gβ- and gγ-turns in proteins revisited: A new set of amino acid turn-type dependent positional preferences and potentials
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The number of β-turns in a representative set of 426 protein three-dimensional crystal structures selected from the recent Protein Data Bank has nearly doubled and the number of γ-turns in a representative set of 320 proteins has increased over seven times since the previous analysis. β-turns (7153) and γ-turns (911) extracted from these proteins were used to derive a revised set of type-dependent amino acid positional preferences and potentials. Compared with previous results, the preference for proline, methionine and tryptophan has increased and the preference for glutamine, valine, glutamic acid and alanine has decreased for β-turns. Certain new amino acid preferences were observed for both turn types and individual amino acids showed turn-type dependent positional preferences. The rationale for new amino acid preferences are discussed in the light of hydrogen bonds and other interactions involving the turns. Where main-chain hydrogen bonds of the type NH(i + 3)→CO(i) were not observed for some β-turns, other main-chain hydrogen bonds or solvent interactions were observed that possibly stabilize such β-turns. A number of unexpected isolated β-turns with proline at i + 2 position were also observed. The NH(i + 2)→CO(i) hydrogen bond was observed for almost all γ-turns. Nearly 20% classic γ-turns and 43% inverse gturns are isolated turns.
KeywordsAmino acid preferences amino acid potentials β- and γ-turns in proteins
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