1987: Evolution of Catalytic Function, Vol. LII
Organizer: James Watson
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 399ß 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
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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 |
