Quantum mechanical study of secondary structure formation in protected dipeptides.
An extensive computational study of the conformational preferences of three capped dipeptides: Ac-Xxx-Phe-NH(2), Xxx = Gly, Ala, Val is reported. On the basis of local second-order Møller-Plesset perturbation theory (LMP2) and DFT computations we were able to identify the experimentally observed conformers as gamma(L)-gamma(L)(g-) and beta-turn I(g+) in Ac-Gly-Phe-NH(2), and Ac-Ala-Phe-NH(2), and as the closely related gamma(L)(g+)-gamma(L)(g-) and beta-turn I(a,g+) in Ac-Val-Phe-NH(2). In contrast to the experimental observation that peptides with bulky side chain have a propensity for beta-turns, we show that in Ac-Val-Phe-NH(2) the minimum energy structure corresponds to the experimentally non detected beta-strand.
Sarić
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A
Department of Chemistry, Columbia University, NY 10027, New York, USA.
Hrenar
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T
Malis
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M
Doslić
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N
D004151:Dipeptides / Q000737:chemistry*; D004583:Electrons; D056004:Molecular Dynamics Simulation; D017433:Protein Structure, Secondary; D011789:Quantum Theory; D013055:Spectrophotometry, Infrared
D004151:Dipeptides