Howard Schachman University of California Professor of Molecular Biology: Discussions of His Research Over His Scientific Career From the 1940s Until 2010 Interviews conducted by Sondra Schlesinger (2007-2010) Copyright © 2010 by The Regents of the University of California Since 1954 the Regional Oral History Office has been interviewing leading participants in or well-placed witnesses to major events in the development of Northern California, the West, and the nation. Oral History is a method of collecting historical information through tape-recorded interviews between a narrator with firsthand knowledge of historically significant events and a well- informed interviewer, with the goal of preserving substantive additions to the historical record. The tape recording is transcribed, lightly edited for continuity and clarity, and reviewed by the interviewee. The corrected manuscript is bound with photographs and illustrative materials and placed in The Bancroft Library at the University of California, Berkeley, and in other research collections for scholarly use. Because it is primary material, oral history is not intended to present the final, verified, or complete narrative of events. It is a spoken account, offered by the interviewee in response to questioning, and as such it is reflective, partisan, deeply involved, and irreplaceable. ********************************* All uses of this manuscript are covered by a legal agreement between The Regents of the University of California, Howard Schachman, and Sondra Schlesinger, dated November 11, 2010. The manuscript is thereby made available for research purposes. All literary rights in the manuscript, including the right to publish, are reserved to The Bancroft Library of the University of California, Berkeley. Excerpts up to 1000 words from this interview may be quoted for publication without seeking permission as long as the use is non-commercial and properly cited. Requests for permission to quote for publication should be addressed to The Bancroft Library, Head of Public Services, Mail Code 6000, University of California, Berkeley, 94720-6000, and should follow instructions available online at http://bancroft.berkeley.edu/ROHO/collections/cite.html It is recommended that this oral history be cited as follows: Howard Schachman, “University of California Professor of Molecular Biology: Discussions of His Research Over His Scientific Career From the 1940s Until 2010,” conducted by Sondra Schlesinger between 2007 and 2010, Regional Oral History Office, The Bancroft Library, University of California, Berkeley, 2010. Howard at the ultracentrifuge in 1966 iv Table of Contents–Howard Schachman Introduction vi Acknowledgement vii Audio File 1 Oct 18 and 22, 2007, January 16, 2008 1 Howard’s move from engineering to biology–how he was hired as a technician to work for Max Lauffer at the Rockefeller Institute for Medical Research, Princeton, New Jersey–use of the Sharples centrifuge for purifying tobacco mosaic virus (TMV)–graduate school at Harvard but getting his PhD at Princeton–the navy–move to the University of California, Berkeley with Wendell Stanley(1948)– initial studies with TMV and the use of the ultracentrifuge– measuring the compressibility of particles–synthetic boundary cells–Ed Pickels and Spinco, work on rabbit papilloma virus–Robley Williams, TMV and the electron microscope. Audio File 2 January 21, 2008 29 Homogeneity of TMV–discovery of ribosomes in E. coli–discovery of chromatophores in Rhodospirillum rubrum–research on DNA and development of ultraviolet absorption optics for the ultracentrifuge with Spinco–development of a photoelectric absorption scanning apparatus and a double beam instrument at Berkeley–a Rayleigh interferometer with Ed Pickels–initial work with Arthur Kornberg to show by sedimentation that DNA was synthesized in vitro–suggests to Matt Meselson the use of cesium chloride for the Meselson-Stahl experiment that showed that DNA replicates by a semi-conservative mechanism. v Reflections on research and collaborations with the ultracentrifuge 48 Audio File 3 January 22, 2008 49 Sabbatical with Arthur Kornberg in St. Louis–summer at Woods Hole –discovery of copolymer of deoxyadenylate-thymidylate in alternating sequence–discussions about Kornberg’s lab and Washington University –Howard’s humorous talk called “Money Transferase” at the Gordon Conference–Aspartic transcarbamylase (ATCase) and collaboration with John Gerhardt–catalytic and regulatory subunits of the enzyme. Audio File 4 March 17 and 19, 2008 66 Thoughts about Ann Forman, a student in Howard’s lab–agreement among those working on ATCase that the catalytic chains were organized as two trimers and the regulatory chains were organized as three dimers–study of hybrid subunits of aldolase to show protein is a tetramer–studies with hybrids of catalytic subunits of ATCase to show protein is a trimer–cross-linked regulatory dimers reassociate with catalytic trimers indicating that dimers must exist endogenously– George Stark and binding studies with N-(phosphonacetyl)-l-aspartate (PALA) a bi-substrate analog–ATCase can exist as two trimers and two regulatory dimers but is less stable–ATCase contains zinc– assembly mechanisms–beginning of genetic experiments–pyrB, the gene that codes for catalytic trimers, previously identified– Schachman laboratory identifies pyrI gene by sequencing–pyrB and pyrI are an operon–site-directed mutagenesis experiments begin in the lab–Howard talks about his role in getting coordinates of X-ray structures deposited in the Brookhaven Bank. Audio File 5 August 20 and 22, 2008 88 Summary of ATCase trimers and dimers and discussion about oligomers–site-directed mutagenesis and hybridization of subunits– further discussion of monkey models and why trimers are more stable than dimers–discussion of assembly mechanism–reflections comparing the significance of the discovery of ribosomes and the satisfaction derived from his studies proving the compressibility of particles in the ultracentrifuge–discussion of conformational states of ATCase on binding of ligands–studies of assembly of ATCase in vivo in E. coli–ATCase and allosteric interactions–discussion of the Monod, Wyman, Changeux model of conformational changes in enzymes on interacting with substrates or inhibitors–allostery and global conformational changes of ATCase using radioactive PALA (N-(phosphonacetyl)-L-aspartate)–ligand-promoted conformational changes–reversibility of ATCase and story about Jeff Foote. Audio File 6 January 23, 2009 111 Dissociation and reassociation of catalytic trimers–crystallographic vi studies showed that the individual catalytic chains in ATCase are folded into two clearly identifiable domains–genetic engineering to study the catalytic chain, separating the polypeptide into two fragments –experiments showing that two separated fragments assemble in the test tube and in E. coli–genetic engineering experiments to introduce new N- and C- termini in the polypeptide chain. Audio File 7 March 8, 2010 122 Collaboration with Tom Alper on x-ray studies of the catalytic subunit of ATCase–genetic engineering to study the regulatory subunit–a seventy amino acid peptide of the regulatory subunit binds to the catalytic trimer affecting the activity–collaboration with Lewis Kay in Toronto on NMR studies of ATCase–further x-ray studies with Howard’s last postdoctoral student and Tom Alper. Audio File 8 July 19, 2010 131 Awards Howard has received–President of ASBMB and FASEB–meetings with lawyers about fraud versus misconduct in science–Howard proposes fabrication, falsification, and plagiarism as definition of misconduct–Howard serves as an ombudsman for Harold Varmus when Harold heads the NIH–AAAS awards Howard the Scientific Freedom and Responsibility Award–ASBMB establishes the Howard K. Schachman Public Service Award. Vita 144 List of Publications 146 Sondra Schlesinger biosketch 166 Illustrations “Money Transferase” at the Gordon Conference 61 Another of Howard’s humorous slides 61 Monkey model showing one catalytic trimer and one 71 regulatory dimer Monkey model showing three regulatory dimers and one trimer 72 10 steps of reversible and non-reversible steps in assembly 80 Hybridization scheme to demonstrate shared active sites 92 Scheme for the assembly of ATCase from subunits 95 Ribbon diagram of single chain of catalytic subunit of ATCase 113 Another ribbon diagram with numbered amino acids 119 Diagram showing circularly permuted catalytic chains of ATCase 121 vii INTRODUCTION by Sondra Schlesinger Howard’s career at the University of California has spanned over 60 years––a period that has seen many changes in the world and also in Howard’s field of biochemistry. The field of molecular biology did not even exist when Howard arrived at Berkeley. In 1948, the year that Howard joined the faculty at Berkeley, biologists had not yet recognized that DNA was the genetic material. O. T. Avery, C. M. McLeod and M. McCarthy published their landmark discovery in 1944 showing that it was DNA, not protein, that was responsible for bacterial transformation. Those results did not convince everyone and the oft-cited Hershey-Chase experiment showing that only the DNA of the bacteriophage need enter the bacterial cell for phage replication was not published until 1952. In the early 1940s, although most scientists agreed that proteins consisted of amino acids linked together in a linear array, how they were synthesized and their three- dimensional complexities were unimagined. The Bancroft Library at the