COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE

VOLUME LII COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY

VOLUME LII

Evolution of Catalytic Function

COLD SPRING HARBOR LABORATORY 1987 COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY VOLUME LII 1987 by The Cold Spring Harbor Laboratory International Standard Book Number 0-87969-054-2 International Standard Serial Number 0091-7451 Library of Congress Catalog Card Number 34-8174

Printed in the United States of America All rights reserved

COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY

Founded in 1933 by REGINALD G. HARRIS Director of the Biological Laboratory 1924 to 1936

Previous Symposia Volumes

I (1933) Surface Phenomena XXV (1960) Biological Clocks II (1934) Aspects of Growth XXVI (1961) Cellular Regulatory Mechanisms III (1935) Photochemical Reactions XXVII (1962) Basic Mechanisms in Animal Virus Biology IV (1936) Excitation Phenomena XXVIII (1963) Synthesis and Structure of Macromolecules V (1937) Internal Secretions XXIX (1964) Human Genetics VI (1938) Protein XXX (1965) Sensory Receptors VII (1939) Biological Oxidations XXXI (1966) The Genetic Code VIII (1940) Permeability and the of Cell Membranes XXXII (1967) Antibodies IX (1941) Genes and Chromosomes: Structure and Organi- XXXIII (1968) Replication of DNA in Microorganisms zation. XXXIV (1969) The Mechanism of Protein Synthesis X (1942) The Relation of Hormones to Development XXXV (1970) Transcription of Genetic Material XI (1946) Heredity and Variation in Microorganisms XXXVI (1971) Structure and Function of Proteins at the XII (1947) Nucleic Acids and Nucleoproteins Three-dimensional Level XIII (1948) Biological Applications of Tracer Elements XXXVII (1972) The Mechanism of Muscle Contraction XIV (1949) Amino Acids and Proteins XXXVIII (1973) Chromosome Structure and Function XV (1950) Origin and Evolution of Man XXXIX (1974) Tumor Viruses XVI (1951) Genes and Mutations XL (1975) The Synapse XVII (1952) The Neuron XLI (1976) Origins of Lymphocyte Diversity XVIII (1953) Viruses XLII (1977) Chromatin XIX (1954) The Mammalian Fetus: Physiological Aspects of XLIII (1978) DNA: Replication and Recombination Development XLIV (1979) Viral Oncogenes XX (1955) Population Genetics: The Nature and Causes of XLV (1980) Movable Genetic Elements Genetic Variability in Population XLVI (1981) Organization of the Cytoplasm XX1 (1956) Genetic Mechanisms: Structure and Function XLVII (1982) Structures of DNA XXII (1957) Population Studies: Animal Ecology and De- XLVIII (1983) Molecular Neurobiology mography XLIX (1984) Recombination at the DNA Level XXIII (1958) Exchange of Genetic Material: Mechanism and L (1985) of Development Consequences LI (1986) Molecular Biology of Homo sapiens XXIV (1959) Genetics and Twentieth Century

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ALTMAN, SIDNEY, Dept. of Biology, Yale University, CEDERGREN, ROBERT, Dept. of , Universi- New Haven, Connecticut ty of Montreal, Canada ARMSTRONG,JOHN, Dept. of Drug Metabolism, Smith, CHOTHIA, CYRUS, MRC Laboratory of Molecular Biol- Kline & French Research Ltd., Welwyn Hefts, ogy, Cambridge, England England CRAIK, CHARLES, Dept. of Pharmaceutical Chemistry, BAKER, MICHAEL,University of California, San Diego, University of California, San Francisco La Jolla CREIGHTON, THOMAS, MRC Laboratory of Molecular BALDWIN, ANNE, Dept. of Biochemistry, Stanford Biology, Cambridge, England University Medical Center, California DARNELL, JAMES, Rockefeller University, New York, BALDWIN, ROBERT, Dept. of Biochemistry, Stanford New York University Medical Center, California DAUTER, ZBIGNIEW, European Molecular Biology BALL, ANDREWL., Dept. of Microbiology, University Laboratory, Hamburg, Federal Republic of of Alabama, Birmingham Germany BARTLETT, PAUL, Dept. of Chemistry, University of DAVIES, WAYNE, Allelix, Inc., Mississauga, Ontario, California, Berkeley Canada BASHFORD, DONALD, Dept. of Chemistry, Harvard DEGRADO, WILLIAM, E.I. du Pont de Nemours and University, Cambridge, Company, Wilmington, Delaware BELFORD, MARLENE, Wadsworth Laboratories, New DOMANICO, PAUL, E.I. du Pont de Nemours and Com- York State Dept. of Health, Albany pany, Wilmington, Delaware BENKOVlC, STEPHEN, Dept. of Chemistry, Pennsylvania DOOLITTLE, RUSSELL, Dept. of Chemistry, University State University, University Park of California, San Diego, La Jolla BENNER, STEVEN, Laboratory for Organic Chemistry, DOOLI~LE, W. FORD, Dept. of Biochemistry, Swiss Federal Institute of Technology, Zurich Dalhousie University, Halifax, Nova Scotia, BERG, JEREMY, Dept. of Chemistry, Johns Hopkins Canada University, Baltimore, Maryland DORIT, ROBERT, Dept. of Cellular and Developmental BIEBRICHER, CHRISTOF, Dept. of Biochemical Kinetics, Biology, , Cambridge, Mas- Max-Planck Institut, Gottingen, Federal Repub- sachusetts lic of Germany DOUDNA, JENNIFER, Dept. of Molecular Biology, Mas- BLAKE, COLIN C.F., Laboratory of Molecular sachusetts General Hospital, . Biophysics, University of Oxford, England EIGEN, MANFRED, Dept. of Biophysikalische Chemie, BOSWELL, ROSS, Dept. of Haematological Medicine, Max-Planck Institute, Gottingen, Federal Re- Clinical School, En- public of Germany gland EISENBERG, DAVID, Dept. of Chemistry, University of BOUBLIK, MILOSLAV, Dept. of Biochemistry, Roche California, Los Angeles Institute of Molecular Biology, Nutley, New EISENSTEIN, EDWARD, Dept. of Molecular Biology and Jersey Virus Laboratory, University of California, Ber- BR~NDI~N, CARL, Dept. of Chemistry and Molecular keley Biology, Uppsala Biomedical Center, Sweden EPSTEIN, LLOYD, Dept. of Biological Science, Florida BRESLOW, RONALD, Dept. of Chemistry, Columbia State University, Tallahassee University, New York, New York ERIKSSON, ELISABETH, Dept. of Molecular Biology, BRUICE, THOMAS, Dept. of Chemistry, University of Uppsala University, Sweden California, Santa Barbara FERRIS, JAMES, Dept. of Chemistry, Rensselaer Poly- BURKE, JOHN, Dept. of Chemistry, Williams College, technic Institute, Troy, New York Williamstown, Massachusetts FITCH, WALTER, Dept. of Biological Sciences, Uni- CARRELL, ROBIN, Dept. of Haematology, University of versity of Southern California, Los Angeles Cambridge, England FREY, PERRY, Enzyme Institute, University of Wiscon- CARTER, PAUL, , South San Francisco, sin, Madison California GARDELL, STEPHEN, Dept. of Biological Chemistry, CAVALIER-SMITH, THOMAS, Dept. of Biophysics, Cell Merck, Sharpe & Dohme Research Laboratories, and Molecular Biology, Kings College, London, West Point, Pennsylvania England GERBI, SUSAN, Division of Biology and Medicine, CECH, THOMAS, Dept. of Chemistry and Biochemistry, Brown University, Providence, Rhode Island University of Colorado, Boulder GILBERT, WALTER, Dept. of Cellular and Developmen- vi SYMPOSIUM PARTICIPANTS

tal Biology, Harvard University, Cambridge, KORANT, BRUCE, Dept. of Central Research and De- Massachusetts velopment, E.I. du Pont de Nemours & Com- GG, MITIKO, Dept. of Biology, Kyushu University, pany, Wilmington, Delaware Higashi-ku Fukuoka-shi, Japan KOSHLAND, DANIEL, Dept. of Biochemistry, Universi- GOODMAN, MORRIS, Anatomy Department, Wayne ty of California, Berkeley State University School of Medicine, Detroit, KOSTER, HUBERT, MilliGen-Division of Millipore, Bed- Michigan ford, Massachusetts GRABOWSKI, PAULA, Center for Cancer Research, KREMSKY, JONATHAN, Genetics Institute, Cambridge, Massachusetts Institute of Technology, Cam- Massachusetts bridge KRENITSKV, THOMAS, Dept. of Experimental Therapy, GREGORY, STEVEN, Dept. of Experimental Biology, Wellcome Research Laboratories, Research Tri- Roswell Park Memorial Institute, Buffalo, New angle Park, North Carolina York KRETSINGER, ROBERT, Dept. of Biology, University of GUMPORT, RICHARD, Dept. of Biochemistry, Universi- Virginia, Charlottesville ty of Illinois, Urbana KRUG, ROBERT, Dept. of Molecular Biology and Virol- HACKERT, MARVIN, Dept. of Chemistry, University of ogy, Memorial Sloan-Kettering Cancer Center, Texas, Austin New York, New York HALL, TIMOTHY, Dept. of Biology, Texas A&M Uni- KURKINEN, MARKKU, UMDNJ-Robert Wood-Johnson versity, College Station Medical School, Piscataway, New Jersey HARAYAMA, SHIGEAKI, Dept. of Medical Biochemistry, LAI, MICHAEL, Dept. of Microbiology, University of University of Geneva, Switzerland Southern California School of Medicine, Los HILVERT, DONALD, Dept. of Molecular Biology, Angeles Scripps Clinic and Research Foundation, La LAKE, JIM, Dept. of Biology, University of Southern Jolla, California California, Los Angeles HINGORAN1, VIJAY, Dept. of Biological Chemistry, LASKOWSKI, MICHAEL, JR., Dept. of Chemistry, Pur- University of Illinois, Chicago due University, West Lafayette, Indiana HUMPHREYS, JOHN, Dept. of Biotechnology, Miles LERNER, RICHARD, Dept. of Molecular Biology, The Laboratories, Inc., Elkhart, Indiana Research Institute of Scripps Clinic, La Jolla, INOUE, TAN, The Salk Institute, La Jolla, California California JENCKS, WILLIAM, Dept. of Biochemistry, Brandeis LEVITT, MICHAEL, Dept. of Chemistry, Weizmann In- University, Waltham, Massachusetts stitute, Rehovot, Israel JONES, ALWYN, Dept. of Molecular Biology, Universi- LI, WEN-HsIUNG, Dept. of Demographic and Popula- ty of Uppsala, Sweden tion Genetics, University of Texas Health Sci- JOYCE, GERALD, The Salk Institute For Biological ence Center, Houston Studies, San Diego, California MANDECKI, WLODEK, Abbott Laboratories, Abbott JUKES, THOMAS, Space Sciences Laboratory, Universi- Park, Illinois ty of California, Berkeley MANDIYAN, VALSAN, Dept. of Biochemistry, Roche JURKA, JERZY, Dept. of Biostatistics, Dana Farber Institute of Molecular Biology, Nutley, New Cancer Institute, Boston, Massachusetts Jersey KARPLUS, MARTIN, Dept. of Biophysics, Harvard Uni- MARSH, LOREN, Dept. of Biology, Texas A&M Uni- versity, Cambridge, Massachusetts versity, College Station KELLER, WALTER, Dept. of Cell and Molecular Biolo- MASSEY, RICHARD, IGEN Inc., Rockville, Maryland gy, German Cancer Research Center, Heidel- MATrHEWS, CHARLES, Dept. of Chemistry, Pennsyl- berg, Federal Republic of Germany vania State University, University Park KENDALL, DEBRA, Dept. of Bioorganic Chemistry and McLACHLAN, ANDREW, MRC Laboratory of Molecu- Biochemistry, Rockefeller University, New York, lar Biology, Cambridge, England New York MERTZ, RONALD, Max-Planck-Institut f/Jr Biochemie, KIM, BVUNG-DONG, Dept. of Plant Science, University Martinsried, Federal Republic of Germany of Rhode Island, Kingston MICHEL, FRANqOIS, Centre de Genetique Moleculaire KLAR, AMAR, Cold Spring Harbor Laboratory, New du CNRS, Gif-sur-Yvette, France York MILKMAN, ROGER, Dept. of Biology, University of KLUG, AARON, MRC Laboratory of Molecular Biolo- Iowa, Iowa City gy, Cambridge, England MILLER, STANLEY, Dept. of Chemistry, University of KNOWLES, JEREMY, Dept. of Chemistry, Harvard Uni- California, San Diego, La Jolla versity, Cambridge, Massachusetts MILLS, DONALD, Dept. of Genetics and Development, KOLAKOFSKY, DANIEL, Dept. of Microbiology, Uni- College of Physicians, versity of Geneva Medical School, Switzerland Surgeons, New York, New York KOMIVES, ELIZABETH, Dept. of Chemistry, Harvard MIYATA, TAKASHI, Dept. of Biology, Kyushu Universi- University, Cambridge, Massachusetts ty, Fukuoka, Japan SYMPOSIUM PARTICIPANTS vii

MOORE, PETER, Dept. of Chemistry, Yale University, and Biochemistry, Yale University, New Haven, New Haven, Connecticut Connecticut MORAS, DINO, Institute de Biologie Moleculaire and ROBERTUS, JON, Dept. of Chemistry, University of Cellulaire, Strasbourg, France Texas, Austin MOWBRAY, SHERRY, Dept. of Biochemistry, University SAAVEDRA, RAUL, Dept. of Biology, California Insti- of California, Berkeley tute of Technology, Pasadena NIERHAUS, KNUD, Max-Planck-Institut f/Jr Molekulare SANTER, MELVIN, Dept. of Biology, Haverford Col- Genetik, Berlin, Federal Republic of Germany lege, Pennsylvania NINIO, JACQUES, Institut Jacques Monod, Paris, France SCHEINMAN, ANDREW, Dept. of Molecular Biology, NOLLER, HARRY, University of California, Santa Cruz University of California, Los Angeles NOMURA, MASAYASU,Dept. of Biochemistry, Universi- SCHULTZ, PETER, Dept. of Chemistry, University of ty of California, Irvine California, Berkeley NORTH, GEOFFREY, Nature, London, England SCHULZ, GEORG, Institut f/it Organische Chemie und OLSEN, GARY, Dept. of Biology and Institute of Biochemie, Universitat Freiburg, Federal Re- Molecular and Cellular Biology, Indiana Uni- public of Germany versity, Bloomington SCHWARTZ, ALAN, Dept. of Exobiology, University of ORGEL, LESLIE, Chemical Evolution Laboratory, Salk Nijmegen, The Netherlands Institute for Biological Studies, San Diego, SHARP, PmLLIP, Center for Cancer Research, Mas- California sachusetts Institute of Technology, Cambridge OSAWA, SYOzO, Biology Laboratory of Molecular SHUB, DAVID, Dept. of Biological Sciences, State Uni- Genetics, Nagoya University, Japan versity of New York, Albany OZEKI, HARUO, Dept. of Biophysics, Kyoto Universi- SIGLER, PAUL, Dept. of Biochemistry and Molecular ty, Japan Biology, University of Chicago, Illinois PACE, NICK, Dept. of Biochemistry, Texas A&M Uni- STACY, DAVID, St. Joseph's Hospital, Atlanta, Georgia versity, College Station STEITZ, THOMAS, Dept. of Molecular Biophysics and PACE, NORMAN, Dept. of Biology, Indiana University, Biochemistry, Yale University, New Haven, Con- Bloomington necticut PEEBLES, CRAIG, Dept. of Biological Science, Universi- STEWART, CARO-BETH, Dept. of biochemistry and ty of Pittsburgh, Pennsylvania Biophysics, University of California, San Fran- PENNY, DAVID, DEPT. of Botany and Zoology, Massey cisco University, Palmerston North, New Zealand STOLZFUS, ARLIN, Dept. of Biology, University of PERUTZ, MAX, MRC Laboratory of Molecular Biolo- Iowa, Iowa City gy, Cambridge, England STUBBE, JOANNE, Dept. of Biochemistry, University of PETSKO, GREGORY, Dept. of Chemistry, Massachusetts Wisconsin, Madison Institute of Technology, Cambridge SUGIMOTO, NAOKI, Dept. of Chemistry, University of PETrER, RUSSELL, Dept. of Chemistry, University of Rochester, New York Pittsburgh, Pennsylvania SYMONS, ROBERT, Dept. of Biochemistry, University of PICCIRILLI, JOE, Laboratorium f/Jr Organische Chemie, Adelaide, Australia ETH Zentrum, Zurich, Switzerland TABAK, HENK, Dept. of Molecular Biology, University PtLKIS, SIMON, Dept. of Physiology and Biophysics, of Amsterdam, The Netherlands State University New York, Stony Brook TAKAHASHI, TADASHI,Biotechnology Developing Cen- PLUCKTHUN, ANDREAAS, Dept. of Molecular Biology, ter, Olympus Corporation, Lake Success, New Ludwig-Maximilians-Universitat, Martinsried, York Federal Republic of Germany THILLET, JOELLE, Institut Jacques Monod, Paris, POWELL, MICHAEL, IGEN Inc., Rockville, Maryland France QUIOCHO, FLORANTE, Baylor College of Medicine, THOMPSON, BOB, Dept. of Biology, University of Col- Houston, Texas orado, Boulder RAJAVASHISTH, TRIPATHI, School of Medicine, Uni- THORSNESS, PETER, Dept. of Biochemistry, University versity of California, Los Angeles of California, Berkeley RAO, NAGIARAJA,Molecular Genetics Research, Lilly TINOCO, IGNACIO, JR., Dept. of Chemistry, University Corporate Center, Indianapolis, Indiana of California, Berkeley REANNEY, DARRYL, Science Focus, East Hawthorn, TOMITA, FUSAO, Kato Memorial Bioscience Laborat- Victoria, Australia ries, Kyowa Hakko Kogyo Co. Ltd., Tokyo, REYNOLDS, FREDERICK, Oncogene Science Inc., Japan Mineola, New York TURNER, DOUGLAS, Dept. of Chemistry, University of RHEINBERGER, HANS-JORG, Max-Planck-Institut f/Jr Rochester, New York Molekulare Genetik, Berlin, Federal Republic of UHLENBECK, OLKE, Dept. of Chemistry and Biochem- Germany istry, University of Colorado, Boulder RICHARDS, FREDERIC, Dept. of Molecular Biophysics VYAS, NAND, Howard Hughes Medical Institute, viii SYMPOSIUM PARTICIPANTS

Structural Biology Laboratory, University of WESTHEIMER, FRANK, Dept. of Chemistry, Harvard Texas, Houston University, Cambridge, Massachusetts WATSON, JAMES, Cold Spring Harbor Laboratory, New WILLS, PETER, Dept. of , University of Auck- York land, New Zealand WEINER, ALAN, Dept. of Molecular Biophysics and Wimmer, Eckard, Dept. of Microbiology, State Uni- Biochemistry, Yale University School of versity New York, Stony Brook Medicine, New Haven, Connecticut YANAGAWA, HIROSHI, Mitsubishi-Kasei Institute of WEISS, ROBERT, Howard Hughes Medical Institute, Life Sciences, Tokyo, Japan University of Utah, Salt Lake City YONATH, ADA, Dept. of Structural Chemistry, Weiz- WELLS, JAMES, Dept. of Biocatalysis, Genentech, mann Institute, Rehovot, Israel South San Francisco, California ZARLING, DAVID, Dept. of Molecular Biology, SRI WERTZ, GAIL, Dept. of Microbiology, University of International, Menlo Park, California Alabama, Birmingham First row: W. Fitch; J. Berg, T. Bruice; J. Darnell Second row: S. Deodhar, G.M. Browne, J. Maroney; W. Gilbert, M. Nomura, T. Jukes Third row: Picnic First row: P. Sigler, M. Hackert; W. Gilbert, J. Knowles, R. Dorit Second row." P. Sharp, J. Hicks, T. Grodzicker; M. Karplus, R. Baldwin Third row: M. Perutz; D. Eisenberg, L.A. Hazen; C. Chothia First row: D.E. Koshland, S. Mowbray; J. Knowles; G. Petsko, A. McLachlan Second row: D. Eisenberg, A. Klug, W. Gilbert; P. Sharp, R. Lerner, E. Watson Third row: S. Benkovic; M. Mathews, T. Cech; T. Steitz First row: G. Petsko; M. Eigen, T. Jukes; F. Richards Second row: T.A. Jones; R. Doolittle, D. Koshland; D. Eisenberg, M. Cozza, J. Ebert Third row: A. Klug, J. Robertus; Picnic Fourth row: J. Ninio, L. Orgel Foreword

For all too long, RNA never had the essential simplicity we wanted from it. Unlike DNA, the closer we got to it, the more complex it seemed. Initially, we focused on its informational properties, postulating that it carried the genetic information from DNA to the cytoplasmic sites of protein synthesis. It then seemed natural to believe that the main RNA molecules within ribosomes were the templates for the ordering of amino acids during protein synthesis. Quickly, however, this idea was overturned with the discovery first of transfer RNA and then of the true templates, messenger RNA itself. These seminal discoveries had the positive impact of permitting the basic outlines of protein synthesis to be established, as well as permitting the elucidation of the genetic code. At the same time, the dilemma arose of why RNA played so many different roles. In some profound way, the explanation had to lie in the molecular events that gave rise to the origin of life. Rationally thinking about events so distant in the past, however, was then and still is a major intellectual challenge. rose to the occasion by postulating that RNA had to have an enzymatic role, as well as template and structural roles, functioning during the early stages of life as the enzyme for its own self-replication. Under this scheme, the first genetic molecule was RNA, with DNA coming later, after the essential outlines of the genetic code were established. But logical as this idea was, it had little impact, and for almost 20 years, thinking about the origin of life was regarded at best as a safe haven for minds unable to keep up with the extraordinary rush of a recombinant-DNA-driven assault on the nature of life as it exists today. Then in 1982, the discovery of the first example RNA self-splicing suddenly led to the realization that RNA molecules do have the capability to act as ~athlysts. Over the past several years, many more examples of self-splicing have been found, and the fact that the catalytic activity of RNase P resides in its RNA component has been demonstrated. With Crick's conjecture now a fact and with the recent rapid progress in understanding today's enzymes and ribosomes, the time had thus arrived to bring together a diverse collection of pure , biochemists, molecular biologists, and evolutionary biologists to discuss the evolutionary events that may have given rise to the living organisms that now exist on earth. As a title, we chose the Evolution of Catalytic Function to help assure that this Symposium would bring together minds that think in terms of chemistry, as well as about genetic information. The first plans for this our 52nd Symposium arose at a meeting at Harvard in August 1986 between Walter Gilbert, Jeremy Knowles, and myself. Subsequently, I greatly benefited from suggestions given by Leslie Orgel, Daniel Koshland, Russell Doolittle, Tom Cech, and Jim Darnell. The final program comprised 110 speakers, each speaking some 30 minutes. These presentations led to one of our intellectually most demanding meetings, since the talks were arranged to be longer than customary in view of the very diverse nature of the audience, which this year consisted of some 167 scientists. The majority of this year's attendees presented papers, resembling the situation in the very first Symposia. At its start, I worried that our program might be too wide-ranging for true intellectual exchanges. But by the end, I was more than pleased by the high spirits expressed by virtually all participants, who felt that this was a truly historic gathering in which the need to think evolutionary had at last become an accepted way of thinking for molecular biologists. Helping assure this success were the wide-ranging opening talks by Daniel Koshland, Leslie Orgel, and as well as the gracefully lucid summary by Alan Weiner. The bringing together of so many speakers required many sources of financial backing. In addition to our long-time Symposium supporters, the National Cancer Institute/ National Institutes of Health, the National Science Foundation, and the Department of Energy, we are greatly indebted to special help provided by the Sloan Foundation and the Lucille E Markey Charitable Trust. Essential funds were also provided by our Corporate Sponsor Program, which provides core support for the Cold Spring Harbor Meetings Programs: Abbott Laboratories; American Cyanamid Company; Amersham International

Xlll xiv FOREWORD

plc; AMGen; Becton Dickinson and Company; Boehringer Mannheim GmbH; Bristol- Myers Company; Cetus Corporation; Ciba-Geigy Corporation; Diagnostic Products Cor- poration; E.I. du Pont de Nemours & Company; Eastman Kodak Company; Genentech, Inc.; Genetics Institute; Hoffman-La Roche Inc.; Johnson & Johnson; Eli Lilly and Company; Millipore Corporation; Monsanto Company; Oncogene Science, Inc.; Pall Corporation; Pfizer Inc.; The Procter & Gamble Company; Schering-Plough Corporation; Smith Kline & French Laboratories; Tambrands Inc.; The Upjohn Company; The Wellcome Research Laboratories; Burrough Wellcome Co.; and Wyeth Laboratories. Our Meetings Office staff, Maureen Berejka, Karen Otto, Diane Tighe, Michela McBride, and Barbara Ward, again performed at a high level, looking after the registration and housing of Symposium participants and making each of our participants feel thorough- ly wanted. The audiovisual setups were again ably provided by Herb Parsons, and the massive correspondence and telephoning needed to put together a Symposium was cheerfully performed by Andrea Stephenson. As in the past several years, our Publications Department has worked hard to ensure the publication of these books by the end of the year, and for their efforts we are indebted to Nancy Ford, Managing Director of Publications, and editors Patricia Barker and Dorothy Brown, ably assisted by Joan Ebert and Mary Cozza.

James D. Watson, Director October 19, 1987 Contents

Symposium Participants V Foreword xiii

Opening Remarks Evolution of Catalytic Function D.E. Koshland, Jr. Evolution of the Genetic Apparatus: A Review L.E. Orget

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. Trarnontano, 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. Schuhz 97 Engineering of Antibodies with a Known Three-dimensional Structure A. Pliick- thun, R. Glockshuber, I. Pfitzinger, A. Skerra, and J. StadlmiHler 105

RNA Anatomy Conformational Changes and Dynamics of tRNAs: Evidence from Hydrolysis Pat- terns A.C. Dock-Bregeon and D. Moras 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 1. 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 147

XV xvi CONTENTS

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 in the Phage T4 td Gene M. Belfort, P.S. Chandry, and J. Pedersen-Lane 181 A Family of Autocatalytic Group I in Bacteriophage T4 D.A. Shub, M.-Q. Xu, J.M. Gott, A. Zeeh, and L.D. Wilson 193 Long-range Intron- 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. Kriimer, and W Keller 287

Templates Replication and Evolution of Short-chained RNA Species Replicated by Qfl 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. Krdusslich, 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. 0. 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. Briinger, R. Elber, and J. Kuriyan 381 CONTENTS xvii

The C-peptide Helix from Ribonuclease A Considered as an Autonomous Folding Unit K.R. Shoemaker, R. 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 13 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 Recognition A. Klug and D. Rhodes 473 Some Evolutionary Relationships of the Primary Biological Catalysts Glutamine Synthetase and RuBisCO D. Eisenberg, R.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. BriindOn, 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, P.A. Pemberton, and D.R. Boswell 527 The Role of Protein Folding in the Evolution of Protein Sequences T. Stackhouse, J.J. Onuffer, C.R. Matthews, S.A. Ahmed, and E.W. Miles 537 Positive Darwinian Selection in Evolution of Protein Inhibitors of Serine Protein- ases M. Laskowski, Jr., L 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 xviii CONTENTS

Crystallography and Site-directed Mutagenesis of Yeast Triosephosphate 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 Serine 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. Sourer, 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 Ribo- somal 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 CONTENTS xix

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 L M. Henderson 857 Male-driven Molecular Evolution: A Model and 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 Introns

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. G6 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

Author Index 943

Subject Index 945