Theoretical studies on peptide conformation

Abstract

It is now well established that the biological activities of polypeptides and proteins are intimately connected with their 3-dimensional structures and so the determinations of these provide insight into their mode of action. In this context, theoretical studies of analyzing possible peptide and polypeptide conformations which have engaged the interest of this department for the last several years have contributed significantly to a better understanding of biological structure-function relationship in such systems. This thesis embodies the results of theoretical studies undertaken by the author on some pertinent aspects of peptide conformation and these are detailed in chapters distributed in two parts. Part I entitled as: "Theoretical Studies on Peptide Structures" consists of Chapters 2 and 3 and Part II entitled as: "Conformational Studies on Peptides Containing Disulfide Bridges" consists of Chapters 4, 5 and 6. These two parts, however, are intimately connected as the studies reported in these are based on the same ideas of peptide conformation. In what follows, brief summaries of each chapter are given. The first chapter is a general introduction to the thesis and reviews briefly the classical empirical formalism of studying polypeptide conformation which has been employed in this thesis. It introduces the method of analyzing allowed polypeptide conformations on the basis of the so-called hard sphere approximation extending it on to the method of calculation of conformational energy using classical empirical potential functions. Brief descriptions of the various terms which have been included in the energy calculations in studies reported in the subsequent chapters and the constants used therein are also given. A characteristic feature of peptide, polypeptide and protein structures is that they are composed overwhelmingly of the trans form of the peptide unit C?-CO-NH-C? and the cis form has occasionally been observed for the peptide linkage X?-Pro. In Chapter 2, this problem of the very rare occurrence of cis peptide units in proteins and polypeptides has been looked into on the basis of conformational analysis. The intrinsic higher energy of the cis form offers only a partial answer for this phenomenon of almost total absence of cis peptide units. It is shown that this rarity arises because a cis peptide unit when it occurs within an all-trans polypeptide chain introduces severe conformational restrictions locally. This has been arrived at by performing conformational energy calculations on a segment of a polypeptide chain composed of three peptide units and consisting of the atoms C?-NH-C? (R?,R?)-CO-NH-C? (R?,R?)-CO-NH-C? (R?,R?) groups of the middle two amino-acid residues. Two examples have been studied, namely, the sequence trans-trans-trans (ttt) and trans-cis-trans (tct) with the amino acids being the examples Ala-Ala to represent the general case and Ala-Pro to represent the X-Pro case. It is found that the tct configuration can occur only to an extent of 0.1% for Ala-Ala sequence but for the Ala-Pro sequence this can be about 5% or higher. In the latter case a larger probability for the occurrence of cis peptide units is found to be primarily due to the possibility of having, in such a case, an open bend-like structure very well stabilized by dipole-dipole interaction between the terminal trans peptide units. Such cis-Pro bends have been observed in protein crystal structures. This analysis has indicated that, for non-prolyl residues the probability for the occurrence of cis peptide units is not negligible and these can still be expected to occur in some rare examples. On the other hand for prolyl residue cis units are likely to occur not infrequently and should be looked for in protein crystal structures. In recent years, a significant amount of work has been done towards the refinement of empirical potential functions employed for energy calculations. These functions, especially for non-bonded interactions differ for the various groups of workers; even then, it is a general observation that they yield similar minimum-energy conformation.