Functional motions in biomolecules: Insights from computational studies at multiple scales

A.W. VAN WYNSBERGHE; L. MA; X. CHEN; Q. CUI

doi:10.1142/9789812778789_0010

Functional motions in biomolecules: Insights from computational studies at multiple scales

A.W. VAN WYNSBERGHE, L. MA, X. CHEN, Q. CUI^*

^*Corresponding author for this work

Research output: Book Chapters | Papers in Conference Proceedings › Book Chapter › Research › peer-review

1 Citation (Scopus)

Abstract

Motions at both the domain and local scales are important to the function of biomolecules. In this chapter, we discuss computational techniques for probing these functional motions. These include atomistic simulations that characterize the energetics of local motions, various normal-mode based methods that capture the directionality of domain scale motions, as well as effective coarse-grained methods necessary for probing motions at very large length and time scales. The values and limitations of these techniques are illustrated by selected applications used to analyze the role of local motions in enzyme catalysis, mechanochemical coupling in signaling proteins and biomolecular motors, and gating of the mechanosensitive channel. A number of outstanding and emerging questions regarding functional motions in biomolecular systems are briefly discussed.

Original language	English
Title of host publication	Computational Structural Biology: Methods and Applications
Editors	Torsten SCHWEDE, Manuel PEITSCH
Publisher	World Scientific Publishing Co.
Chapter	10
Pages	253-297
Number of pages	45
ISBN (Electronic)	9789814472418
ISBN (Print)	9789812778772
DOIs	https://doi.org/10.1142/9789812778789_0010
Publication status	Published - 2008
Externally published	Yes

Bibliographical note

Q. Cui and X. Chen acknowledge other group members and collaborators who made significant contributions to the work discussed here. The studies reviewed have been generously supported from a Research Innovation Award from the Research Corporation and the National Institutes of Health (R01-GM071428-01) to Q. Cui and a CAREER award to X. Chen (CMMI-0643726) from the National Science Foundation. Q. Cui also acknowledges an Alfred P. Sloan Research Fellowship. Computational resources from the National Center for Supercomputing Applications at the University of Illinois are greatly appreciated.

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title = "Functional motions in biomolecules: Insights from computational studies at multiple scales",

abstract = "Motions at both the domain and local scales are important to the function of biomolecules. In this chapter, we discuss computational techniques for probing these functional motions. These include atomistic simulations that characterize the energetics of local motions, various normal-mode based methods that capture the directionality of domain scale motions, as well as effective coarse-grained methods necessary for probing motions at very large length and time scales. The values and limitations of these techniques are illustrated by selected applications used to analyze the role of local motions in enzyme catalysis, mechanochemical coupling in signaling proteins and biomolecular motors, and gating of the mechanosensitive channel. A number of outstanding and emerging questions regarding functional motions in biomolecular systems are briefly discussed.",

author = "{VAN WYNSBERGHE}, A.W. and L. MA and X. CHEN and Q. CUI",

note = "Q. Cui and X. Chen acknowledge other group members and collaborators who made significant contributions to the work discussed here. The studies reviewed have been generously supported from a Research Innovation Award from the Research Corporation and the National Institutes of Health (R01-GM071428-01) to Q. Cui and a CAREER award to X. Chen (CMMI-0643726) from the National Science Foundation. Q. Cui also acknowledges an Alfred P. Sloan Research Fellowship. Computational resources from the National Center for Supercomputing Applications at the University of Illinois are greatly appreciated.",

year = "2008",

doi = "10.1142/9789812778789_0010",

language = "English",

isbn = "9789812778772",

pages = "253--297",

editor = "Torsten SCHWEDE and Manuel PEITSCH",

booktitle = "Computational Structural Biology: Methods and Applications",

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}

Functional motions in biomolecules: Insights from computational studies at multiple scales. / VAN WYNSBERGHE, A.W.; MA, L.; CHEN, X. et al.
Computational Structural Biology: Methods and Applications. ed. / Torsten SCHWEDE; Manuel PEITSCH. World Scientific Publishing Co., 2008. p. 253-297.

Research output: Book Chapters | Papers in Conference Proceedings › Book Chapter › Research › peer-review

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AU - MA, L.

AU - CHEN, X.

AU - CUI, Q.

N1 - Q. Cui and X. Chen acknowledge other group members and collaborators who made significant contributions to the work discussed here. The studies reviewed have been generously supported from a Research Innovation Award from the Research Corporation and the National Institutes of Health (R01-GM071428-01) to Q. Cui and a CAREER award to X. Chen (CMMI-0643726) from the National Science Foundation. Q. Cui also acknowledges an Alfred P. Sloan Research Fellowship. Computational resources from the National Center for Supercomputing Applications at the University of Illinois are greatly appreciated.

PY - 2008

Y1 - 2008

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AB - Motions at both the domain and local scales are important to the function of biomolecules. In this chapter, we discuss computational techniques for probing these functional motions. These include atomistic simulations that characterize the energetics of local motions, various normal-mode based methods that capture the directionality of domain scale motions, as well as effective coarse-grained methods necessary for probing motions at very large length and time scales. The values and limitations of these techniques are illustrated by selected applications used to analyze the role of local motions in enzyme catalysis, mechanochemical coupling in signaling proteins and biomolecular motors, and gating of the mechanosensitive channel. A number of outstanding and emerging questions regarding functional motions in biomolecular systems are briefly discussed.

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Functional motions in biomolecules: Insights from computational studies at multiple scales

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Bibliographical note

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