........ published in NEWSLETTER # 54
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........ published in NEWSLETTER # 54
STATISTICAL MECHANICS, PROTEIN STRUCTURE AND PROTEIN SUBSTRATE INTERACTIONS
by Professor S. Doniach, University, Stanford/CA (U.S.A.)
This volume contains 33 chapters written by invited speakers and some participants at the NATO Advanced Research Workshop held at Cargese, Corsica in June 1993. The aim of the meeting which resulted in a state_of_the_art publication (NATO ASI SERIES B325), was to bring together scientists working on a number of different aspects of the structure and function of proteins viewed at the detailed molecular level.
Currently there is considerable interest in the "protein folding problem". This is motivated from two different points of view: understanding the "second genetic code" relating the primary sequence of a protein to its three dimensional structure; and understanding the specifics of the kinetic pathway (or pathways) along which proteins proceed from a completely denatured or unfolded state to the final native fold. Current progress in the field includes the realization that partially folded states of protein may occur in a "molten globule" form in which the protein is compact and contains considerable secondary structure, but is nevertheless disordered. A group of chapters in the book surveys the state of experimental knowledge of these folding intermediates. At the theoretical level, several authors discuss much simplified models for studying generic features of protein folding in which the protein is represented by a very simple "string of beads" type of model on a lattice.
The problem of constructing the structure from the sequence can be considerably helped by the methods of nuclear magnetic resonance which yield a set of constraints determining which regions of the polypeptide chain are in contact with one another. These are discussed at both the empirical and more theoretical levels. At another level, the job of trying to construct a three dimensional protein structure from the primary sequence can be tackled by the methods of computer science, starting from the database of known protein structures. A group of chapters focuses on various methods of doing this and their degree of success.
Other chapters include material on basic interactions, computatinal methods for exploring conformation space, the computer simulation of the structure of membrane proteins, and experimental and theoretical analysis of protein_substrate interactions, including antibody_antigen docking and x_ray crystallography of proteinase inhibitors.
All in all, the book provides a selection of different approaches to the computer simulation of protein structures linked with recent experimental progress in determining different aspects of protein structures, both in crystalline and non_crystalline forms.
It should be of interest both to biochemists isnterested in knowing more about computer simulation methods of representing protein structures and to physicists and computer scientists seeking more insight into the experimental aspects of protein structure determination and understanding.
Reference books: A183, A246, B325