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 LII: Evolution of Catalytic Function 1987 |
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From left: Dr. D. Esienberg, Dr. Aaron Klug, Dr. Walter Gilbert, Mrs. Lita Annenberg Hazen, Dr. James Watson  SYMPOSIUM SYNOPSIS LIST OF PARTICIPANTS CONTENTS OF SYMPOSIUM VOLUME PHOTOGRAPHS PUBLISHED VOLUME  |
Evolution of Catalytic Function
Symposium Volume LII Contents
Symposium Participants v
Foreword xiii
Opening Remarks
Evolution of Catalytic Function D. E. Koshland, Jr. 1
Evolution of the Genetic Apparatus: A Review L. E. Orgel 9
Primordial Soup
Which Organic Compounds Could Have Occurred on the Prebiotic Earth? S. L. Miller 17
Prebiotic Synthesis: Problems and Challenges J. P. Ferris 29
In Search of RNA Ancestors A. W Schwartz, J. Visscher, R. Van der Woerd, and C. G. Bakker 37
Nonenzymatic Template-directed Synthesis of Informational Macromolecules G. F. Joyce 41
Natural Selection, Protein Engineering, and the Last Riboorganism: Rational Model Building in Biochemistry S A. Benner, R. K. Allemann, A. D. Ellington, L. Ge, A. Glasfeld, G. F. Leanz, T. Krauch, L. J. MacPherson, S. Moroney, J. A. Piccirilli, and E. Weinhold 53
Essentials of Catalysis
Economics of Enzyme Catalysis W P. Jencks 65
Artificial Enzymes R. Breslow 75
Phosphorus-containing Peptide Analogs as Peptidase Inhibitors P. A. Bartlett, C. K. Marlowe, P. P. Giannousis, and J. E. Hanson 83
Catalytic Antibodies A. Tramontano, K. Janda, A. D. Napper, S. J. Benkovic, and R. A. Lerner 91
Antibody Catalysis by Transition State Stabilization S. J. Pollack and P. G. Schultz 97
Engineering of Antibodies with a Known Three-dimensional Structure A. Pluck- thun, R. Glockshuber, I. Pfitzinger, A. Skerra, and J. Stadlmüller 105
RNA
Anatomy
Conforniational Changes and Dynamics of tRNAs: Evidence from Hydrolysis Pat terns A. C. Dock-Bregeon and D. Morasv 113
Improved Parameters for Prediction of RNA Structure D.H. Turner, N. Sugimoto, J. A. Jaeger, C. E. Longfellow, S. M. Freier, and R. Kierzek 123
RNA Structure from A to Z. I. Tinoco, Jr., P. W. Davis, C. C. Hardin, J. D. Puglisi, G. T. Walker, and J. Wyatt 135
Catalysis
Structures Involved in Tetrahymena rRNA Self-splicing and RNA Enzyme Activity M.D. Been, E. T. Barfod, J. M. Burke, J. V. Price, N. K. Tanner, A. J. Zaug, and T.R. Cech
Implications of Intermolecularly Catalyzed Reactions by the Tetrahymena Ribo zyme P.S. Kay and T. Inoue 159
Internal Guide Sequence and Reaction Specificity of Group I Self-splicing In- trons R. W. Davies, R. B. Waring, and P. Towner 165
Genetic Dissection of an RNA Enzyme J. A. Doudna, A. S. Gerber, J. M. Cherry, and J. W Szostak 173
Genetic Delineation of Functional Components of the Group I Intron in the Phage T4 td Gene M. Belfort, P.S. Chandry, and J. Pedersen-Lane 181
A Family of Autocatalytic Group I Introns in Bacteriophage T4 D. A. Shub, M. -Q. Xu, J. M. Gott, A. Zeeh, and L. D. Wilson 193
Long-range Intron-Exon and Intron-Intron Pairings Involved in Self-splicing of Class II Catalytic Introns F. Michel and A. Jacquier 201
Reactions Mediated by Yeast Mitochondrial Group I and II Introns H. F. Tabak, G. Van der Horst, A. J. Winter, J. Smit, R. Van der Veen, J. H. J. M. Kwakman, L.A. Grivell, and A. C. Arnberg 213
Group II Intron Self-splicing: Development of Alternative Reaction Conditions and Identification of a Predicted Intermediate C. L. Peebles, E. J. Benatan, K. A. Jarrell, and P.S. Perlman 223
Characteristics of Ribonuclease P from Various Organisms N. Lawrence, D. Wesolowski, H. Gold, M. Bartkiewicz, C. Guerrier-Takada, W. H. McClain, and S. Altman 233
Structure and Catalytic Function in Ribonuclease P N. R. Pace, C. Reich, B. D. James, G. J. Olsen, B. Pace, and D. S. Waugh 239
Structural and Ionic Requirements for Self-cleavage of Virusoid RNAs and trans Self-cleavage of Viroid RNA A. C. Forster, A. C. Jeffries, C. C. Sheldon, and R.H. Symons 249
Transcripts of Newt Satellite DNA Self-cleave In Vitro L. M. Epstein and J. G. Gall 261
Characterization of Two RNA-catalyzed RNA Cleavage Reactions J. R. Sampson, F. X. Sullivan, L. S. Behlen, A. B. DiRenzo, and O. C. Uhlenbeck 267
Splicing of Messenger RNA Precursors P. A. Sharp, M. M. Konarska, P. J. Grabow- ski, A. I. Lamond, R. Marciniak, and S. R. Seiler 277
Different Small Nuclear Ribonucleoprotein Particles Are Involved in Different Steps of Splicing Complex Formation D. Frendewey, A. Kramer, and W. Keller 287
Templates
Replication and Evolution of Short-chained RNA Species Replicated by Qb Rep licase C. K. Biebricher 299
New Concepts for Dealing with the Evolution of Nucleic Acids M. Eigen 307
Evolution of the RNA Coliphages: The Role of Secondary Structures during RNA Replication C. Priano, F. R. Kramer, and D. R. Mills 321
Evidence Implicating a tRNA Heritage for the Promoters of Positive-strand RNA Synthesis in Brome Mosaic and Related Viruses L. E. Marsh and T. C. Hall 331
Molecular Events Leading to Poliovirus Genome Replication A.V. Paul, C. -F. Yang, S.-K. Jang, R.. J. Kuhn, H. Tada, M. Nicklin, H. -G. Kräusslich, C. -K. Lee, and E. Wimmer 343
Transcription and Replication of Influenza Virion RNA in the Nucleus of Infected Cells R. M. Krug, C. St. Angelo, B. Broni, and G. Shapiro 353
Coronavirus: A Jumping RNA Transcription M. M. C. Lai, S. Makino, L. H. Soe, C. -K. Shieh, J. G. Keck, and J. O. Fleming 359
The Switch from Transcription to Replication of a Negative-strand RNA Virus G. W Wertz, M. B. Howard, N. Davis, and J. Patton 367
The Translational Requirement for La Crosse Virus S-mRNA Synthesis D. Kolakof- sky, C. Bellocq, and R. Raju 373
Putting a Protein Together
Molecular Dynamics: Applications to Proteins M. Karplus, A. T. Brünger, R. Elber, and J. Kuriyan 381
The C-peptide Helix from Ribonuclease A Considered as an Autonomous Folding Unit K. R. Shoemaker, B. Fairman, P.S. Kim, E. J. York, J. M. Stewart, and R. L. Baldwin 391
The Evolution of Protein Structures C. Chothia and A. M. Lesk 399
ß Turns in Early Evolution: Chirality, Genetic Code, and Biosynthetic Pathways J. Jurka and T. F. Smith 407
Gene Duplication and the Origin of Repetitive Protein Structures A. D. McLachlan 411
Internal Packing and Protein Structural Classes J. W Ponder and F.M. Richards 421
Proteins
Structure
Structural and Functional Relationships in the Adenylate Kinase Family G.E. Schulz 429
Facing up to Membranes: Structure/Function Relationships in Phospholipases A. Achari, D. Scott, P. Barlow, J. C. Vidal, Z. Otwinowski, S. Brunie, and P. B. Sigler 441
Atomic Protein Structures Reveal Basic Features of Binding of Sugars and Ionic Substrates and Calcium Cation F. A. Quiocho, N. K. Vyas, J. S. Sack, and M. N. Vyas 453
Structural Studies of Klenow Fragment: An Enzyme with Two Active Sites T. A. Steitz, L. Beese, P.S. Freemont, J. M. Friedman, and M. R. Sanderson 465
Zinc Fingers: A Novel Protein Fold for Nucleic Acid Recognition A. KIug and D. Rhodes 473
Some Evolutionary Relationships of the Primary Biological Catalysts Glutamine Synthetase and RuBisCO D. Eisenberg, B. J. Almassy, C. A. Janson, M. S. Chapman, S. W. Suh, D. Cascio, and W. W. Smith 483
Structural and Evolutionary Aspects of the Key Enzymes in Photorespiration; RuBis- CO and Glycolate Oxidase C. -I. Brändén, G. Schneider, Y. Lindqvist, I. Andersson, S. Knight, and G. Lorimer 491
Calcium Coordination and the Calmodulin Fold: Divergent versus Convergent Evolu- tion R. H. Kretsinger 499
Biosynthesis, Processing, and Evolution of Bovine Pancreatic Trypsin Inhibitor T. E. Creighton and I. G. Charles 511
The Design of a Four-helix Bundle Protein W. F. DeGrado, L. Regan, and S. P. Ho 521
The Serpins: Evolution and Adaptation in a Family of Protease Inhibitors R. W. Carrell, PA. Pemberton, and D. B. Boswell 527
The Role of Protein Folding in the Evolution of Protein Sequences T. Stackhouse, J. J. Onuffer, C. B. Matthews, S. A. Ahmed, and E. W. Miles 537
Positive Darwinian Selection in Evolution of Protein Inhibitors of Seine Protein- ases M. Laskowski, Jr., I. Kato, W. J. Kohr, S. J. Park, M. Tashiro, and H. E. Whatley 545
Cofactors
Stereochemistry of Cooperative Mechanisms in Hemoglobin M. F. Perutz, G. Fermi, B. Luisi, B. Shaanan, and R. C. Liddington 555
Porphyrin Iron(III) Mixed Function Oxidases: An Evolutionary Endpoint for Transi- tion Metal(III) Reactions with Oxygen Donors T. C. Bruice 567
S-Adenosylmethionine and the Mechanism of Hydrogen Transfer in the Lysine 2,3-Aminomutase Reaction P A. Frey and M. L. Moss 571
Metal Ions in Proteins: Structural and Functional Roles J. M. Berg 579
Lactobacillus leichmannii and Escherichia coli Ribonucleotide Reductases: Chemical and Structural Similarities A. I. Lin, G. W. Ashley, and J. Stubbe 587
Function
The Development of Enzyme Catalytic Efficiency: An Experimental Approach J. D. Hermes, S. C. Blacklow, and J. R. Knowles 597
Crystallography and Site-directed Mutagenesis of Yeast Thosephosphate Isomerase: What Can We Learn about Catalysis from a "Simple" Enzyme? T. C. Alber, R. C. Davenport, Jr., D. A. Giammona, E. Lolis, G. A. Petsko, and D. Ringe 603
Evolution of Catalysis in the Seine Proteases J. N. Higaki, B. W Gibson, and C. S. Craik 615
Transmission of Regulatory Conformational Changes through Proteins P E. Thors- ness, S. L. Mowbray, and D. E. Koshland, Jr. 623
Implications for Enzymic Catalysis from Free-energy Reaction Coordinate Profiles C. A. Fierke, R. D. Kuchta, K. A. Johnson, and S. J. Benkovic 631
Kinetic Devices in Protein Synthesis, DNA Replication, and Mismatch Repair J. Ninio 639
On the Evolution of Specificity and Catalysis in Subtilisin J. A. Wells, B. C. Cunning- ham, T. P Graycar, D. A. Estell, and P Carter 647
Ribosomes
The Role of RNA and Protein in Ribosome Function: A Review of Early Reconstitu tion Studies and Prospects for Future Studies M. Nomura 653
New Aspects of Structure, Assembly, Evolution, and Function of Ribosomes K. H. Nierhaus, R. Brimacombe, V. Nowotny, C. L. Pon, H. -J. Rheinberger, B. Witt- mann-Liebold, and H. G. Wittmann 665
Evolving Ribosome Structure and Function: rRNA and the Translation Mech- anism M. Oakes, A. Scheinman, M. Rivera, D. Soufer, G. Shankweiler, and J. Lake 675
Slippery Runs, Shifty Stops, Backward Steps, and Forward Hops: -2, -1, +1, +2, +5, and +6 Ribosomal Frameshifting R. .B. Weiss, D. M. Dunn, J. F. Atkins, and R.. F. Gesteland 687
Studies on the Architecture and Function of 16S rRNA H. F. Noller, S. Stern, D. Moazed, T. Powers, P. Svensson, and L. -M. Changchien 695
Evolution of Eukaryotic rRNA: Constraints Imposed by RNA Interactions S. A. Gerbi, C. Jeppesen, B. Stebbins-Boaz, and M. Ares, Jr 709
On the Modus Operandi of the Ribosome P. B. Moore 721
Approaches to the Determination of the Three-dimensional Architecture of Ribosomal Particles A. Yonath, K. R. Leonard, S. Weinstein, and H. G. Wittmann 729
Protein Synthesis and the Genetic Code
Peptide-specific Ribosomes, Genomic Tags, and the Origin of the Genetic Code N. Maizels and A. M. Weiner 743
Genetic Error and Genome Design D. C. Reanney 751
The Phylogeny of tRNA Sequences Provides Evidence for Ambiguity Reduction in the Origin of the Genetic Code W M. Fitch and K. Upper 759
Evolution of Anticodons: Variations in the Genetic Code T. H. Jukes, S. Osawa, A. Muto, and N. Lehman 769
Role of Directional Mutation Pressure in the Evolution of the Eubacterial Genetic Code S. Osawa, T. H. Jukes, A. Muto, F. Yamao, T. Ohama, and Y. Andachi 777
Genetic System of Chloroplasts H. Ozeki, K. Ohyama, H. Inokuchi, H. Fukuzawa, T. Kohchi, T. Sano, K. Nakahigashi, and K. Umesono 791
Evolutionary Trees
The Origin of Cells: A Symbiosis between Genes, Catalysts, and Membranes T. Cavalier-Smith 805
Earliest Phylogenetic Branchings: Comparing rRNA-based Evolutionary Trees In- ferred with Various Techniques G. J. Olsen 825
Prokaryotes and Archaebacteria Are Not Monophyletic: Rate Invariant Analysis of rRNA Genes Indicates That Eukaryotes and Eocytes Form a Monophyletic Taxon J. A. Lake 839
Reconstruction of Phylogenetic Trees and Estimation of Divergence Times Under Nonconstant Rates of Evolution W. -H. Li, K. H. Wolfe, J. Sourdis, and P. M. Sharp 847
Reliability of Evolutionary Trees D. Penny, M.D. Hendy, and I. M. Henderson 857
Male-driven Molecular Evolution: A Model and Nucleotide Sequence Analysis T. Miyata, H. Hayashida, K. Kuma, K. Mitsuyasu, and T. Yasunaga 863
Reconstructing the Evolution of Vertebrate Blood Coagulation from a Consideration of the Amino Acid Sequences of Clotting Proteins R. F. Doolittle and D. F. Feng 869
Globins: A Case Study in Molecular Phylogeny M. Goodman, J. Czelusniak, B. F. Koop, D. A. Tagle, and J. L. Slightom 875
Sequence Convergence and Functional Adaptation of Stomach Lysozymes from Foregut Fermenters C. -B. Stewart and A. C. Wilson 891
Exons and latrons
The Exon Theory of Genes W. Gilbert 901
What Introns Have to Tell Us: Hierarchy in Genome Evolution W. F. Doolittle 907
Protein Architecture and the Origin of Introns M. Go and M. Nosaka 915
Exon and Domain Evolution in the Proenzymes of Blood Coagulation and Fi- brinolysis C. C. F. Blake, K. Harlos, and S. K. Holland 925
Summary
A. M. Weiner 933
Foreword xiii
Opening Remarks
Evolution of Catalytic Function D. E. Koshland, Jr. 1
Evolution of the Genetic Apparatus: A Review L. E. Orgel 9
Primordial Soup
Which Organic Compounds Could Have Occurred on the Prebiotic Earth? S. L. Miller 17
Prebiotic Synthesis: Problems and Challenges J. P. Ferris 29
In Search of RNA Ancestors A. W Schwartz, J. Visscher, R. Van der Woerd, and C. G. Bakker 37
Nonenzymatic Template-directed Synthesis of Informational Macromolecules G. F. Joyce 41
Natural Selection, Protein Engineering, and the Last Riboorganism: Rational Model Building in Biochemistry S A. Benner, R. K. Allemann, A. D. Ellington, L. Ge, A. Glasfeld, G. F. Leanz, T. Krauch, L. J. MacPherson, S. Moroney, J. A. Piccirilli, and E. Weinhold 53
Essentials of Catalysis
Economics of Enzyme Catalysis W P. Jencks 65
Artificial Enzymes R. Breslow 75
Phosphorus-containing Peptide Analogs as Peptidase Inhibitors P. A. Bartlett, C. K. Marlowe, P. P. Giannousis, and J. E. Hanson 83
Catalytic Antibodies A. Tramontano, K. Janda, A. D. Napper, S. J. Benkovic, and R. A. Lerner 91
Antibody Catalysis by Transition State Stabilization S. J. Pollack and P. G. Schultz 97
Engineering of Antibodies with a Known Three-dimensional Structure A. Pluck- thun, R. Glockshuber, I. Pfitzinger, A. Skerra, and J. Stadlmüller 105
RNA
Anatomy
Conforniational Changes and Dynamics of tRNAs: Evidence from Hydrolysis Pat terns A. C. Dock-Bregeon and D. Morasv 113
Improved Parameters for Prediction of RNA Structure D.H. Turner, N. Sugimoto, J. A. Jaeger, C. E. Longfellow, S. M. Freier, and R. Kierzek 123
RNA Structure from A to Z. I. Tinoco, Jr., P. W. Davis, C. C. Hardin, J. D. Puglisi, G. T. Walker, and J. Wyatt 135
Catalysis
Structures Involved in Tetrahymena rRNA Self-splicing and RNA Enzyme Activity M.D. Been, E. T. Barfod, J. M. Burke, J. V. Price, N. K. Tanner, A. J. Zaug, and T.R. Cech
Implications of Intermolecularly Catalyzed Reactions by the Tetrahymena Ribo zyme P.S. Kay and T. Inoue 159
Internal Guide Sequence and Reaction Specificity of Group I Self-splicing In- trons R. W. Davies, R. B. Waring, and P. Towner 165
Genetic Dissection of an RNA Enzyme J. A. Doudna, A. S. Gerber, J. M. Cherry, and J. W Szostak 173
Genetic Delineation of Functional Components of the Group I Intron in the Phage T4 td Gene M. Belfort, P.S. Chandry, and J. Pedersen-Lane 181
A Family of Autocatalytic Group I Introns in Bacteriophage T4 D. A. Shub, M. -Q. Xu, J. M. Gott, A. Zeeh, and L. D. Wilson 193
Long-range Intron-Exon and Intron-Intron Pairings Involved in Self-splicing of Class II Catalytic Introns F. Michel and A. Jacquier 201
Reactions Mediated by Yeast Mitochondrial Group I and II Introns H. F. Tabak, G. Van der Horst, A. J. Winter, J. Smit, R. Van der Veen, J. H. J. M. Kwakman, L.A. Grivell, and A. C. Arnberg 213
Group II Intron Self-splicing: Development of Alternative Reaction Conditions and Identification of a Predicted Intermediate C. L. Peebles, E. J. Benatan, K. A. Jarrell, and P.S. Perlman 223
Characteristics of Ribonuclease P from Various Organisms N. Lawrence, D. Wesolowski, H. Gold, M. Bartkiewicz, C. Guerrier-Takada, W. H. McClain, and S. Altman 233
Structure and Catalytic Function in Ribonuclease P N. R. Pace, C. Reich, B. D. James, G. J. Olsen, B. Pace, and D. S. Waugh 239
Structural and Ionic Requirements for Self-cleavage of Virusoid RNAs and trans Self-cleavage of Viroid RNA A. C. Forster, A. C. Jeffries, C. C. Sheldon, and R.H. Symons 249
Transcripts of Newt Satellite DNA Self-cleave In Vitro L. M. Epstein and J. G. Gall 261
Characterization of Two RNA-catalyzed RNA Cleavage Reactions J. R. Sampson, F. X. Sullivan, L. S. Behlen, A. B. DiRenzo, and O. C. Uhlenbeck 267
Splicing of Messenger RNA Precursors P. A. Sharp, M. M. Konarska, P. J. Grabow- ski, A. I. Lamond, R. Marciniak, and S. R. Seiler 277
Different Small Nuclear Ribonucleoprotein Particles Are Involved in Different Steps of Splicing Complex Formation D. Frendewey, A. Kramer, and W. Keller 287
Templates
Replication and Evolution of Short-chained RNA Species Replicated by Qb Rep licase C. K. Biebricher 299
New Concepts for Dealing with the Evolution of Nucleic Acids M. Eigen 307
Evolution of the RNA Coliphages: The Role of Secondary Structures during RNA Replication C. Priano, F. R. Kramer, and D. R. Mills 321
Evidence Implicating a tRNA Heritage for the Promoters of Positive-strand RNA Synthesis in Brome Mosaic and Related Viruses L. E. Marsh and T. C. Hall 331
Molecular Events Leading to Poliovirus Genome Replication A.V. Paul, C. -F. Yang, S.-K. Jang, R.. J. Kuhn, H. Tada, M. Nicklin, H. -G. Kräusslich, C. -K. Lee, and E. Wimmer 343
Transcription and Replication of Influenza Virion RNA in the Nucleus of Infected Cells R. M. Krug, C. St. Angelo, B. Broni, and G. Shapiro 353
Coronavirus: A Jumping RNA Transcription M. M. C. Lai, S. Makino, L. H. Soe, C. -K. Shieh, J. G. Keck, and J. O. Fleming 359
The Switch from Transcription to Replication of a Negative-strand RNA Virus G. W Wertz, M. B. Howard, N. Davis, and J. Patton 367
The Translational Requirement for La Crosse Virus S-mRNA Synthesis D. Kolakof- sky, C. Bellocq, and R. Raju 373
Putting a Protein Together
Molecular Dynamics: Applications to Proteins M. Karplus, A. T. Brünger, R. Elber, and J. Kuriyan 381
The C-peptide Helix from Ribonuclease A Considered as an Autonomous Folding Unit K. R. Shoemaker, B. Fairman, P.S. Kim, E. J. York, J. M. Stewart, and R. L. Baldwin 391
The Evolution of Protein Structures C. Chothia and A. M. Lesk 399
ß Turns in Early Evolution: Chirality, Genetic Code, and Biosynthetic Pathways J. Jurka and T. F. Smith 407
Gene Duplication and the Origin of Repetitive Protein Structures A. D. McLachlan 411
Internal Packing and Protein Structural Classes J. W Ponder and F.M. Richards 421
Proteins
Structure
Structural and Functional Relationships in the Adenylate Kinase Family G.E. Schulz 429
Facing up to Membranes: Structure/Function Relationships in Phospholipases A. Achari, D. Scott, P. Barlow, J. C. Vidal, Z. Otwinowski, S. Brunie, and P. B. Sigler 441
Atomic Protein Structures Reveal Basic Features of Binding of Sugars and Ionic Substrates and Calcium Cation F. A. Quiocho, N. K. Vyas, J. S. Sack, and M. N. Vyas 453
Structural Studies of Klenow Fragment: An Enzyme with Two Active Sites T. A. Steitz, L. Beese, P.S. Freemont, J. M. Friedman, and M. R. Sanderson 465
Zinc Fingers: A Novel Protein Fold for Nucleic Acid Recognition A. KIug and D. Rhodes 473
Some Evolutionary Relationships of the Primary Biological Catalysts Glutamine Synthetase and RuBisCO D. Eisenberg, B. J. Almassy, C. A. Janson, M. S. Chapman, S. W. Suh, D. Cascio, and W. W. Smith 483
Structural and Evolutionary Aspects of the Key Enzymes in Photorespiration; RuBis- CO and Glycolate Oxidase C. -I. Brändén, G. Schneider, Y. Lindqvist, I. Andersson, S. Knight, and G. Lorimer 491
Calcium Coordination and the Calmodulin Fold: Divergent versus Convergent Evolu- tion R. H. Kretsinger 499
Biosynthesis, Processing, and Evolution of Bovine Pancreatic Trypsin Inhibitor T. E. Creighton and I. G. Charles 511
The Design of a Four-helix Bundle Protein W. F. DeGrado, L. Regan, and S. P. Ho 521
The Serpins: Evolution and Adaptation in a Family of Protease Inhibitors R. W. Carrell, PA. Pemberton, and D. B. Boswell 527
The Role of Protein Folding in the Evolution of Protein Sequences T. Stackhouse, J. J. Onuffer, C. B. Matthews, S. A. Ahmed, and E. W. Miles 537
Positive Darwinian Selection in Evolution of Protein Inhibitors of Seine Protein- ases M. Laskowski, Jr., I. Kato, W. J. Kohr, S. J. Park, M. Tashiro, and H. E. Whatley 545
Cofactors
Stereochemistry of Cooperative Mechanisms in Hemoglobin M. F. Perutz, G. Fermi, B. Luisi, B. Shaanan, and R. C. Liddington 555
Porphyrin Iron(III) Mixed Function Oxidases: An Evolutionary Endpoint for Transi- tion Metal(III) Reactions with Oxygen Donors T. C. Bruice 567
S-Adenosylmethionine and the Mechanism of Hydrogen Transfer in the Lysine 2,3-Aminomutase Reaction P A. Frey and M. L. Moss 571
Metal Ions in Proteins: Structural and Functional Roles J. M. Berg 579
Lactobacillus leichmannii and Escherichia coli Ribonucleotide Reductases: Chemical and Structural Similarities A. I. Lin, G. W. Ashley, and J. Stubbe 587
Function
The Development of Enzyme Catalytic Efficiency: An Experimental Approach J. D. Hermes, S. C. Blacklow, and J. R. Knowles 597
Crystallography and Site-directed Mutagenesis of Yeast Thosephosphate Isomerase: What Can We Learn about Catalysis from a "Simple" Enzyme? T. C. Alber, R. C. Davenport, Jr., D. A. Giammona, E. Lolis, G. A. Petsko, and D. Ringe 603
Evolution of Catalysis in the Seine Proteases J. N. Higaki, B. W Gibson, and C. S. Craik 615
Transmission of Regulatory Conformational Changes through Proteins P E. Thors- ness, S. L. Mowbray, and D. E. Koshland, Jr. 623
Implications for Enzymic Catalysis from Free-energy Reaction Coordinate Profiles C. A. Fierke, R. D. Kuchta, K. A. Johnson, and S. J. Benkovic 631
Kinetic Devices in Protein Synthesis, DNA Replication, and Mismatch Repair J. Ninio 639
On the Evolution of Specificity and Catalysis in Subtilisin J. A. Wells, B. C. Cunning- ham, T. P Graycar, D. A. Estell, and P Carter 647
Ribosomes
The Role of RNA and Protein in Ribosome Function: A Review of Early Reconstitu tion Studies and Prospects for Future Studies M. Nomura 653
New Aspects of Structure, Assembly, Evolution, and Function of Ribosomes K. H. Nierhaus, R. Brimacombe, V. Nowotny, C. L. Pon, H. -J. Rheinberger, B. Witt- mann-Liebold, and H. G. Wittmann 665
Evolving Ribosome Structure and Function: rRNA and the Translation Mech- anism M. Oakes, A. Scheinman, M. Rivera, D. Soufer, G. Shankweiler, and J. Lake 675
Slippery Runs, Shifty Stops, Backward Steps, and Forward Hops: -2, -1, +1, +2, +5, and +6 Ribosomal Frameshifting R. .B. Weiss, D. M. Dunn, J. F. Atkins, and R.. F. Gesteland 687
Studies on the Architecture and Function of 16S rRNA H. F. Noller, S. Stern, D. Moazed, T. Powers, P. Svensson, and L. -M. Changchien 695
Evolution of Eukaryotic rRNA: Constraints Imposed by RNA Interactions S. A. Gerbi, C. Jeppesen, B. Stebbins-Boaz, and M. Ares, Jr 709
On the Modus Operandi of the Ribosome P. B. Moore 721
Approaches to the Determination of the Three-dimensional Architecture of Ribosomal Particles A. Yonath, K. R. Leonard, S. Weinstein, and H. G. Wittmann 729
Protein Synthesis and the Genetic Code
Peptide-specific Ribosomes, Genomic Tags, and the Origin of the Genetic Code N. Maizels and A. M. Weiner 743
Genetic Error and Genome Design D. C. Reanney 751
The Phylogeny of tRNA Sequences Provides Evidence for Ambiguity Reduction in the Origin of the Genetic Code W M. Fitch and K. Upper 759
Evolution of Anticodons: Variations in the Genetic Code T. H. Jukes, S. Osawa, A. Muto, and N. Lehman 769
Role of Directional Mutation Pressure in the Evolution of the Eubacterial Genetic Code S. Osawa, T. H. Jukes, A. Muto, F. Yamao, T. Ohama, and Y. Andachi 777
Genetic System of Chloroplasts H. Ozeki, K. Ohyama, H. Inokuchi, H. Fukuzawa, T. Kohchi, T. Sano, K. Nakahigashi, and K. Umesono 791
Evolutionary Trees
The Origin of Cells: A Symbiosis between Genes, Catalysts, and Membranes T. Cavalier-Smith 805
Earliest Phylogenetic Branchings: Comparing rRNA-based Evolutionary Trees In- ferred with Various Techniques G. J. Olsen 825
Prokaryotes and Archaebacteria Are Not Monophyletic: Rate Invariant Analysis of rRNA Genes Indicates That Eukaryotes and Eocytes Form a Monophyletic Taxon J. A. Lake 839
Reconstruction of Phylogenetic Trees and Estimation of Divergence Times Under Nonconstant Rates of Evolution W. -H. Li, K. H. Wolfe, J. Sourdis, and P. M. Sharp 847
Reliability of Evolutionary Trees D. Penny, M.D. Hendy, and I. M. Henderson 857
Male-driven Molecular Evolution: A Model and Nucleotide Sequence Analysis T. Miyata, H. Hayashida, K. Kuma, K. Mitsuyasu, and T. Yasunaga 863
Reconstructing the Evolution of Vertebrate Blood Coagulation from a Consideration of the Amino Acid Sequences of Clotting Proteins R. F. Doolittle and D. F. Feng 869
Globins: A Case Study in Molecular Phylogeny M. Goodman, J. Czelusniak, B. F. Koop, D. A. Tagle, and J. L. Slightom 875
Sequence Convergence and Functional Adaptation of Stomach Lysozymes from Foregut Fermenters C. -B. Stewart and A. C. Wilson 891
Exons and latrons
The Exon Theory of Genes W. Gilbert 901
What Introns Have to Tell Us: Hierarchy in Genome Evolution W. F. Doolittle 907
Protein Architecture and the Origin of Introns M. Go and M. Nosaka 915
Exon and Domain Evolution in the Proenzymes of Blood Coagulation and Fi- brinolysis C. C. F. Blake, K. Harlos, and S. K. Holland 925
Summary
A. M. Weiner 933
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