Theoretical and Experimental Aspects of Protein Folding

This article is based on the second and third of four lectures that I presented at the International Summer School of Biophysics. The first lecture, entitled Recent developments in the theory of water, aqueous solutions and protein hydration, has already been summarized in several review articles (Scheraga, 1979 Paterson et al., 1981 Nemethy et al., 1981), and the fourth lecture, entitled Enzyme - substrate interactions, has likewise been summarized in two recent reviews (Pincus and Scheraga, 1981  

Scheraga et al., 1982). In the two lectures constituting this article, we describe some of our theoretical and experimental work designed to gain an understanding of the interactions that lead to the observed conformational behavior of biological macromolecules, either as individual molecules or as complexes with other molecules. The theoretical aspects of the problem are dealt with first this is then followed by a discussion of experimental studies on protein conformation. 

Several empirical potential functions are used to calculate the conformational energy of a polypeptide. The one in most frequent use in our laboratory is ECEPP (Empirical Conformational Energy Program for Peptides)(Momany et al., 1975 Pottle et al., 1980). It was parameterized (Momany et al., 1974a) and tested (Momany et al., 1974b) on the crystals listed in Table 1 of a paper by Scheraga (1974) and on gas-phase data (Momany et al.. 

For energetic reasons that are understood (Zimmerman and Scheraga, 

the peptide group is maintained in the planar trans conformation except for peptide groups preceding proline in such cases, both trans and cis conformations are allowed. 

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