs: FREAD, knowledge base of

PDB fragments; and PETRA, ab initio from database of computer-generated conformers

Adding side chains

SCWRL program Side chain placement with a rotamer library

TABLE I (continued) Description/URL

(continued)

8a J Moult, K Fidelis, A Zemla et al., Proteins 53(6): 334–339 (Suppl.), 6 (2003).

9 L Holm and C Sander, Science 273, 595 (1996).

10 L J McGuffin, K Bryson, and D T Jones, Bioinformatics 16, 404 (2000).

11 D T Jones, FEBS Lett 423, 281 (1998).

12 P A Bates, L A Kelley, R M MacCallum, and M J E Sternberg, Proteins 5(Suppl.), 39 (2001).

13 L A Kelley, R M MacCallum, and M J E Sternberg, J Mol Biol 299, 501 (2000).

14 D Fischer, Pac Symp Biocomp 119 (2000).

15 L Rychlewski, L Jaroszewski, W Li, and A Godzik, Protein Sci 9, 232 (2000).

16 D Xu, O H Crawford, P F LoCascio, and Y Xu, Proteins 5(Suppl.), 140 (2001).

17 D T Jones, J Mol Biol 287, 797 (1999).

18 J Shi, T L Blundell, and K Mizuguchi, J Mol Biol 310, 243 (2001).

19 R L Dunbrack, Jr., Proteins 3(Suppl.), 81 (1999).

20 Dean and Blundell (in press).

21 R Luthy, J U Bowie, and D Eisenberg, Nature 356, 83 (1992).

22 J M Word, S C Lovell, J S Richardson, and D C Richardson, J Mol Biol 285, 1735 (1999).

TABLE I (continued) Description/URL

Complete, high-resolution maps are also available for Homo sapiens, Musmusculus, Rattus norvegicus, Danio rerio (zebrafish), Avena sativa (oat), Hor-deum vulgare (barley), Oryza sativa (rice), Triticum aestivum (wheat), andZea mays (maize) From these and from more traditional sources, the aminoacid sequences of about 1,300,000 proteins are available About half ofthese protein sequences belong to 2000 recognized homolog families, ofwhich about 1000 contain at least one determined tertiary structure AsFischer et al.25noted, ‘‘What non-expert biologists need is to be able to applyautomatic tools for their prediction needs, and on a large, genomic scale.’’Second Half of Genetic Code

Since the pioneering experiments of Anfinsen26on the renaturation ofRNase A, it has been shown for several proteins and inferred for manyothers that the amino acid sequence of a protein determines its tertiarystructure No other assembly mechanism is required, although chaperonesmay protect the protein from hydrolysis and/or rescue the folding proteinfrom local minima The genetically encoded amino acid sequence deter-mines the tertiary structure of the protein Understanding that foldingprocess and the resultant structure is the second half of the genetic code.Hierarchy of Structures

The linear sequence of amino acids, or residues, is referred to as the mary structure Secondary structure refers to the spatial, or conformational,relationships of residues to those nearby in sequence; they fall predomi-nantly into two regular patterns:  helix and  strand The remaining resi-dues are traditionally grouped together as coils or turns These may befurther classified into supersecondary structure elements; examples include

pri- hairpin (consecutive  helices in a compact arrangement),  cornerI(consecutive  helices in a noncompact arrangement),  hairpin (hydro-gen-bonded consecutive  strands),  corner (non-hydrogen-bonded con-secutive  strands), –– unit (parallel hydrogen-bonded  strands withintervening  helix), and split –– unit (parallel non-hydrogen-bonded

 strands with intervening  helix) Tertiary structure refers to the dimensional relationships of these elements of secondary structurewithin a single polypeptide chain, or monomer Most proteins are parts oflarger complexes that contain several constituent polypeptides chains; therelationship among these chains comprises the quaternary structure

three-23 Siew et al (in press).

24 J Janin, Proteins 47, 257 (2002).

25 D Fischer, A Elofsson, L Rychlewski, F Pazos, A Valencia, B Rost, A R Ortiz, and

R L Dunbrack, Jr., Proteins 5(Suppl.), 171 (2001).

26 C Anfinsen, Science 181, 223 (1973).

Parameterization of Protein Structure

All proteins consist of an unbranched polypeptide chain made from the

20 genetically encoded -amino acids The bond angles and bond lengths ofthe main-chain atoms are nearly the same,
0.01 A˚ , for all 20 and for theirposttranslationally modified derivatives The peptide bond is nearly planarand almost always trans; the few exceptions for proline are noted in thelegend toFig 2 This means that models of proteins are built of units ofstandard dimensions ‘‘Atoms’’ in this discussion means all atoms excepthydrogen In most cases the standard bond lengths and angles fix the pos-ition of the hydrogens However, free rotation about the single bonds ofmethyl, amine, hydroxyl, and sulfhydryl groups leaves those hydrogens un-defined; this is a concern for refinement of both crystal structures and ofmodels The posttranslational modifications of amino acids are notconsidered in most prediction schemes

Dihedral Angles and Ramachandran (f,c) Plot

Given common bond lengths and angles, the trace of the polypeptidechain and carbonyl oxygen, plus -carbon for all residues excepting glycine,can be fully described by just two dihedral angles—
, —defined and illus-trated in Fig 1 As was predicted by Ramachandran and Sassiekharan27and subsequently observed in many crystal structures, the range of allowed

, values is restricted to a small area of the Ramachandran plot Onlymore recently has it been fully appreciated, from examination of crystalstructures refined with high-resolution (1.5 A˚ ) X-ray diffraction data, thatthe area of the
, plot actually occupied by amino acids in proteins is evenmore restricted and significantly different from that originally predicted.28Further, these areas and their occupancies differ characteristically, almostlike a fingerprint, for each residue (Fig 2)

Just as evaluation of high-resolution crystal structures revealed discrete

, values, so too side chains assume discrete dihedral angles,  , as marized in rotamer libraries.29The number of  angles available per aminoacid are as follows: Gly, Ala, Pro ¼ 0; Ser, Thr, Cys, Val ¼ 1; Asp, Asn,Leu, Ile, His, Phe, Tyr, Trp¼ 2; Glu, Gln, Met ¼ 3; Arg, Lys ¼ 4 Whennormalized for average frequency of occurrence, there are 1.75 degrees

sum-of freedom for the side chain sum-of the average residue Predictions sum-of ary structure do not consider  angles Structure predictions do not initiallyconsider the dihedral values of side chains; however, these are important

second-27 G N Ramachandran and V Sassiekharan, Adv Protein Chem 28, 283 (1968).

28 S Hovmo¨ller, T Zhou, and T Ohlson, Acta Crystallogr D Biol Crystallogr 58, 768 (2002).

29 S C Lovell, J M Word, J S Richardson, and D C Richardson, Proteins 40, 389 (2000).

Fig 1 Definition of
and with examples (A) Trialanine As drawn,
n ¼ 180 and

n ¼ 180 C n , N n , H n , C n  1 , O n  1 , and C n  1 are all contained in one plane; C n , C n ,

O n , N n þ 1 , H n þ 1 and C n þ 1 are contained in another Positive rotation, increasing the value

of the dihedral angle, is indicated by the arrows, proceeding along the peptide chain (N ! C) Some find it easier to visualize
by looking from C toward N; in that case, positive rotation would be indicated by the arrow in the opposite sense; see (B) n  1 ¼ 180 At the N terminus
n is not defined without the amide group being involved in a peptide bond
n þ 1 ¼

180 At the C terminus, n þ 1 is not defined without the carboxylate group being involved in

a peptide bond (B)
n ¼ 109 and n ¼ 121 as seen in the R, or polyproline II, conformation for alanine ( Fig 2A ).

parameters when evaluating or refining a predicted structure The sidechains are the only difference among the amino acids; their order carriesthe hidden message that directs the polypeptide to fold into its tertiarystructure.

It is generally assumed that linkers between domains (characterized inSection II.A, below) are more flexible than are the domains themselves andcorrespondingly that loops are more flexible than  helices and  strands.However, it is best to be alert to the exceptions Dalal et al.30solved the

‘‘Paracelsus challenge’’ by changing a -sheet protein to an -helical tein by selectively changing less than 50% of the residues ResiduesHis40–Met67 of G-actin form an  helix in one crystal structure and a turn in another31; seeFig 3 The important point is that most proteins form

pro-an ensemble of structures; they must if they are to function like chines It is misleading to speak of the structure of a protein We assumethat the sequences that enjoy alternate conformations in proteins are notstrongly predicted to form one or another type of structure

microma-Protein Data Bank

The Protein Data Bank (PDB), as of January 2003 contained 18,482protein, 1932 nucleic acid, and 18 carbohydrate structures Many pro-tein families have multiple entries, reflecting different complexes, dif-ferent (site-directed) mutants, different isoforms, or space groups of

Fig 2 Ramachandran plot(s) for individual residues from structures determined at high resolution (A) Alanine prefers to be in an -helical conformation Of the two regions in the  region, the left region (S,
¼ 140and ¼ 140) is found in  sheets (B) Asparagine has a complicated pattern of conformations with a large fraction in the turns, or left-handed -helix, region (T at
¼ 60and ¼ 35; see Fig 1B ) and in the two bridging areas U and V It is rarely found in  strands (C) Isoleucine prefers to be in  sheets (S,
¼ 117and ¼ 128) (D) Glycine is the only amino acid without a C and thus can have conformations that are sterically hindered in all other amino acids Notice that the turn region, T, is the most occupied The letters G, L, H, R, S, and T [together with U and V; see (B)] denote the eight discrete conformations assumed by amino acids in proteins (E) Pro is the most restricted amino acid Because its amine group is not available to form hydrogen bonds it is unusual in

 sheets and is found in only the first three positions of  helices (F) Although proline can have the conformation needed for an  helix, the amino acid just before proline nearly always has a  conformation, making proline a terminator of  helices (after Hovmo¨ller et al 28 ) About 5% of prolines occur with the peptide bond cis This is not explicitly stated in the PDB file In some lower-resolution structures a cis-proline has been built trans, thereby distorting the local geometry.

30 S Dalal, S Balasubramanian, and L Regan, Nat Struct Biol 4, 548 (1997).

31 L R Otterbein, P Graceffa, and R Dominguez, Science 293, 708 (2001).

crystallization Conversely, there are classes of proteins that are represented, such as membrane proteins and large multidomain proteins.Distinct subfamilies are represented in the VAST nonredundant databasewith a 10 7 E (for expectation) value cutoff (http://www.ncbi.nlm.nih.gov/

under-Fig 3 Illustration of alternative shapes of regions of the same protein Residues His40–Met67 of G-actin form an  helix in one crystal structure and a  turn in another Redrawn after Otterbein et al 31

Structure/VAST/vast.shtml) or in the pdbselect database (pages.fhgiessen.de/ hg12640/pdbselect/recent.pdb_select25) of 1949 chainswith a 25% identity threshold used in the nonredundant PDB-select list.The Web sites of the PDB and of all other databases, servers, and programsare indicated inTable Iand are not explicitly referenced in text.

http://home-The reliability and the errors associated with structures in the PDBvary The atomic coordinates of atoms given in the PDB are, on average,accurate to within 0.2 A˚ for structures determined at 2.5-A˚ resolutionand R ¼ 22% and to within 0.15 A˚ for 1.5 A˚ resolution and R ¼ 19%.(R¼ i ¼ 1n [lobs  lcalc]i, and i ¼ 1n lobs, where n ¼ number of reflec-tions, lobs ¼ observed intensity, and lcalc ¼ calculated intensity) Tem-perature factor B < 20 A˚2indicates good order; B > 30 A˚2indicates highvibration and/or disorder of packing of the proteins within the crystal lattice.When modeling a target sequence against the known structure of a homolog,

it is desirable to consider both the similarity of sequences of target and plate and the reliability of the known structure, both overall and in specificregions of disorder, often in turns at the surface of the protein

tem-Structures of proteins in solution determined by nuclear magnetic onance (NMR) provide invaluable information about the dynamics andmobilities of proteins Usually those regions assigned high mobility byNMR accord with those having high B values in crystal structures NMRalso directly observes hydrogen atoms, unlike X-ray crystallography, andquantitatively measures the strength of proton interactions, as in hydrogenbonding Unless explicitly stated, most prediction programs rely heavily orsolely on crystal structures

res-Physical versus Knowledge-Based Methods

The refinement of protein structures by energy minimization involvesmany empirical formulas that only approximate the exact functions.These empirical functions contain constants whose optimal values are notknown Further, it is especially difficult to estimate the entropic contri-bution to the free energy of the entire system In spite of the theoreticallyattractive approach of predicting protein structures from physical prin-ciples, these methods cannot yet predict a protein model that yields aRamachandran plot distribution similar to that empirically observed.Today the primary value of physical based methods in structure prediction

is in identifying steric violations, internal voids, uncompensated charges,and unfulfilled hydrogen bond donors in either experimentally determined

or in predicted structures Thus, all of the structure prediction servers andprograms—homolog comparison, fold recognition and threading, and new(ab initio)—are based on knowledge of the structures of other proteins,with little regard for ligands present or solvent employed in crystallization

Classifications of Protein Structure

of that family than with any members of another protein family Conversely,members of different families may or may not be homologous Other lines ofevidence (i.e., similar fold, function, cofactors) may indicate homology, butthis cannot be demonstrated by statistical analysis of the sequences Thisraises the fascinating question of the ultimate origin of protein families.Many proteins consist of several distinct domains, each of which is char-acterized by a single hydrophobic core and/or by being a distinct unit as rep-resented in an evolutionary dendrogram The entire polypeptide chainoriginated by gene splicing Each constituent domain has its own evolution-ary history and is homologous to other members of its own family Domainsare frequently joined by flexible linkers and the relationships among thesedomains often change with the functional state of the protein If success isencountered in predicting the structures of the domains of a multidomainmonomer, there is still the problem of determining the spatial relationshipbetween domains—a problem similar to prediction of quaternary structure

Classifications of Structure

Proteins can be classified by structure, in addition to sequence This isinherently much more difficult because sequences are discrete; structuresare not There is still controversy and a significant element of subjectivejudgment in defining the difference or similarity between two proteinstructures It is reassuring that several protocols or algorithms provide

32 T C Wood and W R Pearson, J Mol Biol 291, 977 (1999).