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Volumn 64, Issue 1, 2006, Pages 210-218

Analyzing large-scale structural change in proteins: Comparison of principal component projection and Sammon mapping

Author keywords

Conformational change; Dimensionality reduction techniques; Protein flexibility

Indexed keywords

BACTERIAL ENZYME; NUCLEASE; PROTEIN P21; RAS PROTEIN;

EID: 33744814656     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.20981     Document Type: Article
Times cited : (37)

References (63)
  • 1
    • 0028335096 scopus 로고
    • Structural mechanisms for domain movements in proteins
    • Gerstein M, Lesk A, Chothia C. Structural mechanisms for domain movements in proteins. Biochemistry 1994;33(22):6739-6749.
    • (1994) Biochemistry , vol.33 , Issue.22 , pp. 6739-6749
    • Gerstein, M.1    Lesk, A.2    Chothia, C.3
  • 2
    • 0028292635 scopus 로고
    • Harmonic and anharmonic aspects in the dynamics of BPTI: A normal mode analysis and principal component analysis
    • Hayward S, Kitao A, Go N. Harmonic and anharmonic aspects in the dynamics of BPTI: a normal mode analysis and principal component analysis. Protein Sci 1994;3:936-943.
    • (1994) Protein Sci , vol.3 , pp. 936-943
    • Hayward, S.1    Kitao, A.2    Go, N.3
  • 4
    • 0027732618 scopus 로고
    • Effect of solvent of collective motions in globular protein
    • Hayward S, Kitao A, Hirata F, Go N. Effect of solvent of collective motions in globular protein. J Mol Biol 1993;234:1204-1217.
    • (1993) J Mol Biol , vol.234 , pp. 1204-1217
    • Hayward, S.1    Kitao, A.2    Hirata, F.3    Go, N.4
  • 5
    • 0346216028 scopus 로고    scopus 로고
    • Principal components of the protein dynamical transition
    • Tournier A, Smith JC. Principal components of the protein dynamical transition. Phys Rev Lett 2003;91(20):208106.
    • (2003) Phys Rev Lett , vol.91 , Issue.20 , pp. 208106
    • Tournier, A.1    Smith, J.C.2
  • 6
    • 0031043056 scopus 로고    scopus 로고
    • A new method for analyzing protein sequence relationships based on Sammon maps
    • Agrafiotis DK. A new method for analyzing protein sequence relationships based on Sammon maps. Protein Sci 1997;6(2):287-293.
    • (1997) Protein Sci , vol.6 , Issue.2 , pp. 287-293
    • Agrafiotis, D.K.1
  • 7
    • 0042314795 scopus 로고    scopus 로고
    • Indexing and mapping of proteins using a modified nonlinear Sammon projection
    • Apostol I, Szpankowski W. Indexing and mapping of proteins using a modified nonlinear Sammon projection. J Comp Chem 1999;20(10):1049-1059.
    • (1999) J Comp Chem , vol.20 , Issue.10 , pp. 1049-1059
    • Apostol, I.1    Szpankowski, W.2
  • 8
    • 0034909184 scopus 로고    scopus 로고
    • Visualization of expression clusters using Sammon's non-linear mapping
    • Ewing RM, Cherry JM. Visualization of expression clusters using Sammon's non-linear mapping. Bioinformatics 2001;17:658-659.
    • (2001) Bioinformatics , vol.17 , pp. 658-659
    • Ewing, R.M.1    Cherry, J.M.2
  • 9
    • 0027393187 scopus 로고
    • Statistical clustering techniques for the analysis of long molecular dynamics trajectories: Analysis of 2.2-ns trajectories of YPGDV
    • Karpen ME, Tobias DJ, Brooks CL. Statistical clustering techniques for the analysis of long molecular dynamics trajectories: analysis of 2.2-ns trajectories of YPGDV. Biochemistry 1993;32:412-420.
    • (1993) Biochemistry , vol.32 , pp. 412-420
    • Karpen, M.E.1    Tobias, D.J.2    Brooks, C.L.3
  • 10
    • 16344374494 scopus 로고    scopus 로고
    • Thermal unfolding simulations of a multimeric protein-transition state and unfolding pathways
    • Duan J, Nilsson L. Thermal unfolding simulations of a multimeric protein-transition state and unfolding pathways. Proteins 2005;59:170-182.
    • (2005) Proteins , vol.59 , pp. 170-182
    • Duan, J.1    Nilsson, L.2
  • 11
    • 0000231955 scopus 로고
    • Conjugate peak refinement: An algorithm for finding reaction paths and accurate transition states in systems with many degrees of freedom
    • Fischer S, Karplus M. Conjugate peak refinement: an algorithm for finding reaction paths and accurate transition states in systems with many degrees of freedom. Chem Phys Lett 1992;194:252-261.
    • (1992) Chem Phys Lett , vol.194 , pp. 252-261
    • Fischer, S.1    Karplus, M.2
  • 12
    • 17844381111 scopus 로고    scopus 로고
    • A continuous path for the T→R allosteric transition of hemoglobin
    • Olsen K, Fischer S, Karplus M. A continuous path for the T→R allosteric transition of hemoglobin. Biophys J 2000;78:394A.
    • (2000) Biophys J , vol.78
    • Olsen, K.1    Fischer, S.2    Karplus, M.3
  • 13
    • 17844406890 scopus 로고    scopus 로고
    • Automated computation of low-energy pathways for complex rearrangements in proteins: Application to the conformational switch of Ras p21
    • Noe F, Ille F, Smith JC, Fischer S. Automated computation of low-energy pathways for complex rearrangements in proteins: application to the conformational switch of Ras p21. Proteins 2005;59:534-544.
    • (2005) Proteins , vol.59 , pp. 534-544
    • Noe, F.1    Ille, F.2    Smith, J.C.3    Fischer, S.4
  • 15
    • 0000325341 scopus 로고
    • On lines and planes of closest fit to systems of points in space
    • Pearson K. On lines and planes of closest fit to systems of points in space. London, Edinburgh and Dublin Philos Mag J Sci 1901;2:572.
    • (1901) London, Edinburgh and Dublin Philos Mag J Sci , vol.2 , pp. 572
    • Pearson, K.1
  • 16
    • 58149421595 scopus 로고
    • Analysis of a complex of statistical variables into principal components
    • Hotelling H. Analysis of a complex of statistical variables into principal components. J Educ Psychol 1933;24:417-441, 498-520.
    • (1933) J Educ Psychol , vol.24 , pp. 417-441
    • Hotelling, H.1
  • 17
    • 0031043161 scopus 로고    scopus 로고
    • Nucleation mechanisms in protein folding
    • Fersht AR. Nucleation mechanisms in protein folding. Curr Opin Struct Biol 1997;7:3-9.
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 3-9
    • Fersht, A.R.1
  • 18
    • 0000577041 scopus 로고
    • Large-amplitude nonlinear motions in proteins
    • Garcia ANE. Large-amplitude nonlinear motions in proteins. Phys Rev Lett 1992;68:2696-2699.
    • (1992) Phys Rev Lett , vol.68 , pp. 2696-2699
    • Garcia, A.N.E.1
  • 19
    • 0001693358 scopus 로고    scopus 로고
    • Quantitative visualization of a macromolecular potential energy funnel
    • Becker OM. Quantitative visualization of a macromolecular potential energy funnel. J Mol Struct (THEOCHEM) 1997;398-399:507-516.
    • (1997) J Mol Struct (THEOCHEM) , vol.398-399 , pp. 507-516
    • Becker, O.M.1
  • 20
    • 0000127140 scopus 로고
    • Method for estimating the configurational entropy of macromolecules
    • Karplus M, Kushick JN. Method for estimating the configurational entropy of macromolecules. Macromolecules 1981;14:325-332.
    • (1981) Macromolecules , vol.14 , pp. 325-332
    • Karplus, M.1    Kushick, J.N.2
  • 21
    • 0025318327 scopus 로고
    • Motions of an alpha-helical polypeptide: Comparison of molecular and harmonic dynamics
    • Perahia D, Levy RM, Karplus M. Motions of an alpha-helical polypeptide: comparison of molecular and harmonic dynamics. Biopolymers 1990;29:645-677.
    • (1990) Biopolymers , vol.29 , pp. 645-677
    • Perahia, D.1    Levy, R.M.2    Karplus, M.3
  • 22
    • 0026076090 scopus 로고
    • Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations
    • Ichiye T, Karplus M. Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations. Proteins 1991;11:205-217.
    • (1991) Proteins , vol.11 , pp. 205-217
    • Ichiye, T.1    Karplus, M.2
  • 23
    • 0029818017 scopus 로고    scopus 로고
    • The consistency of large concerted motions in proteins in molecular dynamics simulations
    • De Groot BL, Van Aalten DMF, Amadei A, Berendsen HJC. The consistency of large concerted motions in proteins in molecular dynamics simulations. Biophys J 1996;71(4):1707-1713.
    • (1996) Biophys J , vol.71 , Issue.4 , pp. 1707-1713
    • De Groot, B.L.1    Van Aalten, D.M.F.2    Amadei, A.3    Berendsen, H.J.C.4
  • 24
    • 0030888546 scopus 로고    scopus 로고
    • Model-free methods of analyzing domain motions in proteins from simulations: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme
    • Hayward S, Kitao A, Berendsen HJC. Model-free methods of analyzing domain motions in proteins from simulations: a comparison of normal mode analysis and molecular dynamics simulation of lysozyme. Proteins 1997;24:425-437.
    • (1997) Proteins , vol.24 , pp. 425-437
    • Hayward, S.1    Kitao, A.2    Berendsen, H.J.C.3
  • 25
    • 0031910020 scopus 로고    scopus 로고
    • Locally accessible conformations of proteins: Multiple molecular dynamics simulations of crambin
    • Caves LS, Evanseck JD, Karplus M. Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin. Protein Sci 1998;7(3):649-666.
    • (1998) Protein Sci , vol.7 , Issue.3 , pp. 649-666
    • Caves, L.S.1    Evanseck, J.D.2    Karplus, M.3
  • 26
    • 0025294520 scopus 로고
    • Refinement of protein dynamic structure: Normal mode refinement
    • Kidera A, Go N. Refinement of protein dynamic structure: normal mode refinement. Proc Natl Acad Sci USA 1990;87:3718-3722.
    • (1990) Proc Natl Acad Sci USA , vol.87 , pp. 3718-3722
    • Kidera, A.1    Go, N.2
  • 27
    • 0028058108 scopus 로고
    • Collective motions in proteins investigated by X-ray diffuse scattering
    • Mizuguchi K, Kidera A, Go N. Collective motions in proteins investigated by X-ray diffuse scattering. Proteins 1994;18:34-48.
    • (1994) Proteins , vol.18 , pp. 34-48
    • Mizuguchi, K.1    Kidera, A.2    Go, N.3
  • 28
    • 0032546743 scopus 로고    scopus 로고
    • Are there non-trivial dynamic cross-correlations in proteins?
    • Abseher R, Nilges M. Are there non-trivial dynamic cross-correlations in proteins? J Mol Biol 1998;279:911-920.
    • (1998) J Mol Biol , vol.279 , pp. 911-920
    • Abseher, R.1    Nilges, M.2
  • 29
    • 0029586726 scopus 로고
    • Essential dynamics of the cellular retinol binding protein: Evidence for ligand induced conformational changes
    • Van Aalten DMF, Findlay JBC, Amadei A, Berendsen HJC. Essential dynamics of the cellular retinol binding protein: evidence for ligand induced conformational changes. Protein Eng 1995;8:1129-1136.
    • (1995) Protein Eng , vol.8 , pp. 1129-1136
    • Van Aalten, D.M.F.1    Findlay, J.B.C.2    Amadei, A.3    Berendsen, H.J.C.4
  • 31
    • 84887006810 scopus 로고
    • A nonlinear mapping for data structure analysis
    • Sammon JW Jr. A nonlinear mapping for data structure analysis. IEEE Trans Comput 1969;C-18:401-409.
    • (1969) IEEE Trans Comput , vol.C-18 , pp. 401-409
    • Sammon Jr., J.W.1
  • 33
    • 0029552020 scopus 로고
    • A novel representation of protein structure
    • Barlow TW, Richards WG. A novel representation of protein structure. J Mol Graph 1995;13:373-376.
    • (1995) J Mol Graph , vol.13 , pp. 373-376
    • Barlow, T.W.1    Richards, W.G.2
  • 34
    • 0029159959 scopus 로고
    • X-ray structures of the myosin motor domain of Dictyostelium discoideum complexed with MgADP.cntdot.BeFx and MgADP.cntdot.AlF4
    • Fisher AJ, Smith CA, Thoden J, et al. X-ray structures of the myosin motor domain of Dictyostelium discoideum complexed with MgADP.cntdot.BeFx and MgADP.cntdot.AlF4-. Biochemistry 1995;34(28):8960-8972.
    • (1995) Biochemistry , vol.34 , Issue.28 , pp. 8960-8972
    • Fisher, A.J.1    Smith, C.A.2    Thoden, J.3
  • 35
    • 0029960235 scopus 로고    scopus 로고
    • .vanadate complex of the Dictyostelium discoideum myosin motor domain to 1.9 Å resolution
    • .vanadate complex of the Dictyostelium discoideum myosin motor domain to 1.9 Å resolution. Biochemistry 1996;35(17):5404- 5417.
    • (1996) Biochemistry , vol.35 , Issue.17 , pp. 5404-5417
    • Smith, C.A.1    Rayment, I.2
  • 36
    • 0015214368 scopus 로고
    • Mechanism of adenosine triphosphate hydrolysis by actomyosin
    • Lymn RW, Taylor EW. Mechanism of adenosine triphosphate hydrolysis by actomyosin. Biochemistry 1971;10(25):4617-4624.
    • (1971) Biochemistry , vol.10 , Issue.25 , pp. 4617-4624
    • Lymn, R.W.1    Taylor, E.W.2
  • 37
    • 0032883413 scopus 로고    scopus 로고
    • Structural mechanism of muscle contraction
    • Geeves MA, Holmes KC. Structural mechanism of muscle contraction. Annu Rev Biochem 1999;68:687-728.
    • (1999) Annu Rev Biochem , vol.68 , pp. 687-728
    • Geeves, M.A.1    Holmes, K.C.2
  • 38
    • 0018361151 scopus 로고
    • Hemoglobin: The structural changes related to ligand binding and its allosteric mechanism
    • Baldwin J, Chothia C. Hemoglobin: the structural changes related to ligand binding and its allosteric mechanism. J Mol Biol 1979;129:175-220.
    • (1979) J Mol Biol , vol.129 , pp. 175-220
    • Baldwin, J.1    Chothia, C.2
  • 39
    • 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 HJC. 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.C.2
  • 40
    • 0032420786 scopus 로고    scopus 로고
    • Conformational features of a truncated staphylococcal nuclease R (SNR135) and their implications for catalysis
    • Zhou B, Jing GZ. Conformational features of a truncated staphylococcal nuclease R (SNR135) and their implications for catalysis. Arch Biochem Biophys 1998;360:33-40.
    • (1998) Arch Biochem Biophys , vol.360 , pp. 33-40
    • Zhou, B.1    Jing, G.Z.2
  • 41
    • 0034700307 scopus 로고    scopus 로고
    • pH dependence of stability of staphylococcal nuclease: Evidence of substantial electrostatic interactions in the denatured state
    • Whitten ST, Garcia-Moreno B. pH dependence of stability of staphylococcal nuclease: evidence of substantial electrostatic interactions in the denatured state. Biochemistry 2000;39:14292-14304.
    • (2000) Biochemistry , vol.39 , pp. 14292-14304
    • Whitten, S.T.1    Garcia-Moreno, B.2
  • 42
    • 0027988297 scopus 로고
    • Backbone dynamics of a highly disordered 131 residue fragment of staphylococcal nuclease
    • Alexandrescu AT, Shortle D. Backbone dynamics of a highly disordered 131 residue fragment of staphylococcal nuclease. J Mol Biol 1994;242:527-546.
    • (1994) J Mol Biol , vol.242 , pp. 527-546
    • Alexandrescu, A.T.1    Shortle, D.2
  • 43
    • 0034142113 scopus 로고    scopus 로고
    • Correlation between changes in nuclear magnetic resonance order parameters and conformational entropy: Molecular dynamics simulations of native and denatured staphylococcal nuclease
    • Wrabl JO, Shortle D, Woolf TB. Correlation between changes in nuclear magnetic resonance order parameters and conformational entropy: molecular dynamics simulations of native and denatured staphylococcal nuclease. Proteins 2000;38:123-133.
    • (2000) Proteins , vol.38 , pp. 123-133
    • Wrabl, J.O.1    Shortle, D.2    Woolf, T.B.3
  • 44
    • 0030066904 scopus 로고    scopus 로고
    • Mapping the structure of a non-native state of staphylococcal nuclease
    • Ermacora MR, Ledman DW, Fox RO. Mapping the structure of a non-native state of staphylococcal nuclease. Nat Struct Biol 1996;3:59-65.
    • (1996) Nat Struct Biol , vol.3 , pp. 59-65
    • Ermacora, M.R.1    Ledman, D.W.2    Fox, R.O.3
  • 45
    • 0029786948 scopus 로고    scopus 로고
    • A dynamic bundle of four adjacent hydrophobic segments in the denatured state of staphylococcal nuclease
    • Wang Yi, Shortle A. A dynamic bundle of four adjacent hydrophobic segments in the denatured state of staphylococcal nuclease. Protein Sci 1996;5:1898-1906.
    • (1996) Protein Sci , vol.5 , pp. 1898-1906
    • Yi, W.1    Shortle, A.2
  • 46
    • 0024963569 scopus 로고
    • Residual structure in large fragments of staphylococcal nuclease: Effects of amino acid substitution
    • Shortle D, Meeker AK. Residual structure in large fragments of staphylococcal nuclease: effects of amino acid substitution. Biochemistry 1989;28:936-944.
    • (1989) Biochemistry , vol.28 , pp. 936-944
    • Shortle, D.1    Meeker, A.K.2
  • 48
    • 0037441481 scopus 로고    scopus 로고
    • Molecular dynamics simulations reveals a surface salt bridge forming a kinetic trap in unfolding of truncated staphylococcal nuclease
    • Gruia AD, Fischer S, Smith JC. Molecular dynamics simulations reveals a surface salt bridge forming a kinetic trap in unfolding of truncated staphylococcal nuclease. Proteins 2003;50:507-515.
    • (2003) Proteins , vol.50 , pp. 507-515
    • Gruia, A.D.1    Fischer, S.2    Smith, J.C.3
  • 51
    • 0025117674 scopus 로고
    • Molecular switch for signal transduction: Structural differences between active and inactive forms of protooncogenic Ras proteins
    • Milburn MV, Tong L, deVos AM, et al. Molecular switch for signal transduction: structural differences between active and inactive forms of protooncogenic Ras proteins. Science 1990;247:939-945.
    • (1990) Science , vol.247 , pp. 939-945
    • Milburn, M.V.1    Tong, L.2    DeVos, A.M.3
  • 52
    • 0025740753 scopus 로고
    • The structure of ras protein: A model for a universal molecular switch
    • Wittinghofer A, Pai E. The structure of ras protein: a model for a universal molecular switch. Trends Biochem Sci 1991;16:382-387.
    • (1991) Trends Biochem Sci , vol.16 , pp. 382-387
    • Wittinghofer, A.1    Pai, E.2
  • 53
    • 0029089593 scopus 로고
    • Ras-effector interactions, the problem of specificity
    • Wittinghofer A, Herrmann C. Ras-effector interactions, the problem of specificity. FEBS Lett 1995;369:52-56.
    • (1995) FEBS Lett , vol.369 , pp. 52-56
    • Wittinghofer, A.1    Herrmann, C.2
  • 54
    • 0030711616 scopus 로고    scopus 로고
    • Molecular switch in signal transduction: Reaction paths of the conformational changes in ras p21
    • Ma J, Karplus M. Molecular switch in signal transduction: reaction paths of the conformational changes in ras p21. Proc Natl Sci USA 1997;94:11905-11910.
    • (1997) Proc Natl Sci USA , vol.94 , pp. 11905-11910
    • Ma, J.1    Karplus, M.2
  • 55
    • 0000689085 scopus 로고
    • Predicting slow structural transitions in macromolecular systems: Conformational flooding
    • Grubmüller H. Predicting slow structural transitions in macromolecular systems: conformational flooding. Phys Rev E 1995;52:2893-2906.
    • (1995) Phys Rev E , vol.52 , pp. 2893-2906
    • Grubmüller, H.1
  • 56
    • 0040488445 scopus 로고    scopus 로고
    • Functional significance of hierarchical tiers in carbonmonoxy myoglobin: Conformational substrates and transitions studied by conformational flooding simulations
    • Schulze BG, Grubmüller H, Evanseck JD. Functional significance of hierarchical tiers in carbonmonoxy myoglobin: conformational substrates and transitions studied by conformational flooding simulations. J Am Chem Soc 2000;12:8700-8711.
    • (2000) J Am Chem Soc , vol.12 , pp. 8700-8711
    • Schulze, B.G.1    Grubmüller, H.2    Evanseck, J.D.3
  • 59
    • 0029967692 scopus 로고    scopus 로고
    • Towards an exhaustive sampling of the configurational spaces of the two forms of the peptide hormone guanylin
    • De Groot BL, Amadei A, Van Aalten DM, Berendsen HJ. Towards an exhaustive sampling of the configurational spaces of the two forms of the peptide hormone guanylin. J Biomol Struct Dyn 1996;13:741-751.
    • (1996) J Biomol Struct Dyn , vol.13 , pp. 741-751
    • De Groot, B.L.1    Amadei, A.2    Van Aalten, D.M.3    Berendsen, H.J.4
  • 60
    • 11144226928 scopus 로고    scopus 로고
    • Phylogeny of protein-folding trajectories reveals a unique pathway to native structure
    • Ota M, Ikeguchi M, Kidera A. Phylogeny of protein-folding trajectories reveals a unique pathway to native structure. Proc Natl Acad Sci USA 2004;101(51):17658-17663.
    • (2004) Proc Natl Acad Sci USA , vol.101 , Issue.51 , pp. 17658-17663
    • Ota, M.1    Ikeguchi, M.2    Kidera, A.3
  • 61
    • 0030322828 scopus 로고    scopus 로고
    • Homology modeling by distance geometry
    • Aszodi A, Taylor WR. Homology modeling by distance geometry. Fold Des 1996;1:325-334.
    • (1996) Fold Des , vol.1 , pp. 325-334
    • Aszodi, A.1    Taylor, W.R.2
  • 62
    • 0030623726 scopus 로고    scopus 로고
    • Distance geometry based comparative modelling
    • Aszodi A, Munro RE, Taylor WR. Distance geometry based comparative modelling. Fold Des 1997;2:S3-S6.
    • (1997) Fold Des , vol.2
    • Aszodi, A.1    Munro, R.E.2    Taylor, W.R.3
  • 63
    • 41349089279 scopus 로고    scopus 로고
    • Convergence of sampling in protein simulations
    • Hess B. Convergence of sampling in protein simulations. Phys Rev E 2002;65:031910.
    • (2002) Phys Rev E , vol.65 , pp. 031910
    • Hess, B.1


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