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Volumn 109, Issue 6, 2015, Pages 1101-1109

Structure-Encoded Global Motions and Their Role in Mediating Protein-Substrate Interactions

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; PROTEIN BINDING;

EID: 84941804038     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2015.06.004     Document Type: Review
Times cited : (49)

References (74)
  • 1
    • 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
    • (2005) Structure , vol.13 , pp. 893-904
    • Yang, L.W.1    Bahar, I.2
  • 2
    • 64849101493 scopus 로고    scopus 로고
    • Protein dynamism and evolvability
    • N. Tokuriki, and D.S. Tawfik Protein dynamism and evolvability Science 324 2009 203 207
    • (2009) Science , vol.324 , pp. 203-207
    • Tokuriki, N.1    Tawfik, D.S.2
  • 3
    • 84865525384 scopus 로고    scopus 로고
    • Sequence evolution correlates with structural dynamics
    • Y. Liu, and I. Bahar Sequence evolution correlates with structural dynamics Mol. Biol. Evol. 29 2012 2253 2263
    • (2012) Mol. Biol. Evol. , vol.29 , pp. 2253-2263
    • Liu, Y.1    Bahar, I.2
  • 4
    • 64849111005 scopus 로고    scopus 로고
    • Sending signals dynamically
    • R.G. Smock, and L.M. Gierasch Sending signals dynamically Science 324 2009 198 203
    • (2009) Science , vol.324 , pp. 198-203
    • Smock, R.G.1    Gierasch, L.M.2
  • 5
    • 84873054389 scopus 로고    scopus 로고
    • Toward understanding allosteric signaling mechanisms in the ATPase domain of molecular chaperones
    • Y. Liu, and I. Bahar Toward understanding allosteric signaling mechanisms in the ATPase domain of molecular chaperones Pac. Symp. Biocomput. 15 2010 269 280
    • (2010) Pac. Symp. Biocomput. , vol.15 , pp. 269-280
    • Liu, Y.1    Bahar, I.2
  • 6
    • 77952938726 scopus 로고    scopus 로고
    • Global dynamics of proteins: Bridging between structure and function
    • I. Bahar, and T.R. Lezon E. Eyal Global dynamics of proteins: bridging between structure and function Annu. Rev. Biophys 39 2010 23 42
    • (2010) Annu. Rev. Biophys , vol.39 , pp. 23-42
    • Bahar, I.1    Lezon, T.R.2    Eyal, E.3
  • 8
    • 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
  • 10
    • 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
  • 11
    • 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
  • 12
    • 0033557178 scopus 로고    scopus 로고
    • Analysis of domain motions in large proteins
    • K. Hinsen, A. Thomas, and M.J. Field Analysis of domain motions in large proteins Proteins 34 1999 369 382
    • (1999) Proteins , vol.34 , pp. 369-382
    • Hinsen, K.1    Thomas, A.2    Field, M.J.3
  • 13
    • 0032932341 scopus 로고    scopus 로고
    • Tertiary and quaternary conformational changes in aspartate transcarbamylase: A normal mode study
    • A. Thomas, and K. Hinsen D. Perahia Tertiary and quaternary conformational changes in aspartate transcarbamylase: a normal mode study Proteins 34 1999 96 112
    • (1999) Proteins , vol.34 , pp. 96-112
    • Thomas, A.1    Hinsen, K.2    Perahia, D.3
  • 14
    • 0035132230 scopus 로고    scopus 로고
    • Anisotropy of fluctuation dynamics of proteins with an elastic network model
    • A.R. Atilgan, and S.R. Durell I. Bahar Anisotropy of fluctuation dynamics of proteins with an elastic network model Biophys. J. 80 2001 505 515
    • (2001) Biophys. J. , vol.80 , pp. 505-515
    • Atilgan, A.R.1    Durell, S.R.2    Bahar, I.3
  • 15
    • 58149161251 scopus 로고    scopus 로고
    • Systematic multiscale parameterization of heterogeneous elastic network models of proteins
    • E. Lyman, J. Pfaendtner, and G.A. Voth Systematic multiscale parameterization of heterogeneous elastic network models of proteins Biophys. J. 95 2008 4183 4192
    • (2008) Biophys. J. , vol.95 , pp. 4183-4192
    • Lyman, E.1    Pfaendtner, J.2    Voth, G.A.3
  • 16
    • 68149141470 scopus 로고    scopus 로고
    • Protein elastic network models and the ranges of cooperativity
    • L. Yang, G. Song, and R.L. Jernigan Protein elastic network models and the ranges of cooperativity Proc. Natl. Acad. Sci. USA 106 2009 12347 12352
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 12347-12352
    • Yang, L.1    Song, G.2    Jernigan, R.L.3
  • 17
    • 84863662039 scopus 로고    scopus 로고
    • Elastic network models are robust to variations in formalism
    • N. Leioatts, T.D. Romo, and A. Grossfield Elastic network models are robust to variations in formalism J. Chem. Theory Comput. 8 2012 2424 2434
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 2424-2434
    • Leioatts, N.1    Romo, T.D.2    Grossfield, A.3
  • 18
    • 84878381053 scopus 로고    scopus 로고
    • Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics
    • G. Zhao, and J.R. Perilla P. Zhang Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics Nature 497 2013 643 646
    • (2013) Nature , vol.497 , pp. 643-646
    • Zhao, G.1    Perilla, J.R.2    Zhang, P.3
  • 19
    • 84901999641 scopus 로고    scopus 로고
    • Light harvesting by lamellar chromatophores in Rhodospirillum photometricum
    • D.E. Chandler, and J. Strumpfer K. Schulten Light harvesting by lamellar chromatophores in Rhodospirillum photometricum Biophys. J. 106 2014 2503 2510
    • (2014) Biophys. J. , vol.106 , pp. 2503-2510
    • Chandler, D.E.1    Strumpfer, J.2    Schulten, K.3
  • 21
    • 69349101503 scopus 로고    scopus 로고
    • Quantifying uncertainty and sampling quality in biomolecular simulations
    • A. Grossfield, and D.M. Zuckerman Quantifying uncertainty and sampling quality in biomolecular simulations Annu. Rep. Comput. Chem. 5 2009 23 48
    • (2009) Annu. Rep. Comput. Chem. , vol.5 , pp. 23-48
    • Grossfield, A.1    Zuckerman, D.M.2
  • 22
    • 79955874370 scopus 로고    scopus 로고
    • Equilibrium sampling in biomolecular simulations
    • D.M. Zuckerman Equilibrium sampling in biomolecular simulations Annu. Rev. Biophys 40 2011 41 62
    • (2011) Annu. Rev. Biophys , vol.40 , pp. 41-62
    • Zuckerman, D.M.1
  • 23
    • 84881430324 scopus 로고    scopus 로고
    • Coupled global and local changes direct substrate translocation by neurotransmitter-sodium symporter ortholog LeuT
    • M.H. Cheng, and I. Bahar Coupled global and local changes direct substrate translocation by neurotransmitter-sodium symporter ortholog LeuT Biophys. J. 105 2013 630 639
    • (2013) Biophys. J. , vol.105 , pp. 630-639
    • Cheng, M.H.1    Bahar, I.2
  • 24
    • 84856225222 scopus 로고    scopus 로고
    • X-ray structures of LeuT in substrate-free outward-open and apo inward-open states
    • H. Krishnamurthy, and E. Gouaux X-ray structures of LeuT in substrate-free outward-open and apo inward-open states Nature 481 2012 469 474
    • (2012) Nature , vol.481 , pp. 469-474
    • Krishnamurthy, H.1    Gouaux, E.2
  • 26
    • 84887404259 scopus 로고    scopus 로고
    • X-ray structure of dopamine transporter elucidates antidepressant mechanism
    • A. Penmatsa, K.H. Wang, and E. Gouaux X-ray structure of dopamine transporter elucidates antidepressant mechanism Nature 503 2013 85 90
    • (2013) Nature , vol.503 , pp. 85-90
    • Penmatsa, A.1    Wang, K.H.2    Gouaux, E.3
  • 27
    • 84930675499 scopus 로고    scopus 로고
    • Insights into the mechanisms of dopamine transporter function modulation by emphetamine, orphenadrine and cocaine biding
    • M.H. Cheng, and E. Block I. Bahar Insights into the mechanisms of dopamine transporter function modulation by emphetamine, orphenadrine and cocaine biding Front. Neurol. 6 2015 134
    • (2015) Front. Neurol. , vol.6 , pp. 134
    • Cheng, M.H.1    Block, E.2    Bahar, I.3
  • 28
    • 84901376917 scopus 로고    scopus 로고
    • Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model
    • A. Das, and M. Gur B. Roux Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model PLOS Comput. Biol. 10 2014 e1003521
    • (2014) PLOS Comput. Biol. , vol.10 , pp. e1003521
    • Das, A.1    Gur, M.2    Roux, B.3
  • 29
    • 84872781515 scopus 로고    scopus 로고
    • Structural biology. (Pseudo-)symmetrical transport
    • L.R. Forrest Structural biology. (Pseudo-)symmetrical transport Science 339 2013 399 401
    • (2013) Science , vol.339 , pp. 399-401
    • Forrest, L.R.1
  • 30
    • 0014029736 scopus 로고
    • Simple allosteric model for membrane pumps
    • O. Jardetzky Simple allosteric model for membrane pumps Nature 211 1966 969 970
    • (1966) Nature , vol.211 , pp. 969-970
    • Jardetzky, O.1
  • 31
    • 84867092080 scopus 로고    scopus 로고
    • Alternating-access mechanism in conformationally asymmetric trimers of the betaine transporter BetP
    • C. Perez, and C. Koshy C. Ziegler Alternating-access mechanism in conformationally asymmetric trimers of the betaine transporter BetP Nature 490 2012 126 130
    • (2012) Nature , vol.490 , pp. 126-130
    • Perez, C.1    Koshy, C.2    Ziegler, C.3
  • 32
    • 70149090164 scopus 로고    scopus 로고
    • The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding
    • A. Bakan, and I. Bahar The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding Proc. Natl. Acad. Sci. USA 106 2009 14349 14354
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 14349-14354
    • Bakan, A.1    Bahar, I.2
  • 33
    • 66249135330 scopus 로고    scopus 로고
    • Allosteric transitions of supramolecular systems explored by network models: Application to chaperonin GroEL
    • Z. Yang, P. Májek, and I. Bahar Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL PLOS Comput. Biol. 5 2009 e1000360
    • (2009) PLOS Comput. Biol. , vol.5 , pp. e1000360
    • Yang, Z.1    Májek, P.2    Bahar, I.3
  • 34
    • 77955833735 scopus 로고    scopus 로고
    • Predicting order of conformational changes during protein conformational transitions using an interpolated elastic network model
    • M. Tekpinar, and W. Zheng Predicting order of conformational changes during protein conformational transitions using an interpolated elastic network model Proteins 78 2010 2469 2481
    • (2010) Proteins , vol.78 , pp. 2469-2481
    • Tekpinar, M.1    Zheng, W.2
  • 35
    • 84904151157 scopus 로고    scopus 로고
    • Opening and closing of a toroidal group II chaperonin revealed by a symmetry constrained elastic network model
    • H. Lee, and S. Seo M.K. Kim Opening and closing of a toroidal group II chaperonin revealed by a symmetry constrained elastic network model Protein Sci. 23 2014 703 713
    • (2014) Protein Sci. , vol.23 , pp. 703-713
    • Lee, H.1    Seo, S.2    Kim, M.K.3
  • 36
    • 73649085109 scopus 로고    scopus 로고
    • Mechanical coupling in myosin V: A simulation study
    • V. Ovchinnikov, B.L. Trout, and M. Karplus Mechanical coupling in myosin V: a simulation study J. Mol. Biol. 395 2010 815 833
    • (2010) J. Mol. Biol. , vol.395 , pp. 815-833
    • Ovchinnikov, V.1    Trout, B.L.2    Karplus, M.3
  • 37
    • 84856707117 scopus 로고    scopus 로고
    • Myosin-V as a mechanical sensor: An elastic network study
    • M. Düttmann, and Y. Togashi A.S. Mikhailov Myosin-V as a mechanical sensor: an elastic network study Biophys. J. 102 2012 542 551
    • (2012) Biophys. J. , vol.102 , pp. 542-551
    • Düttmann, M.1    Togashi, Y.2    Mikhailov, A.S.3
  • 38
    • 84867488922 scopus 로고    scopus 로고
    • Complex intramolecular mechanics of G-actin - An elastic network study
    • M. Düttmann, and M. Mittnenzweig A.S. Mikhailov Complex intramolecular mechanics of G-actin - an elastic network study PLoS ONE 7 2012 e45859
    • (2012) PLoS ONE , vol.7 , pp. e45859
    • Düttmann, M.1    Mittnenzweig, M.2    Mikhailov, A.S.3
  • 39
    • 84898991793 scopus 로고    scopus 로고
    • Allosteric transitions of the maltose transporter studied by an elastic network model
    • C.H. Li, and Y.X. Yang C.X. Wang Allosteric transitions of the maltose transporter studied by an elastic network model Biopolymers 101 2014 758 768
    • (2014) Biopolymers , vol.101 , pp. 758-768
    • Li, C.H.1    Yang, Y.X.2    Wang, C.X.3
  • 40
    • 80053084303 scopus 로고    scopus 로고
    • Large collective motions regulate the functional properties of glutamate transporter trimers
    • J. Jiang, and I.H. Shrivastava S.G. Amara Large collective motions regulate the functional properties of glutamate transporter trimers Proc. Natl. Acad. Sci. USA 108 2011 15141 15146
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 15141-15146
    • Jiang, J.1    Shrivastava, I.H.2    Amara, S.G.3
  • 41
    • 84858763413 scopus 로고    scopus 로고
    • Constraints imposed by the membrane selectively guide the alternating access dynamics of the glutamate transporter GltPh
    • T.R. Lezon, and I. Bahar Constraints imposed by the membrane selectively guide the alternating access dynamics of the glutamate transporter GltPh Biophys. J. 102 2012 1331 1340
    • (2012) Biophys. J. , vol.102 , pp. 1331-1340
    • Lezon, T.R.1    Bahar, I.2
  • 42
    • 77952721198 scopus 로고    scopus 로고
    • Independent and cooperative motions of the Kv1.2 channel: Voltage sensing and gating
    • A. Yeheskel, T. Haliloglu, and N. Ben-Tal Independent and cooperative motions of the Kv1.2 channel: voltage sensing and gating Biophys. J. 98 2010 2179 2188
    • (2010) Biophys. J. , vol.98 , pp. 2179-2188
    • Yeheskel, A.1    Haliloglu, T.2    Ben-Tal, N.3
  • 43
    • 77955897919 scopus 로고    scopus 로고
    • Normal mode gating motions of a ligand-gated ion channel persist in a fully hydrated lipid bilayer model
    • E.J. Bertaccini, J.R. Trudell, and E. Lindahl Normal mode gating motions of a ligand-gated ion channel persist in a fully hydrated lipid bilayer model ACS Chem. Neurosci. 1 2010 552 558
    • (2010) ACS Chem. Neurosci. , vol.1 , pp. 552-558
    • Bertaccini, E.J.1    Trudell, J.R.2    Lindahl, E.3
  • 44
    • 78650570871 scopus 로고    scopus 로고
    • Pore opening and closing of a pentameric ligand-gated ion channel
    • F. Zhu, and G. Hummer Pore opening and closing of a pentameric ligand-gated ion channel Proc. Natl. Acad. Sci. USA 107 2010 19814 19819
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 19814-19819
    • Zhu, F.1    Hummer, G.2
  • 45
    • 79551615831 scopus 로고    scopus 로고
    • Decrypting the sequence of structural events during the gating transition of pentameric ligand-gated ion channels based on an interpolated elastic network model
    • W. Zheng, and A. Auerbach Decrypting the sequence of structural events during the gating transition of pentameric ligand-gated ion channels based on an interpolated elastic network model PLOS Comput. Biol. 7 2011 e1001046
    • (2011) PLOS Comput. Biol. , vol.7 , pp. e1001046
    • Zheng, W.1    Auerbach, A.2
  • 46
    • 84870013769 scopus 로고    scopus 로고
    • Energetics and ion permeation characteristics in a glutamate-gated chloride (GluCl) receptor channel
    • M.H. Cheng, and R.D. Coalson Energetics and ion permeation characteristics in a glutamate-gated chloride (GluCl) receptor channel J. Phys. Chem. B 116 2012 13637 13643
    • (2012) J. Phys. Chem. B , vol.116 , pp. 13637-13643
    • Cheng, M.H.1    Coalson, R.D.2
  • 47
    • 84919668874 scopus 로고    scopus 로고
    • Structure, dynamics and implied gating mechanism of a human cyclic nucleotide-gated channel
    • Y. Gofman, and C. Schärfe N. Ben-Tal Structure, dynamics and implied gating mechanism of a human cyclic nucleotide-gated channel PLOS Comput. Biol. 10 2014 e1003976
    • (2014) PLOS Comput. Biol. , vol.10 , pp. e1003976
    • Gofman, Y.1    Schärfe, C.2    Ben-Tal, N.3
  • 48
    • 80053142382 scopus 로고    scopus 로고
    • Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins
    • L. Meireles, and M. Gur I. Bahar Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins Protein Sci. 20 2011 1645 1658
    • (2011) Protein Sci. , vol.20 , pp. 1645-1658
    • Meireles, L.1    Gur, M.2    Bahar, I.3
  • 49
    • 77449138099 scopus 로고    scopus 로고
    • Modeling G protein-coupled receptors for structure-based drug discovery using low-frequency normal modes for refinement of homology models: Application to H3 antagonists
    • B.K. Rai, and G.J. Tawa C. Humblet Modeling G protein-coupled receptors for structure-based drug discovery using low-frequency normal modes for refinement of homology models: application to H3 antagonists Proteins 78 2010 457 473
    • (2010) Proteins , vol.78 , pp. 457-473
    • Rai, B.K.1    Tawa, G.J.2    Humblet, C.3
  • 50
    • 84884204842 scopus 로고    scopus 로고
    • The interplay of structure and dynamics: Insights from a survey of HIV-1 reverse transcriptase crystal structures
    • J.M. Seckler, and N. Leioatts A. Grossfield The interplay of structure and dynamics: insights from a survey of HIV-1 reverse transcriptase crystal structures Proteins 81 2013 1792 1801
    • (2013) Proteins , vol.81 , pp. 1792-1801
    • Seckler, J.M.1    Leioatts, N.2    Grossfield, A.3
  • 51
    • 84859211500 scopus 로고    scopus 로고
    • ATP-triggered conformational changes delineate substrate-binding and -folding mechanics of the GroEL chaperonin
    • D.K. Clare, and D. Vasishtan H.R. Saibil ATP-triggered conformational changes delineate substrate-binding and -folding mechanics of the GroEL chaperonin Cell 149 2012 113 123
    • (2012) Cell , vol.149 , pp. 113-123
    • Clare, D.K.1    Vasishtan, D.2    Saibil, H.R.3
  • 52
    • 84907486031 scopus 로고    scopus 로고
    • Evol and ProDy for bridging protein sequence evolution and structural dynamics
    • A. Bakan, and A. Dutta I. Bahar Evol and ProDy for bridging protein sequence evolution and structural dynamics Bioinformatics 30 2014 2681 2683
    • (2014) Bioinformatics , vol.30 , pp. 2681-2683
    • Bakan, A.1    Dutta, A.2    Bahar, I.3
  • 53
    • 84907822084 scopus 로고    scopus 로고
    • Crystal structure of a symmetric football-shaped GroEL:GroES2-ATP14 complex determined at 3.8Å reveals rearrangement between two GroEL rings
    • A. Koike-Takeshita, and T. Arakawa T. Shimamura Crystal structure of a symmetric football-shaped GroEL:GroES2-ATP14 complex determined at 3.8Å reveals rearrangement between two GroEL rings J. Mol. Biol. 426 2014 3634 3641
    • (2014) J. Mol. Biol. , vol.426 , pp. 3634-3641
    • Koike-Takeshita, A.1    Arakawa, T.2    Shimamura, T.3
  • 54
    • 0035368238 scopus 로고    scopus 로고
    • The Lys103Asn mutation of HIV-1 RT: A novel mechanism of drug resistance
    • Y. Hsiou, and J. Ding E. Arnold The Lys103Asn mutation of HIV-1 RT: a novel mechanism of drug resistance J. Mol. Biol. 309 2001 437 445
    • (2001) J. Mol. Biol. , vol.309 , pp. 437-445
    • Hsiou, Y.1    Ding, J.2    Arnold, E.3
  • 55
    • 0028924567 scopus 로고
    • Mechanism of inhibition of HIV-1 reverse transcriptase by non-nucleoside inhibitors
    • R. Esnouf, and J. Ren D. Stuart Mechanism of inhibition of HIV-1 reverse transcriptase by non-nucleoside inhibitors Nat. Struct. Biol. 2 1995 303 308
    • (1995) Nat. Struct. Biol. , vol.2 , pp. 303-308
    • Esnouf, R.1    Ren, J.2    Stuart, D.3
  • 56
    • 0028947588 scopus 로고
    • High resolution structures of HIV-1 RT from four RT-inhibitor complexes
    • J. Ren, and R. Esnouf D. Stammers High resolution structures of HIV-1 RT from four RT-inhibitor complexes Nat. Struct. Biol. 2 1995 293 302
    • (1995) Nat. Struct. Biol. , vol.2 , pp. 293-302
    • Ren, J.1    Esnouf, R.2    Stammers, D.3
  • 57
    • 38949218425 scopus 로고    scopus 로고
    • Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes
    • L. Yang, and G. Song R.L. Jernigan Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes Structure 16 2008 321 330
    • (2008) Structure , vol.16 , pp. 321-330
    • Yang, L.1    Song, G.2    Jernigan, R.L.3
  • 58
    • 61449106774 scopus 로고    scopus 로고
    • Principal component analysis of native ensembles of biomolecular structures (PCA-NEST): Insights into functional dynamics
    • L.W. Yang, and E. Eyal A. Kitao Principal component analysis of native ensembles of biomolecular structures (PCA-NEST): insights into functional dynamics Bioinformatics 25 2009 606 614
    • (2009) Bioinformatics , vol.25 , pp. 606-614
    • Yang, L.W.1    Eyal, E.2    Kitao, A.3
  • 59
    • 84904630632 scopus 로고    scopus 로고
    • Local packing density is the main structural determinant of the rate of protein sequence evolution at site level
    • S.W. Yeh, and T.T. Huang J. Echave Local packing density is the main structural determinant of the rate of protein sequence evolution at site level Biomed Res. Int 2014 2014 572409
    • (2014) Biomed Res. Int , vol.2014 , pp. 572409
    • Yeh, S.W.1    Huang, T.T.2    Echave, J.3
  • 60
    • 84883471917 scopus 로고    scopus 로고
    • From sequence and forces to structure, function, and evolution of intrinsically disordered proteins
    • J.D. Forman-Kay, and T. Mittag From sequence and forces to structure, function, and evolution of intrinsically disordered proteins Structure 21 2013 1492 1499
    • (2013) Structure , vol.21 , pp. 1492-1499
    • Forman-Kay, J.D.1    Mittag, T.2
  • 61
    • 83755178457 scopus 로고    scopus 로고
    • Direct-coupling analysis of residue coevolution captures native contacts across many protein families
    • F. Morcos, and A. Pagnani M. Weigt Direct-coupling analysis of residue coevolution captures native contacts across many protein families Proc. Natl. Acad. Sci. USA 108 2011 E1293 E1301
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. E1293-E1301
    • Morcos, F.1    Pagnani, A.2    Weigt, M.3
  • 62
    • 84869447010 scopus 로고    scopus 로고
    • Protein structure prediction from sequence variation
    • D.S. Marks, T.A. Hopf, and C. Sander Protein structure prediction from sequence variation Nat. Biotechnol. 30 2012 1072 1080
    • (2012) Nat. Biotechnol. , vol.30 , pp. 1072-1080
    • Marks, D.S.1    Hopf, T.A.2    Sander, C.3
  • 63
    • 84856090271 scopus 로고    scopus 로고
    • PSICOV: Precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments
    • D.T. Jones, and D.W. Buchan M. Pontil PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments Bioinformatics 28 2012 184 190
    • (2012) Bioinformatics , vol.28 , pp. 184-190
    • Jones, D.T.1    Buchan, D.W.2    Pontil, M.3
  • 64
    • 84994885238 scopus 로고    scopus 로고
    • Sequence co-evolution gives 3D contacts and structures of protein complexes
    • T.A. Hopf, and C.P. Schärfe D.S. Marks Sequence co-evolution gives 3D contacts and structures of protein complexes eLife 3 2014 e03430
    • (2014) ELife , vol.3 , pp. e03430
    • Hopf, T.A.1    Schärfe, C.P.2    Marks, D.S.3
  • 65
    • 84899072164 scopus 로고    scopus 로고
    • FreeContact: Fast and free software for protein contact prediction from residue co-evolution
    • L. Kaján, and T.A. Hopf B. Rost FreeContact: fast and free software for protein contact prediction from residue co-evolution BMC Bioinformatics 15 2014 85
    • (2014) BMC Bioinformatics , vol.15 , pp. 85
    • Kaján, L.1    Hopf, T.A.2    Rost, B.3
  • 66
    • 84931078182 scopus 로고    scopus 로고
    • Comparative study of the effectiveness and limitations of current methods for detecting sequence coevolution
    • W. Mao, and C. Kaya I. Bahar Comparative study of the effectiveness and limitations of current methods for detecting sequence coevolution Bioinformatics 15 2015 1929 1937
    • (2015) Bioinformatics , vol.15 , pp. 1929-1937
    • Mao, W.1    Kaya, C.2    Bahar, I.3
  • 67
    • 79953823548 scopus 로고    scopus 로고
    • A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis
    • G. Bhabha, and J. Lee P.E. Wright A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis Science 332 2011 234 238
    • (2011) Science , vol.332 , pp. 234-238
    • Bhabha, G.1    Lee, J.2    Wright, P.E.3
  • 68
    • 49049096095 scopus 로고    scopus 로고
    • Evolutionary conservation of protein vibrational dynamics
    • S. Maguid, S. Fernandez-Alberti, and J. Echave Evolutionary conservation of protein vibrational dynamics Gene 422 2008 7 13
    • (2008) Gene , vol.422 , pp. 7-13
    • Maguid, S.1    Fernandez-Alberti, S.2    Echave, J.3
  • 69
    • 84930715900 scopus 로고    scopus 로고
    • Structure, dynamics, assembly, and evolution of protein complexes
    • J.A. Marsh, and S.A. Teichmann Structure, dynamics, assembly, and evolution of protein complexes Annu. Rev. Biochem. 84 2015 5.1 5.25
    • (2015) Annu. Rev. Biochem. , vol.84 , pp. 51-525
    • Marsh, J.A.1    Teichmann, S.A.2
  • 70
    • 84901445186 scopus 로고    scopus 로고
    • Protein flexibility facilitates quaternary structure assembly and evolution
    • J.A. Marsh, and S.A. Teichmann Protein flexibility facilitates quaternary structure assembly and evolution PLoS Biol. 12 2014 e1001870
    • (2014) PLoS Biol. , vol.12 , pp. e1001870
    • Marsh, J.A.1    Teichmann, S.A.2
  • 71
    • 84875686450 scopus 로고    scopus 로고
    • Structural dynamics flexibility informs function and evolution at a proteome scale
    • Z.N. Gerek, S. Kumar, and S.B. Ozkan Structural dynamics flexibility informs function and evolution at a proteome scale Evolut. Applic. 6 2013 423 433
    • (2013) Evolut. Applic. , vol.6 , pp. 423-433
    • Gerek, Z.N.1    Kumar, S.2    Ozkan, S.B.3
  • 72
    • 84861139691 scopus 로고    scopus 로고
    • Collective dynamics differentiates functional divergence in protein evolution
    • T.J. Glembo, and D.W. Farrell S.B. Ozkan Collective dynamics differentiates functional divergence in protein evolution PLOS Comput. Biol. 8 2012 e1002428
    • (2012) PLOS Comput. Biol. , vol.8 , pp. e1002428
    • Glembo, T.J.1    Farrell, D.W.2    Ozkan, S.B.3
  • 73
    • 84922379085 scopus 로고    scopus 로고
    • Evolution of conformational dynamics determines the conversion of a promiscuous generalist into a specialist enzyme
    • T. Zou, and V.A. Risso S.B. Ozkan Evolution of conformational dynamics determines the conversion of a promiscuous generalist into a specialist enzyme Mol. Biol. Evol. 32 2015 132 143
    • (2015) Mol. Biol. Evol. , vol.32 , pp. 132-143
    • Zou, T.1    Risso, V.A.2    Ozkan, S.B.3
  • 74
    • 77649097195 scopus 로고    scopus 로고
    • Structural and functional roles of coevolved sites in proteins
    • S. Chakrabarti, and A.R. Panchenko Structural and functional roles of coevolved sites in proteins PLoS ONE 5 2010 e8591
    • (2010) PLoS ONE , vol.5 , pp. e8591
    • Chakrabarti, S.1    Panchenko, A.R.2


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