Molecular Dynamics and Small-Angle X-ray Scattering: Comparison of Computational and Experimental Approaches to Studying Structures of Biological Complexes

IF 0.6 4区材料科学 Q4 CRYSTALLOGRAPHY

Crystallography Reports Pub Date : 2024-11-14 DOI:10.1134/S1063774524601540

M. V. Petoukhov, T. V. Rakitina, Yu. K. Agapova, D. E. Petrenko, D. D. Podshivalov, V. I. Timofeev, G. S. Peters, Yu. A. Gaponov, E. V. Bocharov, E. V. Shtykova

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Abstract

The results of investigation of DNA-protein complexes by two independent structural methods, namely, molecular dynamics (MD) and small-angle X-ray scattering (SAXS), were compared. Molecular dynamics is a computational method enabling the visualization of the behavior of macromolecules in real media, which is based on the laws of physics, but it is limited by numerous simplifications. Small-angle X-ray scattering is an X-ray method, which allows the reconstruction of the three-dimensional structure of a system in solution from a one-dimensional small-angle scattering profile, but it faces the problem of ambiguity in solving inverse problems. The use of structural characteristics of the complexes determined by SAXS for the validation of 3D structural models generated by MD simulations made it possible to significantly reduce the ambivalence of theoretical predictions and demonstrated the efficiency of a combination of MD simulations and SAXS for solving problems of structural biology.

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分子动力学和小角 X 射线散射：比较研究生物复合物结构的计算和实验方法

通过分子动力学（MD）和小角 X 射线散射（SAXS）这两种独立的结构方法对 DNA 蛋白复合物的研究结果进行了比较。分子动力学是一种计算方法，可以将大分子在真实介质中的行为可视化，它以物理定律为基础，但受到许多简化的限制。小角 X 射线散射是一种 X 射线方法，可以根据一维小角散射剖面重建溶液中系统的三维结构，但在解决逆问题时面临模糊性问题。利用 SAXS 确定的复合物结构特征来验证 MD 模拟生成的三维结构模型，可以大大降低理论预测的矛盾性，并证明了 MD 模拟和 SAXS 结合解决结构生物学问题的效率。

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来源期刊

Crystallography Reports 化学-晶体学

CiteScore

1.10

自引率

28.60%

发文量

审稿时长

4-8 weeks

期刊介绍： Crystallography Reports is a journal that publishes original articles short communications, and reviews on various aspects of crystallography: diffraction and scattering of X-rays, electrons, and neutrons, determination of crystal structure of inorganic and organic substances, including proteins and other biological substances; UV-VIS and IR spectroscopy; growth, imperfect structure and physical properties of crystals; thin films, liquid crystals, nanomaterials, partially disordered systems, and the methods of studies.