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Volumn 107, Issue 6, 2014, Pages 1415-1425

Ligand-induced protein responses and mechanical signal propagation described by linear response theories

Author keywords

[No Author keywords available]

Indexed keywords

CARBON MONOXIDE; LIGAND; MYOGLOBIN;

EID: 84909592217     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2014.07.049     Document Type: Article
Times cited : (19)

References (45)
  • 1
    • 0025163070 scopus 로고
    • Deoxymyoglobin studied by the conformational normal mode analysis. II. The conformational change upon oxygenation
    • Seno, Y., and N. Go¯. 1990. Deoxymyoglobin studied by the conformational normal mode analysis. II. The conformational change upon oxygenation. J. Mol. Biol. 216:111-126.
    • (1990) J. Mol. Biol. , vol.216 , pp. 111-126
    • Seno, Y.1    Go, N.2
  • 2
    • 18144418170 scopus 로고    scopus 로고
    • Protein structural change upon ligand binding: Linear response theory
    • Ikeguchi, M., J. Ueno, ..., A. Kidera. 2005. Protein structural change upon ligand binding: linear response theory. Phys. Rev. Lett. 94:078102.
    • (2005) Phys. Rev. Lett. , vol.94 , pp. 078102
    • Ikeguchi, M.1    Ueno, J.2    Kidera, A.3
  • 3
    • 34547401903 scopus 로고    scopus 로고
    • Primary protein response after ligand photodissociation in carbonmonoxy myoglobin
    • Sato, A., Y. Gao, ..., Y. Mizutani. 2007. Primary protein response after ligand photodissociation in carbonmonoxy myoglobin. Proc. Natl. Acad. Sci. USA. 104:9627-9632.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 9627-9632
    • Sato, A.1    Gao, Y.2    Mizutani, Y.3
  • 4
    • 0030079898 scopus 로고    scopus 로고
    • Picosecond structural dynamics of myoglobin following photolysis of carbon monoxide
    • Causgrove, T. P., and R. B. Dyer. 1996. Picosecond structural dynamics of myoglobin following photolysis of carbon monoxide. J. Phys. Chem. 100:3273-3277.
    • (1996) J. Phys. Chem. , vol.100 , pp. 3273-3277
    • Causgrove, T.P.1    Dyer, R.B.2
  • 5
    • 30044434744 scopus 로고    scopus 로고
    • Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state
    • Tobi, D., and I. Bahar. 2005. Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state. Proc. Natl. Acad. Sci. USA. 102:18908-18913.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 18908-18913
    • Tobi, D.1    Bahar, I.2
  • 6
    • 84868122211 scopus 로고    scopus 로고
    • Response of rotation-translation blocked proteins using Langevin dynamics on a locally harmonic landscape
    • Manson, A. C., and R. D. Coalson. 2012. Response of rotation-translation blocked proteins using Langevin dynamics on a locally harmonic landscape. J. Phys. Chem. B. 116:12142-12158.
    • (2012) J. Phys. Chem. B. , vol.116 , pp. 12142-12158
    • Manson, A.C.1    Coalson, R.D.2
  • 7
    • 68149131936 scopus 로고    scopus 로고
    • Dynamic linear response theory for conformational relaxation of proteins
    • Essiz, S. G., and R. D. Coalson. 2009. Dynamic linear response theory for conformational relaxation of proteins. J. Phys. Chem. B. 113:10859-10869.
    • (2009) J. Phys. Chem. B. , vol.113 , pp. 10859-10869
    • Essiz, S.G.1    Coalson, R.D.2
  • 8
    • 79953905577 scopus 로고    scopus 로고
    • Classification and annotation of the relationship between protein structural change and ligand binding
    • Amemiya, T., R. Koike, ..., A. Kidera. 2011. Classification and annotation of the relationship between protein structural change and ligand binding. J. Mol. Biol. 408:568-584.
    • (2011) J. Mol. Biol. , vol.408 , pp. 568-584
    • Amemiya, T.1    Koike, R.2    Kidera, A.3
  • 9
    • 84857554750 scopus 로고    scopus 로고
    • PSCDB: A database for protein structural change upon ligand binding
    • Amemiya, T., R. Koike, ..., M. Ota. 2012. PSCDB: a database for protein structural change upon ligand binding. Nucleic Acids Res. 40:D554-D558.
    • (2012) Nucleic Acids Res. , vol.40 , pp. D554-D558
    • Amemiya, T.1    Koike, R.2    Ota, M.3
  • 11
    • 0002121327 scopus 로고
    • Stochastic problems in physics and astronomy
    • Chandrasekhar, S. 1943. Stochastic problems in physics and astronomy. Rev. Mod. Phys. 15:1-89.
    • (1943) Rev. Mod. Phys. , vol.15 , pp. 1-89
    • Chandrasekhar, S.1
  • 12
    • 0027732618 scopus 로고
    • Effect of solvent on collective motions in globular protein
    • Hayward, S., A. Kitao, ..., N. Go. 1993. Effect of solvent on collective motions in globular protein. J. Mol. Biol. 234:1207-1217.
    • (1993) J. Mol. Biol. , vol.234 , pp. 1207-1217
    • Hayward, S.1    Kitao, A.2    Go, N.3
  • 13
    • 0000991642 scopus 로고
    • Harmonic dynamics of proteins: Normal modes and fluctuations in bovine pancreatic trypsin inhibitor
    • Brooks, B., and M. Karplus. 1983. Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc. Natl. Acad. Sci. USA. 80:6571-6575.
    • (1983) Proc. Natl. Acad. Sci. USA , vol.80 , pp. 6571-6575
    • Brooks, B.1    Karplus, M.2
  • 14
    • 0020771265 scopus 로고
    • Dynamics of a small globular protein in terms of low-frequency vibrational modes
    • Go, N., T. Noguti, and T. Nishikawa. 1983. Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc. Natl. Acad. Sci. USA. 80:3696-3700.
    • (1983) Proc. Natl. Acad. Sci. USA , vol.80 , pp. 3696-3700
    • Go, N.1    Noguti, T.2    Nishikawa, T.3
  • 15
    • 0000998079 scopus 로고
    • The effects of solvent on the conformation and the collective motions of protein: Normal mode analysis and molecular dynamics simulations of melittin in water and in vacuum
    • Kitao, A., F. Hirata, and N. Go¯. 1991. The effects of solvent on the conformation and the collective motions of protein: Normal mode analysis and molecular dynamics simulations of melittin in water and in vacuum. Chem. Phys. 158:447-472.
    • (1991) Chem. Phys. , vol.158 , pp. 447-472
    • Kitao, A.1    Hirata, F.2    Go, N.3
  • 16
    • 61449106774 scopus 로고    scopus 로고
    • Principal component analysis of native ensembles of biomolecular structures (PCA-NEST): Insights into functional dynamics
    • Yang, L.W., E. Eyal, ..., A. Kitao. 2009. Principal component analysis of native ensembles of biomolecular structures (PCA-NEST): insights into functional dynamics. Bioinformatics. 25:606-614.
    • (2009) Bioinformatics , vol.25 , pp. 606-614
    • Yang, L.W.1    Eyal, E.2    Kitao, A.3
  • 17
    • 0038853525 scopus 로고    scopus 로고
    • Crystal structures of myoglobin-ligand complexes at near-atomic resolution
    • Vojtechovský, J., K. Chu, ..., I. Schlichting. 1999. Crystal structures of myoglobin-ligand complexes at near-atomic resolution. Biophys. J. 77:2153-2174.
    • (1999) Biophys. J. , vol.77 , pp. 2153-2174
    • Vojtechovský, J.1    Chu, K.2    Schlichting, I.3
  • 18
  • 19
    • 84893482610 scopus 로고
    • A solution for the best rotation to relate two sets of vectors
    • Kabsch, W. 1976. A solution for the best rotation to relate two sets of vectors. Acta Crystallogr. A. 32:922-923.
    • (1976) Acta Crystallogr. A , vol.32 , pp. 922-923
  • 20
    • 36149010019 scopus 로고
    • Some studies concerning rotating axes and polyatomic molecules
    • Eckart, C. 1935. Some studies concerning rotating axes and polyatomic molecules. Phys. Rev. 47:552-558.
    • (1935) Phys. Rev. , vol.47 , pp. 552-558
    • Eckart, C.1
  • 21
    • 34249945151 scopus 로고    scopus 로고
    • Insights into equilibrium dynamics of proteins from comparison of NMR and x-ray data with computational predictions
    • Yang, L. W., E. Eyal, ..., I. Bahar. 2007. Insights into equilibrium dynamics of proteins from comparison of NMR and x-ray data with computational predictions. Structure. 15:741-749.
    • (2007) Structure , vol.15 , pp. 741-749
    • Yang, L.W.1    Eyal, E.2    Bahar, I.3
  • 22
    • 33747829284 scopus 로고    scopus 로고
    • oGNM: Online computation of structural dynamics using the Gaussian Network Model
    • Yang, L. W., A. J. Rader, ..., I. Bahar. 2006. oGNM: online computation of structural dynamics using the Gaussian Network Model. Nucleic Acids Res. 34:W24-W31.
    • (2006) Nucleic Acids Res. , vol.34 , pp. W24-W31
    • Yang, L.W.1    Rader, A.J.2    Bahar, I.3
  • 23
    • 0028409107 scopus 로고
    • Discovery of new ligand binding pathways in myoglobin by random mutagenesis
    • Huang, X., and S. G. Boxer. 1994. Discovery of new ligand binding pathways in myoglobin by random mutagenesis. Nat. Struct. Biol. 1:226-229.
    • (1994) Nat. Struct. Biol. , vol.1 , pp. 226-229
    • Huang, X.1    Boxer, S.G.2
  • 24
    • 77954257799 scopus 로고    scopus 로고
    • ConSurf 2010: Calculating evolutionary conservation in sequence and structure of proteins and nucleic acids
    • Ashkenazy, H., E. Erez, ..., N. Ben-Tal. 2010. ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res. 38:W529-W533.
    • (2010) Nucleic Acids Res. , vol.38 , pp. W529-W533
    • Ashkenazy, H.1    Erez, E.2    Ben-Tal, N.3
  • 25
    • 0029156486 scopus 로고
    • A double mutant of sperm whale myoglobin mimics the structure and function of elephant myoglobin
    • Zhao, X., K. Vyas, ..., D. F. Bocian. 1995. A double mutant of sperm whale myoglobin mimics the structure and function of elephant myoglobin. J. Biol. Chem. 270:20763-20774.
    • (1995) J. Biol. Chem. , vol.270 , pp. 20763-20774
    • Zhao, X.1    Vyas, K.2    Bocian, D.F.3
  • 26
    • 0142242162 scopus 로고    scopus 로고
    • Structural dynamics of myoglobin: Ligand migration and binding in valine 68 mutants
    • Nienhaus, K., P. Deng, ..., G. U. Nienhaus. 2003. Structural dynamics of myoglobin: ligand migration and binding in valine 68 mutants. J. Biol. Chem. 278:42532-42544.
    • (2003) J. Biol. Chem. , vol.278 , pp. 42532-42544
    • Nienhaus, K.1    Deng, P.2    Nienhaus, G.U.3
  • 27
    • 7444230904 scopus 로고    scopus 로고
    • Unveiling functional protein motions with picosecond x-ray crystallography and molecular dynamics simulations
    • Hummer, G., F. Schotte, and P. A. Anfinrud. 2004. Unveiling functional protein motions with picosecond x-ray crystallography and molecular dynamics simulations. Proc. Natl. Acad. Sci. USA. 101:15330-15334.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 15330-15334
    • Hummer, G.1    Schotte, F.2    Anfinrud, P.A.3
  • 28
    • 22444450449 scopus 로고    scopus 로고
    • Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion
    • Ota, N., and D. A. Agard. 2005. Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion. J. Mol. Biol. 351:345-354.
    • (2005) J. Mol. Biol. , vol.351 , pp. 345-354
    • Ota, N.1    Agard, D.A.2
  • 29
    • 33749029273 scopus 로고    scopus 로고
    • Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling
    • Sharp, K., and J. J. Skinner. 2006. Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling. Proteins. 65:347-361.
    • (2006) Proteins , vol.65 , pp. 347-361
    • Sharp, K.1    Skinner, J.J.2
  • 30
    • 65949104571 scopus 로고    scopus 로고
    • Frequency-resolved communication maps for proteins and other nanoscale materials
    • Leitner, D.M. 2009. Frequency-resolved communication maps for proteins and other nanoscale materials. J. Chem. Phys. 130:195101.
    • (2009) J. Chem. Phys. , vol.130 , pp. 195101
    • Leitner, D.M.1
  • 31
    • 80051867711 scopus 로고    scopus 로고
    • Communication maps computed for homodimeric hemoglobin: Computational study of water-mediated energy transport in proteins
    • Gnanasekaran, R., J. K. Agbo, and D. M. Leitner. 2011. Communication maps computed for homodimeric hemoglobin: computational study of water-mediated energy transport in proteins. J. Chem. Phys. 135:065103.
    • (2011) J. Chem. Phys. , vol.135 , pp. 065103
    • Gnanasekaran, R.1    Agbo, J.K.2    Leitner, D.M.3
  • 32
    • 58949102247 scopus 로고    scopus 로고
    • Signaling pathways of PDZ2 domain: A molecular dynamics interaction correlation analysis
    • Kong, Y., and M. Karplus. 2009. Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis. Proteins. 74:145-154.
    • (2009) Proteins , vol.74 , pp. 145-154
    • Kong, Y.1    Karplus, M.2
  • 33
    • 33749055796 scopus 로고    scopus 로고
    • Markov propagation of allosteric effects in biomolecular systems: Application to GroEL-GroES
    • Chennubhotla, C., and I. Bahar. 2006. Markov propagation of allosteric effects in biomolecular systems: application to GroEL-GroES. Mol. Syst. Biol. 2:36.
    • (2006) Mol. Syst. Biol. , vol.2 , pp. 36
    • Chennubhotla, C.1    Bahar, I.2
  • 34
    • 0033536602 scopus 로고    scopus 로고
    • Evolutionarily conserved pathways of energetic connectivity in protein families
    • Lockless, S. W., and R. Ranganathan. 1999. Evolutionarily conserved pathways of energetic connectivity in protein families. Science. 286:295-299.
    • (1999) Science , vol.286 , pp. 295-299
    • Lockless, S.W.1    Ranganathan, R.2
  • 35
    • 35648944297 scopus 로고    scopus 로고
    • A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis
    • Ghosh, A., and S. Vishveshwara. 2007. A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis. Proc. Natl. Acad. Sci. USA. 104:15711-15716.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 15711-15716
    • Ghosh, A.1    Vishveshwara, S.2
  • 36
    • 22944454879 scopus 로고    scopus 로고
    • Heat flow in proteins: Computation of thermal transport coefficients
    • Yu, X., and D. M. Leitner. 2005. Heat flow in proteins: computation of thermal transport coefficients. J. Chem. Phys. 122:54902.
    • (2005) J. Chem. Phys. , vol.122 , pp. 54902
    • Yu, X.1    Leitner, D.M.2
  • 37
    • 34848882812 scopus 로고    scopus 로고
    • Signal propagation in proteins and relation to equilibrium fluctuations
    • Chennubhotla, C., and I. Bahar. 2007. Signal propagation in proteins and relation to equilibrium fluctuations. PLOS Comput. Biol. 3:1716-1726.
    • (2007) PLOS Comput. Biol. , vol.3 , pp. 1716-1726
    • Chennubhotla, C.1    Bahar, I.2
  • 38
    • 0038047431 scopus 로고    scopus 로고
    • Watching a protein as it functions with 150-ps time-resolved x-ray crystallography
    • Schotte, F., M. Lim, ..., P. A. Anfinrud. 2003. Watching a protein as it functions with 150-ps time-resolved x-ray crystallography. Science. 300:1944-1947.
    • (2003) Science , vol.300 , pp. 1944-1947
    • Schotte, F.1    Lim, M.2    Anfinrud, P.A.3
  • 39
    • 49649084492 scopus 로고    scopus 로고
    • Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms
    • Okazaki, K., and S. Takada. 2008. Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms. Proc. Natl. Acad. Sci. USA. 105:11182-11187.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 11182-11187
    • Okazaki, K.1    Takada, S.2
  • 40
    • 84986472098 scopus 로고
    • Conformational dynamics of polypeptides and proteins in the dihedral angle space and in the cartesian coordinate space: Normal mode analysis of deca-alanine
    • Kitao, A., and N. Go¯. 1991. Conformational dynamics of polypeptides and proteins in the dihedral angle space and in the cartesian coordinate space: normal mode analysis of deca-alanine. J. Comput. Chem. 12:359-368.
    • (1991) J. Comput. Chem. , vol.12 , pp. 359-368
    • Kitao, A.1    Go, N.2
  • 41
    • 0000081668 scopus 로고
    • Collective variable description of native protein dynamics
    • Hayward, S., and N. Go. 1995. Collective variable description of native protein dynamics. Annu. Rev. Phys. Chem. 46:223-250.
    • (1995) Annu. Rev. Phys. Chem. , vol.46 , pp. 223-250
    • Hayward, S.1    Go, N.2
  • 42
    • 14844286108 scopus 로고    scopus 로고
    • Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes
    • Ma, J. 2005. Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. Structure. 13:373-380.
    • (2005) Structure , vol.13 , pp. 373-380
    • Ma, J.1
  • 43
    • 20444409186 scopus 로고    scopus 로고
    • Coupling between catalytic site and collective dynamics: A requirement for mechanochemical activity of enzymes
    • Yang, L. W., and I. Bahar. 2005. Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes. Structure. 13:893-904.
    • (2005) Structure , vol.13 , pp. 893-904
    • Yang, L.W.1    Bahar, I.2
  • 44
    • 33644517853 scopus 로고    scopus 로고
    • Functional modes of proteins are among the most robust
    • Nicolay, S., and Y. H. Sanejouand. 2006. Functional modes of proteins are among the most robust. Phys. Rev. Lett. 96:078104.
    • (2006) Phys. Rev. Lett. , vol.96 , pp. 078104
    • Nicolay, S.1    Sanejouand, Y.H.2
  • 45
    • 77952938726 scopus 로고    scopus 로고
    • Global dynamics of proteins: Bridging between structure and function
    • Bahar, I., T. R. Lezon, ..., E. Eyal. 2010. Global dynamics of proteins: bridging between structure and function. Annu. Rev. Biophys. 39:23-42.
    • (2010) Annu. Rev. Biophys. , vol.39 , pp. 23-42
    • Bahar, I.1    Lezon, T.R.2    Eyal, E.3


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