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Development and validation of force-field parameters for molecular simulations of peptides and proteins containing open-shell residues

✍ Scribed by Barone, Vincenzo; Capecchi, Gabriella; Brunel, Yvon; Andri�s, Marie-Louise Dheu; Subra, Robert

Publisher
John Wiley and Sons
Year
1997
Tongue
English
Weight
375 KB
Volume
18
Category
Article
ISSN
0192-8651

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✦ Synopsis

Parameters suitable for extending the AMBER force field for nucleic acids and proteins to open-shell derivatives of amino acid residues are Ž w x proposed and tested. Two new atom types radical carbon CE and hydrogen w x. directly bonded to it HE are introduced, whose parameters have been determined by a best fitting of quantum-mechanical computations of the simplest Ž . analogue of glycine radical GlyR in a peptide. The new force field is able to fit the reference results concerning both the structural parameters and the relative stabilities of the different conformers. It has been next applied to a conformational study of the distortions induced by extraction of the glycine H ␣ atom in an initially helical structure of a dodecamer of alanine including a central glycine residue. Our results show that the helical structure corresponds to a local energy minimum, but deeper minima are found which correspond to a fully planar GlyR residue included in a distorted helical sequence.

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