메뉴 건너뛰기




Volumn 24, Issue 5, 2016, Pages 826-837

Identifying Allosteric Hotspots with Dynamics: Application to Inter- and Intra-species Conservation

Author keywords

[No Author keywords available]

Indexed keywords

ALLOSTERISM; ARTICLE; BINDING SITE; COMPARATIVE STUDY; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; EXOME; GENE FREQUENCY; HUMAN; HUMAN GENOME; NEXT GENERATION SEQUENCING; PRIORITY JOURNAL; PURIFYING SELECTION; SPECIES CONSERVATION; SURFACE PROPERTY; ALLOSTERIC SITE; ANIMAL; CHEMISTRY; CONSERVED SEQUENCE; PROCEDURES; SEQUENCE ANALYSIS; SOFTWARE;

EID: 84962708550     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2016.03.008     Document Type: Article
Times cited : (49)

References (51)
  • 4
    • 77954257799 scopus 로고    scopus 로고
    • ConSurf 2010: Calculating evolutionary conservation in sequence and structure of proteins and nucleic acids
    • H. Ashkenazy, E. Erez, E. Martz, T. Pupko, and N. Ben-Tal ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids Nucleic Acids Res. 38 2010 W529 W533
    • (2010) Nucleic Acids Res. , vol.38 , pp. W529-W533
    • Ashkenazy, H.1    Erez, E.2    Martz, E.3    Pupko, T.4    Ben-Tal, N.5
  • 7
    • 67749137351 scopus 로고    scopus 로고
    • Functional annotations improve the predictive score of human disease-related mutations in proteins
    • R. Calabrese, E. Capriotti, P. Fariselli, P.L. Martelli, and R. Casadio Functional annotations improve the predictive score of human disease-related mutations in proteins Hum. Mutat. 30 2009 1237 1244
    • (2009) Hum. Mutat. , vol.30 , pp. 1237-1244
    • Calabrese, R.1    Capriotti, E.2    Fariselli, P.3    Martelli, P.L.4    Casadio, R.5
  • 8
    • 74549149999 scopus 로고    scopus 로고
    • Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure
    • J.A. Capra, R.A. Laskowski, J.M. Thornton, M. Singh, and T.A. Funkhouser Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure PLoS Comput. Biol. 5 2009 e1000585
    • (2009) PLoS Comput. Biol. , vol.5 , pp. e1000585
    • Capra, J.A.1    Laskowski, R.A.2    Thornton, J.M.3    Singh, M.4    Funkhouser, T.A.5
  • 9
    • 84876210821 scopus 로고    scopus 로고
    • ConSurf: Using evolutionary data to raise testable hypotheses about protein function
    • G. Celniker, G. Nimrod, H. Ashkenazy, F. Glaser, E. Martz, and et al. ConSurf: using evolutionary data to raise testable hypotheses about protein function Isr. J. Chem. 13 2013 199 206
    • (2013) Isr. J. Chem. , vol.13 , pp. 199-206
    • Celniker, G.1    Nimrod, G.2    Ashkenazy, H.3    Glaser, F.4    Martz, E.5
  • 10
    • 33749055796 scopus 로고    scopus 로고
    • Markov propagation of allosteric effects in biomolecular systems: Application to GroEL-GroES
    • C. Chennubhotla, and I. Bahar Markov propagation of allosteric effects in biomolecular systems: application to GroEL-GroES Mol. Syst. Biol. 2 2006 36
    • (2006) Mol. Syst. Biol. , vol.2 , pp. 36
    • Chennubhotla, C.1    Bahar, I.2
  • 11
    • 84877580262 scopus 로고    scopus 로고
    • Structure and dynamics of molecular networks: A novel paradigm of drug discovery
    • P. Csermely, T. Korcsmáros, H.J.M. Kiss, G. London, and R. Nussinov Structure and dynamics of molecular networks: a novel paradigm of drug discovery Pharmacol. Ther. 138 2013 333 408
    • (2013) Pharmacol. Ther. , vol.138 , pp. 333-408
    • Csermely, P.1    Korcsmáros, T.2    Kiss, H.J.M.3    London, G.4    Nussinov, R.5
  • 12
    • 33745461893 scopus 로고    scopus 로고
    • Residues crucial for maintaining short paths in network communication mediate signaling in proteins
    • A. del Sol, H. Fujihashi, D. Amoros, and R. Nussinov Residues crucial for maintaining short paths in network communication mediate signaling in proteins Mol. Syst. Biol. 2 2006 2006.0019
    • (2006) Mol. Syst. Biol. , vol.2 , pp. 20060019
    • Del Sol, A.1    Fujihashi, H.2    Amoros, D.3    Nussinov, R.4
  • 15
    • 84923139220 scopus 로고    scopus 로고
    • Comparing the intrinsic dynamics of multiple protein structures using elastic network models
    • E. Fuglebakk, S.P. Tiwari, and N. Reuter Comparing the intrinsic dynamics of multiple protein structures using elastic network models Biochim. Biophys. Acta 1850 2015 911 922
    • (2015) Biochim. Biophys. Acta , vol.1850 , pp. 911-922
    • Fuglebakk, E.1    Tiwari, S.P.2    Reuter, N.3
  • 17
    • 55249123363 scopus 로고    scopus 로고
    • Variations in clique and community patterns in protein structures during allosteric communication: Investigation of dynamically equilibrated structures of methionyl tRNA synthetase complexes
    • A. Ghosh, and S. Vishveshwara Variations in clique and community patterns in protein structures during allosteric communication: investigation of dynamically equilibrated structures of methionyl tRNA synthetase complexes Biochemistry 47 2008 11398 11407
    • (2008) Biochemistry , vol.47 , pp. 11398-11407
    • Ghosh, A.1    Vishveshwara, S.2
  • 19
    • 2542445427 scopus 로고    scopus 로고
    • ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information
    • F. Glaser, T. Pupko, I. Paz, R.E. Bell, D. Bechor-Shental, and et al. ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information Bioinformatics 19 2003 163 164
    • (2003) Bioinformatics , vol.19 , pp. 163-164
    • Glaser, F.1    Pupko, T.2    Paz, I.3    Bell, R.E.4    Bechor-Shental, D.5
  • 20
    • 68749107059 scopus 로고    scopus 로고
    • Protein sectors: Evolutionary units of three-dimensional structure
    • N. Halabi, O. Rivoire, S. Leibler, and R. Ranganathan Protein sectors: evolutionary units of three-dimensional structure Cell 138 2009 774 786
    • (2009) Cell , vol.138 , pp. 774-786
    • Halabi, N.1    Rivoire, O.2    Leibler, S.3    Ranganathan, R.4
  • 21
    • 0003742069 scopus 로고
    • Department of Biochemistry and Molecular Biology, University College London
    • S.J. Hubbard, and J.M. Thornton 'NACCESS', Computer Program 1993 Department of Biochemistry and Molecular Biology, University College London
    • (1993) 'Naccess', Computer Program
    • Hubbard, S.J.1    Thornton, J.M.2
  • 23
    • 84951747918 scopus 로고    scopus 로고
    • Dynamics-driven allostery in protein kinases
    • A.P. Kornev, and S.S. Taylor Dynamics-driven allostery in protein kinases Trends Biochem. Sci. 40 2015 628 647
    • (2015) Trends Biochem. Sci. , vol.40 , pp. 628-647
    • Kornev, A.P.1    Taylor, S.S.2
  • 24
    • 23144448512 scopus 로고    scopus 로고
    • ConSurf 2005: The projection of evolutionary conservation scores of residues on protein structures
    • M. Landau, I. Mayrose, Y. Rosenberg, F. Glaser, E. Martz, T. Pupko, and N. Ben-Tal ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures Nucleic Acids Res. 33 2005 W299 W302
    • (2005) Nucleic Acids Res. , vol.33 , pp. W299-W302
    • Landau, M.1    Mayrose, I.2    Rosenberg, Y.3    Glaser, F.4    Martz, E.5    Pupko, T.6    Ben-Tal, N.7
  • 29
    • 18844409482 scopus 로고    scopus 로고
    • Quantifying allosteric effects in proteins
    • D. Ming, and M.E. Wall Quantifying allosteric effects in proteins Proteins 59 2005 697 707
    • (2005) Proteins , vol.59 , pp. 697-707
    • Ming, D.1    Wall, M.E.2
  • 30
    • 80053440006 scopus 로고    scopus 로고
    • Binding leverage as a molecular basis for allosteric regulation
    • S. Mitternacht, and I.N. Berezovsky Binding leverage as a molecular basis for allosteric regulation PLoS Comput. Biol. 7 2011 e1002148
    • (2011) PLoS Comput. Biol. , vol.7 , pp. e1002148
    • Mitternacht, S.1    Berezovsky, I.N.2
  • 31
    • 79952685998 scopus 로고    scopus 로고
    • A geometry-based generic predictor for catalytic and allosteric sites
    • S. Mitternacht, and I.N. Berezovsky A geometry-based generic predictor for catalytic and allosteric sites Protein Eng. Des. Sel. 24 2011 405 409
    • (2011) Protein Eng. Des. Sel. , vol.24 , pp. 405-409
    • Mitternacht, S.1    Berezovsky, I.N.2
  • 32
    • 0242268469 scopus 로고    scopus 로고
    • Nonlinear elasticity, protein quakes, and the energy landscapes of functional transitions in proteins
    • O. Miyashita, J.N. Onuchic, and P.G. Wolynes Nonlinear elasticity, protein quakes, 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
  • 33
    • 0035026704 scopus 로고    scopus 로고
    • Predicting deleterious amino acid substitutions
    • P.C. Ng, and S. Henikoff Predicting deleterious amino acid substitutions Genome Res. 11 2001 863 874
    • (2001) Genome Res. , vol.11 , pp. 863-874
    • Ng, P.C.1    Henikoff, S.2
  • 34
    • 77950456409 scopus 로고    scopus 로고
    • Assessing the structural conservation of protein pockets to study functional and allosteric sites: Implications for drug discovery
    • A. Panjkovich, and X. Daura Assessing the structural conservation of protein pockets to study functional and allosteric sites: implications for drug discovery BMC Struct. Biol. 10 2010 9
    • (2010) BMC Struct. Biol. , vol.10 , pp. 9
    • Panjkovich, A.1    Daura, X.2
  • 35
    • 84867744642 scopus 로고    scopus 로고
    • Exploiting protein flexibility to predict the location of allosteric sites
    • A. Panjkovich, and X. Daura Exploiting protein flexibility to predict the location of allosteric sites BMC Bioinformatics 13 2012 273
    • (2012) BMC Bioinformatics , vol.13 , pp. 273
    • Panjkovich, A.1    Daura, X.2
  • 36
    • 84455167671 scopus 로고    scopus 로고
    • Hot spots for allosteric regulation on protein surfaces
    • K.A. Reynolds, R.N. McLaughlin, and R. Ranganathan Hot spots for allosteric regulation on protein surfaces Cell 147 2011 1564 1575
    • (2011) Cell , vol.147 , pp. 1564-1575
    • Reynolds, K.A.1    McLaughlin, R.N.2    Ranganathan, R.3
  • 38
  • 40
    • 13844296720 scopus 로고    scopus 로고
    • A systems biology perspective on protein structural dynamics and signal transduction
    • F. Rousseau, and J. Schymkowitz A systems biology perspective on protein structural dynamics and signal transduction Curr. Opin. Struct. Biol. 15 2005 23 30
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 23-30
    • Rousseau, F.1    Schymkowitz, J.2
  • 41
    • 0026743174 scopus 로고
    • Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and residue confidence levels
    • R.B. Russell, and G.J. Barton Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels Proteins 14 1992 309 323
    • (1992) Proteins , vol.14 , pp. 309-323
    • Russell, R.B.1    Barton, G.J.2
  • 44
    • 1642304065 scopus 로고    scopus 로고
    • Structural determinants of allosteric ligand activation in RXR heterodimers
    • A.I. Shulman, C. Larson, D.J. Mangelsdorf, and R. Ranganathan Structural determinants of allosteric ligand activation in RXR heterodimers Cell 116 2004 417 429
    • (2004) Cell , vol.116 , pp. 417-429
    • Shulman, A.I.1    Larson, C.2    Mangelsdorf, D.J.3    Ranganathan, R.4
  • 45
    • 84891837451 scopus 로고    scopus 로고
    • The Human Gene Mutation Database: Building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine
    • P.D. Stenson, M. Mort, E.V. Ball, K. Shaw, A.D. Phillips, and D.N. Cooper The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine Hum. Genet. 133 2014 1 9
    • (2014) Hum. Genet. , vol.133 , pp. 1-9
    • Stenson, P.D.1    Mort, M.2    Ball, E.V.3    Shaw, K.4    Phillips, A.D.5    Cooper, D.N.6
  • 46
    • 0037219686 scopus 로고    scopus 로고
    • Evolutionarily conserved networks of residues mediate allosteric communication in proteins
    • G.M. Süel, S.W. Lockless, M.A. Wall, and R. Ranganathan Evolutionarily conserved networks of residues mediate allosteric communication in proteins Nat. Struct. Biol. 10 2003 59 69
    • (2003) Nat. Struct. Biol. , vol.10 , pp. 59-69
    • Süel, G.M.1    Lockless, S.W.2    Wall, M.A.3    Ranganathan, R.4
  • 47
    • 0035532141 scopus 로고    scopus 로고
    • Estimating the number of clusters in a data set via the gap statistic
    • R. Tibshirani, G. Walther, and T. Hastie Estimating the number of clusters in a data set via the gap statistic J. R. Stat. Soc. 63 2001 411 423
    • (2001) J. R. Stat. Soc. , vol.63 , pp. 411-423
    • Tibshirani, R.1    Walther, G.2    Hastie, T.3
  • 48
    • 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
  • 49
    • 0033621104 scopus 로고    scopus 로고
    • Folding and binding cascades: Shifts in energy landscapes
    • C. Tsai, B. Ma, and R. Nussinov Folding and binding cascades: shifts in energy landscapes Proc. Natl. Acad. Sci. USA 96 1999 9970 9972
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 9970-9972
    • Tsai, C.1    Ma, B.2    Nussinov, R.3
  • 50
    • 84865063074 scopus 로고    scopus 로고
    • Exploring residue component contributions to dynamical network models of allostery
    • A.T. Vanwart, J. Eargle, Z. Luthey-Schulten, and R.E. Amaro Exploring residue component contributions to dynamical network models of allostery J. Chem. Theor. Comput. 8 2012 2949 2961
    • (2012) J. Chem. Theor. Comput. , vol.8 , pp. 2949-2961
    • Vanwart, A.T.1    Eargle, J.2    Luthey-Schulten, Z.3    Amaro, R.E.4
  • 51
    • 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.