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The Symposia, 1933 — 2003

1987:   Evolution of Catalytic Function, Vol. LII

Organizer: James Watson


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Symposium Participants    v
Foreword    xiiiOpening RemarksEvolution of Catalytic Function D. E. Koshland, Jr.    1Evolution of the Genetic Apparatus: A Review L. E. Orgel    9Primordial SoupWhich Organic Compounds Could Have Occurred on the Prebiotic Earth? S. L. Miller    17Prebiotic Synthesis: Problems and Challenges J. P. Ferris    29In Search of RNA Ancestors A. W Schwartz, J. Visscher, R. Van der Woerd, and C. G. Bakker    37Nonenzymatic Template-directed Synthesis of Informational Macromolecules G. F. Joyce    41Natural 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    53Essentials of CatalysisEconomics of Enzyme Catalysis W P. Jencks    65Artificial Enzymes R. Breslow    75Phosphorus-containing Peptide Analogs as Peptidase Inhibitors P. A. Bartlett, C. K. Marlowe, P. P. Giannousis, and J. E. Hanson    83Catalytic Antibodies A. Tramontano, K. Janda, A. D. Napper, S. J. Benkovic, and R. A. Lerner    91Antibody Catalysis by Transition State Stabilization S. J. Pollack and P. G. Schultz     97Engineering of Antibodies with a Known Three-dimensional Structure A. Pluck- thun, R. Glockshuber, I. Pfitzinger, A. Skerra, and J. Stadlmüller     105RNAAnatomyConforniational Changes and Dynamics of tRNAs: Evidence from Hydrolysis Pat terns A. C. Dock-Bregeon and D. Morasv    113Improved Parameters for Prediction of RNA Structure D.H. Turner, N. Sugimoto, J. A. Jaeger, C. E. Longfellow, S. M. Freier, and R. Kierzek    123RNA Structure from A to Z. I. Tinoco, Jr., P. W. Davis, C. C. Hardin, J. D. Puglisi, G. T. Walker, and J. Wyatt    135CatalysisStructures 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. CechImplications of Intermolecularly Catalyzed Reactions by the Tetrahymena Ribo zyme P.S. Kay and T. Inoue    159Internal Guide Sequence and Reaction Specificity of Group I Self-splicing In- trons R. W. Davies, R. B. Waring, and P. Towner    165Genetic Dissection of an RNA Enzyme J. A. Doudna, A. S. Gerber, J. M. Cherry, and J. W Szostak     173Genetic Delineation of Functional Components of the Group I Intron in the Phage T4 td Gene M. Belfort, P.S. Chandry, and J. Pedersen-Lane    181A Family of Autocatalytic Group I Introns in Bacteriophage T4 D. A. Shub, M. -Q. Xu, J. M. Gott, A. Zeeh, and L. D. Wilson    193Long-range Intron-Exon and Intron-Intron Pairings Involved in Self-splicing of Class II Catalytic Introns F. Michel and A. Jacquier    201Reactions 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    213Group 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    223Characteristics of Ribonuclease P from Various Organisms N. Lawrence, D. Wesolowski, H. Gold, M. Bartkiewicz, C. Guerrier-Takada, W. H. McClain, and S. Altman    233Structure and Catalytic Function in Ribonuclease P N. R. Pace, C. Reich, B. D. James, G. J. Olsen, B. Pace, and D. S. Waugh    239Structural 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    249Transcripts of Newt Satellite DNA Self-cleave In Vitro L. M. Epstein and J. G. Gall     261Characterization of Two RNA-catalyzed RNA Cleavage Reactions J. R. Sampson, F. X. Sullivan, L. S. Behlen, A. B. DiRenzo, and O. C. Uhlenbeck     267Splicing of Messenger RNA Precursors P. A. Sharp, M. M. Konarska, P. J. Grabow- ski, A. I. Lamond, R. Marciniak, and S. R. Seiler    277Different Small Nuclear Ribonucleoprotein Particles Are Involved in Different Steps of Splicing Complex Formation D. Frendewey, A. Kramer, and W. Keller    287TemplatesReplication and Evolution of Short-chained RNA Species Replicated by Qb Rep licase C. K. Biebricher    299New Concepts for Dealing with the Evolution of Nucleic Acids M. Eigen    307Evolution of the RNA Coliphages: The Role of Secondary Structures during RNA Replication C. Priano, F. R. Kramer, and D. R. Mills    321Evidence 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    331Molecular 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    343Transcription and Replication of Influenza Virion RNA in the Nucleus of Infected Cells R. M. Krug, C. St. Angelo, B. Broni, and G. Shapiro    353Coronavirus: A Jumping RNA Transcription M. M. C. Lai, S. Makino, L. H. Soe, C. -K. Shieh, J. G. Keck, and J. O. Fleming    359The Switch from Transcription to Replication of a Negative-strand RNA Virus G. W Wertz, M. B. Howard, N. Davis, and J. Patton     367The Translational Requirement for La Crosse Virus S-mRNA Synthesis D. Kolakof- sky, C. Bellocq, and R. Raju     373Putting a Protein TogetherMolecular Dynamics: Applications to Proteins M. Karplus, A. T. Brünger, R. Elber, and J. Kuriyan    381The 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     399ü Turns in Early Evolution: Chirality, Genetic Code, and Biosynthetic Pathways J. Jurka and T. F. Smith     407Gene Duplication and the Origin of Repetitive Protein Structures A. D. McLachlan     411Internal Packing and Protein Structural Classes J. W Ponder and F.M. Richards    421ProteinsStructureStructural and Functional Relationships in the Adenylate Kinase Family G.E. Schulz     429Facing 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    441Atomic 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    453Structural 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     465Zinc Fingers: A Novel Protein Fold for Nucleic Acid Recognition A. KIug and D. Rhodes     473Some 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


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


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


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


A. M. Weiner    933