Abstract
There have been many studies of dipeptide structure at a high level of accuracy using quantum chemical methods. Such calculations are resource-consuming (in terms of memory, CPU and other computational imperatives) which is the reason why most previous studies were restricted to the two simplest amino-acid residue types, glycine and alanine. We improve on this by extending the scope of residue types to include all 20 naturally occurring residue types. Our results reveal differences in secondary structure preferences for the all residue types. There are in most cases very deep energy troughs corresponding either to the polyproline II (collagen) helix and the α-helix or both. The β-strand was not strongly favoured energetically although the extent of this depression in the energy surface is, while not “deeper” (energetically), has a wider extent than the other two types of secondary structure. There is currently great interest in the question of cotranslational folding, the extent to which the nascent polypeptide begins to fold prior to emerging from the ribosome exit tunnel. Accordingly, while most previous quantum studies of dipeptides were carried out in the (simulated) gas or aqueous phase, we wished to consider the first step in polypeptide biosynthesis on the ribosome where neither gas nor aqueous conditions apply. We used a dielectric constant that would be compatible with the water-poor macromolecular (ribosome) environment.
Highlights
Throughout this and our previous work, and in keeping with the usage adopted by previous authors (Gould et al 1994; Bywater and Veryazov 2013; Carrascoza et al 2014), we study constructs that we refer to as primitive dipeptides with a N-acetyl-(XXX) (2)-N′-methylamine as a generic structure in which XXX represents the defining amino
The results presented here can be used by protein chemists as a guide to what the most likely secondary structure propensities are for each of the amino acid types
There has been much interest in determining the structure of dipeptides. These efforts have been restricted to the case of primitive dipeptides where the central residue type is glycine or alanine, and no account was made of the effect of solvent
Summary
There are many reasons why there has been so much interest in calculating peptide conformations (Gould et al 1994; Wu et al 2010; Bellesia et al 2010; Hovmoller et al 2002; Bywater and Veryazov 2013; Carrascoza et al 2014). Most previous studies (Gould et al 1994; Wu et al 2010) were concerned with small peptides per se, in the gas or aqueous phase, while we addressed the latter question, that of peptide biosynthesis Throughout this and our previous work, and in keeping with the usage adopted by previous authors (Gould et al 1994; Bywater and Veryazov 2013; Carrascoza et al 2014), we study constructs that we refer to as primitive dipeptides with a N-acetyl-(XXX) (2)-N′-methylamine as a generic structure in which XXX represents the defining amino. A previous publication (Carrascoza et al 2014) reported studies of the entire set of amino acids, with somewhat different results, as discussed below
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