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Issue 18, 2010
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Quantum mechanical study of secondary structure formation in protected dipeptides

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Abstract

An extensive computational study of the conformational preferences of three capped dipeptides: Ac-Xxx-Phe-NH2, 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 γLγL(g−) and β-turn I(g+) in Ac-Gly-Phe-NH2, and Ac-Ala-Phe-NH2, and as the closely related γL(g+)γL(g−) and β-turn I(a,g+) in Ac-Val-Phe-NH2. In contrast to the experimental observation that peptides with bulky side chain have a propensity for β-turns, we show that in Ac-Val-Phe-NH2 the minimum energy structure corresponds to the experimentally non detected β-strand.

Graphical abstract: Quantum mechanical study of secondary structure formation in protected dipeptides

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Article information


Submitted
03 Nov 2009
Accepted
05 Feb 2010
First published
16 Mar 2010

Phys. Chem. Chem. Phys., 2010,12, 4678-4685
Article type
Paper

Quantum mechanical study of secondary structure formation in protected dipeptides

A. <strong xmlns="http://www.rsc.org/schema/rscart38">Š</strong>ari<strong xmlns="http://www.rsc.org/schema/rscart38">ć</strong>, T. Hrenar, M. Mali<strong xmlns="http://www.rsc.org/schema/rscart38">š</strong> and N. Do<strong xmlns="http://www.rsc.org/schema/rscart38">š</strong>li<strong xmlns="http://www.rsc.org/schema/rscart38">ć</strong>, Phys. Chem. Chem. Phys., 2010, 12, 4678
DOI: 10.1039/B923041F

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