Towards Physical Understanding of Molecular Recognition in the Cell: Recent Evolution of Molecular Dynamics Techniques and Free Energy Theories

Takefumi Yamashita

doi:doi:10.11648/j.bs.20160205.11

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Towards Physical Understanding of Molecular Recognition in the Cell: Recent Evolution of Molecular Dynamics Techniques and Free Energy Theories

Takefumi Yamashita

Published in Biomedical Sciences (Volume 2, Issue 5)

Received: 29 September 2016 Accepted: 19 October 2016 Published: 21 November 2016

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Abstract

In cells, molecules do not arbitrarily interact with others; interact only with molecules of a particular type. This molecular recognition is a very important molecular function as one of the molecular bases on which the cells sustain their lives. Recently, it has been found that molecular recognition, which occurs not only between protein and protein but also between RNA and protein, plays important roles in the cell. Understanding of the molecular recognition at the atomic level is one of the challenging problems in the field of molecular biology and biochemistry. In this review, we address the theoretical and practical aspects of molecular dynamics simulation, which has become an important tool for studying the molecular recognition. From the theoretical viewpoint, many free energy calculation methods based on statistical mechanics have been developed. As for the practical aspects, it is important that the evolution of the computing technique not only enabled long-time simulations, but also enhanced prediction accuracy of simulations with developing new reliable force fields. By the recent development of theory and technology, the challenging tasks such as analysis and prediction of conformational distribution, structural change, and free energy of protein and/or nucleic acid systems are becoming possible.

Published in	Biomedical Sciences (Volume 2, Issue 5)
DOI	10.11648/j.bs.20160205.11
Page(s)	34-47
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2024. Published by Science Publishing Group

Keywords

Molecular Dynamics, Binding Free Energy, Simulation, Molecular Recognition, Protein, RNA

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Takefumi Yamashita. (2016). Towards Physical Understanding of Molecular Recognition in the Cell: Recent Evolution of Molecular Dynamics Techniques and Free Energy Theories. Biomedical Sciences, 2(5), 34-47. https://doi.org/10.11648/j.bs.20160205.11

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ACS Style

Takefumi Yamashita. Towards Physical Understanding of Molecular Recognition in the Cell: Recent Evolution of Molecular Dynamics Techniques and Free Energy Theories. Biomed. Sci. 2016, 2(5), 34-47. doi: 10.11648/j.bs.20160205.11

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AMA Style

Takefumi Yamashita. Towards Physical Understanding of Molecular Recognition in the Cell: Recent Evolution of Molecular Dynamics Techniques and Free Energy Theories. Biomed Sci. 2016;2(5):34-47. doi: 10.11648/j.bs.20160205.11

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@article{10.11648/j.bs.20160205.11,
  author = {Takefumi Yamashita},
  title = {Towards Physical Understanding of Molecular Recognition in the Cell: Recent Evolution of Molecular Dynamics Techniques and Free Energy Theories},
  journal = {Biomedical Sciences},
  volume = {2},
  number = {5},
  pages = {34-47},
  doi = {10.11648/j.bs.20160205.11},
  url = {https://doi.org/10.11648/j.bs.20160205.11},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.bs.20160205.11},
  abstract = {In cells, molecules do not arbitrarily interact with others; interact only with molecules of a particular type. This molecular recognition is a very important molecular function as one of the molecular bases on which the cells sustain their lives. Recently, it has been found that molecular recognition, which occurs not only between protein and protein but also between RNA and protein, plays important roles in the cell. Understanding of the molecular recognition at the atomic level is one of the challenging problems in the field of molecular biology and biochemistry. In this review, we address the theoretical and practical aspects of molecular dynamics simulation, which has become an important tool for studying the molecular recognition. From the theoretical viewpoint, many free energy calculation methods based on statistical mechanics have been developed. As for the practical aspects, it is important that the evolution of the computing technique not only enabled long-time simulations, but also enhanced prediction accuracy of simulations with developing new reliable force fields. By the recent development of theory and technology, the challenging tasks such as analysis and prediction of conformational distribution, structural change, and free energy of protein and/or nucleic acid systems are becoming possible.},
 year = {2016}
}

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TY  - JOUR
T1  - Towards Physical Understanding of Molecular Recognition in the Cell: Recent Evolution of Molecular Dynamics Techniques and Free Energy Theories
AU  - Takefumi Yamashita
Y1  - 2016/11/21
PY  - 2016
N1  - https://doi.org/10.11648/j.bs.20160205.11
DO  - 10.11648/j.bs.20160205.11
T2  - Biomedical Sciences
JF  - Biomedical Sciences
JO  - Biomedical Sciences
SP  - 34
EP  - 47
PB  - Science Publishing Group
SN  - 2575-3932
UR  - https://doi.org/10.11648/j.bs.20160205.11
AB  - In cells, molecules do not arbitrarily interact with others; interact only with molecules of a particular type. This molecular recognition is a very important molecular function as one of the molecular bases on which the cells sustain their lives. Recently, it has been found that molecular recognition, which occurs not only between protein and protein but also between RNA and protein, plays important roles in the cell. Understanding of the molecular recognition at the atomic level is one of the challenging problems in the field of molecular biology and biochemistry. In this review, we address the theoretical and practical aspects of molecular dynamics simulation, which has become an important tool for studying the molecular recognition. From the theoretical viewpoint, many free energy calculation methods based on statistical mechanics have been developed. As for the practical aspects, it is important that the evolution of the computing technique not only enabled long-time simulations, but also enhanced prediction accuracy of simulations with developing new reliable force fields. By the recent development of theory and technology, the challenging tasks such as analysis and prediction of conformational distribution, structural change, and free energy of protein and/or nucleic acid systems are becoming possible.
VL  - 2
IS  - 5
ER  -

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Author Information

Takefumi Yamashita

Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, the University of Tokyo, Tokyo, Japan

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APA Style

Takefumi Yamashita. (2016). Towards Physical Understanding of Molecular Recognition in the Cell: Recent Evolution of Molecular Dynamics Techniques and Free Energy Theories. Biomedical Sciences, 2(5), 34-47. https://doi.org/10.11648/j.bs.20160205.11

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ACS Style

Takefumi Yamashita. Towards Physical Understanding of Molecular Recognition in the Cell: Recent Evolution of Molecular Dynamics Techniques and Free Energy Theories. Biomed. Sci. 2016, 2(5), 34-47. doi: 10.11648/j.bs.20160205.11

Copy | Download

AMA Style

Takefumi Yamashita. Towards Physical Understanding of Molecular Recognition in the Cell: Recent Evolution of Molecular Dynamics Techniques and Free Energy Theories. Biomed Sci. 2016;2(5):34-47. doi: 10.11648/j.bs.20160205.11

Copy | Download

@article{10.11648/j.bs.20160205.11,
  author = {Takefumi Yamashita},
  title = {Towards Physical Understanding of Molecular Recognition in the Cell: Recent Evolution of Molecular Dynamics Techniques and Free Energy Theories},
  journal = {Biomedical Sciences},
  volume = {2},
  number = {5},
  pages = {34-47},
  doi = {10.11648/j.bs.20160205.11},
  url = {https://doi.org/10.11648/j.bs.20160205.11},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.bs.20160205.11},
  abstract = {In cells, molecules do not arbitrarily interact with others; interact only with molecules of a particular type. This molecular recognition is a very important molecular function as one of the molecular bases on which the cells sustain their lives. Recently, it has been found that molecular recognition, which occurs not only between protein and protein but also between RNA and protein, plays important roles in the cell. Understanding of the molecular recognition at the atomic level is one of the challenging problems in the field of molecular biology and biochemistry. In this review, we address the theoretical and practical aspects of molecular dynamics simulation, which has become an important tool for studying the molecular recognition. From the theoretical viewpoint, many free energy calculation methods based on statistical mechanics have been developed. As for the practical aspects, it is important that the evolution of the computing technique not only enabled long-time simulations, but also enhanced prediction accuracy of simulations with developing new reliable force fields. By the recent development of theory and technology, the challenging tasks such as analysis and prediction of conformational distribution, structural change, and free energy of protein and/or nucleic acid systems are becoming possible.},
 year = {2016}
}

Copy | Download

TY  - JOUR
T1  - Towards Physical Understanding of Molecular Recognition in the Cell: Recent Evolution of Molecular Dynamics Techniques and Free Energy Theories
AU  - Takefumi Yamashita
Y1  - 2016/11/21
PY  - 2016
N1  - https://doi.org/10.11648/j.bs.20160205.11
DO  - 10.11648/j.bs.20160205.11
T2  - Biomedical Sciences
JF  - Biomedical Sciences
JO  - Biomedical Sciences
SP  - 34
EP  - 47
PB  - Science Publishing Group
SN  - 2575-3932
UR  - https://doi.org/10.11648/j.bs.20160205.11
AB  - In cells, molecules do not arbitrarily interact with others; interact only with molecules of a particular type. This molecular recognition is a very important molecular function as one of the molecular bases on which the cells sustain their lives. Recently, it has been found that molecular recognition, which occurs not only between protein and protein but also between RNA and protein, plays important roles in the cell. Understanding of the molecular recognition at the atomic level is one of the challenging problems in the field of molecular biology and biochemistry. In this review, we address the theoretical and practical aspects of molecular dynamics simulation, which has become an important tool for studying the molecular recognition. From the theoretical viewpoint, many free energy calculation methods based on statistical mechanics have been developed. As for the practical aspects, it is important that the evolution of the computing technique not only enabled long-time simulations, but also enhanced prediction accuracy of simulations with developing new reliable force fields. By the recent development of theory and technology, the challenging tasks such as analysis and prediction of conformational distribution, structural change, and free energy of protein and/or nucleic acid systems are becoming possible.
VL  - 2
IS  - 5
ER  -

Copy | Download