Steered molecular dynamics analysis of the role of cofilin in increasing the flexibility of actin filaments

Jae In Kim, Junpyo Kwon, Inchul Baek, Sung Soo Na

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Cofilin is one of the most essential regulatory proteins and participates in the process of disassembling actin filaments. Cofilin induces conformational changes to actin filaments, and both the bending and torsional rigidity of the filament. In this study, we investigate the effects of cofilin on the mechanical properties of actin filaments using computational methods. Three models defined by their number of bound cofilins are constructed using coarse-grained MARTINI force field, and they are then extended with steered molecular dynamics simulation. After obtaining the stress–strain curves of the models, we calculate their Young's moduli and other mechanical properties that have not yet been determined for actin filaments. We analyze the cause of the different behaviors of the three models based on their atomistic geometrical differences. Finally, it is demonstrated that cofilin binding causes changes in the distances, angles, and stabilities of the residues in actin filaments.

Original languageEnglish
Pages (from-to)27-35
Number of pages9
JournalBiophysical Chemistry
Volume218
DOIs
Publication statusPublished - 2016 Nov 1

Fingerprint

Actin Depolymerizing Factors
Molecular Dynamics Simulation
Actin Cytoskeleton
Dynamic analysis
Molecular dynamics
Actins
Mechanical properties
Elastic Modulus
Computational methods
Rigidity
Elastic moduli
Computer simulation
Proteins

Keywords

  • Actin
  • Cofilin
  • Mechanical property
  • SMD

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Organic Chemistry

Cite this

Steered molecular dynamics analysis of the role of cofilin in increasing the flexibility of actin filaments. / Kim, Jae In; Kwon, Junpyo; Baek, Inchul; Na, Sung Soo.

In: Biophysical Chemistry, Vol. 218, 01.11.2016, p. 27-35.

Research output: Contribution to journalArticle

@article{6165140912774f4898adb12d52a18144,
title = "Steered molecular dynamics analysis of the role of cofilin in increasing the flexibility of actin filaments",
abstract = "Cofilin is one of the most essential regulatory proteins and participates in the process of disassembling actin filaments. Cofilin induces conformational changes to actin filaments, and both the bending and torsional rigidity of the filament. In this study, we investigate the effects of cofilin on the mechanical properties of actin filaments using computational methods. Three models defined by their number of bound cofilins are constructed using coarse-grained MARTINI force field, and they are then extended with steered molecular dynamics simulation. After obtaining the stress–strain curves of the models, we calculate their Young's moduli and other mechanical properties that have not yet been determined for actin filaments. We analyze the cause of the different behaviors of the three models based on their atomistic geometrical differences. Finally, it is demonstrated that cofilin binding causes changes in the distances, angles, and stabilities of the residues in actin filaments.",
keywords = "Actin, Cofilin, Mechanical property, SMD",
author = "Kim, {Jae In} and Junpyo Kwon and Inchul Baek and Na, {Sung Soo}",
year = "2016",
month = "11",
day = "1",
doi = "10.1016/j.bpc.2016.08.002",
language = "English",
volume = "218",
pages = "27--35",
journal = "Biophysical Chemistry",
issn = "0301-4622",
publisher = "Elsevier",

}

TY - JOUR

T1 - Steered molecular dynamics analysis of the role of cofilin in increasing the flexibility of actin filaments

AU - Kim, Jae In

AU - Kwon, Junpyo

AU - Baek, Inchul

AU - Na, Sung Soo

PY - 2016/11/1

Y1 - 2016/11/1

N2 - Cofilin is one of the most essential regulatory proteins and participates in the process of disassembling actin filaments. Cofilin induces conformational changes to actin filaments, and both the bending and torsional rigidity of the filament. In this study, we investigate the effects of cofilin on the mechanical properties of actin filaments using computational methods. Three models defined by their number of bound cofilins are constructed using coarse-grained MARTINI force field, and they are then extended with steered molecular dynamics simulation. After obtaining the stress–strain curves of the models, we calculate their Young's moduli and other mechanical properties that have not yet been determined for actin filaments. We analyze the cause of the different behaviors of the three models based on their atomistic geometrical differences. Finally, it is demonstrated that cofilin binding causes changes in the distances, angles, and stabilities of the residues in actin filaments.

AB - Cofilin is one of the most essential regulatory proteins and participates in the process of disassembling actin filaments. Cofilin induces conformational changes to actin filaments, and both the bending and torsional rigidity of the filament. In this study, we investigate the effects of cofilin on the mechanical properties of actin filaments using computational methods. Three models defined by their number of bound cofilins are constructed using coarse-grained MARTINI force field, and they are then extended with steered molecular dynamics simulation. After obtaining the stress–strain curves of the models, we calculate their Young's moduli and other mechanical properties that have not yet been determined for actin filaments. We analyze the cause of the different behaviors of the three models based on their atomistic geometrical differences. Finally, it is demonstrated that cofilin binding causes changes in the distances, angles, and stabilities of the residues in actin filaments.

KW - Actin

KW - Cofilin

KW - Mechanical property

KW - SMD

UR - http://www.scopus.com/inward/record.url?scp=84984608898&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84984608898&partnerID=8YFLogxK

U2 - 10.1016/j.bpc.2016.08.002

DO - 10.1016/j.bpc.2016.08.002

M3 - Article

C2 - 27589672

AN - SCOPUS:84984608898

VL - 218

SP - 27

EP - 35

JO - Biophysical Chemistry

JF - Biophysical Chemistry

SN - 0301-4622

ER -