Program for PDB 50th Anniversary ACA Transactions Symposium 2021: Function Follows Form: Celebrating the 50th Anniversary of the Protein Data Bank

The 2021 ACA Meeting Transactions Symposium, entitled “Function Follows Form: Celebrating the 50th Anniversary of the Protein Data Bank,” will celebrate the 50th anniversary of the Protein Data Bank. Since 1971, 3D macromolecular structure data have been expertly archived, validated, biocurated, and safeguarded by the PDB, the first open-access digital data resource in biology. The 2021 ACA Transactions Symposium is dedicated to celebrating the manifold contributions to fundamental biology, biomedicine, bioenergy, and bioengineering/biotechnology made by PDB Data Depositors and PDB Data Consumers over the past five decades. Meeting participants working in macromolecular crystallography and practitioners of cryogenic electron microscopy, tomography, and diffraction will have the opportunity to learn first-hand from internationally recognized experts contributing to our understanding of the intrinsic relationship between 3D structure and function across the biological and biomedical sciences. Invited presentations by ten high profile experimental and computational structural biologists working in the United States, Canada, and South America will be augmented by two short talks selected from abstracts. At the close of the symposium, speakers will be invited to contribute to a short round table discussion regarding future directions in structural biology and the important role that the RCSB Protein Data Bank can play over the next 50 years.

Sponsored by:

     

Friday July 30th Schedule:

12:00pm-12:05pm Welcome and Introductions

12:05pm-12:45pm Keynote: Cynthia Wolberger - Johns Hopkins, Baltimore, MD

Cynthia Wolberger is a Professor of Biophysics and Biophysical Chemistry at the Johns Hopkins University School of Medicine, where her group studies the structural basis of transcription regulation and ubiquitin signaling using cryo-EM and x-ray crystallography. She received an A.B. in Physics from Cornell University and a Ph.D. in Biophysics from Harvard University, and did postdoctoral research at UCSF and at the Johns Hopkins School of Medicine. In both her graduate and postdoctoral studies, she studied the structural basis of transcription factor binding to DNA. Since establishing her own research group at Johns Hopkins, she has made major contributions to the understanding of the molecular mechanisms underlying combinatorial regulation of transcription, post-translational modification of histone proteins, and ubiquitin signaling. A current focus or her research is on the interplay between histone ubiquitination and regulation of transcription. Dr. Wolberger is a recipient of the Dorothy Crowfoot Hodgkin Award of the Protein Society and is a Fellow of the Biophysical Society and the American Association for the Advancement of Science. She was elected to the National Academy of Sciences and the American Academy of Arts and Sciences. Dr. Wolberger has been a member of the ACA since 1992.

12:45pm-1:00pm: Mike Martynowycz - HHMI/UCLA, Los Angeles, CA

Dr. Martynowycz earned bachelor degree from Loyola University Chicago, where he double majored in Mathematics and Theoretical Physics. He later earned a master’s degree in Physics from the Illinois Institute of Technology. His master’s work was conducted at the Adler Planetarium and Astronomy Museum as an NSF fellow. He earned a PhD in Physics is from the Illinois Institute of Technology, where he was the Dean’s fellow and won two subsequent laboratory fellowships from Argonne National Laboratory. His postdoctoral career in the Gonen lab began at the Howard Hughes Medical Institute’s Janelia Research Campus and now at the University of California Los Angeles. His current research focuses on developing novel cryogenic electron microscopy methods.

1:00pm-1:20pm Coffee Break

1:20pm-1:45pm Plenary: John Rubinstein - Sick Kid’s Hospital, Toronto, Canada

A native of Toronto, John Rubinstein received his BSc from the University of Guelph, graduating in 1998. For his PhD he moved to England to work with Dr. Richard Henderson and Sir John Walker at the MRC laboratories in Cambridge. He completed his PhD research and a postdoctoral fellowship before returning to Canada for a second short postdoctoral fellowship at U of T. He started his own research group at The Hospital for Sick Children in 2006, where he holds a Canada Research Chair, and studies the structural biology of bioenergetics and develops new methods in cryoEM to facilitate this work. He has been recognized by the Burton Medal of the Microscopy Society of America, the New Investigator award of the Canadian Society of Molecular Biosciences, the Lars Ernster Lectureship in Bioenergetics, and most recently a Doctorate of Philosophy honoris causa from Stockholm University.

1:45pm-2:10pm Plenary: Squire J. Booker - Penn State, State College, PA

Squire J. Booker is an Evan Pugh Professor of Chemistry and of Biochemistry and Molecular Biology at The Pennsylvania State University, and holds the Eberly Family Distinguished Chair in Science. He is also an Investigator of the Howard Hughes Medical Institute. Booker received a BA degree with a concentration in Chemistry from Austin College (Sherman, Texas) in 1987. He earned his Ph.D. degree from the Massachusetts Institute of Technology under Professor JoAnne Stubbe (1994), and was supported by NSF–NATO and NIH Fellowships for postdoctoral studies in the laboratories of Dr. Daniel Mansuy (Université René Descartes, Paris, France) and Professor Perry Frey (Institute for Enzyme Research, University of Wisconsin–Madison), respectively. In 1999 he moved to The Pennsylvania State University as an independent investigator. Booker’s research is concerned with novel mechanisms and pathways for the biosynthesis of various natural products and cellular metabolites, with a particular focus on enzymes that use S-adenosylmethionine and iron-sulfur clusters to catalyze reactions via radical mechanisms.

2:10pm-2:35pm Plenary: Rafael M. Couñago- SGC/UNICAMP, Brazil

Rafael M. Couñago leads a research group at the Medicinal Chemistry Center at the University of Campinas (UNICAMP) in São Paulo, Brazil and uses structural biology tools to understand protein function and to develop small-molecule modulators of proteins involved in human diseases. Rafael obtained his PhD from Rice University (TX-US) under the supervision of Yousif Shamoo, and did post-doctoral training with Kurt Krause at the University of Otago (NZ) and with Bostjan Kobe at the University of Queensland (AUS). In 2015, he joined the Structural Genomics Consortium site at UNICAMP, serving as its CSO from 2018 to 2020.

2:35pm-3:00pm Plenary: Erica Ollman Saphire - La Jolla Institute for Immunology, La Jolla, CA

Erica Ollmann Saphire, Ph.D. is a Professor at the La Jolla Institute for Immunology. Her research explains, at the molecular level, how and why viruses like Ebola and Lassa are pathogenic and provides the roadmap for medical defense. Her team has solved the structures of the Ebola, Sudan, Marburg and Lassa virus glycoproteins, explained how they remodel these structures as they drive themselves into cells, how their proteins suppress immune function and where human antibodies can defeat these viruses. Dr. Saphire, herself, solved the first crystal structure of the entire human antibody, revealing at the same time, the hexameric assembly by which the IgG activates the complement cascade for immune protection. Another discovery from her lab expanded the central dogma of molecular biology by proving that certain viral proteins actually rearrange into different structures at different times for different functions. A recent discovery revealed why neutralizing antibodies had been so difficult to elicit against Lassa virus, and provided not only the templates for the needed vaccine, but the molecule itself: a Lassa surface glycoprotein engineered to remain in the right conformation to inspire the needed antibody response. This molecule is the basis for international vaccine efforts against Lassa. Dr. Saphire was also the galvanizing force behind the Viral Hemorrhagic Fever Immunotherapeutic Consortium and is the Director of this organization. This consortium, an NIH-funded Center of Excellence in Translational Research, unites 44 previously competing academic, industrial and government labs across five continents to understand and provide antibody therapeutics against Ebola, Marburg, Lassa and other viruses. In all these endeavors, she has used molecular insight to bring together scientists and policymakers alike for scientific advancement and social change.

Dr. Saphire’s work has been recognized at the White House with the Presidential Early Career Award in Science and Engineering, with young investigator awards from the International Congress of Antiviral Research, the American Society for Microbiology, and the MRC Centre for Virus Research in the United Kingdom. She has also been recognized with an Investigator in the Pathogenesis of Infectious Disease Award from the Burroughs Wellcome Fund, and by the Surhain Sidhu award for the most outstanding contribution to the field of diffraction by a person within five years of the Ph.D. She has been awarded a Fulbright Global Scholar fellowship from the United States Department of State and a Mercator Fellowship from Deutsche Forschungsgemeinschaft, to develop international collaborations around human health and molecular imaging through cryoelectron microscopy. Recently, she was asked by the Bill and Melinda Gates Foundation to head up the Coronavirus Immunotherapeutic Consortium, and is working with Operation Warp Speed to advance antibody therapeutics against SARS-CoV-2.

3:00pm-3:25pm Speaker Panel Discussion: Leaning In -- PDB in the Next 50 Years

3:25pm-3:30pm Concluding Remarks and Acknowledgements

Saturday July 31st Schedule:

11:00am-11:05am Welcome and Introduction

11:05am-11:55am Nobel Lecture: Frances H. Arnold - CalTech, Pasadena, CA

Frances Arnold is the Linus Pauling Professor of Chemical Engineering, Bioengineering and Biochemistry at the California Institute of Technology. Arnold pioneered directed enzyme evolution, for which she was awarded the Nobel Prize in Chemistry in 2018. Arnold was recently appointed to co-chair the President’s Council of Advisors on Science and Technology. Among other awards, Arnold has received the Charles Stark Draper Prize of the US National Academy of Engineering (2011), the US National Medal of Technology and Innovation (2011), and the Millennium Technology Prize (2016). She was the first woman elected to all three US National Academies of Science, Medicine, and Engineering and was appointed to the Pontifical Academy of Sciences in 2019. Co-inventor on more than 60 patents, Arnold was inducted into the US Inventors Hall of Fame in 2014. She co-founded three companies in sustainable chemistry and renewable energy (Gevo, Provivi, Aralez Bio) and serves on several public and private company boards. She earned a B.S. in Mechanical and Aerospace Engineering from Princeton University and a Ph.D. in Chemical Engineering from the University of California, Berkeley.

11:55am-12:00pm Concluding Remarks and Acknowledgements

12:00pm-12:05pm Welcome and Introductions

12:05pm-12:45pm Keynote: Wayne A. Hendrickson - Columbia, New York, NY

Wayne A. Hendrickson is a University Professor at Columbia University in the Department of Biochemistry and Molecular Biophysics and Violin Family Professor in the Department of Physiology and Cellular Biophysics.   He is also Scientific Director of the New York Structural Biology Center.   Hendrickson has a B.A. from the University of Wisconsin at River Falls, a Ph.D. in biophysics at Johns Hopkins University with Warner Love, and postdoctoral research experience with Jerome Karle at the Naval Research Laboratory.  He and his colleagues use x-ray crystallography and electron microscopy as well as biochemical and cellular analyses to study biomolecular properties in atomic detail.  The current emphasis is on membrane receptors and cellular signaling, molecular chaperones and protein folding, viral proteins and HIV infection, and technology for membrane protein production and analysis. Hendrickson’s advances in diffraction methodology have contributed significantly to the emergence of structural biology as a major force in modern biology and molecular medicine.  

12:45pm-1:00pm: Wladek Minor - Department of Molecular Physiology and Biological Physics, University of Virginia

Prof. Wladek Minor received his Ph.D. in 1978 from the University of Warsaw in Solid State Physics. He joined the University of Virginia faculty in 1995. He was tenured in 1998 and promoted to full professor in 2003. In 2016, he became Harrison Distinguished Professor of Molecular Physiology and Biological Physics. He has been developing experimental protocols and computational methods for neutron scattering and X-ray diffraction since graduate school. After starting his independent career, he continued developing software within HKL, HKL-2000, and HKL-3000. He also worked on advanced solutions to other crystallographic problems: (a) Identification and refinement of metals in macromolecular structures; (b) Determination and analysis of macromolecular structures related to drug transport and drug discovery; (c) Reproducibility, ligand identification, and validation in structural biology; (d) Data mining, management, and access to primary experimental data; (e) Protocols and tools for more reliable structure determination, including the application of AI; (f) Analysis of COVID-19 structures and actions necessary to prepare for a possible future pandemic. He published more than 230 papers that attracted more than 46,000 citations. He is a co-author of more than 450 Protein Data Bank deposits. Dr. Minor has trained over 110 people that are very successful in academia, industry, and medicine. Dr. Minor's research is often reported in general media outlets (https://minorlab.org/news), which helps taxpayers understand why investments in basic science are the best investments for the country's future.  

1:00pm-1:20pm Coffee Break

1:20pm-1:45pm Plenary: Chris Sander - Harvard Medical School, Boston, MA

Chris Sander joined the Harvard community in 2016 as Director of the cBio Center at the Dana-Farber Cancer Institute in the Department of Data Science, Professor of Cell Biology at Harvard Medical School, and Associate Member of the Broad Institute.

During his time as a postdoc, he was inspired by the first completely sequenced genome to switch fields from theoretical physics to theoretical biology. He later founded two computational biology departments—at the European Molecular Biology Laboratory and Memorial Sloan Kettering Cancer Center—and co-founded the research branch of the European Bioinformatics Institute and a biotech startup with Millennium Pharmaceuticals.

One of his key mentors was Shneior Lifson at the Weizmann Institute, where he collaborated with Michael Levitt on the first computation of normal modes of protein molecules and with Lifson on contact prediction in proteins. With Wolfgang Kabsch at a Max Planck Institute in Heidelberg he developed the DSSP tool for pattern recognition of structural features in protein 3D structures; with Burkhard Rost, the PhD/Prof method of protein secondary structure prediction, one of the first applications of machine learning in structural biology; with Peer Bork, module analysis of proteins; with Alfonso Valencia et al., contact prediction from correlated mutations; with Liisa Holm, the Dali method for searching similar structures in the PDB by contact map comparison and one of the first computational maps of the universe of protein structures; with Reva and Antipin, MutationAssessor, one of the first fully unsupervised methods for the prediction of mutation effects; with Niki Schultz and Ethan Cerami, the widely used cBioPortal for Cancer Genomics.

In structural biology, his most interesting accomplishment to date, with his collaborators, especially Debora Marks, in 2010/2011 was the first successful computation of correct 3D folds of many proteins from sequences alone, using the maximum entropy concept from statistical physics and the extraordinary power of molecular evolution - now known as the EVfold and Evcouplings method; and, the development of 3Dseq, a fourth method of experimental determination of protein structure using experimental evolution.

1:45pm-2:10pm Plenary: Eva Nogales - UC Berkeley/HHMI, Berkeley, CA

Eva Nogales obtained her BS in Physics from the Universidad Autónoma de Madrid. During her graduate work at the SRS in the UK, she used SAXS and cryo-EM to investigate tubulin assembly. Her postdoctoral work with Ken Downing at the Lawrence Berkeley National Lab produced the first atomic structure of tubulin using electron crystallography. She joined the Molecular and Cell Biology faculty at UC Berkeley in 1998. Since 2000 she is an HHMI Investigator. Presently she is a Professor of Biochemistry, Biophysics and Structural Biology in the MCB department at UC Berkeley and a Senior Faculty Scientist at the Lawrence Berkeley National Lab.

The Nogales lab is dedicated to gaining mechanistic insight into the control of gene expression and the microtubule cytoskeleton. Her lab uses cryo-EM for the direct visualization of macromolecular architecture, functional states, and regulatory interactions. Eva Nogales has received the Dorothy Hodgkin Award from the Protein Society, the Mildred Cohn Award from ASBMB, the Porter Lecture Award from ASCB, and the Biophysical Society Lectureship. She is a fellow of ASCB and the Biophysical Society, a member of the National Academy of Sciences, the American Academy of Arts and Sciences, and a Foreign Associate of EMBO.

2:35pm-3:00pm Plenary: Andrej Sali - RCSB PDB/UCSF, San Francisco, CA

Andrej Sali received his BSc degree in chemistry from the University of Ljubljana, Slovenia, in 1987, under the supervision of Professor Vito Turk; and his PhD from Birkbeck College, University of London, UK, in 1991, developing the MODELLER program for comparative modeling of protein structures under the supervision of Professor Tom L. Blundell. He was then a postdoc with Professor Martin Karplus at Harvard University as a Jane Coffin Childs Memorial Fund fellow, studying lattice Monte Carlo models of protein folding. From 1995 to 2002, he was first an Assistant Professor and then an Associate Professor at The Rockefeller University. In 2003, he moved to University of California, San Francisco, as a Professor of Computational Biology in the Department of Bioengineering and Therapeutic Sciences. He was recognized as Sinsheimer Scholar (1996), an Alfred P. Sloan Research Fellow (1998), an Irma T. Hirschl Trust Career Scientist (2000), the Zois Award of Science Ambassador of Republic of Slovenia (2007), a Fellow of International Society for Computational Biology (2014), Jubilee Professor of Indian Academy of Sciences (2017), Bijvoet Medal recipient (2018), and member of National Academy of Sciences of USA (2018). He has been an Editor of Structure since 2002. Dr. Sali develops and applies computational methods for determining and modulating structures and functions of proteins and their assemblies.

3:00pm-3:25pm Speaker Panel Discussion: Leaning In – PDB in the Next 50 Years

3:25pm-3:30pm Concluding Remarks and Acknowledgements