메뉴 건너뛰기




Volumn 99, Issue 3, 2010, Pages 933-943

Manipulation of conformational change in proteins by single-residue perturbations

Author keywords

[No Author keywords available]

Indexed keywords

ADENYLATE KINASE; AMINO ACID; CHAPERONIN 60; PROTEIN;

EID: 77955680967     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2010.05.020     Document Type: Article
Times cited : (127)

References (42)
  • 1
    • 0022111715 scopus 로고
    • Normal modes for specific motions of macromolecules: Application to the hinge-bending mode of lysozyme
    • Brooks, B., and M. Karplus. 1985. Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme. Proc. Natl. Acad. Sci. USA. 82:4995-4999.
    • (1985) Proc. Natl. Acad. Sci. USA , vol.82 , pp. 4995-4999
    • Brooks, B.1    Karplus, M.2
  • 2
    • 0028331255 scopus 로고
    • Normal-mode analysis of protein dynamics
    • Case, D. A. 1994. Normal-mode analysis of protein dynamics. Curr. Opin. Struct. Biol. 4:285-290.
    • (1994) Curr. Opin. Struct. Biol. , vol.4 , pp. 285-290
    • Case, D.A.1
  • 3
    • 0032533790 scopus 로고    scopus 로고
    • Analysis of domain motions by approximate normal mode calculations
    • Hinsen, K. 1998. Analysis of domain motions by approximate normal mode calculations. Proteins. 33:417-429.
    • (1998) Proteins , vol.33 , pp. 417-429
    • Hinsen, K.1
  • 4
    • 0035044995 scopus 로고    scopus 로고
    • Conformational change of proteins arising from normal mode calculations
    • Tama, F., and Y. H. Sanejouand. 2001. Conformational change of proteins arising from normal mode calculations. Protein Eng. 14:1-6.
    • (2001) Protein Eng , vol.14 , pp. 1-6
    • Tama, F.1    Sanejouand, Y.H.2
  • 5
    • 0035132230 scopus 로고    scopus 로고
    • Anisotropy of fluctuation dynamics of proteins with an elastic network model
    • Atilgan, A. R., S. R. Durell, I. Bahar. 2001. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys. J. 80:505-515.
    • (2001) Biophys. J. , vol.80 , pp. 505-515
    • Atilgan, A.R.1    Durell, S.R.2    Bahar, I.3
  • 6
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
    • Bahar, I., A. R. Atilgan, and B. Erman. 1997. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold. Des. 2:173-181.
    • (1997) Fold. Des. , vol.2 , pp. 173-181
    • Bahar, I.1    Atilgan, A.R.2    Erman, B.3
  • 7
    • 70450065485 scopus 로고    scopus 로고
    • Identification of specificity and promiscuity of PDZ domain interactions through their dynamic behavior
    • Gerek, Z. N., O. Keskin, and S. B. Ozkan. 2009. Identification of specificity and promiscuity of PDZ domain interactions through their dynamic behavior. Proteins. 77:796-811.
    • (2009) Proteins , vol.77 , pp. 796-811
    • Gerek, Z.N.1    Keskin, O.2    Ozkan, S.B.3
  • 8
    • 33749521415 scopus 로고    scopus 로고
    • Optimization and evaluation of a coarse-grained model of protein motion using x-ray crystal data
    • Kondrashov, D. A., Q. Cui, and G. N. Phillips, Jr. 2006. Optimization and evaluation of a coarse-grained model of protein motion using x-ray crystal data. Biophys. J. 91:2760-2767.
    • (2006) Biophys. J. , vol.91 , pp. 2760-2767
    • Kondrashov, D.A.1    Cui, Q.2    Phillips Jr., G.N.3
  • 9
    • 68149141470 scopus 로고    scopus 로고
    • Protein elastic network models and the ranges of cooperativity
    • Yang, L., G. Song, and R. L. Jernigan. 2009. Protein elastic network models and the ranges of cooperativity. Proc. Natl. Acad. Sci. USA. 106:12347-12352.
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 12347-12352
    • Yang, L.1    Song, G.2    Jernigan, R.L.3
  • 10
    • 0032530836 scopus 로고    scopus 로고
    • A database of macromolecular motions
    • Gerstein, M., and W. Krebs. 1998. A database of macromolecular motions. Nucleic Acids Res. 26:4280-4290.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 4280-4290
    • Gerstein, M.1    Krebs, W.2
  • 11
    • 34250001164 scopus 로고    scopus 로고
    • Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: A case study of antibodies
    • Keskin, O. 2007. Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies. BMC Struct. Biol. 7:31.
    • (2007) BMC Struct. Biol. , vol.7 , pp. 31
    • Keskin, O.1
  • 12
    • 34547586177 scopus 로고    scopus 로고
    • MinActionPath: Maximum likelihood trajectory for large-scale structural transitions in a coarsegrained locally harmonic energy landscape
    • Web Server issue
    • Franklin, J., P. Koehl, M. Delarue. 2007. MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarsegrained locally harmonic energy landscape. Nucleic Acids Res. 35 (Web Server issue):W477-W482.
    • (2007) Nucleic Acids Res. , vol.35
    • Franklin, J.1    Koehl, P.2    Delarue, M.3
  • 13
    • 0036708474 scopus 로고    scopus 로고
    • Efficient generation of feasible pathways for protein conformational transitions
    • Kim, M. K., R. L. Jernigan, and G. S. Chirikjian. 2002. Efficient generation of feasible pathways for protein conformational transitions. Biophys. J. 83:1620-1630.
    • (2002) Biophys. J. , vol.83 , pp. 1620-1630
    • Kim, M.K.1    Jernigan, R.L.2    Chirikjian, G.S.3
  • 14
    • 24644483073 scopus 로고    scopus 로고
    • Large amplitude conformational change in proteins explored with a plastic network model: Adenylate kinase
    • Maragakis, P., and M. Karplus. 2005. Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase. J. Mol. Biol. 352:807-822.
    • (2005) J. Mol. Biol. , vol.352 , pp. 807-822
    • Maragakis, P.1    Karplus, M.2
  • 15
    • 34548304871 scopus 로고    scopus 로고
    • Protein conformational transitions explored by mixed elastic network models
    • Zheng, W., B. R. Brooks, and G. Hummer. 2007. Protein conformational transitions explored by mixed elastic network models. Proteins. 69:43-57.
    • (2007) Proteins , vol.69 , pp. 43-57
    • Zheng, W.1    Brooks, B.R.2    Hummer, G.3
  • 16
    • 68149163617 scopus 로고    scopus 로고
    • Large-scale evaluation of dynamically important residues in proteins predicted by the perturbation analysis of a coarse-grained elastic model
    • Zheng, W., and M. Tekpinar. 2009. Large-scale evaluation of dynamically important residues in proteins predicted by the perturbation analysis of a coarse-grained elastic model. BMC Struct. Biol. 9:45.
    • (2009) BMC Struct. Biol. , vol.9 , pp. 45
    • Zheng, W.1    Tekpinar, M.2
  • 17
    • 33646145523 scopus 로고    scopus 로고
    • Can conformational change be described by only a few normal modes?
    • Petrone, P., and V. S. Pande. 2006. Can conformational change be described by only a few normal modes? Biophys. J. 90:1583-1593.
    • (2006) Biophys. J. , vol.90 , pp. 1583-1593
    • Petrone, P.1    Pande, V.S.2
  • 18
    • 21644473891 scopus 로고    scopus 로고
    • Representing receptor flexibility in ligand docking through relevant normal modes
    • Cavasotto, C. N., J. A. Kovacs, and R. A. Abagyan. 2005. Representing receptor flexibility in ligand docking through relevant normal modes. J. Am. Chem. Soc. 127:9632-9640.
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 9632-9640
    • Cavasotto, C.N.1    Kovacs, J.A.2    Abagyan, R.A.3
  • 19
    • 48749126860 scopus 로고    scopus 로고
    • Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking
    • Dobbins, S. E., V. I. Lesk, and M. J. Sternberg. 2008. Insights into protein flexibility: the relationship between normal modes and conformational change upon protein-protein docking. Proc. Natl. Acad. Sci. USA. 105:10390-10395.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 10390-10395
    • Dobbins, S.E.1    Lesk, V.I.2    Sternberg, M.J.3
  • 20
    • 34547666968 scopus 로고    scopus 로고
    • How well can we understand large-scale protein motions using normal modes of elastic network models?
    • Yang, L., G. Song, and R. L. Jernigan. 2007. How well can we understand large-scale protein motions using normal modes of elastic network models? Biophys. J. 93:920-929.
    • (2007) Biophys. J. , vol.93 , pp. 920-929
    • Yang, L.1    Song, G.2    Jernigan, R.L.3
  • 21
    • 0035479570 scopus 로고    scopus 로고
    • Coordination topology and stability for the native and binding conformers of chymotrypsin inhibitor 2
    • Baysal, C., and A. R. Atilgan. 2001. Coordination topology and stability for the native and binding conformers of chymotrypsin inhibitor 2. Proteins. 45:62-70.
    • (2001) Proteins , vol.45 , pp. 62-70
    • Baysal, C.1    Atilgan, A.R.2
  • 22
    • 0034622725 scopus 로고    scopus 로고
    • Identifying the adaptive mechanism in globular proteins: Fluctuations in densely packed regions manipulate flexible parts
    • Yilmaz, L. S., and A. R. Atilgan. 2000. Identifying the adaptive mechanism in globular proteins: fluctuations in densely packed regions manipulate flexible parts. J. Chem. Phys. 113:4454-4464.
    • (2000) J. Chem. Phys. , vol.113 , pp. 4454-4464
    • Yilmaz, L.S.1    Atilgan, A.R.2
  • 23
    • 58149496872 scopus 로고    scopus 로고
    • Modeling the mechanical response of proteins to anisotropic deformation
    • Sacquin-Mora, S., and R. Lavery. 2009. Modeling the mechanical response of proteins to anisotropic deformation. ChemPhysChem. 10:115-118.
    • (2009) ChemPhysChem , vol.10 , pp. 115-118
    • Sacquin-Mora, S.1    Lavery, R.2
  • 24
    • 13844276692 scopus 로고    scopus 로고
    • Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model
    • Zheng, W., and B. Brooks. 2005. Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model. J. Mol. Biol. 346:745-759.
    • (2005) J. Mol. Biol. , vol.346 , pp. 745-759
    • Zheng, W.1    Brooks, B.2
  • 25
    • 33645102817 scopus 로고    scopus 로고
    • Interactions in native binding sites cause a large change in protein dynamics
    • Ming, D., and M. E. Wall. 2006. Interactions in native binding sites cause a large change in protein dynamics. J. Mol. Biol. 358:213-223.
    • (2006) J. Mol. Biol. , vol.358 , pp. 213-223
    • Ming, D.1    Wall, M.E.2
  • 26
    • 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
  • 27
    • 73449126303 scopus 로고    scopus 로고
    • Perturbation-response scanning reveals ligand entry-exit mechanisms of ferric binding protein
    • Atilgan, C., and A. R. Atilgan. 2009. Perturbation-response scanning reveals ligand entry-exit mechanisms of ferric binding protein. PLOS Comput. Biol. 5:e1000544.
    • (2009) PLOS Comput. Biol. , vol.5
    • Atilgan, C.1    Atilgan, A.R.2
  • 29
    • 0035342460 scopus 로고    scopus 로고
    • Elucidating the structural mechanisms for biological activity of the chemokine family
    • Baysal, C., and A. R. Atilgan. 2001. Elucidating the structural mechanisms for biological activity of the chemokine family. Proteins. 43:150-160.
    • (2001) Proteins , vol.43 , pp. 150-160
    • Baysal, C.1    Atilgan, A.R.2
  • 30
    • 0000134445 scopus 로고
    • Vibrational normal-mode spectrum of globular proteins
    • Benavraham, D. 1993. Vibrational normal-mode spectrum of globular proteins. Phys. Rev. B Condens. Matter. 47:14559-14560.
    • (1993) Phys. Rev. B Condens. Matter , vol.47 , pp. 14559-14560
    • Benavraham, D.1
  • 31
    • 0346057951 scopus 로고    scopus 로고
    • Small-world communication of residues and significance for protein dynamics
    • Atilgan, A. R., P. Akan, and C. Baysal. 2004. Small-world communication of residues and significance for protein dynamics. Biophys. J. 86:85-91.
    • (2004) Biophys. J. , vol.86 , pp. 85-91
    • Atilgan, A.R.1    Akan, P.2    Baysal, C.3
  • 32
    • 61649124866 scopus 로고    scopus 로고
    • Allostery wiring diagrams in the transitions that drive the GroEL reaction cycle
    • Tehver, R., J. Chen, and D. Thirumalai. 2009. Allostery wiring diagrams in the transitions that drive the GroEL reaction cycle. J. Mol. Biol. 387:390-406.
    • (2009) J. Mol. Biol. , vol.387 , pp. 390-406
    • Tehver, R.1    Chen, J.2    Thirumalai, D.3
  • 33
    • 40849084893 scopus 로고    scopus 로고
    • Kinetic model for the coupling between allosteric transitions in GroEL and substrate protein folding and aggregation
    • Tehver, R., and D. Thirumalai. 2008. Kinetic model for the coupling between allosteric transitions in GroEL and substrate protein folding and aggregation. J. Mol. Biol. 377:1279-1295.
    • (2008) J. Mol. Biol. , vol.377 , pp. 1279-1295
    • Tehver, R.1    Thirumalai, D.2
  • 34
    • 0033005899 scopus 로고    scopus 로고
    • Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes
    • Betancourt, M. R., and D. Thirumalai. 1999. Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes. Protein Sci. 8:361-369.
    • (1999) Protein Sci , vol.8 , pp. 361-369
    • Betancourt, M.R.1    Thirumalai, D.2
  • 35
    • 0034967287 scopus 로고    scopus 로고
    • Identification of important amino acid residues that modulate binding of Escherichia coli GroEL to its various cochaperones
    • Klein, G., and C. Georgopoulos. 2001. Identification of important amino acid residues that modulate binding of Escherichia coli GroEL to its various cochaperones. Genetics. 158:507-517.
    • (2001) Genetics , vol.158 , pp. 507-517
    • Klein, G.1    Georgopoulos, C.2
  • 36
    • 0034064511 scopus 로고    scopus 로고
    • Conservation among HSP60 sequences in relation to structure, function, and evolution
    • Brocchieri, L., and S. Karlin. 2000. Conservation among HSP60 sequences in relation to structure, function, and evolution. Protein Sci. 9:476-486.
    • (2000) Protein Sci , vol.9 , pp. 476-486
    • Brocchieri, L.1    Karlin, S.2
  • 37
    • 0034003828 scopus 로고    scopus 로고
    • Identifying the determinants in the equatorial domain of Buchnera GroEL implicated in binding Potato leafroll virus
    • Hogenhout, S. A., F. van der Wilk, J. F. van den Heuvel. 2000. Identifying the determinants in the equatorial domain of Buchnera GroEL implicated in binding Potato leafroll virus. J. Virol. 74:4541-4548.
    • (2000) J. Virol. , vol.74 , pp. 4541-4548
    • Hogenhout, S.A.1    Van Der Wilk, F.2    Van Den Heuvel, J.F.3
  • 38
    • 37249032102 scopus 로고    scopus 로고
    • Dynamic personalities of proteins
    • Henzler-Wildman, K., and D. Kern. 2007. Dynamic personalities of proteins. Nature. 450:964-972.
    • (2007) Nature , vol.450 , pp. 964-972
    • Henzler-Wildman, K.1    Kern, D.2
  • 39
    • 0025635858 scopus 로고
    • Mechanism of adenylate kinase. Critical evaluation of the x-ray model and assignment of the AMP site
    • Yan, H. G., T. Dahnke, M. D. Tsai. 1990. Mechanism of adenylate kinase. Critical evaluation of the x-ray model and assignment of the AMP site. Biochemistry. 29:10956-10964.
    • (1990) Biochemistry , vol.29 , pp. 10956-10964
    • Yan, H.G.1    Dahnke, T.2    Tsai, M.D.3
  • 40
    • 36849039429 scopus 로고    scopus 로고
    • A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
    • Henzler-Wildman, K. A., M. Lei, D. Kern. 2007. A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature. 450:913-916.
    • (2007) Nature , vol.450 , pp. 913-916
    • Henzler-Wildman, K.A.1    Lei, M.2    Kern, D.3
  • 41
    • 36849048228 scopus 로고    scopus 로고
    • Intrinsic motions along an enzymatic reaction trajectory
    • Henzler-Wildman, K. A., V. Thai, D. Kern. 2007. Intrinsic motions along an enzymatic reaction trajectory. Nature. 450:838-844.
    • (2007) Nature , vol.450 , pp. 838-844
    • Henzler-Wildman, K.A.1    Thai, V.2    Kern, D.3
  • 42
    • 70350131719 scopus 로고    scopus 로고
    • Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation in proteins
    • Schrank, T. P., D.W. Bolen, and V. J. Hilser. 2009. Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation in proteins. Proc. Natl. Acad. Sci. USA. 106:16984-16989.
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 16984-16989
    • Schrank, T.P.1    Bolen, D.W.2    Hilser, V.J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.