help button home button Biophys. J.
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS

Biophysical Journal 68: 5-12 (1995)
© 1995 the Biophysical Society

This Article
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Tirion, M M
Right arrow Articles by Holmes, K C
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Tirion, M M
Right arrow Articles by Holmes, K C

Normal modes as refinement parameters for the F-actin model.

M M Tirion, D ben-Avraham, M Lorenz and K C Holmes

Department of Physics, Clarkson University, Potsdam, New York 13699-5820.

ABSTRACT

The slow normal modes of G-actin were used as structural parameters to refine the F-actin model against 8-A resolution x-ray fiber diffraction data. The slowest frequency normal modes of G-actin pertain to collective rearrangements of domains, motions that are characterized by correlation lengths on the order of the resolution of the fiber diffraction data. Using a small number of normal mode degrees of freedom (< or = 12) improved the fit to the data significantly. The refined model of F-actin shows that the nucleotide binding cleft has narrowed and that the DNase I binding loop has twisted to a lower radius, consistent with other refinement techniques and electron microscopy data. The methodology of a normal mode refinement is described, and the results, as applied to actin, are detailed.




This article has been cited by other articles:


Home page
 J. Cell Biol.Home page
I. Rouiller, X.-P. Xu, K. J. Amann, C. Egile, S. Nickell, D. Nicastro, R. Li, T. D. Pollard, N. Volkmann, and D. Hanein
The structural basis of actin filament branching by the Arp2/3 complex
J. Cell Biol., March 5, 2008; 180(5): 887 - 895.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
J.-W. Chu and G. A. Voth
Coarse-Grained Modeling of the Actin Filament Derived from Atomistic-Scale Simulations
Biophys. J., March 1, 2006; 90(5): 1572 - 1582.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
M. McKane, K.-K. Wen, I. R. Boldogh, S. Ramcharan, L. A. Pon, and P. A. Rubenstein
A Mammalian Actin Substitution in Yeast Actin (H372R) Causes a Suppressible Mitochondria/Vacuole Phenotype
J. Biol. Chem., October 28, 2005; 280(43): 36494 - 36501.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
J. S. Allingham, A. Zampella, M. V. D'Auria, and I. Rayment
Structures of microfilament destabilizing toxins bound to actin provide insight into toxin design and activity
PNAS, October 11, 2005; 102(41): 14527 - 14532.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
T. Oda, K. Namba, and Y. Maeda
Position and Orientation of Phalloidin in F-Actin Determined by X-Ray Fiber Diffraction Analysis
Biophys. J., April 1, 2005; 88(4): 2727 - 2736.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
B. Wawro, S. Y. Khaitlina, A. Galinska-Rakoczy, and H. Strzelecka-Golaszewska
Role of Actin DNase-I-Binding Loop in Myosin Subfragment 1-Induced Polymerization of G-actin: Implications for the Mechanism of Polymerization
Biophys. J., April 1, 2005; 88(4): 2883 - 2896.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
J. Moraczewska, J. Gruszczynska-Biegala, M. J. Redowicz, S. Yu. Khaitlina, and H. Strzelecka-Golaszewska
The DNase-I Binding Loop of Actin May Play a Role in the Regulation of Actin-Myosin Interaction by Tropomyosin/Troponin
J. Biol. Chem., July 23, 2004; 279(30): 31197 - 31204.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
M. Delarue and P. Dumas
On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models
PNAS, May 4, 2004; 101(18): 6957 - 6962.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
Yu. S. Borovikov, I. V. Dedova, C. G. dos Remedios, N. N. Vikhoreva, P. G. Vikhorev, S. V. Avrova, T. L. Hazlett, and B. W. Van Der Meer
Fluorescence Depolarization of Actin Filaments in Reconstructed Myofibers: The Effect of S1 or pPDM-S1 on Movements of Distinct Areas of Actin
Biophys. J., May 1, 2004; 86(5): 3020 - 3029.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
Y. Wu and J. Ma
Refinement of F-Actin Model against Fiber Diffraction Data by Long-Range Normal Modes
Biophys. J., January 1, 2004; 86(1): 116 - 124.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
D. Ming, Y. Kong, Y. Wu, and J. Ma
Substructure synthesis method for simulating large molecular complexes
PNAS, January 7, 2003; 100(1): 104 - 109.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
R. Musib, G. Wang, L. Geng, and P. A. Rubenstein
Effect of Polymerization on the Subdomain 3/4 Loop of Yeast Actin
J. Biol. Chem., June 14, 2002; 277(25): 22699 - 22709.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
M. R. Bubb, L. Govindasamy, E. G. Yarmola, S. M. Vorobiev, S. C. Almo, T. Somasundaram, M. S. Chapman, M. Agbandje-McKenna, and R. McKenna
Polylysine Induces an Antiparallel Actin Dimer That Nucleates Filament Assembly. CRYSTAL STRUCTURE AT 3.5-A RESOLUTION
J. Biol. Chem., May 31, 2002; 277(23): 20999 - 21006.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
R. Mendelson and E. P. Morris
The structure of the acto-myosin subfragment 1 complex: Results of searches using data from electron microscopy and x-ray crystallography
PNAS, August 5, 1997; 94(16): 8533 - 8538.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
L. Feng, E. Kim, W.-L. Lee, C. J. Miller, B. Kuang, E. Reisler, and P. A. Rubenstein
Fluorescence Probing of Yeast Actin Subdomain 3/4 Hydrophobic Loop 262-274. ACTIN-ACTIN AND ACTIN-MYOSIN INTERACTIONS IN ACTIN FILAMENTS
J. Biol. Chem., July 4, 1997; 272(27): 16829 - 16837.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
B. Kuang and P. A. Rubenstein
The Effects of Severely Decreased Hydrophobicity in a Subdomain 3/4 Loop on the Dynamics and Stability of Yeast G-actin
J. Biol. Chem., February 14, 1997; 272(7): 4412 - 4418.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
B. Kuang and P. A. Rubenstein
Beryllium Fluoride and Phalloidin Restore Polymerizability of a Mutant Yeast Actin (V266G,L267G) with Severely Decreased Hydrophobicity in a Subdomain 3/4 Loop
J. Biol. Chem., January 10, 1997; 272(2): 1237 - 1247.
[Abstract] [Full Text] [PDF]

Home page
 International Journal of High Performance Computing ApplicationsHome page
M. T. Nelson, W. Humphrey, A. Gursoy, A. Dalke, L. V. Kale, R. D. Skeel, and K. Schulten
NAMD: a Parallel, Object-Oriented Molecular Dynamics Program
International Journal of High Performance Computing Applications, December 1, 1996; 10(4): 251 - 268.
[Abstract] [PDF]

Home page
 J. Biol. Chem.Home page
J. H. Gerson, E. Kim, A. Muhlrad, and E. Reisler
Tropomyosin-Troponin Regulation of Actin Does Not Involve Subdomain 2 Motions
J. Biol. Chem., May 18, 2001; 276(21): 18442 - 18449.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
G. M. Hynes and K. R. Willison
Individual Subunits of the Eukaryotic Cytosolic Chaperonin Mediate Interactions with Binding Sites Located on Subdomains of beta -Actin
J. Biol. Chem., June 16, 2000; 275(25): 18985 - 18994.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
Copyright © 1995 by the Biophysical Society.