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Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics

1
Institute of Transformative Bio-Molecules (WPI), Nagoya University, Nagoya, Aichi 464-8601, Japan
2
Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
3
RIKEN-Center for Computational Science, Kobe, Hyogo 650-0047, Japan
*
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2018, 19(11), 3401; https://doi.org/10.3390/ijms19113401
Received: 1 October 2018 / Revised: 20 October 2018 / Accepted: 27 October 2018 / Published: 30 October 2018
(This article belongs to the Special Issue Protein Structural Dynamics)
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Abstract

Protein structural biology came a long way since the determination of the first three-dimensional structure of myoglobin about six decades ago. Across this period, X-ray crystallography was the most important experimental method for gaining atomic-resolution insight into protein structures. However, as the role of dynamics gained importance in the function of proteins, the limitations of X-ray crystallography in not being able to capture dynamics came to the forefront. Computational methods proved to be immensely successful in understanding protein dynamics in solution, and they continue to improve in terms of both the scale and the types of systems that can be studied. In this review, we briefly discuss the limitations of X-ray crystallography in studying protein dynamics, and then provide an overview of different computational methods that are instrumental in understanding the dynamics of proteins and biomacromolecular complexes. View Full-Text
Keywords: hybrid modeling; integrative modeling; molecular dynamics; X-ray crystallography hybrid modeling; integrative modeling; molecular dynamics; X-ray crystallography
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Srivastava, A.; Nagai, T.; Srivastava, A.; Miyashita, O.; Tama, F. Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics. Int. J. Mol. Sci. 2018, 19, 3401.

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