Interaction of Lysine‐Alanine‐Alanine tripeptide with a fragment of DNA: An empirical potential study | Zendy

Hobza Pavel | Zendy; Nachtigallová Dana | Zendy; Havlas Zdeněk | Zendy; Maloň Petr | Zendy; Šponar Jaroslav | Zendy

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Interaction of Lysine‐Alanine‐Alanine tripeptide with a fragment of DNA: An empirical potential study

Author(s) -

Hobza Pavel,

Nachtigallová Dana,

Havlas Zdeněk,

Maloň Petr,

Šponar Jaroslav

Publication year - 1991

Publication title -

journal of computational chemistry

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 0.907

H-Index - 188

eISSN - 1096-987X

pISSN - 0192-8651

DOI - 10.1002/jcc.540120103

Subject(s) - tripeptide , intramolecular force , chemistry , intermolecular force , alanine , dna , peptide , stereochemistry , fragment (logic) , computational chemistry , crystallography , molecule , amino acid , biochemistry , organic chemistry , computer science , programming language

Interaction of a rigid fragment of B‐DNA (polyanionic as well as screened by Na + cations) with the flexible tripeptide Lys‐Ala‐Ala (in both L and D configurations) were investigated with the aid of an empirical potential. The potential consists of intramolecular (MM2 potential) and intermolecular (pair potential described in reference 1) parts; hence total energy is formed by intra‐ and intermolecular components. The results demonstrate that intramolecular relaxation of the peptide results in a considerable decrease in total energy. While energies of DNA complexes with L‐Lys‐L‐Ala‐L‐Ala were comparable to those with D‐Lys‐D‐Ala‐D‐Ala the respective geometries exhibit considerable differences.

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