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GIAO-PCM Calculations on Alanine Diamide Models Aimed at Predicting Protein Secondary Structures

Hudáky, Ilona and Jákli, Imre and Náray-Szabó, Gábor and Perczel, András (2012) GIAO-PCM Calculations on Alanine Diamide Models Aimed at Predicting Protein Secondary Structures. J Comput Chem. ISSN 0192-8651 (print), 1096-987X (online) (Submitted)

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Abstract

In this paper we extend our theoretical studies dealing with the dependence of relative proton and carbon chemical shifts (CSs) of protein backbone atoms on their conformational position. In an earlier paper (A. Czajlik, I. Hudáky, A. Perczel, J Comp Chem 2011, 32, 3362) we reported on a fair agreement between calculated and observed backbone CSs as a function of backbone conformation. Applying the polarizable continuum model (PCM) in this work, we compare relative CSs of fully optimized alanine diamide conformers with gas phase calculations and experimental results. Along a path on the Ramachandran surface, we collated calculated relative CSs obtained with and without explicit water molecules, as well as with and without considering the PCM reaction field. Furthermore, we traced the energetically relevant reaction paths along the torsional angle ψ connecting the lowest energy minima (helical, extended, polyproline II and inverse γ-turn) on the Ramachandran plot, with the prospect to facilitate identifying them by their relative CSs. We found that consideration of the solvent effect of the environment around a diamide model improves the agreement with experimental findings on abundant conformers. This agreement is of the level achieved previously by a thorough gas phase investigation on considerably larger oligoalanine models. By relating DeltaδCα, DeltaδHα and DeltaδCβ values of polyproline II and inverse γ-turn to the experimentally well characterized helical and extended data, our calculations contribute to protein secondary structure prediction based on nuclear magnetic CSs

Item Type: Article
Subjects: Q Science / természettudomány > QD Chemistry / kémia > QD02 Physical chemistry / fizikai kémia
Q Science / természettudomány > QH Natural history / természetrajz > QH301 Biology / biológia > QH3015 Molecular biology / molekuláris biológia
Depositing User: Prof Gábor Náray-Szabó
Date Deposited: 23 Feb 2012 11:01
Last Modified: 26 Sep 2012 09:58
URI: http://real.mtak.hu/id/eprint/2901

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