STRUCTURAL BIOINFORMATICS STUDY OF THE STRUCTURAL BASIS OF SUBSTRATE SPECIFICITY OF PURINE NUCLEOSIDE PHOSPHORYLASE FROM THERMUS THERMOPHILUS

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Abstract

Molecular dynamics simulations were performed for wild-type purine nucleoside phosphorylase in complexes with two substrates (adenosine and guanosine). The MD simulations were also performed for the mutant form of the enzyme with the same substrates. The free energy changes upon the formation of the complexes were evaluated from the molecular dynamics trajectories by the MM-GBSA method.

About the authors

I. F. Garipov

Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics,” Russian Academy of Sciences, Moscow, 119333 Russia

Email: ildar.garipov.f@gmail.com
Россия, Москва

V. I. Timofeev

Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics,” Russian Academy of Sciences, Moscow, 119333 Russia; National Research Centre “Kurchatov Institute,” Moscow, 123182 Russia

Email: ildar.garipov.f@gmail.com
Россия, Москва; Россия, Москва

E. A. Zayats

Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia

Email: ildar.garipov.f@gmail.com
Россия, Москва

Yu. A. Abramchikc

Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia

Email: ildar.garipov.f@gmail.com
Россия, Москва

M. A. Kostromina

Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia

Email: ildar.garipov.f@gmail.com
Россия, Москва

I. D. Konstantinova

Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia

Email: ildar.garipov.f@gmail.com
Россия, Москва

R. S. Esipov

Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia

Author for correspondence.
Email: ildar.garipov.f@gmail.com
Россия, Москва

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