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Improved Modeling of Peptidic Foldamers Using a Quantum Chemical Parametrization Based on Torsional Minimum Energy Path Matching

Wacha, András and Beke‐Somfai, Tamás and Nagy, Tibor (2019) Improved Modeling of Peptidic Foldamers Using a Quantum Chemical Parametrization Based on Torsional Minimum Energy Path Matching. ChemPlusChem, 84 (7). pp. 927-941. ISSN 2192-6506

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Abstract

The increasing interest in novel foldamer constructs demands an accurate computational treatment on an extensive timescale. However, it is still a challenge to derive a force field (FF) that can reproduce the experimentally known fold while also allowing the spontaneous exploration of other structures. Here, aiming at a realistic reproduction of backbone torsional barriers, the relevant proper dihedrals of acyclic β2‐, β3‐ and β2,3‐amino acids were added to the CHARMM FF and optimized using a novel, self‐consistent iterative procedure based on quantum chemical relaxed scans. The new FF was validated by molecular dynamics simulations on three acyclic peptides. While they resided most of the time in their preferred fold (>80 % in helices and >50 % in hairpin), they also visited other conformations. Owing to the CHARMM36m‐consistent parametrization, the proposed extension is suitable for exploring new foldamer structures and assemblies, and their interactions with diverse biomolecules.

Item Type: Article
Subjects: Q Science / természettudomány > QD Chemistry / kémia > QD02 Physical chemistry / fizikai kémia
Q Science / természettudomány > QD Chemistry / kémia > QD04 Organic chemistry / szerves kémia
Depositing User: Tibor Nagy
Date Deposited: 26 Sep 2019 08:59
Last Modified: 26 Sep 2019 08:59
URI: http://real.mtak.hu/id/eprint/101449

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