Molecular dynamics and small-angle x-ray scattering: a comparison computational and experimental approaches to studying the structure of biological complexes

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Abstract

The results of studying DNA-protein complexes using two independent structural methods – molecular dynamics (MD) and small-angle X-ray scattering (SAXS) – are compared. MD is a computational method that allows visualization of macromolecule behavior in real environmental conditions based on the laws of physics but suffers from numerous simplifications. SAXS is an X-ray method that allows the reconstruction of the three-dimensional structure of an object in solution based on the one-dimensional profile of small-angle scattering, which presents the problem of ambiguity in solving inverse problems. The use of structural characteristics of complexes obtained by the SAXS method for validating 3D structural models obtained in MD experiments has significantly reduced the ambivalence of theoretical predictions and demonstrated the effectiveness of combining MD and SAXS methods for solving structural biology problems.

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M. V. Petoukhov

Shubnikov Institute of Crystallography of Kurchatov Complex of Crystallography and Photonics of NRC “Kurchatov Institute”; Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences; A.N. Frumkin Institute of Physical Chemistry and Electrochemistry of Russian Academy of Sciences

Author for correspondence.
Email: pmxmvl@yandex.ru
Russian Federation, Moscow; Moscow; Moscow

T. V. Rakitina

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

Email: pmxmvl@yandex.ru
Russian Federation, 123182 Moscow; Moscow

Yu. K. Agapova

National Research Centre "Kurchatov Institute"

Email: pmxmvl@yandex.ru
Russian Federation, 123182 Moscow

D. E. Petrenko

National Research Centre "Kurchatov Institute"

Email: pmxmvl@yandex.ru
Russian Federation, 123182 Moscow

D. D. Podshivalov

National Research Centre "Kurchatov Institute"; M.V. Lomonosov Moscow State University

Email: pmxmvl@yandex.ru
Russian Federation, 123182 Moscow; Moscow

V. I. Timofeev

Shubnikov Institute of Crystallography of Kurchatov Complex of Crystallography and Photonics of NRC “Kurchatov Institute”

Email: pmxmvl@yandex.ru
Russian Federation, Moscow

G. S. Peters

National Research Centre "Kurchatov Institute"

Email: pmxmvl@yandex.ru
Russian Federation, 123182 Moscow

Yu. A. Gaponov

National Research Centre "Kurchatov Institute"

Email: pmxmvl@yandex.ru
Russian Federation, 123182 Moscow

E. V. Bocharov

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

Email: pmxmvl@yandex.ru
Russian Federation, Moscow

E. V. Shtykova

Shubnikov Institute of Crystallography of Kurchatov Complex of Crystallography and Photonics of NRC “Kurchatov Institute”; A.N. Frumkin Institute of Physical Chemistry and Electrochemistry of Russian Academy of Sciences

Email: pmxmvl@yandex.ru
Russian Federation, Moscow; Moscow

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