Understanding and Predicting Protein Structure

Gustaf H. Carlson School of Chemistry, Clark University, 950 Main Street, Worcester, Massachusetts, 01610, USA email dmierke clarku.edu 

Department of Pharmacology and Molecular Toxicology, University of Massachusetts, Medical Center, 55 Lake Avenue, North, Worcester, Massachusetts 01655, USA 

The generation of protein sequences (or equivalently the DNA sequences which provide the protein sequence) is accelerating at a great pace. In the foreseeable future the complete human genome will be sequenced. The challenge for the protein chemist is to assimilate and utilize this information [1], Given the strong correlation between structure and function, the question is therefore the determination of structure from the primary protein sequence. 

In this chapter, some methods currently employed in the prediction of tertiary structure from the protein sequence will be highlighted This is not intended to be a comprehensive review of the literature, a goal that would require an entire book of this size and would quickly become outdated. Instead, the aim is to provide some of the basic tenets of the theories and methods utilized with a few select references to the original literature. Hopefully this will serve as a starting point to delve into this very exciting and ongoing field of research. 

The goal of protein-structure prediction is to derive the tertiary structure of the protein (defined as the manner in which the protein is bent or folded in three dimensions) given the sequence of amino acids (referred to as the primary structure). In between the primary and tertiary structure is the secondary structure which consists of regularly recurring arrangements of the protein chain in one-dimension (i e, a-helices and (3-sheets) 

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John M. Troyer and Fred E. Cohen, Simplified Models for Understanding and Predicting Protein Structure. 

Simplified Models for Understanding and Predicting Protein Structure... 

This review is an updated revision of a contribution by j. M. Troyer and F. E. Cohen, in Molecular Conformation and Biological Interactions. P. Balaram and S. Ramaseshan, Eds., Indian Academy of Sciences, Bangalore, India, 1991. Simplified Models for Understanding and Predicting Protein Structure. 

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