Insights into Actin Polymerization and Nucleation Using a Coarse-Grained Model.

Biophysical Journal
Brandon G HoranDimitrios Vavylonis

Abstract

We studied actin filament polymerization and nucleation with molecular dynamics simulations and a previously established coarse-grained model having each residue represented by a single interaction site located at the Cα atom. We approximate each actin protein as a fully or partially rigid unit to identify the equilibrium structural ensemble of interprotein complexes. Monomers in the F-actin configuration bound to both barbed and pointed ends of a short F-actin filament at the anticipated locations for polymerization. Binding at both ends occurred with similar affinity. Contacts between residues of the incoming subunit and the short filament were consistent with expectation from models based on crystallography, x-ray diffraction, and cryo-electron microscopy. Binding at the barbed and pointed end also occurred at an angle with respect to the polymerizable bound structure, and the angle range depended on the flexibility of the D-loop. Additional barbed end bound states were seen when the incoming subunit was in the G-actin form. Consistent with an activation barrier for pointed end polymerization, G-actin did not bind at an F-actin pointed end. In all cases, binding at the barbed end also occurred in a configuration similar to t...Continue Reading

References

Apr 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·S H Northrup, H P Erickson
Mar 1, 1988·The Journal of Cell Biology·R MillonigU Aebi
Jan 1, 1985·Annual Review of Biophysics and Biophysical Chemistry·O G Berg, P H von Hippel
Nov 24, 1986·Physical Review Letters·R H Swendsen, J S Wang
Dec 22, 1999·Journal of Molecular Biology·D SeptJ A McCammon
Jan 7, 2000·Journal of Molecular Biology·E M De La CruzT D Pollard
Jul 21, 2001·Biophysical Journal·D Sept, J A McCammon
Jul 28, 2001·Science·L R OtterbeinR Dominguez
Aug 29, 2002·Nature Cell Biology·Ikuko FujiwaraShin'ichi Ishiwata
Jun 19, 2003·The Journal of Biological Chemistry·Philip Graceffa, Roberto Dominguez
Sep 8, 2004·Biochemistry·Peteranne B JoelKathleen M Trybus
Jun 9, 2005·Proceedings of the National Academy of Sciences of the United States of America·Dimitrios VavylonisBen O'Shaughnessy
Sep 2, 2005·Proceedings of the National Academy of Sciences of the United States of America·Jhih-Wei Chu, Gregory A Voth
Dec 20, 2005·Biophysical Journal·Jhih-Wei Chu, Gregory A Voth
Jan 31, 2006·Biophysical Journal·Evgeny B Stukalin, Anatoly B Kolomeisky
Feb 18, 2006·Molecular Cell·Dimitrios VavylonisThomas D Pollard
Aug 9, 2006·Journal of Molecular Biology·Vadim A KlenchinIvan Rayment
May 23, 2007·Proceedings of the National Academy of Sciences of the United States of America·Ikuko FujiwaraThomas D Pollard
May 29, 2007·Biophysical Journal·Xiange ZhengDavid Sept
Dec 18, 2007·Journal of Molecular Biology·Young C Kim, Gerhard Hummer
Aug 30, 2008·Proceedings of the National Academy of Sciences of the United States of America·Young C KimGerhard Hummer
Jan 23, 2009·Nature·Toshiro OdaAkihiro Narita
Jul 22, 2009·Proceedings of the National Academy of Sciences of the United States of America·Jim PfaendtnerGregory A Voth
Jan 16, 2010·Proceedings of the Japan Academy. Series B, Physical and Biological Sciences·Naoki Watanabe
Apr 7, 2010·Biochemistry·Elena E GrintsevichAndras Muhlrad
Jun 12, 2010·Proceedings of the National Academy of Sciences of the United States of America·Anna M DuckaTomasz Sitar
Oct 12, 2010·Nature Structural & Molecular Biology·Vitold E GalkinEdward H Egelman
Feb 15, 2011·Annual Review of Biophysics·Roberto Dominguez, Kenneth C Holmes
Mar 8, 2011·The EMBO Journal·Akihiro NaritaYuichiro Maéda
Oct 6, 2011·Journal of Structural Biology·Unai SilvánCora-Ann Schoenenberger
Apr 10, 2012·Structure·Marissa G Saunders, Gregory A Voth
Sep 6, 2012·Biophysical Journal·Osman N YogurtcuSean X Sun
Sep 27, 2012·Biophysical Journal·Zeynep A Oztug DurerEmil Reisler
Oct 3, 2012·Proceedings of the National Academy of Sciences of the United States of America·Hyeran KangEnrique M De La Cruz
Nov 7, 2012·Proceedings of the National Academy of Sciences of the United States of America·Weihua ZhengPeter G Wolynes
Jan 26, 2013·Biopolymers·Dmitri S Kudryashov, Emil Reisler
Jun 4, 2013·Cell Reports·Xiaorui ChenJianpeng Ma
Dec 24, 2013·Biophysical Journal·Hyeran KangEnrique M De La Cruz
Jan 3, 2014·Physiological Reviews·Laurent BlanchoinJulie Plastino

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Citations

Jan 17, 2021·International Journal of Molecular Sciences·Harper SmithDmitri S Kudryashov
Nov 18, 2020·Proceedings of the National Academy of Sciences of the United States of America·Vilmos ZsolnayGregory A Voth
Sep 13, 2021·Biophysical Journal·Aaron D RosenbloomThomas D Pollard

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