메뉴 건너뛰기




Volumn 75, Issue 5, 1998, Pages 2178-2187

Dependence of protein stability on the structure of the denatured state: Free energy calculations of 156V mutation in human lysozyme

Author keywords

[No Author keywords available]

Indexed keywords

LYSOZYME; MUTANT PROTEIN;

EID: 0031722981     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(98)77661-1     Document Type: Article
Times cited : (25)

References (50)
  • 1
    • 0001655657 scopus 로고
    • Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations
    • Beglov, D. and B. Roux. 1994. Finite representation of an infinite bulk system: solvent boundary potential for computer simulations. J. Chem. Phys. 100:9050-9063.
    • (1994) J. Chem. Phys. , vol.100 , pp. 9050-9063
    • Beglov, D.1    Roux, B.2
  • 2
    • 0024578173 scopus 로고
    • Free energy via molecular simulation: Application to chemical and biomolecular systems
    • Beveridge, B. L., and F. M. DiCapua. 1989. Free energy via molecular simulation: application to chemical and biomolecular systems. Annu. Rev. Biophys. Biophys. Chem. 18:431-492.
    • (1989) Annu. Rev. Biophys. Biophys. Chem. , vol.18 , pp. 431-492
    • Beveridge, B.L.1    DiCapua, F.M.2
  • 3
    • 0027968902 scopus 로고
    • Free energy simulations: The meaning of the individual contributions from a component analysis
    • Boresch, S., G. Archontis, and M. Karplus. 1994. Free energy simulations: the meaning of the individual contributions from a component analysis. Proteins Struct. Funct. Genet. 20:25-33.
    • (1994) Proteins Struct. Funct. Genet. , vol.20 , pp. 25-33
    • Boresch, S.1    Archontis, G.2    Karplus, M.3
  • 4
    • 0029584358 scopus 로고
    • The meaning of component analysis: Decomposition of the free energy in terms of specific interaction
    • Boresch, S., and M. Karplus. 1995. The meaning of component analysis: decomposition of the free energy in terms of specific interaction. J. Mol. Biol. 254:801-807.
    • (1995) J. Mol. Biol. , vol.254 , pp. 801-807
    • Boresch, S.1    Karplus, M.2
  • 5
    • 0028858516 scopus 로고
    • Decomposition of interaction free energies in proteins and other complex systems
    • Brady, G. P., and K. A. Sharp. 1995. Decomposition of interaction free energies in proteins and other complex systems. J. Mol. Biol. 254:77-85.
    • (1995) J. Mol. Biol. , vol.254 , pp. 77-85
    • Brady, G.P.1    Sharp, K.A.2
  • 6
    • 0030601861 scopus 로고    scopus 로고
    • On the decomposition of free energies
    • Brady, G. P., A. Szabo, and K. A. Sharp. 1996. On the decomposition of free energies. J. Mol. Biol. 263:123-125.
    • (1996) J. Mol. Biol. , vol.263 , pp. 123-125
    • Brady, G.P.1    Szabo, A.2    Sharp, K.A.3
  • 7
    • 0028349704 scopus 로고
    • Amide hydrogen exchange in a highly denatured state: Hen egg-white lysozyme in urea
    • Buck. M., S. E. Radford, and C. M. Dobson. 1994. Amide hydrogen exchange in a highly denatured state: hen egg-white lysozyme in urea. J. Mol. Biol. 237:247-254.
    • (1994) J. Mol. Biol. , vol.237 , pp. 247-254
    • Buck, M.1    Radford, S.E.2    Dobson, C.M.3
  • 8
    • 0025856806 scopus 로고
    • Denatured states of proteins
    • Dill, K. A., and D. Shortle. 1991. Denatured states of proteins. Annu. Rev. Biochem. 60:795-825.
    • (1991) Annu. Rev. Biochem. , vol.60 , pp. 795-825
    • Dill, K.A.1    Shortle, D.2
  • 9
    • 5244247401 scopus 로고
    • Atomic level simulations on million particles: The cell multipole method for Coulomb and London nonbond interactions
    • Ding, H.-Q., N. Karasawa, and W. A. Goddard, III. 1992. Atomic level simulations on million particles: the cell multipole method for Coulomb and London nonbond interactions. J. Chem. Phys. 97:4309-4315.
    • (1992) J. Chem. Phys. , vol.97 , pp. 4309-4315
    • Ding, H.-Q.1    Karasawa, N.2    Goddard W.A. III3
  • 10
    • 0026567907 scopus 로고
    • Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect
    • Eriksson, A. E., W. A. Baase, X.-J. Zhang, D. W. Heinz, M. Blaber, E. P. Baldwin, and B. W. Matthews. 1992. Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. Science. 255:178-183.
    • (1992) Science , vol.255 , pp. 178-183
    • Eriksson, A.E.1    Baase, W.A.2    Zhang, X.-J.3    Heinz, D.W.4    Blaber, M.5    Baldwin, E.P.6    Matthews, B.W.7
  • 11
    • 0025865522 scopus 로고
    • Hydrophobic clustering in nonnative states of a protein: Interpretation of chemical shifts in NMR spectra of denatured states of lysozyme
    • Evans, P. A., K. D. Topping, D. N. Woolfson, and C. M. Dobson. 1991. Hydrophobic clustering in nonnative states of a protein: interpretation of chemical shifts in NMR spectra of denatured states of lysozyme. Proteins Struct. Funct. Genet. 9:248-266.
    • (1991) Proteins Struct. Funct. Genet. , vol.9 , pp. 248-266
    • Evans, P.A.1    Topping, K.D.2    Woolfson, D.N.3    Dobson, C.M.4
  • 12
    • 0027462173 scopus 로고
    • Principles of protein stability derived from protein engineering experiments
    • Fersht, A. R., and L. Serrano. 1993. Principles of protein stability derived from protein engineering experiments. Curr. Opin. Struct. Biol. 3:75-83.
    • (1993) Curr. Opin. Struct. Biol. , vol.3 , pp. 75-83
    • Fersht, A.R.1    Serrano, L.2
  • 13
    • 0000749460 scopus 로고    scopus 로고
    • Toward a description of the conformations of denatured states of proteins. Comparison of a random coil model with NMR measurements
    • Fiebig, K. M., H. Schwalbe, M. Buck, L. J. Smith, and C. M. Dobson. 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.
    • (1996) J. Phys. Chem. , vol.100 , pp. 2661-2666
    • Fiebig, K.M.1    Schwalbe, H.2    Buck, M.3    Smith, L.J.4    Dobson, C.M.5
  • 14
    • 0027495402 scopus 로고
    • Mutations can cause large changes in the conformation of a denatured protein
    • Flanagan, J. M., M. Kataoka, T. Fujisawa, and D. M. Engelman. 1993. Mutations can cause large changes in the conformation of a denatured protein. Biochemistry. 32:10359-10370.
    • (1993) Biochemistry , vol.32 , pp. 10359-10370
    • Flanagan, J.M.1    Kataoka, M.2    Fujisawa, T.3    Engelman, D.M.4
  • 15
    • 0030474922 scopus 로고    scopus 로고
    • The structure, stability, and folding process of amyloidogenic mutant human lysozyme
    • Funahashi, J., K. Takano, K. Ogasahara, Y. Yamagata, and K. Yutani. 1996. The structure, stability, and folding process of amyloidogenic mutant human lysozyme. J. Biochem. 120:1216-1223.
    • (1996) J. Biochem. , vol.120 , pp. 1216-1223
    • Funahashi, J.1    Takano, K.2    Ogasahara, K.3    Yamagata, Y.4    Yutani, K.5
  • 16
    • 0001538909 scopus 로고
    • Canonical dynamics: Equilibrium phase-space distributions
    • Hoover, W. G. 1985. Canonical dynamics: equilibrium phase-space distributions. Phys. Rev. A. 31:1695-1697.
    • (1985) Phys. Rev. A , vol.31 , pp. 1695-1697
    • Hoover, W.G.1
  • 17
    • 0004016501 scopus 로고
    • Comparison of simple potential functions for simulating liquid water
    • Jorgensen, W. L., J. Chandrasekhar, and J. D. Madura. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
    • (1983) J. Chem. Phys. , vol.79 , pp. 926-935
    • Jorgensen, W.L.1    Chandrasekhar, J.2    Madura, J.D.3
  • 18
    • 0004504539 scopus 로고
    • Monte Carlo simulation of differences in free energies of hydration
    • Jorgensen, W. L., and C. Ravimohan. 1985. Monte Carlo simulation of differences in free energies of hydration. J. Chem. Phys. 83:3050-3054.
    • (1985) J. Chem. Phys. , vol.83 , pp. 3050-3054
    • Jorgensen, W.L.1    Ravimohan, C.2
  • 19
    • 0030324821 scopus 로고    scopus 로고
    • X-ray solution scattering studies of protein folding
    • Kataoka, M., and Y. Goto. 1996. X-ray solution scattering studies of protein folding. Folding Des. 1:107-114.
    • (1996) Folding Des. , vol.1 , pp. 107-114
    • Kataoka, M.1    Goto, Y.2
  • 20
    • 0024375463 scopus 로고
    • Energetics of complementary side-chain packing in a protein hydrophobic core
    • Kellis, J. J. T., K. Nyberg, and A. R. Fersht. 1989. Energetics of complementary side-chain packing in a protein hydrophobic core. Biochemistry. 28:4914-4922.
    • (1989) Biochemistry , vol.28 , pp. 4914-4922
    • Kellis, J.J.T.1    Nyberg, K.2    Fersht, A.R.3
  • 21
    • 7044239742 scopus 로고
    • Free energy calculations: Applications to chemical and biochemical phenomena
    • Kollman, P. 1993. Free energy calculations: applications to chemical and biochemical phenomena. Chem. Rev. 93:2395-2417.
    • (1993) Chem. Rev. , vol.93 , pp. 2395-2417
    • Kollman, P.1
  • 22
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • Kraulis, P. J 1991. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24:946-950.
    • (1991) J. Appl. Crystallogr. , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 23
    • 0027955639 scopus 로고
    • Small angle scattering studies of protein folding
    • Lattman, E. E. 1994. Small angle scattering studies of protein folding. Curr. Opin. Struct. Biol. 4:87-92.
    • (1994) Curr. Opin. Struct. Biol. , vol.4 , pp. 87-92
    • Lattman, E.E.1
  • 24
    • 0027255479 scopus 로고
    • Structural and genetic analysis of protein stability
    • Mathews, B. W. 1993. Structural and genetic analysis of protein stability. Annu. Rev. Biochem. 62:139-160.
    • (1993) Annu. Rev. Biochem. , vol.62 , pp. 139-160
    • Mathews, B.W.1
  • 25
    • 0028057108 scopus 로고
    • Raster3D Version 20. A program for photorealistic molecular graphics
    • Merrit, E. A., and M. E. P. Murphy. 1994. Raster3D Version 20. A program for photorealistic molecular graphics. Acta Crystallogr. D. 50:869-873.
    • (1994) Acta Crystallogr. D , vol.50 , pp. 869-873
    • Merrit, E.A.1    Murphy, M.E.P.2
  • 26
    • 0008348735 scopus 로고
    • PRESTO (PRotein Engineering SimulaTOr): A vectorized molecular mechanics program for biopolymers
    • Morikami, K., T. Nakai, A. Kidera, M. Saito, and H. Nakamura. 1992. PRESTO (PRotein Engineering SimulaTOr): a vectorized molecular mechanics program for biopolymers. Comput. Chem. 16:243-248.
    • (1992) Comput. Chem. , vol.16 , pp. 243-248
    • Morikami, K.1    Nakai, T.2    Kidera, A.3    Saito, M.4    Nakamura, H.5
  • 27
    • 84943502952 scopus 로고
    • A molecular dynamics method for simulations in the canonical ensemble
    • Nosé, S. 1984. A molecular dynamics method for simulations in the canonical ensemble. Mol. Phys. 52:255-268.
    • (1984) Mol. Phys. , vol.52 , pp. 255-268
    • Nosé, S.1
  • 28
    • 0028988836 scopus 로고
    • Side-chain determinants of beta-sheet stability
    • Otzen, D. E., and A. R. Fersht. 1995. Side-chain determinants of beta-sheet stability. Biochemistry. 34:5718-5724.
    • (1995) Biochemistry , vol.34 , pp. 5718-5724
    • Otzen, D.E.1    Fersht, A.R.2
  • 29
    • 0028865428 scopus 로고
    • Structural factors contributing to the hydrophobic effect: The partly exposed hydrophobic minicore in chymotrypsin inhibitor 2
    • Otzen, D. E., M. Rheinnecker, and A. R. Fersht. 1995. Structural factors contributing to the hydrophobic effect: the partly exposed hydrophobic minicore in chymotrypsin inhibitor 2. Biochemistry. 34:13051-13058.
    • (1995) Biochemistry , vol.34 , pp. 13051-13058
    • Otzen, D.E.1    Rheinnecker, M.2    Fersht, A.R.3
  • 30
    • 0026777217 scopus 로고
    • Contribution of the hydrophobic effect to globular protein stability
    • Pace, C. N. 1992. Contribution of the hydrophobic effect to globular protein stability. J. Mol. Biol. 226:29-35.
    • (1992) J. Mol. Biol. , vol.226 , pp. 29-35
    • Pace, C.N.1
  • 32
    • 0003819814 scopus 로고
    • Relative melting temperatures of RNase HI mutant proteins from MD simulation/free energy calculations
    • Saito, M., and R. Taninura. 1995. Relative melting temperatures of RNase HI mutant proteins from MD simulation/free energy calculations. Chem. Phys. Lett. 236:156-161.
    • (1995) Chem. Phys. Lett. , vol.236 , pp. 156-161
    • Saito, M.1    Taninura, R.2
  • 33
    • 0030759665 scopus 로고    scopus 로고
    • Structural and dynamical properties of a denatured protein. Heteronuclear 3D NMR experiments and theoretical simulations of lysozyme in 8 M urea
    • Schwalbe, H., K. M. Fiebig, M. Buck, J. A. Jones, S. B. Grimshaw, A. Spencer, S. J. Glaser, L. J. Smith, and C. M. Dobson. 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.
    • (1997) Biochemistry , vol.36 , pp. 8977-8991
    • Schwalbe, H.1    Fiebig, K.M.2    Buck, M.3    Jones, J.A.4    Grimshaw, S.B.5    Spencer, A.6    Glaser, S.J.7    Smith, L.J.8    Dobson, C.M.9
  • 34
    • 0026553768 scopus 로고
    • The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability
    • Serrano, L., J. T. Kellis, Jr., P. Cann, A. Matouschek, and A. R. Fersht. 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.
    • (1992) J. Mol. Biol. , vol.224 , pp. 783-804
    • Serrano, L.1    Kellis J.T., Jr.2    Cann, P.3    Matouschek, A.4    Fersht, A.R.5
  • 35
    • 0030032461 scopus 로고    scopus 로고
    • The denatured state (the other half of the folding equation) and its role in protein stability
    • Shortle, D. 1996. The denatured state (the other half of the folding equation) and its role in protein stability. FASEB J. 10:27-34.
    • (1996) FASEB J. , vol.10 , pp. 27-34
    • Shortle, D.1
  • 36
    • 0025005525 scopus 로고
    • Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease
    • Shortle, D., W. E. Stites, and A. K. Meeker. 1990. Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease. Biochemistry. 29:8033-8041.
    • (1990) Biochemistry , vol.29 , pp. 8033-8041
    • Shortle, D.1    Stites, W.E.2    Meeker, A.K.3
  • 37
    • 0029978353 scopus 로고    scopus 로고
    • Analysis of main chain torsion angles in proteins: Prediction of NMR coupling constants for native and random coil conformations
    • Smith, L. J., K. A. Bolin, H. Schwalbe, M. W. MacArthur, J. M. Thornton, and C. M. Dobson. 1996a. Analysis of main chain torsion angles in proteins: prediction of NMR coupling constants for native and random coil conformations. J. Mol. Biol. 255:494-506.
    • (1996) J. Mol. Biol. , vol.255 , pp. 494-506
    • Smith, L.J.1    Bolin, K.A.2    Schwalbe, H.3    MacArthur, M.W.4    Thornton, J.M.5    Dobson, C.M.6
  • 38
    • 0030320442 scopus 로고    scopus 로고
    • The concept of a random coil. Residual structure in peptides and denatured proteins
    • Smith, L. J., K. M. Fiebig, H. Schwalbe, and C. M. Dobson. 1996b. The concept of a random coil. Residual structure in peptides and denatured proteins. Folding Des. 1:95-106.
    • (1996) Folding Des. , vol.1 , pp. 95-106
    • Smith, L.J.1    Fiebig, K.M.2    Schwalbe, H.3    Dobson, C.M.4
  • 39
    • 0040543046 scopus 로고
    • When are free energy components meaningful?
    • Smith, P. E., and W. F. van Gunsteren. 1994. When are free energy components meaningful? J. Phys. Chem. 98:2366-2379.
    • (1994) J. Phys. Chem. , vol.98 , pp. 2366-2379
    • Smith, P.E.1    Van Gunsteren, W.F.2
  • 41
    • 0032032108 scopus 로고    scopus 로고
    • Improved protein free energy calculation by more accurate treatment of nonbonded energy: Application to chymotrypsin inhibitor 2, V57A
    • Sugita, Y., and A. Kitao. 1998. Improved protein free energy calculation by more accurate treatment of nonbonded energy: application to chymotrypsin inhibitor 2, V57A. Proteins Struct. Funct. Genet. 30:388-400.
    • (1998) Proteins Struct. Funct. Genet. , vol.30 , pp. 388-400
    • Sugita, Y.1    Kitao, A.2
  • 42
    • 0031778441 scopus 로고    scopus 로고
    • Computational analysis of thermal stability: Effect of Ile to Val mutations in human lysozyme
    • Sugita, Y., A. Kitao, and N. Go. 1998. Computational analysis of thermal stability: effect of Ile to Val mutations in human lysozyme. Folding Des. 3:173-181.
    • (1998) Folding Des. , vol.3 , pp. 173-181
    • Sugita, Y.1    Kitao, A.2    Go, N.3
  • 43
    • 0029929557 scopus 로고    scopus 로고
    • 96 to Ala in barnase: Contribution of the difference in stability
    • 96 to Ala in barnase: contribution of the difference in stability. Protein Eng. 9:273-281.
    • (1996) Protein Eng. , vol.9 , pp. 273-281
    • Sun, Y.-C.1    Veenstra, D.L.2    Kollman, P.A.3
  • 44
    • 0028786432 scopus 로고
    • Contribution of hydrophobic residues to the stability of human lysozyme: Calorimetric studies and x-ray structural analysis of the five isoleucine to valine mutants
    • Takano, K., K. Ogasahara, H. Kaneda, Y. Yamagata, S. Fujii, E. Kanaya, M. Kikuchi, M. Oobatake, and K. Yutani. 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.
    • (1995) J. Mol. Biol. , vol.254 , pp. 62-76
    • Takano, K.1    Ogasahara, K.2    Kaneda, H.3    Yamagata, Y.4    Fujii, S.5    Kanaya, E.6    Kikuchi, M.7    Oobatake, M.8    Yutani, K.9
  • 45
    • 0031050618 scopus 로고    scopus 로고
    • Contribution of the hydrophobic effect to the stability of human lysozyme: Calorimetric studies and x-ray structural analyses of the nine valine to alanine mutants
    • Takano, K., Y. Yamagata, S. Fujii, and K. Yutani. 1997. Contribution of the hydrophobic effect to the stability of human lysozyme: calorimetric studies and x-ray structural analyses of the nine valine to alanine mutants. Biochemistry. 36:688-698.
    • (1997) Biochemistry , vol.36 , pp. 688-698
    • Takano, K.1    Yamagata, Y.2    Fujii, S.3    Yutani, K.4
  • 46
    • 0010131264 scopus 로고    scopus 로고
    • Molecular dynamics/free energy perturbation studies of the thermostable V74I mutant of ribonuclease HI
    • Tanimura, R., and M. Saito. 1996. Molecular dynamics/free energy perturbation studies of the thermostable V74I mutant of ribonuclease HI. Mol. Simulation. 16:75-85.
    • (1996) Mol. Simulation , vol.16 , pp. 75-85
    • Tanimura, R.1    Saito, M.2
  • 47
    • 0025732376 scopus 로고
    • Simulation analysis of the stability mutant R96H of T4 lysozyme
    • Tidor, B., and M. Karplus. 1991. Simulation analysis of the stability mutant R96H of T4 lysozyme. Biochemistry. 30:3217-3228.
    • (1991) Biochemistry , vol.30 , pp. 3217-3228
    • Tidor, B.1    Karplus, M.2
  • 48
    • 0026556022 scopus 로고
    • On the interpretation of biochemical data by molecular dynamics computer simulation
    • van Gunsteren, W. F., and A. E. Mark. 1992. On the interpretation of biochemical data by molecular dynamics computer simulation. Eur. J. Biochem. 204:947-961.
    • (1992) Eur. J. Biochem. , vol.204 , pp. 947-961
    • Van Gunsteren, W.F.1    Mark, A.E.2
  • 49
    • 84988053694 scopus 로고
    • An all atom force field for simulations of proteins and nucleic acids
    • Weiner, S. J., P. A. Kollman, D. T. Nguyen, and D. A. Case. 1986. An all atom force field for simulations of proteins and nucleic acids. J. Comput. Chem. 7:230-252.
    • (1986) J. Comput. Chem. , vol.7 , pp. 230-252
    • Weiner, S.J.1    Kollman, P.A.2    Nguyen, D.T.3    Case, D.A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.