Protein Engineering, Vol. 14, No. 1, 1-6,
January 2001
© 2001 Oxford University Press
Conformational change of proteins arising from normal mode calculations
Laboratoire de Physique Quantique, UMR 5626 of CNRS, IRSAMC, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse Cedex, France
A normal mode analysis of 20 proteins in `open' or `closed' forms was performed using simple potential and protein models. The quality of the results was found to depend upon the form of the protein studied, normal modes obtained with the open form of a given protein comparing better with the conformational change than those obtained with the closed form. Moreover, when the motion of the protein is a highly collective one, then, in all cases considered, there is a single low-frequency normal mode whose direction compares well with the conformational change. When it is not, in most cases there is still a single low-frequency normal mode giving a good description of the pattern of the atomic displacements, as they are observed experimentally during the conformational change. Hence a lot of information on the nature of the conformational change of a protein is often found in a single low-frequency normal mode of its open form. Since this information can be obtained through the normal mode analysis of a model as simple as that used in the present study, it is likely that the property captured by such an analysis is for the most part a property of the shape of the protein itself. One of the points that has to be clarified now is whether or not amino acid sequences have been selected in order to allow proteins to follow a single normal mode direction, as least at the very beginning of their conformational change.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  K. M. E. Weimer, B. L. Shane, M. Brunetto, S. Bhattacharyya, and S. Hati Evolutionary Basis for the Coupled-domain Motions in Thermus thermophilus Leucyl-tRNA Synthetase J. Biol. Chem., April 10, 2009; 284(15): 10088 - 10099. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Madden, P. Bohnenkamp, K. Kazerounian, and H. T. Ilies Residue Level Three-dimensional Workspace Maps for Conformational Trajectory Planning of Proteins The International Journal of Robotics Research, April 1, 2009; 28(4): 450 - 463. [Abstract] [PDF]
|
|
|
|
 |
|
 S. S. Ericksen, D. F. Cummings, H. Weinstein, and J. A. Schetz Ligand Selectivity of D2 Dopamine Receptors Is Modulated by Changes in Local Dynamics Produced by Sodium Binding J. Pharmacol. Exp. Ther., January 1, 2009; 328(1): 40 - 54. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. E. Dobbins, V. I. Lesk, and M. J. E. Sternberg Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking PNAS, July 29, 2008; 105(30): 10390 - 10395. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. C. Whitford, S. Gosavi, and J. N. Onuchic Conformational Transitions in Adenylate Kinase: ALLOSTERIC COMMUNICATION REDUCES MISLIGATION J. Biol. Chem., January 25, 2008; 283(4): 2042 - 2048. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X. Liu and H. A. Karimi High-throughput modeling and analysis of protein structural dynamics Brief Bioinform, November 1, 2007; 8(6): 432 - 445. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Franklin, P. Koehl, S. Doniach, and M. Delarue MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape Nucleic Acids Res., July 13, 2007; 35(suppl_2): W477 - W482. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Eyal, C. Chennubhotla, L.-W. Yang, and I. Bahar Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models Bioinformatics, July 1, 2007; 23(13): i175 - i184. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Togashi and A. S. Mikhailov Nonlinear relaxation dynamics in elastic networks and design principles of molecular machines PNAS, May 22, 2007; 104(21): 8697 - 8702. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. I. Garzon, J. Kovacs, R. Abagyan, and P. Chacon DFprot: a webtool for predicting local chain deformability Bioinformatics, April 1, 2007; 23(7): 901 - 902. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Taly, P.-J. Corringer, T. Grutter, L. P. de Carvalho, M. Karplus, and J.-P. Changeux Implications of the quaternary twist allosteric model for the physiology and pathology of nicotinic acetylcholine receptors PNAS, November 7, 2006; 103(45): 16965 - 16970. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. B. Sherman, R. H. Guenther, F. Tama, T. L. Sit, C. L. Brooks, A. M. Mikhailov, E. V. Orlova, T. S. Baker, and S. A. Lommel Removal of Divalent Cations Induces Structural Transitions in Red Clover Necrotic Mosaic Virus, Revealing a Potential Mechanism for RNA Release J. Virol., November 1, 2006; 80(21): 10395 - 10406. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K.-i. Okazaki, N. Koga, S. Takada, J. N. Onuchic, and P. G. Wolynes Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations PNAS, August 8, 2006; 103(32): 11844 - 11849. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Lindahl, C. Azuara, P. Koehl, and M. Delarue NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W52 - W56. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. Zheng, B. R. Brooks, and D. Thirumalai Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations PNAS, May 16, 2006; 103(20): 7664 - 7669. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Sari and I. Andricioaei Rotation of DNA around intact strand in human topoisomerase I implies distinct mechanisms for positive and negative supercoil relaxation Nucleic Acids Res., November 27, 2005; 33(20): 6621 - 6634. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Luo and T. C. Bruice Low-frequency normal mode in DNA HhaI methyltransferase and motions of residues involved in the base flipping PNAS, November 8, 2005; 102(45): 16194 - 16198. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Lindahl and M. Delarue Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization Nucleic Acids Res., August 8, 2005; 33(14): 4496 - 4506. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L.-W. Yang, X. Liu, C. J. Jursa, M. Holliman, A.J. Rader, H. A. Karimi, and I. Bahar iGNM: a database of protein functional motions based on Gaussian Network Model Bioinformatics, July 1, 2005; 21(13): 2978 - 2987. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Hammel, H.-P. Fierobe, M. Czjzek, S. Finet, and V. Receveur-Brechot Structural Insights into the Mechanism of Formation of Cellulosomes Probed by Small Angle X-ray Scattering J. Biol. Chem., December 31, 2004; 279(53): 55985 - 55994. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Suhre and Y.-H. Sanejouand ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement Nucleic Acids Res., July 1, 2004; 32(suppl_2): W610 - W614. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
|
|
W. Zheng and S. Doniach A comparative study of motor-protein motions by using a simple elastic-network model PNAS, November 11, 2003; 100(23): 13253 - 13258. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. Miyashita, J. N. Onuchic, and P. G. Wolynes Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins PNAS, October 28, 2003; 100(22): 12570 - 12575. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Tama, M. Valle, J. Frank, and C. L. Brooks III Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy PNAS, August 5, 2003; 100(16): 9319 - 9323. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Ming, Y. Kong, M. A. Lambert, Z. Huang, and J. Ma How to describe protein motion without amino acid sequence and atomic coordinates PNAS, June 25, 2002; 99(13): 8620 - 8625. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Ming, Y. Kong, S. J. Wakil, J. Brink, and J. Ma Domain movements in human fatty acid synthase by quantized elastic deformational model PNAS, June 11, 2002; 99(12): 7895 - 7899. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Halle Flexibility and packing in proteins PNAS, January 24, 2002; (2002) 32522499. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Halle Flexibility and packing in proteins PNAS, February 5, 2002; 99(3): 1274 - 1279. [Abstract] [Full Text] [PDF]
|
|