Flexibility in biomolecules

Current Topics in Physics: In Honor of Sir Roger J. Elliott

Volumn , Issue , 2005, Pages 97-112

  Thorpe, M F ^a   Chubynsky, Mykyta ^a   Hespenheide, Brandon ^a   Menor, Scott ^a   Jacobs, Donald J ^b   Kuhn, Leslie A ^c   Zavodszky, Maria I ^c   Lei, Ming ^d   Rader, A J ^e   Whiteley, Walter ^f  

^a ARIZONA STATE UNIVERSITY   (United States)

^b CALIFORNIA STATE UNIVERSITY   (United States)

^c Michigan State University   (United States)

^d BRANDEIS UNIVERSITY   (United States)

^e UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

^f YORK UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATION THEORY;

BARNASE; COMPUTATIONAL WORK; HIV-PROTEASE; MONTE CARLO DYNAMICS; REGION DECOMPOSITION; RIGID CORE;

BIOMOLECULES;

EID: 84967361898     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1142/9781860947209_0006     Document Type: Chapter

References (40)

1. Jacobs, D.J., Rader, A.J., Kuhn, L.A. and Thorpe, M.F., Protein flexibility predictions using graph theory, Proteins 44 (2001) 150-165.
2. Laman, G., On graphs and rigidity of plane skeletal structures, J. Eng. Mathematics 4 (1970) 331-340.
3. Graver, J., Servatius, B. and Servatius, H., Graduate Studies in Mathematics, Am. Math. Soc. (1993).
4. Maxwell, J.C., On reciprocal figures and diagrams of forces, Phil. Mag. 27 (1864) 250-261.
5. Hendrickson, B., Siam J. Comput. 21 (1992) 65.
6. Jacobs, D.J. and Thorpe, M.F., Generic rigidity percolation in two dimensions, Phys. Rev. E. 53 (1996) 3682-3693.
7. Whiteley, W., The union of matroids and the rigidity of frameworks, SIAM J. Disc. Math. 1 (1988) 237-255.
8. Jacobs, D.J., Rader, A.J., Kuhn, L.A. and Thorpe, M.F., Protein flexibility predictions using graph theory, Proteins 44 (2001) 150-165.
9. Laman, G., On graphs and rigidity of plane skeletal structures, J. Eng. Mathematics 4 (1970) 331-340.
10. Graver, J., Servatius, B. and Servatius, H., Graduate Studies in Mathematics, Am. Math. Soc. (1993).
11. Maxwell, J.C., On reciprocal figures and diagrams of forces, Phil. Mag. 27 (1864) 250-261.
12. Hendrickson, B., Siam J. Comput. 21 (1992) 65.
13. Jacobs, D.J. and Thorpe, M.F., Generic rigidity percolation in two dimensions, Phys. Rev. E. 53 (1996) 3682-3693.
14. Whiteley, W., The union of matroids and the rigidity of frameworks, SIAM J. Disc. Math. 1 (1988) 237-255.
15. Whiteley, W., The union of matroids and the rigidity of frameworks, Flexibility in Biomolecules 111
16. Tay, T.-S. and Whiteley, W., Recent progress in the rigidity of frameworks, Struct. Topology 9 (1984) 31-38.
17. White, N. and Whiteley, W., The algebraic geometry of motions of bar and body frameworks, SIAM J. Alg. Disc. Math. 8 (1987) 1-32.
18. Crapo, H. and Whiteley, W., Statics of frameworks and motions of panel structures: A projective geometric introduction, Struct. Topology 6 (1982) 43-82.
19. Thorpe, M.F., Protein folding, HIV and drug design, Physics and Technology Forefronts, APS News (February, 2003).
20. Whiteley, W., Infinitesimal motions of a bipartite framework, Pac. J. Math. 110 (1984) 233-255.
21. Jacobs, D.J., Generic rigidity in three-dimensional bond-bending networks, J. Phys. A 31 (1998) 6653-6668.
22. Whiteley,W., Rigidity of molecular structures: Generic and geometric analysis, in Rigidity Theory and Applications, eds. Thorpe,M.F. andDuxbury,P.M. (Academic/Kluwer, 1999), pp. 21-46.
23. Jacobs, D.J., Kuhn, L.A. and Thorpe, M.F., Flexible and rigid regions in proteins, in Rigidity Theory and Applications, eds. Thorpe, M.F. and Duxbury, P.M. (Academic/Kluwer, 1999), pp. 357-384.
24. Thorpe, M.F., Hespenheide, B.M., Yang, Y. and Kuhn, L.A., Flexibility and critical hydrogen bonds in cytochrome c, in Pac. Symp. Biocomput. (2000) 191-202.
25. Thorpe, M.F., Lei, M., Rader, A.J., Jacobs, D.J. and Kuhn, L.A., Protein flexibility and dynamics using constraint theory, J. Mol. Graph. Model. 19 (2001) 60-69.
26. Hespenheide, B.M., Rader, A.J., Thorpe, M.F. and Kuhn, L.A., Identifying protein folding cores from the evolution of flexible regions during unfolding, J. Mol. Graph. Model. 21 (2002) 195-207.
27. Rader, A.J. and Bahar, I., Folding core predictions from network models of proteins, Polymer (2004) 655-668.
28. Li, R. and Woodward, C., The hydrogen exchange core and protein folding, Protein Sci. 8 (1999) 1571-1590.
29. Soss, M. and Toussaint, G.T., Geometric and computational aspects of polymer reconfiguration, J. Math. Chem. 27 (2000) 303-318.
30. Thorpe, M.F., Jacobs, D.J., Chubynsky, M.V. and Rader, A.J., Generic rigidity of network glasses, in Rigidity Theory andApplications, eds.Thorpe,M.F. and Duxbury, P.M. (Kluwer Academic, 1999), pp. 239-277.
31. Jacobs, D.J. and Thorpe, M.F., Generic rigidity percolation: The pebble game, Phys. Rev. Lett. 75 (1995) 4051-4054.
32. Dill, K.A., Dominant forces in protein folding, Biochemistry 29 (1990) 7133-7155.
33. Vriend, G. WHAT IF: A molecular modeling and drug design program, J. Mol. Graph. 8 (1990) 29, 52-56.
34. Williams, M.A., Goodfellow, J.M. and Thornton, J.M., Buried waters and internal cavities in monomeric proteins, Protein Sci. 3 (1994) 1224-1235.
35. Rader, A.J., Hespenheide, B.M., Kuhn, L.A. and Thorpe, M.F., Protein unfolding: Rigidity lost, in Proc. Natl. Acad. Sci. USA 99 (2002) 3540-3545.
36. Lei M., Kuhn, L.A., Zavodszky, M.I. and Thorpe, M.F., Sampling protein conformations and pathways, J. Comput. Chem. 25 (2004) 1133-1148.
37. Zavodszky, M.I., Lei Ming, Thorpe, M.F., Day, A.R. and Kuhn, L.A., Modeling correlated main-chain motions in proteins for flexible molecular recognition, accepted by Proteins: Structure, Function and Genetics (2004).
38. Menor, S. and Thorpe, M.F., unpublished (2004).
39. Bycroft M., Ludvigsen S., Fersht, A.R. and Poulsen, F.M., Determination of the three-dimensional solution structure of barnase using nuclear magnetic resonance spectroscopy, Biochem. 30 (1991) 8697.
40. Mauguen, Y., Hartley, R.W., Dodson, E.J., Dodson, G.G., Bricogne, G., Chothia, C. and Jack, A., Molecular structure of a new family of ribonucleases, Nature 297 (1982) 162.