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Author:

Zhu, Liangliang (Zhu, Liangliang.) | Wu, Jiazhong (Wu, Jiazhong.) | Liu, Ling (Liu, Ling.) | Liu, Yilun (Liu, Yilun.) | Yan, Yuan (Yan, Yuan.) | Cui, Qiang (Cui, Qiang.) | Chen, Xi (Chen, Xi.)

Indexed by:

SCIE EI Scopus

Abstract:

Gating transition of the mechanosensitive channel of large conductance (MscL) represents a good example of important biological processes that are difficult to describe using atomistic simulations due to the large (submicron) length scale and long (millisecond) time scale. Here we develop a novel computational framework that tightly couples continuum mechanics with continuum solvation models to study the detailed gating behavior of E. coli-MscL. The components of protein molecules are modeled by continuum elements that properly describe their shape, material properties and physicochemical features (e.g., charge distribution). The lipid membrane is modeled as a three-layer material in which the lipid head group and tail regions are treated separately, taking into account the fact that fluidic lipid bilayers do not bear shear stress. Coupling between mechanical and chemical responses of the channel is realized by an iterative integration of continuum mechanics (CM) modeling and continuum solvation (CS) computation. Compared to previous continuum mechanics studies, the present model is capable of capturing the most essential features of the gating process in a much more realistic fashion: due mainly to the apolar solvation contribution, the membrane tension for full opening of MscL is reduced substantially to the experimental measured range. Moreover, the pore size stabilizes constantly during gating because of the intricate interactions of the multiple components of the system, implying the mechanism for sub-conducting states of MscL gating. A significant fraction (similar to 2/3) of the gating membrane strain is required to reach the first sub-conducting state of our model, which is featured with a relative conductance of 0.115 to the fully opened state. These trends agree well with experimental observations. We anticipate that the coupled CM/CS modeling framework is uniquely suited for the analysis of many biomolecules and their assemblies under external mechanical stimuli.

Keyword:

Continuum mechanics Continuum solvation model Gating mechanism Mechanosensitive channel Multi-scale simulations

Author Community:

  • [ 1 ] [Zhu, Liangliang; Wu, Jiazhong; Liu, Yilun; Yan, Yuan] Xi An Jiao Tong Univ, Sch Aerosp, State Key Lab Strength & Vibrat Mech Struct, Int Ctr Appl Mech, Xian 710049, Peoples R China
  • [ 2 ] [Zhu, Liangliang; Chen, Xi] Columbia Univ, Dept Earth & Environm Engn, Columbia Nanomech Res Ctr, New York, NY 10027 USA
  • [ 3 ] [Liu, Ling] Utah State Univ, Dept Mech & Aerosp Engn, Logan, UT 84322 USA
  • [ 4 ] [Cui, Qiang] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA
  • [ 5 ] [Cui, Qiang] Univ Wisconsin, Inst Theoret Chem, Madison, WI 53706 USA
  • [ 6 ] [Zhu, Liangliang]Xi An Jiao Tong Univ, Sch Aerosp, State Key Lab Strength & Vibrat Mech Struct, Int Ctr Appl Mech, Xian 710049, Peoples R China
  • [ 7 ] [Wu, Jiazhong]Xi An Jiao Tong Univ, Sch Aerosp, State Key Lab Strength & Vibrat Mech Struct, Int Ctr Appl Mech, Xian 710049, Peoples R China
  • [ 8 ] [Liu, Yilun]Xi An Jiao Tong Univ, Sch Aerosp, State Key Lab Strength & Vibrat Mech Struct, Int Ctr Appl Mech, Xian 710049, Peoples R China
  • [ 9 ] [Yan, Yuan]Xi An Jiao Tong Univ, Sch Aerosp, State Key Lab Strength & Vibrat Mech Struct, Int Ctr Appl Mech, Xian 710049, Peoples R China
  • [ 10 ] [Zhu, Liangliang]Columbia Univ, Dept Earth & Environm Engn, Columbia Nanomech Res Ctr, New York, NY 10027 USA
  • [ 11 ] [Chen, Xi]Columbia Univ, Dept Earth & Environm Engn, Columbia Nanomech Res Ctr, New York, NY 10027 USA
  • [ 12 ] [Liu, Ling]Utah State Univ, Dept Mech & Aerosp Engn, Logan, UT 84322 USA
  • [ 13 ] [Cui, Qiang]Univ Wisconsin, Dept Chem, Madison, WI 53706 USA
  • [ 14 ] [Cui, Qiang]Univ Wisconsin, Inst Theoret Chem, Madison, WI 53706 USA

Reprint Author's Address:

  • Columbia Univ, Dept Earth & Environm Engn, Columbia Nanomech Res Ctr, New York, NY 10027 USA.

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Source :

BIOMECHANICS AND MODELING IN MECHANOBIOLOGY

ISSN: 1617-7959

Year: 2016

Issue: 6

Volume: 15

Page: 1557-1576

3 . 3 2 3

JCR@2016

2 . 9 6 3

JCR@2020

ESI Discipline: MOLECULAR BIOLOGY & GENETICS;

ESI HC Threshold:280

JCR Journal Grade:2

CAS Journal Grade:2

Cited Count:

WoS CC Cited Count: 4

SCOPUS Cited Count: 8

ESI Highly Cited Papers on the List: 0 Unfold All

WanFang Cited Count:

Chinese Cited Count:

30 Days PV: 5

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