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Volumn 15, Issue 5, 2005, Pages 586-592

Coarse-grained normal mode analysis in structural biology

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; CONFORMATION; MACROMOLECULE; MOLECULAR DYNAMICS; MOLECULAR MODEL; PREDICTION; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN STRUCTURE; REVIEW; STRUCTURE ANALYSIS;

EID: 25844431698     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2005.08.007     Document Type: Review
Times cited : (618)

References (68)
  • 1
    • 0020771265 scopus 로고
    • Dynamics of a small globular protein in terms of low-frequency vibrational modes
    • N. Go, T. Noguti, and T. Nishikawa Dynamics of a small globular protein in terms of low-frequency vibrational modes Proc Natl Acad Sci USA 80 1983 3696 3700
    • (1983) Proc Natl Acad Sci USA , vol.80 , pp. 3696-3700
    • Go, N.1    Noguti, T.2    Nishikawa, T.3
  • 2
    • 0000991642 scopus 로고
    • Harmonic dynamics of proteins: Normal modes and fluctuations in bovine pancreatic trypsin inhibitor
    • B. Brooks, and M. Karplus Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor Proc Natl Acad Sci USA 80 1983 6571 6575
    • (1983) Proc Natl Acad Sci USA , vol.80 , pp. 6571-6575
    • Brooks, B.1    Karplus, M.2
  • 3
    • 0028331255 scopus 로고
    • Normal mode analysis of protein dynamics
    • D.A. Case Normal mode analysis of protein dynamics Curr Opin Struct Biol 4 1994 285 290
    • (1994) Curr Opin Struct Biol , vol.4 , pp. 285-290
    • Case, D.A.1
  • 4
    • 0033117937 scopus 로고    scopus 로고
    • Investigating protein dynamics in collective coordinate space
    • A. Kitao, and N. Go Investigating protein dynamics in collective coordinate space Curr Opin Struct Biol 9 1999 164 169
    • (1999) Curr Opin Struct Biol , vol.9 , pp. 164-169
    • Kitao, A.1    Go, N.2
  • 5
    • 14844286108 scopus 로고    scopus 로고
    • Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes
    • J. Ma Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes Structure 13 2005 373 380 This recent insightful review highlights many applications of coarse-grained NMA to large-scale conformational changes. The article discusses the relationship between NMA modes and the underlying energy landscape, along with some limitations of the methods.
    • (2005) Structure , vol.13 , pp. 373-380
    • Ma, J.1
  • 6
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
    • M.M. Tirion Large amplitude elastic motions in proteins from a single-parameter, atomic analysis Phys Rev Lett 77 1996 1905 1908
    • (1996) Phys Rev Lett , vol.77 , pp. 1905-1908
    • Tirion, M.M.1
  • 7
    • 0345973041 scopus 로고    scopus 로고
    • Gaussian dynamics of folded proteins
    • T. Haliloglu, I. Bahar, and B. Erman Gaussian dynamics of folded proteins Phys Rev Lett 79 1997 3090 3093
    • (1997) Phys Rev Lett , vol.79 , pp. 3090-3093
    • Haliloglu, T.1    Bahar, I.2    Erman, B.3
  • 8
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
    • I. Bahar, A.R. Atilgan, and B. Erman Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential Fold Des 2 1997 173 181
    • (1997) Fold des , vol.2 , pp. 173-181
    • Bahar, I.1    Atilgan, A.R.2    Erman, B.3
  • 9
    • 0032533790 scopus 로고    scopus 로고
    • Analysis of domain motions by approximate normal mode calculations
    • K. Hinsen Analysis of domain motions by approximate normal mode calculations Proteins 33 1998 417 429
    • (1998) Proteins , vol.33 , pp. 417-429
    • Hinsen, K.1
  • 11
    • 0035044995 scopus 로고    scopus 로고
    • Conformational change of proteins arising from normal mode calculations
    • F. Tama, and Y.H. Sanejouand Conformational change of proteins arising from normal mode calculations Protein Eng 14 2001 1 6
    • (2001) Protein Eng , vol.14 , pp. 1-6
    • Tama, F.1    Sanejouand, Y.H.2
  • 12
    • 0347753596 scopus 로고    scopus 로고
    • Mixed levels of coarse-graining of large proteins using elastic network model succeeds in extracting the slowest motions
    • O. Kurkcuoglu, R.L. Jernigan, and P. Doruker Mixed levels of coarse-graining of large proteins using elastic network model succeeds in extracting the slowest motions Polymers 45 2004 649 657
    • (2004) Polymers , vol.45 , pp. 649-657
    • Kurkcuoglu, O.1    Jernigan, R.L.2    Doruker, P.3
  • 13
    • 0037079578 scopus 로고    scopus 로고
    • Dynamics of large proteins through hierarchical levels of coarse-grained structures
    • P. Doruker, R.L. Jernigan, and I. Bahar Dynamics of large proteins through hierarchical levels of coarse-grained structures J Comput Chem 23 2002 119 127
    • (2002) J Comput Chem , vol.23 , pp. 119-127
    • Doruker, P.1    Jernigan, R.L.2    Bahar, I.3
  • 14
    • 0034308140 scopus 로고    scopus 로고
    • Building-block approach for determining low-frequency normal modes of macromolecules
    • F. Tama, F.X. Gadea, O. Marques, and Y.H. Sanejouand Building-block approach for determining low-frequency normal modes of macromolecules Proteins 41 2000 1 7
    • (2000) Proteins , vol.41 , pp. 1-7
    • Tama, F.1    Gadea, F.X.2    Marques, O.3    Sanejouand, Y.H.4
  • 15
    • 0036840202 scopus 로고    scopus 로고
    • 2+-ATPase
    • 2+-ATPase Biophys J 83 2002 2457 2474
    • (2002) Biophys J , vol.83 , pp. 2457-2474
    • Li, G.1    Cui, Q.2
  • 16
    • 0037173062 scopus 로고    scopus 로고
    • How to describe protein motion without amino acid sequence and atomic coordinates
    • D. Ming, Y.F. Kong, M.A. Lambert, Z. Huang, and J.P. Ma How to describe protein motion without amino acid sequence and atomic coordinates Proc Natl Acad Sci USA 99 2002 8620 8625
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 8620-8625
    • Ming, D.1    Kong, Y.F.2    Lambert, M.A.3    Huang, Z.4    Ma, J.P.5
  • 17
    • 0036382958 scopus 로고    scopus 로고
    • Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory
    • F. Tama, W. Wriggers, and C.L. Brooks III Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory J Mol Biol 321 2002 297 305
    • (2002) J Mol Biol , vol.321 , pp. 297-305
    • Tama, F.1    Wriggers, W.2    Brooks III, C.L.3
  • 18
    • 0035996990 scopus 로고    scopus 로고
    • Dynamics of proteins in crystals: Comparison of experiment with simple models
    • S. Kundu, J.S. Melton, D.C. Sorensen, and G.N. Phillips Jr. Dynamics of proteins in crystals: comparison of experiment with simple models Biophys J 83 2002 723 732
    • (2002) Biophys J , vol.83 , pp. 723-732
    • Kundu, S.1    Melton, J.S.2    Sorensen, D.C.3    Phillips Jr., G.N.4
  • 19
  • 20
    • 0042424707 scopus 로고    scopus 로고
    • Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy
    • F. Tama, M. Valle, J. Frank, and C.L. Brooks III Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy Proc Natl Acad Sci USA 100 2003 9319 9323
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 9319-9323
    • Tama, F.1    Valle, M.2    Frank, J.3    Brooks III, C.L.4
  • 21
    • 4344685227 scopus 로고    scopus 로고
    • Global ribosome motions revealed with elastic network model
    • Y. Wang, A.J. Rader, I. Bahar, and R.L. Jernigan Global ribosome motions revealed with elastic network model J Struct Biol 147 2004 302 314
    • (2004) J Struct Biol , vol.147 , pp. 302-314
    • Wang, Y.1    Rader, A.J.2    Bahar, I.3    Jernigan, R.L.4
  • 22
    • 9644266693 scopus 로고    scopus 로고
    • Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis
    • F. Tama, and C.L. Brooks III Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis J Mol Biol 345 2005 299 314
    • (2005) J Mol Biol , vol.345 , pp. 299-314
    • Tama, F.1    Brooks III, C.L.2
  • 23
    • 14844300852 scopus 로고    scopus 로고
    • Maturation dynamics of HK97 bacteriophage capsid
    • A.J. Rader, D.H. Vlad, and I. Bahar Maturation dynamics of HK97 bacteriophage capsid Structure 13 2005 413 421
    • (2005) Structure , vol.13 , pp. 413-421
    • Rader, A.J.1    Vlad, D.H.2    Bahar, I.3
  • 24
    • 17844411211 scopus 로고    scopus 로고
    • Normal-modes-based prediction of protein conformational changes guided by distance constraints
    • W. Zheng, and B.R. Brooks Normal-modes-based prediction of protein conformational changes guided by distance constraints Biophys J 88 2005 3109 3117
    • (2005) Biophys J , vol.88 , pp. 3109-3117
    • Zheng, W.1    Brooks, B.R.2
  • 25
    • 10044234207 scopus 로고    scopus 로고
    • The requirement for mechanical coupling between head and S2 domains in smooth muscle myosin ATPase regulation and its implications for dimeric motor function
    • F. Tama, M. Feig, J. Liu, C.L. Brooks III, and K.A. Taylor The requirement for mechanical coupling between head and S2 domains in smooth muscle myosin ATPase regulation and its implications for dimeric motor function J Mol Biol 345 2005 837 854
    • (2005) J Mol Biol , vol.345 , pp. 837-854
    • Tama, F.1    Feig, M.2    Liu, J.3    Brooks III, C.L.4    Taylor, K.A.5
  • 26
    • 1042291214 scopus 로고    scopus 로고
    • Myosin flexibility: Structural domains and collective vibrations
    • I. Navizet, R. Lavery, and R.L. Jernigan Myosin flexibility: structural domains and collective vibrations Proteins 54 2004 384 393
    • (2004) Proteins , vol.54 , pp. 384-393
    • Navizet, I.1    Lavery, R.2    Jernigan, R.L.3
  • 27
    • 13844276692 scopus 로고    scopus 로고
    • Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model
    • W. Zheng, and B.R. Brooks Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model J Mol Biol 346 2005 745 759 A thorough analysis of the dynamics of the myosin motor domain using coarse-grained NMA. Two types of dynamic correlations, fluctuation based and density based, are examined using a subset of dominant modes. Key residues that control the dynamics are shown to be distributed over functional residues.
    • (2005) J Mol Biol , vol.346 , pp. 745-759
    • Zheng, W.1    Brooks, B.R.2
  • 28
    • 5444228752 scopus 로고    scopus 로고
    • Normal-mode analysis suggests protein flexibility modulation throughout RNA polymerase's functional cycle
    • A. Van Wynsberghe, G. Li, and Q. Cui Normal-mode analysis suggests protein flexibility modulation throughout RNA polymerase's functional cycle Biochemistry 43 2004 13083 13096
    • (2004) Biochemistry , vol.43 , pp. 13083-13096
    • Van Wynsberghe, A.1    Li, G.2    Cui, Q.3
  • 29
    • 0346492917 scopus 로고    scopus 로고
    • Folding core predictions from network models of proteins
    • A.J. Rader, and I. Bahar Folding core predictions from network models of proteins Polymers 45 2004 659 668
    • (2004) Polymers , vol.45 , pp. 659-668
    • Rader, A.J.1    Bahar, I.2
  • 31
    • 0036385839 scopus 로고    scopus 로고
    • Elastic properties of proteins: Insight on the folding process and evolutionary selection of native structures
    • C. Micheletti, G. Lattanzi, and A. Maritan Elastic properties of proteins: insight on the folding process and evolutionary selection of native structures J Mol Biol 321 2002 909 921
    • (2002) J Mol Biol , vol.321 , pp. 909-921
    • Micheletti, C.1    Lattanzi, G.2    Maritan, A.3
  • 32
    • 21244506296 scopus 로고    scopus 로고
    • How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues
    • T. Haliloglu, O. Keskin, B. Ma, and R. Nussinov How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues Biophys J 88 2005 1552 1559
    • (2005) Biophys J , vol.88 , pp. 1552-1559
    • Haliloglu, T.1    Keskin, O.2    Ma, B.3    Nussinov, R.4
  • 33
    • 20444409186 scopus 로고    scopus 로고
    • Coupling between catalytic site and collective dynamics: A requirement for mechanochemical activity of enzymes
    • L.W. Yang, and I. Bahar Coupling between catalytic site and collective dynamics: A requirement for mechanochemical activity of enzymes Structure 13 2005 893 904 GNM analysis applied to a set of 98 enzymes shows that the global hinge centers identified by NMA coincide with, or closely communicate with, catalytic sites, emphasizing the importance of conformational dynamics in assisting enzymatic activity.
    • (2005) Structure , vol.13 , pp. 893-904
    • Yang, L.W.1    Bahar, I.2
  • 34
    • 4043116913 scopus 로고    scopus 로고
    • Predictions of protein flexibility: First-order measures
    • J.A. Kovacs, P. Chacon, and R. Abagyan Predictions of protein flexibility: first-order measures Proteins 56 2004 661 668
    • (2004) Proteins , vol.56 , pp. 661-668
    • Kovacs, J.A.1    Chacon, P.2    Abagyan, R.3
  • 35
    • 0036077875 scopus 로고    scopus 로고
    • Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: The elastic network model
    • M. Delarue, and Y.-H. Sanejouand Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model J Mol Biol 320 2002 1011 1024
    • (2002) J Mol Biol , vol.320 , pp. 1011-1024
    • Delarue, M.1    Sanejouand, Y.-H.2
  • 36
    • 0036721233 scopus 로고    scopus 로고
    • Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic
    • W.G. Krebs, V. Alexandrov, C.A. Wilson, N. Echols, H. Yu, and M. Gerstein Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic Proteins 48 2002 682 695
    • (2002) Proteins , vol.48 , pp. 682-695
    • Krebs, W.G.1    Alexandrov, V.2    Wilson, C.A.3    Echols, N.4    Yu, H.5    Gerstein, M.6
  • 37
    • 2342518038 scopus 로고    scopus 로고
    • On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models
    • •• ], this study investigates the use of low-frequency modes derived from NMA for refining structural models.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 6957-6962
    • Delarue, M.1    Dumas, P.2
  • 38
    • 4344716056 scopus 로고    scopus 로고
    • Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM
    • F. Tama, O. Miyashita, and C.L. Brooks III Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM J Struct Biol 147 2004 315 326 This study uses a few of the slowest modes, determined from coarse-grained NMA of high-resolution structures, to generate new optimally deformed structures that are then fitted into cryo-EM maps. This method has been applied to cryo-EM structures of EF-G-bound ribosome, Escherichia coli RNA polymerase and the swollen state of cowpea chlorotic motile virus capsid. This type of EN/NMA-based flexible fitting seems to be a promising tool for predicting and refining cryo-EM structures, and determining the conformational changes of large structures using low-resolution structural data.
    • (2004) J Struct Biol , vol.147 , pp. 315-326
    • Tama, F.1    Miyashita, O.2    Brooks III, C.L.3
  • 39
    • 1642355235 scopus 로고    scopus 로고
    • Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis
    • F. Tama, O. Miyashita, and C.L. Brooks III Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis J Mol Biol 337 2004 985 999
    • (2004) J Mol Biol , vol.337 , pp. 985-999
    • Tama, F.1    Miyashita, O.2    Brooks III, C.L.3
  • 40
    • 17044432465 scopus 로고    scopus 로고
    • Normal mode-based fitting of atomic structure into electron density maps: Application to sarcoplasmic reticulum Ca-ATPase
    • K. Hinsen, N. Reuter, J. Navaza, D.L. Stokes, and J.J. Lacapère Normal mode-based fitting of atomic structure into electron density maps: application to sarcoplasmic reticulum Ca-ATPase Biophys J 88 2005 818 827 This insightful study of the use of coarse-grained NMA for docking high-resolution structures into cryo-EM densities examines the conformational transition between two forms of a large structure. The method, applied to two different atomic structures of sarcoplasmic reticulum Ca-ATPase, shows that only a few modes contribute to the transition between the two forms - a rotation and translation of the cytoplasmic domain with movements of the cytoplasmic loop. The paper also presents a comprehensive summary of how to select the modes that maximize the overlap with the real cryo-EM data, as well as the number of modes needed to optimize the fit.
    • (2005) Biophys J , vol.88 , pp. 818-827
    • Hinsen, K.1    Reuter, N.2    Navaza, J.3    Stokes, D.L.4    Lacapère, J.J.5
  • 41
    • 10344230919 scopus 로고    scopus 로고
    • Automatic domain decomposition of proteins by a Gaussian network model
    • S. Kundu, D.C. Sorensen, and G.N. Phillips Jr. Automatic domain decomposition of proteins by a Gaussian network model Proteins 57 2004 725 733
    • (2004) Proteins , vol.57 , pp. 725-733
    • Kundu, S.1    Sorensen, D.C.2    Phillips Jr., G.N.3
  • 42
    • 2942638203 scopus 로고    scopus 로고
    • Molecular mechanism of domain swapping in proteins: An analysis of slower motions
    • S. Kundu, and R.L. Jernigan Molecular mechanism of domain swapping in proteins: an analysis of slower motions Biophys J 86 2004 3846 3854
    • (2004) Biophys J , vol.86 , pp. 3846-3854
    • Kundu, S.1    Jernigan, R.L.2
  • 43
    • 0037764042 scopus 로고    scopus 로고
    • Molecular dynamics simulations of peptides and proteins with amplified collective motions
    • Z. Zhang, Y. Shi, and H. Liu Molecular dynamics simulations of peptides and proteins with amplified collective motions Biophys J 84 2003 3583 3593 Global modes from NMA are imposed upon an atomic-level MD simulation in order to speed up the exploration of large-scale domain motion in T4 lysozyme and the refolding of an S-peptide analog.
    • (2003) Biophys J , vol.84 , pp. 3583-3593
    • Zhang, Z.1    Shi, Y.2    Liu, H.3
  • 44
    • 0042378853 scopus 로고    scopus 로고
    • Efficiently explore the energy landscape of proteins in molecular dynamics simulations by amplifying collective motions
    • J. He, Z. Zhang, Y. Shi, and H. Liu Efficiently explore the energy landscape of proteins in molecular dynamics simulations by amplifying collective motions J Chem Phys 119 2003 4005 4017
    • (2003) J Chem Phys , vol.119 , pp. 4005-4017
    • He, J.1    Zhang, Z.2    Shi, Y.3    Liu, H.4
  • 45
    • 9244235496 scopus 로고    scopus 로고
    • A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor
    • R. Tatsumi, Y. Fukunishi, and H. Nakamura A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor J Comput Chem 25 2004 1995 2005
    • (2004) J Comput Chem , vol.25 , pp. 1995-2005
    • Tatsumi, R.1    Fukunishi, Y.2    Nakamura, H.3
  • 46
    • 5444269159 scopus 로고    scopus 로고
    • Normal mode analysis using the driven molecular dynamics method. II. An application to biological macromolecules
    • M. Kaledin, A. Brown, A.L. Kaledin, and J.M. Bowman Normal mode analysis using the driven molecular dynamics method. II. An application to biological macromolecules J Chem Phys 121 2004 5646 5653
    • (2004) J Chem Phys , vol.121 , pp. 5646-5653
    • Kaledin, M.1    Brown, A.2    Kaledin, A.L.3    Bowman, J.M.4
  • 47
    • 0036708474 scopus 로고    scopus 로고
    • Efficient generation of feasible pathways for protein conformational transitions
    • M.K. Kim, R.L. Jernigan, and G.S. Chirikjian Efficient generation of feasible pathways for protein conformational transitions Biophys J 83 2002 1620 1630
    • (2002) Biophys J , vol.83 , pp. 1620-1630
    • Kim, M.K.1    Jernigan, R.L.2    Chirikjian, G.S.3
  • 48
    • 0242268469 scopus 로고    scopus 로고
    • Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins
    • O. Miyashita, J.N. Onuchic, and P.G. Wolynes Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins Proc Natl Acad Sci USA 100 2003 12570 12575
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 12570-12575
    • Miyashita, O.1    Onuchic, J.N.2    Wolynes, P.G.3
  • 49
    • 6944227839 scopus 로고    scopus 로고
    • Dynamical transition and proteinquake in photoactive yellow protein
    • K. Itoh, and M. Sasai Dynamical transition and proteinquake in photoactive yellow protein Proc Natl Acad Sci USA 101 2004 14736 14741
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 14736-14741
    • Itoh, K.1    Sasai, M.2
  • 50
    • 13444305369 scopus 로고    scopus 로고
    • Simple energy landscape model for the kinetics of functional transitions in proteins
    • O. Miyashita, P.G. Wolynes, and J.N. Onuchic Simple energy landscape model for the kinetics of functional transitions in proteins J Phys Chem B 109 2005 1959 1969 The transition between two stable equilibrium structures is explored by modeling both end points as ENs. The theoretical basis of this iterative procedure, introduced in [48], is elaborated upon and a more realistic cracking (partial unfolding) model is employed to better estimate the energy barrier associated with adenylate kinase activity.
    • (2005) J Phys Chem B , vol.109 , pp. 1959-1969
    • Miyashita, O.1    Wolynes, P.G.2    Onuchic, J.N.3
  • 51
    • 23244450294 scopus 로고    scopus 로고
    • Exploring the common dynamics of homologous proteins. Application to the globin family
    • S. Maguid, S. Fernandez Alberti, L. Ferrelli, and J. Echave Exploring the common dynamics of homologous proteins. Application to the globin family Biophys J 89 2005 3 13
    • (2005) Biophys J , vol.89 , pp. 3-13
    • Maguid, S.1    Fernandez Alberti, S.2    Ferrelli, L.3    Echave, J.4
  • 52
    • 14844314722 scopus 로고    scopus 로고
    • An analysis of core deformations in protein superfamilies
    • A. Leo-Macias, P. Lopez-Romero, D. Lupyan, D. Zerbino, and A.R. Ortiz An analysis of core deformations in protein superfamilies Biophys J 88 2005 1291 1299 A comparison of the structural dynamics within protein families indicates that the regions with the highest evolutionary fluctuations correspond to the most unconstrained regions. This suggests that structural topology and dynamics play a role in maintaining protein function during evolution.
    • (2005) Biophys J , vol.88 , pp. 1291-1299
    • Leo-Macias, A.1    Lopez-Romero, P.2    Lupyan, D.3    Zerbino, D.4    Ortiz, A.R.5
  • 53
    • 20444384605 scopus 로고    scopus 로고
    • Mining frequent patterns in protein structures: A study of protease families
    • S.C. Chen, and I. Bahar Mining frequent patterns in protein structures: a study of protease families Bioinformatics 20 2004 i77 i85
    • (2004) Bioinformatics , vol.20
    • Chen, S.C.1    Bahar, I.2
  • 54
    • 0032570266 scopus 로고    scopus 로고
    • Correlation between native state hydrogen exchange and cooperative residue fluctuations from a simple model
    • I. Bahar, A. Wallqvist, D.G. Covell, and R.L. Jernigan Correlation between native state hydrogen exchange and cooperative residue fluctuations from a simple model Biochemistry 37 1998 1067 1075
    • (1998) Biochemistry , vol.37 , pp. 1067-1075
    • Bahar, I.1    Wallqvist, A.2    Covell, D.G.3    Jernigan, R.L.4
  • 55
    • 18544386701 scopus 로고    scopus 로고
    • Domain motions and the open-to-closed conformational transition of an enzyme: A normal mode analysis of S-adenosyl-L-homocysteine hydrolase
    • M.M. Wang, R.T. Borchardt, R.L. Schowen, and K. Kuczera Domain motions and the open-to-closed conformational transition of an enzyme: a normal mode analysis of S-adenosyl-L-homocysteine hydrolase Biochemistry 44 2005 7228 7239
    • (2005) Biochemistry , vol.44 , pp. 7228-7239
    • Wang, M.M.1    Borchardt, R.T.2    Schowen, R.L.3    Kuczera, K.4
  • 57
    • 4544280144 scopus 로고    scopus 로고
    • ProMode: A database of normal mode analyses on protein molecules with a full-atom model
    • H. Wako, M. Kato, and S. Endo ProMode: a database of normal mode analyses on protein molecules with a full-atom model Bioinformatics 20 2004 2035 2043
    • (2004) Bioinformatics , vol.20 , pp. 2035-2043
    • Wako, H.1    Kato, M.2    Endo, S.3
  • 58
    • 3242875210 scopus 로고    scopus 로고
    • ElNémo: A normal mode web server for protein movement analysis and the generation of templates for molecular replacement
    • K. Suhre, and Y.H. Sanejouand ElNémo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement Nucleic Acids Res 32 2004 W610 W614
    • (2004) Nucleic Acids Res , vol.32
    • Suhre, K.1    Sanejouand, Y.H.2
  • 59
    • 25444528449 scopus 로고    scopus 로고
    • WEBnm@: A web application for normal mode analyses of proteins
    • S.M. Hollup, G. Salensminde, and N. Reuter WEBnm@: a web application for normal mode analyses of proteins BMC Bioinformatics 6 2005 1 8
    • (2005) BMC Bioinformatics , vol.6 , pp. 1-8
    • Hollup, S.M.1    Salensminde, G.2    Reuter, N.3
  • 60
    • 0037246863 scopus 로고    scopus 로고
    • MolMovDB: Analysis and visualization of conformational change and structural flexibility
    • N. Echols, D. Milburn, and M. Gerstein MolMovDB: analysis and visualization of conformational change and structural flexibility Nucleic Acids Res 31 2003 478 482
    • (2003) Nucleic Acids Res , vol.31 , pp. 478-482
    • Echols, N.1    Milburn, D.2    Gerstein, M.3
  • 61
    • 20444370307 scopus 로고    scopus 로고
    • Molecular mastication mechanics
    • D.A. Kondrashov, and G.N. Phillips Molecular mastication mechanics Structure 13 2005 836 837
    • (2005) Structure , vol.13 , pp. 836-837
    • Kondrashov, D.A.1    Phillips, G.N.2
  • 62
    • 15944387765 scopus 로고    scopus 로고
    • Dual role of interactions between membranous and soluble portions of helical membrane receptors for folding and signaling
    • J. Klein-Seetharaman Dual role of interactions between membranous and soluble portions of helical membrane receptors for folding and signaling Trends Pharma Sci 26 2005 183 189
    • (2005) Trends Pharma Sci , vol.26 , pp. 183-189
    • Klein-Seetharaman, J.1
  • 63
    • 22244438519 scopus 로고    scopus 로고
    • Normal mode analysis suggests a quaternary twist model for the nicotinic receptor gating mechanism
    • A. Taly, M. DeLauro, T. Grutter, M. Nilges, N. Le Novere, P.J. Corringer, and J.P. Changeux Normal mode analysis suggests a quaternary twist model for the nicotinic receptor gating mechanism Biophys J 88 2005 3954 3965
    • (2005) Biophys J , vol.88 , pp. 3954-3965
    • Taly, A.1    Delauro, M.2    Grutter, T.3    Nilges, M.4    Le Novere, N.5    Corringer, P.J.6    Changeux, J.P.7
  • 64
    • 17844380512 scopus 로고    scopus 로고
    • Conformational dynamics of the ligand-binding domain of inward rectifier K channels as revealed by molecular dynamics simulations: Toward an understanding of Kir channel gating
    • S. Haider, A. Grottesi, B.A. Hall, F.M. Ashcroft, and M.S.P. Sansom Conformational dynamics of the ligand-binding domain of inward rectifier K channels as revealed by molecular dynamics simulations: toward an understanding of Kir channel gating Biophys J 88 2005 3310 3320
    • (2005) Biophys J , vol.88 , pp. 3310-3320
    • Haider, S.1    Grottesi, A.2    Hall, B.A.3    Ashcroft, F.M.4    Sansom, M.S.P.5
  • 65
    • 25844440811 scopus 로고    scopus 로고
    • Elastic models for understanding biomolecular machinery: From enzymes to supramolecular assemblies
    • in press.
    • Chennubhotla C, Rader AJ, Yang L-W, Bahar I: Elastic models for understanding biomolecular machinery: from enzymes to supramolecular assemblies. Phys Biol 2005, in press.
    • (2005) Phys Biol
    • Chennubhotla, C.1    Rader, A.J.2    Yang, L.-W.3    Bahar, I.4
  • 66
    • 20344370764 scopus 로고    scopus 로고
    • Allosteric mechanisms of signal transduction
    • J.-P. Changeux, and S.J. Edelstein Allosteric mechanisms of signal transduction Science 308 2005 1424 1428 An excellent review of models of allosteric mechanisms and their applications to understanding regulatory enzymes, nuclear receptors and various membrane receptors. The article emphasizes the intrinsic ability of unliganded structures to undergo conformational changes that accommodate ligand binding and the prior accessibility of functional conformers in the absence of ligand.
    • (2005) Science , vol.308 , pp. 1424-1428
    • Changeux, J.-P.1    Edelstein, S.J.2
  • 67
    • 18844409482 scopus 로고    scopus 로고
    • Quantifying allosteric effects in proteins
    • D.M. Ming, and M.E. Wall Quantifying allosteric effects in proteins Proteins 59 2005 697 707
    • (2005) Proteins , vol.59 , pp. 697-707
    • Ming, D.M.1    Wall, M.E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.