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Volumn 63, Issue 1, 2006, Pages 197-209

An enhanced elastic network model to represent the motions of domain-swapped proteins

Author keywords

Domain motion; Domain rigidity; Domain swapping; Elastic network models; Overlap measure; Transition pathways

Indexed keywords

DIMER; OLIGOMER;

EID: 33645019704     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.20836     Document Type: Article
Times cited : (61)

References (34)
  • 4
    • 0037038372 scopus 로고    scopus 로고
    • Absolute comparison of simulated and experimental protein-folding dynamics
    • Snow CD, Nguyen H, Pande VS, Gruebele M. Absolute comparison of simulated and experimental protein-folding dynamics. Nature 2002;420:102-106.
    • (2002) Nature , vol.420 , pp. 102-106
    • Snow, C.D.1    Nguyen, H.2    Pande, V.S.3    Gruebele, M.4
  • 5
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
    • Tirion MM. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys Rev Lett 1996;77:1905-1908.
    • (1996) Phys Rev Lett , vol.77 , pp. 1905-1908
    • Tirion, M.M.1
  • 6
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
    • Bahar I, Atilgan AR, Erman B. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des 1997;2:173-181.
    • (1997) Fold des , vol.2 , pp. 173-181
    • Bahar, I.1    Atilgan, A.R.2    Erman, B.3
  • 7
    • 0032533790 scopus 로고    scopus 로고
    • Analysis of domain motions by approximate normal mode calculations
    • Hinsen K. Analysis of domain motions by approximate normal mode calculations. Proteins 1998;33:417-429.
    • (1998) Proteins , vol.33 , pp. 417-429
    • Hinsen, K.1
  • 8
    • 0345973041 scopus 로고    scopus 로고
    • Gaussian dynamics of folded proteins
    • Haliloglu T, Bahar I, Erman B. Gaussian dynamics of folded proteins. Phys Rev Lett 1997;79:3090-3093.
    • (1997) Phys Rev Lett , vol.79 , pp. 3090-3093
    • Haliloglu, T.1    Bahar, I.2    Erman, B.3
  • 10
    • 0029560322 scopus 로고
    • Hinge-bending motion in citrate synthase arising from normal mode calculations
    • Marques O, Sanejouand YH. Hinge-bending motion in citrate synthase arising from normal mode calculations. Proteins 1995;23:557-560.
    • (1995) Proteins , vol.23 , pp. 557-560
    • Marques, O.1    Sanejouand, Y.H.2
  • 13
    • 0242438173 scopus 로고    scopus 로고
    • Using motion planning to map protein folding landscapes and analyze folding kinetics of known native structures
    • special issue of Int Conf Comput Mol Biol (RECOMB)
    • Amato NM, Dill Ken A, Song G. Using motion planning to map protein folding landscapes and analyze folding kinetics of known native structures. J Comput Biol 2003;10:239-256 (special issue of Int Conf Comput Mol Biol (RECOMB); 2002).
    • (2002) J Comput Biol , vol.10 , pp. 239-256
    • Amato, N.M.1    Dill Ken, A.2    Song, G.3
  • 14
    • 0042629768 scopus 로고    scopus 로고
    • A path planning-based study of protein folding with a case study of hairpin formation in protein G and L
    • Song G, Thomas SL, Dill KA, Scholtz JM, Amato NM. A path planning-based study of protein folding with a case study of hairpin formation in protein G and L. In Proc Pacific Symp Biocomput (PSB); 2003. p 240-251.
    • (2003) Proc Pacific Symp Biocomput (PSB) , pp. 240-251
    • Song, G.1    Thomas, S.L.2    Dill, K.A.3    Scholtz, J.M.4    Amato, N.M.5
  • 16
    • 0000081668 scopus 로고
    • Collective variable description of native protein dynamics
    • Hayward S, Go N. Collective variable description of native protein dynamics. Annu Rev Phys Chem 1995;46:223-250.
    • (1995) Annu Rev Phys Chem , vol.46 , pp. 223-250
    • Hayward, S.1    Go, N.2
  • 17
    • 0034308140 scopus 로고    scopus 로고
    • Building-block approach for determining low-frequency normal modes of macromolecules
    • Tama F, Gadea FX, Marques O, Sanejouand YH. Building-block approach for determining low-frequency normal modes of macromolecules. Proteins 2000;41:1-7.
    • (2000) Proteins , vol.41 , pp. 1-7
    • Tama, F.1    Gadea, F.X.2    Marques, O.3    Sanejouand, Y.H.4
  • 18
    • 0037079578 scopus 로고    scopus 로고
    • Dynamics of large proteins through hierarchical levels of coarse-grained structures
    • Doruker P, Jernigan RL, Bahar I. Dynamics of large proteins through hierarchical levels of coarse-grained structures. J Comput Chem 2002;23:119-127.
    • (2002) J Comput Chem , vol.23 , pp. 119-127
    • Doruker, P.1    Jernigan, R.L.2    Bahar, I.3
  • 19
    • 0141815545 scopus 로고    scopus 로고
    • Functional motions can be extracted from on-lattice construction of protein structures
    • Doruker P, Jernigan RL. Functional motions can be extracted from on-lattice construction of protein structures. Proteins 2003;53:174-181.
    • (2003) Proteins , vol.53 , pp. 174-181
    • Doruker, P.1    Jernigan, R.L.2
  • 20
    • 0347753596 scopus 로고    scopus 로고
    • Mixed levels of coarse-graining of large proteins using elastic network model succeeds in extracting the slowest motions
    • Kurkcuoglu O, Jernigan RL, Doruker P. Mixed levels of coarse-graining of large proteins using elastic network model succeeds in extracting the slowest motions. Polymer 2004;45:649-657.
    • (2004) Polymer , vol.45 , pp. 649-657
    • Kurkcuoglu, O.1    Jernigan, R.L.2    Doruker, P.3
  • 21
    • 23244465157 scopus 로고    scopus 로고
    • Rigid-cluster models of conformational transitions in macro-molecular machines and assemblies
    • Kim MK, Jernigan RL, Chirikjian GS. Rigid-cluster models of conformational transitions in macro-molecular machines and assemblies. Biophys J 2005;89:43-55.
    • (2005) Biophys J , vol.89 , pp. 43-55
    • Kim, M.K.1    Jernigan, R.L.2    Chirikjian, G.S.3
  • 22
    • 0028077637 scopus 로고
    • Refined structure of dimeric diphtheria toxin at 2.0 A resolution
    • Bennett MJ, Choe S, Eisenberg D. Refined structure of dimeric diphtheria toxin at 2.0 A resolution. Proteins 1994;3:1444-1463.
    • (1994) Proteins , vol.3 , pp. 1444-1463
    • Bennett, M.J.1    Choe, S.2    Eisenberg, D.3
  • 23
    • 2942638203 scopus 로고    scopus 로고
    • Molecular mechanism of domain swapping in proteins: An analysis of slower motions
    • Kundu S, Jernigan RL. Molecular mechanism of domain swapping in proteins: an analysis of slower motions. Biophys J 2004;86:3846-3854.
    • (2004) Biophys J , vol.86 , pp. 3846-3854
    • Kundu, S.1    Jernigan, R.L.2
  • 24
    • 0036108484 scopus 로고    scopus 로고
    • 3D domain swapping: As domains continue to swap
    • Liu Y, Eisenberg D. 3D domain swapping: as domains continue to swap. Protein Sci 2002;11:1285-1299.
    • (2002) Protein Sci , vol.11 , pp. 1285-1299
    • Liu, Y.1    Eisenberg, D.2
  • 25
    • 0029159748 scopus 로고
    • Rigid domains in proteins: An algorithmic approach to their identification
    • Nichols WL, Rose GD, Eyck LF. Ten, Zimm B.H. Rigid domains in proteins: an algorithmic approach to their identification. Proteins 1995;23:38-48.
    • (1995) Proteins , vol.23 , pp. 38-48
    • Nichols, W.L.1    Rose, G.D.2    Eyck, L.F.3    Ten Zimm, B.H.4
  • 26
    • 0030883755 scopus 로고    scopus 로고
    • Protein domain movements: Detection of rigid domains and visualization of hinges in comparisons of atomic coordinates
    • Wriggers W, Schulten K. Protein domain movements: detection of rigid domains and visualization of hinges in comparisons of atomic coordinates. Proteins 1997;29:1-14.
    • (1997) Proteins , vol.29 , pp. 1-14
    • Wriggers, W.1    Schulten, K.2
  • 27
    • 0033557178 scopus 로고    scopus 로고
    • Analysis of domain motions in large proteins
    • Hinsen K, Thomas A, Field MJ. Analysis of domain motions in large proteins. Proteins 1999;34:369-382.
    • (1999) Proteins , vol.34 , pp. 369-382
    • Hinsen, K.1    Thomas, A.2    Field, M.J.3
  • 28
    • 0032006209 scopus 로고    scopus 로고
    • Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and t4 lysozyme
    • Hayward S, Berendsen HJ. Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and t4 lysozyme. Proteins 1998;30:144-154.
    • (1998) Proteins , vol.30 , pp. 144-154
    • Hayward, S.1    Berendsen, H.J.2
  • 29
    • 12944249776 scopus 로고
    • A discussion of the solution for the best rotation to relate two sets of vectors
    • Kabsch W. A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallogr 1978;A34:827-828.
    • (1978) Acta Crystallogr , vol.A34 , pp. 827-828
    • Kabsch, W.1
  • 30
    • 0035044995 scopus 로고    scopus 로고
    • Conformational change of proteins arising from normal mode calculations
    • Tama F, Sanejouand YH. Conformational change of proteins arising from normal mode calculations. Protein Eng 2001;14:1-6.
    • (2001) Protein Eng , vol.14 , pp. 1-6
    • Tama, F.1    Sanejouand, Y.H.2
  • 31
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen bonded and geometrical features
    • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen bonded and geometrical features. Biopolymers 1983;22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 32
    • 0036840202 scopus 로고    scopus 로고
    • A coarse-grained normal mode approach for macromolecules: An efficient implementation and application to ca(2+)-atpase
    • Li G, Cui Q. A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to ca(2+)-atpase. Biophys J 2002;83:2457-2474.
    • (2002) Biophys J , vol.83 , pp. 2457-2474
    • Li, G.1    Cui, Q.2
  • 33
    • 0242558375 scopus 로고    scopus 로고
    • Normal mode analysis of proteins: A comparison of rigid cluster modes with c(alpha) coarse graining
    • Schuyler AD, Chirikjian GS. Normal mode analysis of proteins: a comparison of rigid cluster modes with c(alpha) coarse graining. J Mol Graph Model 2004;22:183-193.
    • (2004) J Mol Graph Model , vol.22 , pp. 183-193
    • Schuyler, A.D.1    Chirikjian, G.S.2
  • 34
    • 0028865843 scopus 로고
    • 3D domain swapping: A mechanism for oligomer assembly
    • Bennett MJ, Schlunegger MP, Eisenberg D. 3D domain swapping: a mechanism for oligomer assembly. Protein Sci 1995;4:2455-2468.
    • (1995) Protein Sci , vol.4 , pp. 2455-2468
    • Bennett, M.J.1    Schlunegger, M.P.2    Eisenberg, D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.