THE RELATIONSHIP BETWEEN PROTEIN STRUCTURE AND FUNCTION, OR HOW HAVE PROTEINS OVER TIME DIVERGED IN FUNCTION? A Seminar Track in the PACIFIC SYMPOSIUM ON BIOCOMPUTING January 5-8, 1998 Kapalua, Hawaii Overview Understanding the relationships between protein structure and function remains a primary focus in structural biology with important consequences in such diverse fields as molecular biology, genetics, biochemistry, protein engineering and bioinformatics. One approach to this problem is to study how nature has re-engineered proteins for new functions through evolutionary processes. This strategy has the potential to reveal fundamental characteristics of protein structures and the explicit manner in which they deliver their associated functions. To understand the structure-function paradigm, the most useful structural information comes the primary amino acid sequences and the tertiary structures. Several recent developments in analysis of the "protein universe" at the tertiary structural level have provided important criteria for understanding the range of family folds that exist and some of the evolutionary relationships associated with them. While the tertiary structure database is small, the sequence databases are large and now include the sequences of the entire genomes of several bacteria, an archaeon and a microbial eukaryote. Many additional genomes will be solved in the near future. With a great deal of protein sequence data at hand, we propose that the computational strategies required to address the "structure-function" problem are now sufficiently developed to support serious attempts to understand the fundamental relationships between protein structure and function. To focus on these issues, papers are solicited from scientists interested in computational approaches to the topics below or to related topics. In particular, we solicit papers that address the interface between automated structural analysis and biological insight. Possible Topics What overall correlations between functional and structural classes of proteins are emerging from analysis of completed genome sequences? Do these correlations require alterations/extensions of our current definitions of function? Tertiary structural relationships can reveal more distant relationships than can normally be identified through sequence analysis alone. How can these two types of information be integrated to extend the insight that can be obtained from either? Given the enormous disparity in the amount of information available at the sequence vs. the tertiary structural level, how can the large volume of sequence information be used to leverage the value that can be obtained from the much smaller volume of tertiary structural information? What are the explicit correlations between protein structure and function? What is the driving force behind the evolution of protein structures to perform new functions? How much of a constraint does a requirement for substrate or ligand recognition impose on mechanisms of evolution? Or a requirement to perform a common chemical step? What are the relationships between the specific function of a protein (i.e., chemical reaction, transport of small or large molecules, binding a small molecule ligand that triggers a downstream function) and its biological role in the cell or organism? Do these relationships correlate with structure in a systematic (or non-systematic) fashion? Submissions Full papers Full papers accepted for this session will be published in a hard-bound archival Proceedings. An electronic proceedings will also be available following the meeting (see http://www-smi.stanford.edu/people/altman/psb97/index.html for electronic proceedings of the papers published from the 1997 PSB meeting). All contributed papers are peer-reviewed by at least three referees. Accepted papers will be allocated up to 12 pages in the Proceedings. Several of these papers, as judged by merit and relevance to the session focus, will be selected for a 30-minute oral presentation to the full assembled conference. To be eligible for publication, full papers must be accompanied by a cover letter stating that it contains original unpublished results not currently under consideration elsewhere. PSB expects to be included in Indicus Medicus, Medline and other indexing services starting this year. Submit 5 copies of full papers to the central PSB address: PSB-98 c/o Section on Medical Informatics Stanford University Medical School, MSOB X215 Stanford, CA 94304-5479 USA We also welcome electronic submission. Format requirements can be found on the PSB web page (http://psb.stanford.edu) or from Russ Altman (altman@smi.stanford.edu). Submit electronic papers directly to Dr. Altman. Poster presentations One page abstracts for standard or computer-interactive poster presentations are also solicited. The one page abstracts should be submitted electronically either as ascii text or as a Microsoft Word file to Russ Altman (altman@smi.stanford.edu). Please contact Dr. Altman if it is not possible to submit your abstract in one of those two formats. Abstracts will be distributed at the meeting separately from the archival proceedings. Important Dates Full paper submissions due: July 14, 1997 Poster abstracts due: August 10, 1997 Notification of paper acceptance: August 22, 1997 Camera-ready copy due: September 22, 1997 Conference: January 5 - 8, 1998 Further Information If you have questions about this symposium track or about submitting a manuscript, please contact the track organizers: Patricia Babbitt. Box 0446 Dept. of Pharm. Chem. University of California San Francisco, CA 94143-0446 Tel.: (+1-415) 476-3784 Fax: (+1-415) 476-0688 email: babbitt@cgl.ucsf.edu url: http://gazzetta.ckm.ucsf.edu/people/babbitt Monica Riley Marine Biological Laboratory 7 MBL St. Woods Hole, MA 02543 Tel.: (+1-508) 289-8612 Fax: (+1-508) 540-6902 email: mriley@mbl.edu url: http://mbl.edu/html/ecoli.html For general information about PSB-98 and registration, accommodation and schedule, contact the PSB '98 - homepage http://psb.stanford.edu or send email to the conference coordinator: psb@cgl.ucsf.edu