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Volumn 86, Issue 5, 2004, Pages 2765-2772

Atomic Mean-Square Displacements in Proteins by Molecular Dynamics: A Case for Analysis of Variance

Author keywords

[No Author keywords available]

Indexed keywords

ANALYSIS OF VARIANCE; ARTICLE; ATOM; CALCULATION; CHEMICAL STRUCTURE; MATHEMATICAL ANALYSIS; MOLECULAR DYNAMICS; PROTEIN STABILITY; THERMOSTABILITY;

EID: 2142820913     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(04)74330-1     Document Type: Article
Times cited : (17)

References (39)
  • 1
    • 0031554925 scopus 로고    scopus 로고
    • Crystal structure of the β-glycosidase from the hyperthermophilic archeon Sulfolobus solfataricus: Resilience as a key factor in thermostability
    • Aguilar, C. F., I. Sanderson, M. Moracci, M. Ciaramella, R. Nucci, M. Rossi, and L. H. Pearl. 1997. Crystal structure of the β-glycosidase from the hyperthermophilic archeon Sulfolobus solfataricus: resilience as a key factor in thermostability. J. Mol. Biol. 271:789-802.
    • (1997) J. Mol. Biol. , vol.271 , pp. 789-802
    • Aguilar, C.F.1    Sanderson, I.2    Moracci, M.3    Ciaramella, M.4    Nucci, R.5    Rossi, M.6    Pearl, L.H.7
  • 2
    • 48749148224 scopus 로고
    • RATTLE: A "velocity" version of the SHAKE algorithm for molecular dynamics calculations
    • Andersen, H. C. 1983. RATTLE: a "velocity" version of the SHAKE algorithm for molecular dynamics calculations. J. Comput. Phys. 52:24-34.
    • (1983) J. Comput. Phys. , vol.52 , pp. 24-34
    • Andersen, H.C.1
  • 4
    • 0029645413 scopus 로고
    • The crystal structure of a cyanogenic β-glucosidase from white clover, a family 1 glycosil hydrolase
    • Barrett, T., C. G. Suresh, S. P. Tolley, E. J. Dodson, and M. A. Hughes. 1995. The crystal structure of a cyanogenic β-glucosidase from white clover, a family 1 glycosil hydrolase. Structure. 3:951-960.
    • (1995) Structure , vol.3 , pp. 951-960
    • Barrett, T.1    Suresh, C.G.2    Tolley, S.P.3    Dodson, E.J.4    Hughes, M.A.5
  • 6
    • 0011689966 scopus 로고
    • Molecular dynamics simulations: Techniques and approaches
    • NATO ASI series C135. A. J. Barnes, W. J. Orville-Thomas, and J. Yarwood, editors. Reidel, New York
    • Berendsen, H. J. C., and W. F. Van Gusteren. 1984. Molecular dynamics simulations: techniques and approaches. In Molecular Liquids, Dynamic and Interaction. NATO ASI series C135. A. J. Barnes, W. J. Orville-Thomas, and J. Yarwood, editors. Reidel, New York. 475-500.
    • (1984) Molecular Liquids, Dynamic and Interaction , pp. 475-500
    • Berendsen, H.J.C.1    Van Gusteren, W.F.2
  • 7
    • 0037375789 scopus 로고    scopus 로고
    • Dynamic fluorescence studies of β-glycosidase mutants from Sulfolobus solfataricus: Effects of single mutations on protein thermostability
    • Bismuto, E., F. Febbraio, S. Limongelli, R. Briante, and R. Nucci. 2003. Dynamic fluorescence studies of β-glycosidase mutants from Sulfolobus solfataricus: effects of single mutations on protein thermostability. Proteins. 51:10-20.
    • (2003) Proteins , vol.51 , pp. 10-20
    • Bismuto, E.1    Febbraio, F.2    Limongelli, S.3    Briante, R.4    Nucci, R.5
  • 8
    • 0036292540 scopus 로고    scopus 로고
    • Effect of molecular confinement on internal enzyme dynamics: Frequency domain fluorometry and molecular dynamics simulation studies
    • Bismuto, E., P. L. Martelli, A. De Maio, D. G. Mita, G. Irace, and R. Casadio. 2002. Effect of molecular confinement on internal enzyme dynamics: frequency domain fluorometry and molecular dynamics simulation studies. Biopolymers. 67:85-95.
    • (2002) Biopolymers , vol.67 , pp. 85-95
    • Bismuto, E.1    Martelli, P.L.2    De Maio, A.3    Mita, D.G.4    Irace, G.5    Casadio, R.6
  • 9
    • 46149128394 scopus 로고
    • Molecular dynamics simulations of rigid molecules
    • Ciccotti, G., and J. P. Ryckaert. 1986. Molecular dynamics simulations of rigid molecules. Comput. Phys. Rep. 4:345-392.
    • (1986) Comput. Phys. Rep. , vol.4 , pp. 345-392
    • Ciccotti, G.1    Ryckaert, J.P.2
  • 10
    • 0033612756 scopus 로고    scopus 로고
    • Stability and activity of mesophilic subtilisin E and its thermophilic homolog: Insights from molecular dynamics simulations
    • Colombo, G., and K. M. Merz. 1999. Stability and activity of mesophilic subtilisin E and its thermophilic homolog: insights from molecular dynamics simulations. J. Am. Chem. Soc. 121:6895-6903.
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 6895-6903
    • Colombo, G.1    Merz, K.M.2
  • 12
    • 0029645404 scopus 로고
    • Structure and mechanisms of glycosyl hydrolases
    • Davies, G., and B. Henrissat. 1995. Structure and mechanisms of glycosyl hydrolases. Structure. 3:853-859.
    • (1995) Structure , vol.3 , pp. 853-859
    • Davies, G.1    Henrissat, B.2
  • 13
    • 0024976853 scopus 로고
    • Dynamical transition of myoglobin revealed by inelastic neutron scattering
    • Doster, W., S. Cusak, and W. Petry. 1989. Dynamical transition of myoglobin revealed by inelastic neutron scattering. Nature. 337:754-756.
    • (1989) Nature , vol.337 , pp. 754-756
    • Doster, W.1    Cusak, S.2    Petry, W.3
  • 15
    • 0033865067 scopus 로고    scopus 로고
    • Structural equilibrium fluctuations in mesophilic and thermophilic α-amylase
    • Fitter, J., and J. Heberle. 2000. Structural equilibrium fluctuations in mesophilic and thermophilic α-amylase. Biophys. J. 79:1629-1636.
    • (2000) Biophys. J. , vol.79 , pp. 1629-1636
    • Fitter, J.1    Heberle, J.2
  • 16
    • 84990647020 scopus 로고
    • The Debye-Waller-factor from villain to hero in protein crystallography
    • Frauenfelder, H. 1989. The Debye-Waller-factor from villain to hero in protein crystallography. Int. J. Quantum Chem. 35:711-715.
    • (1989) Int. J. Quantum Chem. , vol.35 , pp. 711-715
    • Frauenfelder, H.1
  • 17
    • 0018793861 scopus 로고
    • Temperature-dependent X-ray diffraction as a probe of protein structure dynamics
    • Frauenfelder, H., G. Petsko, and D. Tsemoglou. 1979. Temperature-dependent X-ray diffraction as a probe of protein structure dynamics. Nature. 280:558-563.
    • (1979) Nature , vol.280 , pp. 558-563
    • Frauenfelder, H.1    Petsko, G.2    Tsemoglou, D.3
  • 20
    • 0028107325 scopus 로고
    • The effect of engineering surface loops on the thermal stability of Bacillus subtilis neutral protease
    • Hardy. F., G. Vriend, B. van der Vinne, F. Frigerio, G. Grandi, G. Venema, and V. G. Eijsink. 1994. The effect of engineering surface loops on the thermal stability of Bacillus subtilis neutral protease. Protein Eng. 3:425-430.
    • (1994) Protein Eng. , vol.3 , pp. 425-430
    • Hardy, F.1    Vriend, G.2    Van Der Vinne, B.3    Frigerio, F.4    Grandi, G.5    Venema, G.6    Eijsink, V.G.7
  • 21
    • 0023512803 scopus 로고
    • Anisotropy and anharmonicity of atomic fluctuations in proteins: Analysis of a molecular dynamics study
    • Ichiye, T., and M. Karplus. 1987. Anisotropy and anharmonicity of atomic fluctuations in proteins: analysis of a molecular dynamics study. Proteins. 2:236-259.
    • (1987) Proteins , vol.2 , pp. 236-259
    • Ichiye, T.1    Karplus, M.2
  • 22
    • 0034717156 scopus 로고    scopus 로고
    • Stability and stabilization of globular proteins in solution
    • Jaenicke, R. 2000a. Stability and stabilization of globular proteins in solution. J. Biotechnol. 79:193-203.
    • (2000) J. Biotechnol. , vol.79 , pp. 193-203
    • Jaenicke, R.1
  • 23
    • 0034724271 scopus 로고    scopus 로고
    • Do ultrastable proteins from hyperthermophiles have high or low conformational rigidity?
    • Jaenicke, R. 2000b. Do ultrastable proteins from hyperthermophiles have high or low conformational rigidity? Proc. Natl. Acad. Sci. USA. 97:2962-2964.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 2962-2964
    • Jaenicke, R.1
  • 24
    • 84948502362 scopus 로고
    • Superposition of molecular structures using quaternions
    • Kneller, G. R. 1991. Superposition of molecular structures using quaternions. Mol. Simulat. 7:113-119.
    • (1991) Mol. Simulat. , vol.7 , pp. 113-119
    • Kneller, G.R.1
  • 25
    • 0034855858 scopus 로고    scopus 로고
    • How do thermophilic proteins deal with heat?
    • Kumar, S., and R. Nussinov. 2001. How do thermophilic proteins deal with heat? Cell. Mol. Life Sci. 9:1216-1233.
    • (2001) Cell. Mol. Life Sci. , vol.9 , pp. 1216-1233
    • Kumar, S.1    Nussinov, R.2
  • 26
    • 0031467464 scopus 로고    scopus 로고
    • Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin
    • Lazaridis, T., I. Lee, and M. Karplus. 1997. Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin. Protein Sci. 6:2589-2605.
    • (1997) Protein Sci. , vol.6 , pp. 2589-2605
    • Lazaridis, T.1    Lee, I.2    Karplus, M.3
  • 27
    • 0000936038 scopus 로고
    • The calculation of molecular vibration frequencies
    • Lindemann, F. A. 1910. The calculation of molecular vibration frequencies. Physics, Z. 11:609-612.
    • (1910) Physics, Z. , vol.11 , pp. 609-612
    • Lindemann, F.A.1
  • 29
    • 0023430560 scopus 로고
    • Enhanced protein thermostability from site-directed mutations that decrease the entropy of unfolding
    • Matthews, B. W., H. Nicholson, and W. J. Becktel. 1987. Enhanced protein thermostability from site-directed mutations that decrease the entropy of unfolding. Proc. Natl. Acad. Sci. USA. 84:6663-6667.
    • (1987) Proc. Natl. Acad. Sci. USA , vol.84 , pp. 6663-6667
    • Matthews, B.W.1    Nicholson, H.2    Becktel, W.J.3
  • 31
    • 0035139731 scopus 로고    scopus 로고
    • β-glycosidase from Sulfolobus solfataricus
    • Moracci, M., M. Ciaramella, and M. Rossi. 2001. β-glycosidase from Sulfolobus solfataricus. Methods Enzymol. 330:201-215.
    • (2001) Methods Enzymol. , vol.330 , pp. 201-215
    • Moracci, M.1    Ciaramella, M.2    Rossi, M.3
  • 32
    • 84943502952 scopus 로고
    • A molecular dynamics method for simulations in the canonical ensemble
    • Nosè, 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
    • Nosè, S.1
  • 33
    • 0034736267 scopus 로고    scopus 로고
    • Distributions of structural features contributing to thermostability in mesophilic and thermophilic α- β-barrel glycosyl hydrolases
    • Panasik, N., Jr., J. E. Brenchley, and G. K. Farber. 2000. Distributions of structural features contributing to thermostability in mesophilic and thermophilic α- β-barrel glycosyl hydrolases. Biochim. Biophys. Acta. 1543:189-201.
    • (2000) Biochim. Biophys. Acta , vol.1543 , pp. 189-201
    • Panasik Jr., N.1    Brenchley, J.E.2    Farber, G.K.3
  • 34
    • 0020333863 scopus 로고
    • Protein dynamics: Mossbauer spectroscopy on deoxymyoglobin crystals
    • Parak, F., E. W. Knapp, and D. Kucheida. 1982. Protein dynamics: Mossbauer spectroscopy on deoxymyoglobin crystals. J. Mol. Biol. 161:177-194.
    • (1982) J. Mol. Biol. , vol.161 , pp. 177-194
    • Parak, F.1    Knapp, E.W.2    Kucheida, D.3
  • 35
    • 0029932580 scopus 로고    scopus 로고
    • Analysis of protein conformational characteristics related to thermostability
    • Querol, E., J. A. Perez-Pons, and A. Mozo-Villarias. 1996. Analysis of protein conformational characteristics related to thermostability. Protein. Eng. 9:265-271.
    • (1996) Protein. Eng. , vol.9 , pp. 265-271
    • Querol, E.1    Perez-Pons, J.A.2    Mozo-Villarias, A.3
  • 36
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23:327-341.
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 37
    • 0041874658 scopus 로고    scopus 로고
    • The interplay between protein dynamics and frustration of non-bonded interactions as revealed by molecular dynamics simulations
    • Tavernelli, I., and E. Di Iorio. 2001. The interplay between protein dynamics and frustration of non-bonded interactions as revealed by molecular dynamics simulations. Chem. Phys. Lett. 345:287-294.
    • (2001) Chem. Phys. Lett. , vol.345 , pp. 287-294
    • Tavernelli, I.1    Di Iorio, E.2
  • 38
    • 33646650705 scopus 로고
    • Reversible multiple time scale molecular dynamics
    • Tuckerman, M., B. J. Berne, and G. J. Martyna. 1992. Reversible multiple time scale molecular dynamics. J. Chem. Phys. 97:1990-2001.
    • (1992) J. Chem. Phys. , vol.97 , pp. 1990-2001
    • Tuckerman, M.1    Berne, B.J.2    Martyna, G.J.3
  • 39
    • 0001015060 scopus 로고    scopus 로고
    • Equilibrium thermodynamics of homopolymers and clusters: Molecular dynamics and Monte Carlo simulations of systems with square-well interactions
    • Zhou, Y., M. Karplus, J. M. Wichert, and C. K. Hall. 1997. Equilibrium thermodynamics of homopolymers and clusters: molecular dynamics and Monte Carlo simulations of systems with square-well interactions. J. Chem. Phys. 107:10691-10708.
    • (1997) J. Chem. Phys. , vol.107 , pp. 10691-10708
    • Zhou, Y.1    Karplus, M.2    Wichert, J.M.3    Hall, C.K.4


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