Comparison of generalised born/surface area with periodic boundary simulations to study protein unfolding

Molecular Simulation

Volumn 30, Issue 5, 2004, Pages 333-340

  Purkiss, A G ^a   Macdonald, J T ^a   Goodfellow, J M ^a   Slingsby, C ^a  

^a UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

Barnase; Generalised born surface area; Protein molecular dynamics simulation; Protein unfolding

Indexed keywords

DISEASES; FREE ENERGY; KINETIC ENERGY; MOLECULAR DYNAMICS; SOLVENTS; THERMODYNAMICS;

BARNASE; GENERALIZED BORN/SURFACE AREA; PROTEIN MOLECULAR DYNAMICS SIMULATION; PROTEIN UNFOLDING;

PROTEINS;

EID: 11144250815     PISSN: 08927022     EISSN: None     Source Type: Journal    
DOI: 10.1080/08927020410001667566     Document Type: Article

References (41)

1. Booth, D.R., Sunde, M., Bellotti, V., Robinson, C.V., Hutchinson, W.L., Fraser, P.E., Hawkins, P.N., Dobson, C.M., Radford, S.E., Blake, C.C. and Pepys, M.B. (1997) "Instability, unfolding and aggregation of human lysozyme variants underlying amyloid fibrillogenesis", Nature 385, 787.
2. Dobson, C.M. (2003) "Protein folding and disease: a view from the first Horizon Symposium", Nat. Rev. Drug Discov. 2, 154.
3. Dumoulin, M., Last, A.M., Desmyter, A., Decanniere, K., Canet, D., Larsson, G., Spencer, A., Archer, D.B., Sasse, J., Muyldermans, S., Wyns, L., Redfield, C., Matagne, A., Robinson, C.V. and Dobson, C.M. (2003) "A camelid antibody fragment inhibits the formation of amyloid fibrils by human lysozyme", Nature 424, 783.
4. Hammarstrom, P., Wiseman, R.L., Powers, E.T. and Kelly, J.W. (2003) "Prevention of transthyretin amyloid disease by changing protein misfolding energetics", Science 299, 713.
5. Dobson, C. (2002) "Protein misfolding and human disease", Sci. World J. 2, 132.
6. Neira, J.L. and Fersht, A.R. (1999) "Exploring the folding funnel of a polypeptide chain by biophysical studies on protein fragments", J. Mol, Biol. 285, 1309.
7. Neira, J.L., Itzhaki, L.S., Ladurner, A.G., Davis, B., de Prat Gay, G. and Fersht, A.R. (1997) "Following co-operative formation of secondary and tertiary structure in a single protein module", J. Mol, Biol, 268, 185.
8. Fersht, A.R. and Daggett, V. (2002) "Protein folding and unfolding at atomic resolution", Cell 108, 573.
9. Torshin, I.Y. and Harrison, R.W. (2003) "Protein folding: search for basic physical models", Sci. World J. 3, 623.
10. Ivankov, D.N., Garbuzynskiy, S.O., Alm, E., Plaxco, K.W., Baker, D. and Finkelstein, A.V. (2003) "Contact order revisited: influence of protein size on the folding rate", Protein Sci. 12, 2057.
11. Makarov, D.E. and Plaxco, K.W. (2003) "The topomer search model: a simple, quantitative theory of two-state protein folding kinetics", Protein Sci. 12, 17.
12. Chen, Y.R. and Clark, A.C. (2003) "Equilibrium and kinetic folding of an alpha-helical Greek key protein domain: caspase recruitment domain (CARD) of RICK", Biochemistry 42, 6310.
13. Chiti, F., Stefani, M., Taddei, N., Ramponi, G. and Dobson, C.M. (2003) "Rationalization of the effects of mutations on peptide and protein aggregation rates", Nature 424, 805.
14. Klein-Seetharaman, J., Oikawa, M., Grimshaw, S.B., Wirmer, J., Duchardt, E., Ueda, T., Imoto, T., Smith, L.J., Dobson, C.M. and Schwalbe, H. (2002) "Long-range interactions within a normative protein", Science 295, 1719.
15. Jaenicke, R. and Slingsby, C. (2001) "Lens crystallins and their microbial homologs: structure, stability, and function", Crit. Rev. Biochem. Mol. Biol. 36, 435.
16. Benedek, G.B. (1997) "Cataract as a protein condensation disease: the Proctor Lecture", Investig. Ophthalmol. Vis. Sci. 38, 1911.
17. Doyle, S.M., Anderson, E., Zhu, D., Braswell, E.H. and Teschke, C.M. (2003) "Rapid unfolding of a domain populates an aggregation-prone intermediate that can be recognized by GroEL", J. Mol. Biol. 332, 937.
18. Doruker, P., Atilgan, A.R. and Bahar, I. (2000) "Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to alpha-amylase inhibitor", Proteins 40, 512.
19. Zhou, R. (2003) "Free energy landscape of protein folding in water: explicit vs. implicit solvent", Proteins 53, 148.
20. Ferrara, P., Apostolakis, J. and Caflisch, A. (2002) "Evaluation of a fast implicit solvent model for molecular dynamics simulations", Proteins 46, 24.
21. Paci, E., Smith, L.J., Dobson, C.M. and Karplus, M. (2001) "Exploration of partially unfolded states of human alpha-lactalbumin by molecular dynamics simulation", J. Mol. Biol. 306, 329.
22. Li, A. and Daggett, V. (1998) "Molecular dynamics simulation of the unfolding of barnase: characterization of the major intermediate", J. Mol. Biol. 275, 677.
23. Takei, J., Chu, R.A. and Bai, Y. (2000) "Absence of stable intermediates on the folding pathway of barnase", Proc. Natl Acad. Sci. USA 97, 10796.
24. Fersht, A.R. (2000) "A kinetically significant intermediate in the folding of barnase", Proc. Natl Acad. Sci. USA 97, 14121.
25. Arcus, V.L., Vuilleumier, S., Freund, S.M., Bycroft, M. and Fersht, A.R. (1995) "A comparison of the pH, urea, and temperature-denatured states of barnase by heteronuclear NMR: implications for the initiation of protein folding", J. Mol. Biol. 254, 305.
26. Dalby, P.A., Clarke, J., Johnson, CM. and Fersht, A.R. (1998) "Folding intermediates of wild-type and mutants of barnase. II. Correlation of changes in equilibrium amide exchange kinetics with the population of the folding intermediate", J. Mol Biol. 276, 647.
27. Killick, T.R., Freund, S.M. and Fersht, A.R. (1998) "Real-time NMR studies on folding of mutants of barnase and chymotrypsin inhibitor 2", FEBS Lett. 423, 110.
28. Fersht, A.R., Matouschek, A. and Serrano, L. (1992) "The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding", J. Mol. Biol 224, 771.
29. Matouschek, A., Serrano, L. and Fersht, A.R. (1992) "The folding of an enzyme. IV. Structure of an intermediate in the refolding of barnase analysed by a protein engineering procedure", J. Mol Biol 224, 819.
30. Bond, C.J., Wong, K.B., Clarke, J., Fersht, A.R. and Daggett, V. (1997) "Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: description of the folding pathway", Proc. Natl Acad. Sci. USA 94, 13409.
31. Wang, T. and Wade, R.C. (2003) "Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation", Proteins 50, 158.
32. Perlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.S., Cheatham, III, T.E., DeBolt, S., Ferguson, D., Seibel, G. and Kollman, P.A. (1995) "AMBER, a package of computer programs for applying molecular mechancis, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules", Comp. Phys. Commun. 91, 1.
33. Case, D.A., Pearlman, D.A., Caldwell, J.W., Cheatham, T.E., III, Wang, J., Ross, W.S., Simmerling, C.L., Darden, T.A., Merz, K.M., Stanton, R.V., Cheng, A.L., Vincent, J.J., Crowley, M., Tsui, V., Gohlke, H., Radmer, R.J., Duan, Y., Pitera, J., Massova, L., Seibel, G.L., Singh, U.C., Weiner, P.K. and Kollman, P.A. (2002) "AMBER 7", [www.scripps.edu].
34. Tsui, V. and Case, D.A. (2000) "Theory and applications of the generalized Born solvation model in macromolecular simulations", Biopolymers 56, 275.
35. Bashford, D. and Case, D.A. (2000) "Generalized born models of macromolecular solvation effects", Annu. Rev. Phys. Chem. 51, 129.
36. Moraitakis, G., Purkiss, A.G. and Goodfellow, J.M. (2003) "Simulated dynamics and biological macromolecules", Rep. Prog. Phys. 66, 383.
37. Frishman, D. and Argos, P. (1995) "Knowledge-based protein secondary structure assignment", Proteins 23, 566.
38. Hubbard, S.J. and Thornton, J.M. (1993) "NACCESS" [www.http://wolf.bms.umist.ac.uk/naccess/].
39. Purkiss, A.G. (2003) "CONTAX" [www http://people.cryst.bbk.ac. uk/(bpurk01/contax/index.html].
40. Koradi, R., Billeter, M. and Wuthrich, K. (1996) "MOLMOL: a program for display and analysis of macromolecular structures", J. Mol. Graph. 14, 51.
41. Purkiss, A., Slingsby, C. and Goodfellow, J.M. (2000) "Simulation of the highly stable protein: bovine gammaB-crystallin at room and high temperature", Protein Pept. Lett. 7, 211.