FREE-ENERGIES OF AMINO-ACID SIDE-CHAIN ROTAMERS IN ALPHA-HELICES, BETA-SHEETS AND ALPHA-HELIX N-CAPS

Scales have previously been determined for the entropic cost of restri cting amino acid side-chain rotations upon protein folding, giving the rule of thumb that the entropic cost of restricting a single side-cha in bond is approximate to 0.5 kcal mol(-1). However, this result does not consider the distinct preferences shown by amino acid side-chains for particular side-chain chi 1 angles in the folded protein. For exam ple, Glu in an alpha-helix has chi 1 4% gauche(-) (g(-)), 39% trans (t ) and 58% gauche(+) (g(+)) showing that it is most favourable to restr ict Glu chi 1 as g(+) in a helix while g(-) is least favoured. The cha nge in side-chain conformational entropy is the same in both cases, bu t the free energy of each rotamer is different. Here, we determine the energies of every amino acid chi 1 rotamer in alpha-helices, beta-she ets and alpha-helix N-caps and each chi 1 chi 2 rotamer pair in helice s and sheets. The calculation uses observed rotamer distributions in s econdary structure and the coil state, together with experimentally de termined free energy changes for secondary structure formation. The re sults are sets of rotamer energies within a secondary structure that c an be directly compared to each other. For example, we conclude that T yr is the most stable residue in a beta-sheet if only the trans rotame r is accessible; if only the gauche-conformation is available, Thr wou ld be the most stabilising. Previously published scales of amino acid preferences for secondary structure are weighted averages of rotamer e nergies and therefore imply that Thr is the most stabilising substitut ion in a beta-sheet in any side-chain conformation. Both side-chain co nformational entropies and intrinsic secondary structure preferences a re subsumed within our data; the results presented here should therefo re be used in preference to both side-chain conformational entropies a nd intrinsic secondary structure preferences when the rotamer occupied in the folded state is known. The results may be useful in protein en gineering, simulations of binding and folding, prediction of protein s tability and peptide binding energies, and identification of incorrect ly folded structures. (C) 1997 Academic Press Limited.