Computational analysis of thermal stability: Effect of lle→Val mutations in human lysozyme

Folding and Design

Volumn 3, Issue 3, 1998, Pages 173-181

  Sugita, Yuji ^a   Kitao, Akio ^a   Go, Nobuhiro ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

Denatured state structure; Free energy calculation; Human lysozyme; Hydrophobia interaction; Thermal stability

Indexed keywords

ISOLEUCINE; LYSOZYME; VALINE;

ARTICLE; ENZYME CONFORMATION; ENZYME DENATURATION; ENZYME STABILITY; ENZYME STRUCTURE; GENE MUTATION; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; SIMULATION; THERMODYNAMICS;

EID: 0031778441     PISSN: 13590278     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1359-0278(98)00025-X     Document Type: Article

References (41)

1. Kauzmann, W. (1959). Some factors in the interpretation of protein denaturation. Adv. Protein Chem. 14, 1-63.
2. Mathews, B.W. (1993). Structural and genetic analysis of protein stability. Annu. Rev. Biochem. 62, 139-160.
3. Serrano, L, Kellis, J.T., Jr, Cann, P., Matouschek, A. & Fersht. A.R. (1992). The folding of an enzyme II. Substructure of barnase and the contribution of different interactions to protein stability. J. Mol. Biol. 224, 783-804.
4. Eriksson, A.E., et al., & Matthew, B.W. (1992). Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. Science 255, 178-183.
5. Buckle, A.M., Henrick, K., Fersht, A.R. (1993). Crystal structural analysis of mutations in the hydrophobic cores of barnase. J. Mol. Biol. 234, 847-860.
6. Takano, K., et al., & Yutani, K. (1995). Contribution of hydrophobic residues to the stability of human lysozyme: calorimetric studies and X-ray structural analysis of the five isoleucine to valine mutants. J. Mol. Biol. 254, 62-76.
7. Dill, K.A. & Shortle, D. (1991 ). Denatured states of proteins. Annu. Rev. Biochem. 60, 795-825.
8. Evans, P.A., Topping, K.D., Woolfson, D.N. & Dobson, C.M. (1991). Hydrophobic clustering in nonnative states of a protein: interpretation of chemical shifts in NMR spectra of denatured states of lysozyme. Proteins 9, 248-266.
9. Radford, S.E., Buck, M., Topping, K.D., Dobson, C.M. & Evans, P.A. (1992). Hydrogen exchange in native and denatured states of hen egg-white lysozyme. Proteins 14, 237-248.
10. Flanagan, J.M., Kataoka, M., Fujisawa, T. & Engelman, D.M. (1993). Mutations can cause large changes in the conformation of a denatured protein. Biochemistry 32, 10359-10370.
11. Buck, M., Radford, S.E. & Dobson, C.M. (1994). Amide hydrogen exchange in a highly denatured state: hen egg-white lysozyme in urea. J. Mol. Biol. 237, 247-254.
12. Lattman, E.E. (1994). Small angle scattering studies of protein folding. Curr. Opin. Struct. Biol. 4, 87-92.
13. Shortle, D. (1996). The denatured state (the other half of the folding equation) and its role in protein stability. FASEB J. 10, 27-34.
14. Kataoka, M. & Goto, Y. (1996). X-ray solution scattering studies of protein folding. Fold. Des. 1, 107-114.
15. Sugita, Y. & Kitao, A. (1998) Dependence of protein stability on the structure of the denatured state: free energy calculation of 156V mutation in human lysozyme. Biophys. J., in press.
16. Beveridge, B.L. & DiCapua, P.M. (1989). Free energy via molecular simulation: application to chemical and biomolecular systems. Annu. Rev. Biophys. Chem. 18, 431-492.
17. Straatsma, T.P. & McCammon, J.A. (1992). Computational alchemy. Annu. Rev. Phys. Chem. 43, 407-435.
18. van Gunsteren, W.F. & Mark, A.E. (1992). On the interpretation of biochemical data by molecular dynamics computer simulation. Eur. J. Biochem. 204, 947-961.
19. Kollman, P. (1993). Free energy calculations: applications to chemical and biochemical phenomena. Chem. Rev. 93, 2395-2417.
20. Saito, M. (1995). Molecular dynamics/free energy study of a protein in solution with all degrees of freedom and long-range coulomb interactions. J Phys. Chem. 99, 17043-17048.
21. Tanimura, R. & Saito, M. (1996). Molecular dynamics/free energy perturbation studies of the thermostable V74I mutant of ribonuclease HI. Mol. Simulation 16, 75-85.
22. Tidor, B. & Karplus, M. (1991 ). Simulation analysis of the stability mutant R96H of T4 lysozyme. Biochemistry 30, 3217-3228.
23. Yun-Yu, S., Mark, A.E., Cun-Xin, W., Fuhua, H., Berendsen, H.J.C. & van Gunsteren, W.F. (1993). Can the stability of protein mutants be predicted by free energy calculations? Protein Eng. 6, 289-295.
24. Saito, M. & Tanimura, R. (1995). Relative melting temperatures of RNase HI mutant proteins from MD simulation/free energy calculations. Chem. Phys. Lett. 236, 156-161.
25. Sun, Y.-C., Veenstra, D.L. & Kollman, P.A. (1996). Free energy calculations of the mutation of Ile96 to Ala in barnase: contribution of the difference in stability. Protein Eng. 9, 273-281.
26. Sugita, Y. & Kitao, A. (1998) Improved protein free energy calculation by more accurate treatment of nonbonded energy: application to chymotrypsin inhibitor 2. Proteins 30, in press.
27. Rebig, K.M., Schwalbe, H., Buck, M., Smith, L.J. & Dobson, C.M. (1996). Toward a description of the conformations of denatured states of proteins. Comparison of a random coil model with NMR measurements. J. Phys. Chem. 100, 2661-2666.
28. Smith, L.J., Fiebig, K.M., Schwalbe, H. & Dobson, C.M. (1996). The concept of a random coil. Residual structure in peptides and denatured proteins. Fold. Des. 1, 95-106.
29. Smith, L.J., Bolin, K.A., Schwalbe, H., MacArthur, M.W., Thornton, J.M. & Dobson, C.M. (1996). Analysis of mainchain torsion angles in proteins: prediction of NMR coupling constants for native and random coil conformations. J. Mol. Biol. 255, 494-506.
30. Schwalbe, H., et al., & Dobson, C.M. (1997). Structural and dynamical properties of a denatured protein. Heteronuclear 3D NMR experiments and theoretical simulations of lysozyme in 8 M urea. Biochemistry 36, 8977-8991.
31. Weiner, S.J., Kollman, P.A., Nguyen, D.T. & Case, D.A. (1986). An all atom force field for simulations of proteins and nucleic acids. J. Comp. Chem. 7, 230-252.
32. Jorgensen, W.L, Chandrasekhar, J. & Madura, J.D. (1983). Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926-935.
33. Beglov, D. & Roux, B. (1994). Finite representation of an infinite bulk system: solvent boundary potential for computer simulations. J. Chem. Phys. 100, 9050-9063.
34. Ding, H.-Q., Karasawa, N. & Goddard, W.A., III (1992). Atomic level simulations on million particles: the cell multipole method for Coulomb and London nonbond interactions. J. Chem. Phys. 97, 4309-4315.
35. Hoover, W.G. (1985). Canonical dynamics: equilibrium phase-space distributions. Phys. Rev. A 31, 1695-1697.
36. Nosé, S. (1984). A molecular dynamics method for simulations in the canonical ensemble. Mol. Phys. 52, 255-268.
37. Jorgensen, W.L. ≈ Ravimohan, C. (1985). Monte Carlo simulation of difference in free energy of hydration. J. Chem. Phys. 83, 3050-3054.
38. Morikami, K., Nakai, T., Kidera, A., & Saito, M. (1992). PRESTO (PRotein Engineering SimulaTOr). A vectorized molecular mechanics program for biopolymers. Comp. Chem. 16, 243-248
39. Kraulis, PJ. (1991 ). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946-950.
40. Merrit, E.A. & Murphy, M.E.P. (1994). Raster3D version 20. A program for photorealistic molecular graphics. Acta Crystallogr. D 50, 869-873.
41. Kabsch, W. & Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577-2637.