Molecular Dynamics Study of Binding of Substrates Bearing Two Positively Charged Residues to Oligopeptidase B from Serratia proteamaculans


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Resumo

The behavior of the peptide substrates GlyArgArgGly and GlyLysArgGly, which contain arginine or lysine at the Р2 position, in the active site of oligopeptidase В from the gamma-proteobacterium Serratia proteamaculans was studied by molecular dynamics simulations. The nature of the residue at the Р2 position was shown not only to influence the position of this residue and its contacts with the amino-acid environment in the substrate-binding pocket but also to affect the conformational dynamics of the entire peptide. Only the residue at the Р1 position forms persistent contacts with the S1-substrate-binding site of the enzyme, whereas contacts of the residue at the Р2 position may vary depending on its nature. Molecular dynamics simulations are shown to complement and improve the knowledge extracted from X-ray diffraction studies that enable the determination of the three-dimensional structures of molecules in one of numerous alternative conformations.

Sobre autores

Yu. Agapova

National Research Centre “Kurchatov Institute”

Autor responsável pela correspondência
Email: agapova.jk@gmail.com
Rússia, Moscow, 123098

A. Talyzina

Moscow Institute of Physics and Technology

Email: taniarakitina@yahoo.com
Rússia, Dolgoprudnyi, Moscow Region, 141701

Yu. Zeifman

National Research Centre “Kurchatov Institute”

Email: taniarakitina@yahoo.com
Rússia, Moscow, 123098

T. Fateeva

National Research Centre “Kurchatov Institute”

Email: taniarakitina@yahoo.com
Rússia, Moscow, 123098

V. Timofeev

National Research Centre “Kurchatov Institute”; Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics,”
Russian Academy of Sciences

Email: taniarakitina@yahoo.com
Rússia, Moscow, 123098; Moscow, 119333

A. Mikhailova

Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences

Email: taniarakitina@yahoo.com
Rússia, Moscow, 117997

T. Rakitina

National Research Centre “Kurchatov Institute”; Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences

Autor responsável pela correspondência
Email: taniarakitina@yahoo.com
Rússia, Moscow, 123098; Moscow, 117997

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