Amino Acid Pairing Preferences in Parallel β-Sheets in Proteins

Statistical approaches have been applied to examine amino acid pairing preferences within parallel β-sheets. The main chain hydrogen bonding pattern in parallel β-sheets means that, for each residue pair, only one of the residues is involved in main chain hydrogen bonding with the strand containing the partner residue. We call this the hydrogen bonded (HB) residue and the partner residue the non-hydrogen bonded (nHB) residue, and differentiate between the favourability of a pair and that of its reverse pair, e.g. AsnHB-ThrnHB versus ThrHB-AsnnHB. Significantly (p≤0.000001) favoured pairings were rationalised using stereochemical arguments. For instance, AsnHB-ThrnHB and ArgHB-ThrnHB were favoured pairs, where the residues adopted favoured χ1 rotamer positions that allowed side-chain interactions to occur. In contrast, ThrHB-AsnnHB and ThrHB-ArgnHB were not significantly favoured, and could only form side-chain interactions if the residues involved adopted less favourable χ1 conformations. The favourability of hydrophobic pairs e.g. IleHB-IlenHB, ValHB-ValnHB and LeuHB-IlenHB was explained by the residues adopting their most preferred χ1 and χ2 conformations, which enabled them to form nested arrangements. Cysteine-cysteine pairs are significantly favoured, although these do not form intrasheet disulphide bridges. Interactions between positively and negatively charged residues were asymmetrically preferred: those with the negatively charged residue at the HB position were more favoured. This trend was accounted for by the presence of general electrostatic interactions, which, based on analysis of distances between charged atoms, were likely to be stronger when the negatively charged residue is the HB partner. The ArgHB-AspnHB interaction was an exception to this trend and its favourability was rationalised by the formation of specific side-chain interactions. This research provides rules that could be applied to protein structure prediction, comparative modelling and protein engineering and design. The methods used to analyse the pairing preferences are automated and detailed results are available ().