help button home button Biophys. J.
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH
Biophys. J. BioFAST: First Published June 10, 2005. doi:10.1529/biophysj.104.058495
© 2005 by the Biophysical Society.

A more recent version of this article appeared on September 1, 2005.
This Article
Right arrow Full Text (Rapid PDF)
Right arrow supplemental
Right arrow All Versions of this Article:
biophysj.104.058495v1
89/3/1455    most recent
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 Author home page(s):
Joanna Trylska
J. Andrew McCammon
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 Trylska, J.
Right arrow Articles by McCammon, J. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Trylska, J.
Right arrow Articles by McCammon, J. A.

BIOPHYSICAL THEORY AND MODELING

Exploring Global Motions and Correlations in the Ribosome

Joanna Trylska 1*, Valentina Tozzini 2 and J. Andrew McCammon 3

1 University of California at San Diego
2 NEST-INFM-Scuola Normale Superiore
3 University of California - San Diego

* To whom correspondence should be addressed. E-mail: jtrylska{at}mccammon.ucsd.edu.

Submitted on December 22, 2004
Revised on February 28, 2005
Accepted on 20 May 2005


  Abstract
We studied slower global coupled motions of the ribosome with half a microsecond of coarse-grained molecular dynamics. A low resolution anharmonic network model that allows for the evolution of tertiary structure and long-scale sampling, was developed and parameterized. Most importantly, we find that functionally important movements of L7/L12 and L1 lateral stalks are anti-correlated. Other principal directions of motions include widening of the tRNA cleft and the rotation of the small subunit which occurs as one block and is in phase with the movement of L1 stalk. The effect of the dynamical correlation pattern on the elongation process is discussed. Small fluctuations of the 3' tRNA termini and anti-codon nucleotides show tight alignement of substrates for the reaction. Our model provides an efficient and reliable way to study the dynamics of large biomolecular systems composed of both proteins and nucleic acids.

Key Words: coarse-grained models, correlation matrix, functional motions, molecular dynamics, principal component analysis, ribosome




This article has been cited by other articles:


Home page
 Biophys. JHome page
J. I. Sulkowska and M. Cieplak
Selection of Optimal Variants of Go-Like Models of Proteins through Studies of Stretching
Biophys. J., October 1, 2008; 95(7): 3174 - 3191.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
K. Moritsugu and J. C. Smith
REACH Coarse-Grained Biomolecular Simulation: Transferability between Different Protein Structural Classes
Biophys. J., August 15, 2008; 95(4): 1639 - 1648.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H. David-Eden and Y. Mandel-Gutfreund
Revealing unique properties of the ribosome using a network based analysis
Nucleic Acids Res., August 1, 2008; 36(14): 4641 - 4652.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
D. Pan, C.-M. Zhang, S. Kirillov, Y.-M. Hou, and B. S. Cooperman
Perturbation of the tRNA Tertiary Core Differentially Affects Specific Steps of the Elongation Cycle
J. Biol. Chem., June 27, 2008; 283(26): 18431 - 18440.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
A. A. Gorfe, C.-e. A. Chang, I. Ivanov, and J. A. McCammon
Dynamics of the Acetylcholinesterase Tetramer
Biophys. J., February 15, 2008; 94(4): 1144 - 1154.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
K. Moritsugu and J. C. Smith
Coarse-Grained Biomolecular Simulation with REACH: Realistic Extension Algorithm via Covariance Hessian
Biophys. J., November 15, 2007; 93(10): 3460 - 3469.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
A. Arkhipov, P. L. Freddolino, K. Imada, K. Namba, and K. Schulten
Coarse-Grained Molecular Dynamics Simulations of a Rotating Bacterial Flagellum
Biophys. J., December 15, 2006; 91(12): 4589 - 4597.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
C.-E. Chang, T. Shen, J. Trylska, V. Tozzini, and J. A. McCammon
Gated Binding of Ligands to HIV-1 Protease: Brownian Dynamics Simulations in a Coarse-Grained Model
Biophys. J., June 1, 2006; 90(11): 3880 - 3885.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH
Copyright © 2005 by the Biophysical Society.