Comparison of experimental and computed protein anisotropic temperature factors

Proceedings - 2007 IEEE International Conference on Bioinformaticsand Biomedicine Workshops, BIBMW

Volumn , Issue , 2007, Pages 89-96

  Yang, Lei ^a   Song, Guang ^b   Jernigan, Robert L ^a  

^a IOWA STATE UNIVERSITY   (United States)

^b Iowa State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANISOTROPY; BIOCOMMUNICATIONS; BIOINFORMATICS; BIOMOLECULES; COMPUTER NETWORKS; DYNAMICS; INFORMATION SCIENCE; METROPOLITAN AREA NETWORKS; MOLECULES; NETWORK PROTOCOLS; PROTEINS;

ANISOTROPIC TEMPERATURE; ANISOTROPIC TEMPERATURE FACTORS; APPLIED (CO); CONFORMATIONAL CHANGES; GENERAL (CO); IMPROVED MODELS; INTERNAL DYNAMICS; INTERNATIONAL CONFERENCES; MOLECULAR MECHANISMS (MM); MOLECULAR MOTIONS; NETWORK MODELLING; PROTEIN DATA BANK (PDB); PROTEIN MOTIONS; VALIDATION DATA;

MATHEMATICAL MODELS;

EID: 44949260941     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBMW.2007.4425405     Document Type: Conference Paper

References (20)

1. A. R. Atilgan, S. R. Durell, R. L. Jernigan, M. C. Demirel, O. Keskin, and I. Bahar. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys. J., 80:505-515, 2001.
2. I. Bahar, A. R. Atilgan, and B. Erman. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des., 2:173-181, 1997.
3. H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. B. H. Weissig, I. N. Shindyalov, and P. E. Bourne. The protein data bank. Nucleic Acids Res., 28:235-242, 2000.
4. R. Diamond. On the use of normal modes in thermal parameter refinement: theory and applicationto the bovine pancreatic trypsin inhibitor. Acta Cryst. A, 46:625-635, 1990.
5. D. Frenkel and B. Smit. Understanding molecular simulation. Academic Press, 2001.
6. T. Haliloglu, I. Bahar, and B. Erman. Gaussian dynamics of folded proteins. Phys. Rev. Lett., 79:3090-3093, 1997.
7. K. Hinsen. Analysis of domain motions by approximate normal mode calculations. Proteins, 33:417-429, 1998.
8. O. Keskin, I. Bahar, D. Flatow, D. G. Covell, and R. L. Jernigan. Molecular mechanisms of chaperonin GroEL-GroES function. Biochemistry, 41:491-501, 2002.
9. M. K. Kim, R. L. Jernigan, and G. S. Chirikjian. Rigid-cluster models of conformational transitions in macro-molecular machines and assemblies. Biophys. J., 89:43-55, 2005.
10. S. Kundu, J. S. Melton, D. C. Sorensen, and G. N. Phillips Jr. Dynamics of proteins in crystals: comparison of experiment with simple models. Biophys. J., 83:723-732, 2002.
11. J. A. McCammon and S. C. Harvey. Dynamics of proteins and nucleic acids. Cambridge University Press, 1987.
12. E. A. Merritt. Expanding the model: anisotropic displacement parameters in protein structure refinement. Acta Cryst. D, 55:1109-1117, 1999.
13. T. Z. Sen, Y. Feng, J. V. Garcia, A. Kloczkowski, and R. L. Jernigan. The extent of cooperativity of protein motions observed with elastic network models is similar for atomic and coarser-grained models. J. Chem. Theo. Comp., 2:696-704, 2006.
14. G. Song and R. L. Jernigan. vGNM: a better model for understanding the dynamics of proteins in crystals. J. Mol. Biol, 2007. To appear.
15. B. Stec, R. Zhou, and M. M. Teeter. Full-matrix refinement of the protein crambin at 0.83 Å and 130 K. Acta Cryst. D, 51:663-681, 1995.
16. F. Tama, F. X. Gadea, O. Marques, and Y. H. Sane-jouand. Building-block approach for determining low-frequency normal modes of macromolecules. Proteins, 41:1-7,2000.
17. M. M. Tirion. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett., 77:1905-1908, 1996.
18. Y. Wang, A. J. Rader, I. Bahar, and R. L. Jernigan. Global ribosome motions revealed with elastic network model. J. Struct. Biol., 147:302-314, 2004.
19. C. Xu, D. Tobi, and I. Bahar. Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T↔R2 transition. J. Mol. Biol, 333:153-168, 2003.
20. W. Zheng and S. Doniach. A comparative study of motor-protein motions by using a simple elastic network model. Proc. Natl. Acad. Set, 100:13253-13258, 2003.