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Volumn 21, Issue 10, 2013, Pages 1725-1734

Efficient and robust analysis of biomacromolecular flexibility using ensembles of network topologies based on fuzzy noncovalent constraints

Author keywords

[No Author keywords available]

Indexed keywords

ACID LIPASE; CITRATE SYNTHASE;

EID: 84885432778     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2013.07.012     Document Type: Article
Times cited : (20)

References (60)
  • 1
    • 66349117989 scopus 로고    scopus 로고
    • Thermally denatured state determines refolding in lipase: Mutational analysis
    • S. Ahmad, and N.M. Rao Thermally denatured state determines refolding in lipase: mutational analysis Protein Sci. 18 2009 1183 1196
    • (2009) Protein Sci. , vol.18 , pp. 1183-1196
    • Ahmad, S.1    Rao, N.M.2
  • 2
    • 47049084664 scopus 로고    scopus 로고
    • Thermostable Bacillus subtilis lipases: In vitro evolution and structural insight
    • S. Ahmad, M.Z. Kamal, R. Sankaranarayanan, and N.M. Rao Thermostable Bacillus subtilis lipases: in vitro evolution and structural insight J. Mol. Biol. 381 2008 324 340
    • (2008) J. Mol. Biol. , vol.381 , pp. 324-340
    • Ahmad, S.1    Kamal, M.Z.2    Sankaranarayanan, R.3    Rao, N.M.4
  • 3
    • 34447620778 scopus 로고    scopus 로고
    • Using molecular dynamics simulations to provide new insights into protein structure on the nanosecond timescale: Comparison with experimental data and biological inferences for the hyaluronan-binding link module of TSG-6
    • A. Almond, C.D. Blundell, V.A. Higman, A.D. MacKerell, and A.J. Day Using molecular dynamics simulations to provide new insights into protein structure on the nanosecond timescale: Comparison with experimental data and biological inferences for the hyaluronan-binding link module of TSG-6 J. Chem. Theory Comput. 3 2007 1 16
    • (2007) J. Chem. Theory Comput. , vol.3 , pp. 1-16
    • Almond, A.1    Blundell, C.D.2    Higman, V.A.3    Mackerell, A.D.4    Day, A.J.5
  • 5
    • 77952094752 scopus 로고    scopus 로고
    • Effect of interdomain dynamics on the structure determination of modular proteins by small-angle scattering
    • P. Bernadó Effect of interdomain dynamics on the structure determination of modular proteins by small-angle scattering Eur. Biophys. J. 39 2010 769 780
    • (2010) Eur. Biophys. J. , vol.39 , pp. 769-780
    • Bernadó, P.1
  • 9
    • 0343742614 scopus 로고    scopus 로고
    • Automated design of the surface positions of protein helices
    • B.I. Dahiyat, D.B. Gordon, and S.L. Mayo Automated design of the surface positions of protein helices Protein Sci. 6 1997 1333 1337
    • (1997) Protein Sci. , vol.6 , pp. 1333-1337
    • Dahiyat, B.I.1    Gordon, D.B.2    Mayo, S.L.3
  • 10
    • 41149175561 scopus 로고    scopus 로고
    • Revisiting the correlation between proteins' thermoresistance and organisms' thermophilicity
    • Y. Dehouck, B. Folch, and M. Rooman Revisiting the correlation between proteins' thermoresistance and organisms' thermophilicity Protein Eng. Des. Sel. 21 2008 275 278
    • (2008) Protein Eng. Des. Sel. , vol.21 , pp. 275-278
    • Dehouck, Y.1    Folch, B.2    Rooman, M.3
  • 11
    • 30744478915 scopus 로고    scopus 로고
    • Protein flexibility: Its role in structure and mechanism revealed by molecular simulations
    • G. Dodson, and C.S. Verma Protein flexibility: its role in structure and mechanism revealed by molecular simulations Cell. Mol. Life Sci. 63 2006 207 219
    • (2006) Cell. Mol. Life Sci. , vol.63 , pp. 207-219
    • Dodson, G.1    Verma, C.S.2
  • 13
    • 84856397848 scopus 로고    scopus 로고
    • A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking
    • S. Forli, and A.J. Olson A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking J. Med. Chem. 55 2012 623 638
    • (2012) J. Med. Chem. , vol.55 , pp. 623-638
    • Forli, S.1    Olson, A.J.2
  • 14
    • 61649098586 scopus 로고    scopus 로고
    • Statics of the ribosomal exit tunnel: Implications for cotranslational peptide folding, elongation regulation, and antibiotics binding
    • S. Fulle, and H. Gohlke Statics of the ribosomal exit tunnel: implications for cotranslational peptide folding, elongation regulation, and antibiotics binding J. Mol. Biol. 387 2009 502 517
    • (2009) J. Mol. Biol. , vol.387 , pp. 502-517
    • Fulle, S.1    Gohlke, H.2
  • 15
    • 70349299861 scopus 로고    scopus 로고
    • Constraint counting on RNA structures: Linking flexibility and function
    • S. Fulle, and H. Gohlke Constraint counting on RNA structures: linking flexibility and function Methods 49 2009 181 188
    • (2009) Methods , vol.49 , pp. 181-188
    • Fulle, S.1    Gohlke, H.2
  • 16
    • 3042806330 scopus 로고    scopus 로고
    • Change in protein flexibility upon complex formation: Analysis of Ras-Raf using molecular dynamics and a molecular framework approach
    • H. Gohlke, L.A. Kuhn, and D.A. Case Change in protein flexibility upon complex formation: analysis of Ras-Raf using molecular dynamics and a molecular framework approach Proteins 56 2004 322 337
    • (2004) Proteins , vol.56 , pp. 322-337
    • Gohlke, H.1    Kuhn, L.A.2    Case, D.A.3
  • 18
    • 84863155751 scopus 로고    scopus 로고
    • Calculating ensemble averaged descriptions of protein rigidity without sampling
    • L.C. González, H. Wang, D.R. Livesay, and D.J. Jacobs Calculating ensemble averaged descriptions of protein rigidity without sampling PLoS ONE 7 2012 e29176
    • (2012) PLoS ONE , vol.7 , pp. 29176
    • González, L.C.1    Wang, H.2    Livesay, D.R.3    Jacobs, D.J.4
  • 19
    • 0242720597 scopus 로고    scopus 로고
    • Uncovering network systems within protein structures
    • L.H. Greene, and V.A. Higman Uncovering network systems within protein structures J. Mol. Biol. 334 2003 781 791
    • (2003) J. Mol. Biol. , vol.334 , pp. 781-791
    • Greene, L.H.1    Higman, V.A.2
  • 20
    • 0037022347 scopus 로고    scopus 로고
    • Flexibility and packing in proteins
    • B. Halle Flexibility and packing in proteins Proc. Natl. Acad. Sci. USA 99 2002 1274 1279
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 1274-1279
    • Halle, B.1
  • 21
    • 84867508210 scopus 로고    scopus 로고
    • Validation of macromolecular flexibility in solution by small-angle X-ray scattering (SAXS)
    • M. Hammel Validation of macromolecular flexibility in solution by small-angle X-ray scattering (SAXS) Eur. Biophys. J. 41 2012 789 799
    • (2012) Eur. Biophys. J. , vol.41 , pp. 789-799
    • Hammel, M.1
  • 22
    • 37249032102 scopus 로고    scopus 로고
    • Dynamic personalities of proteins
    • K. Henzler-Wildman, and D. Kern Dynamic personalities of proteins Nature 450 2007 964 972
    • (2007) Nature , vol.450 , pp. 964-972
    • Henzler-Wildman, K.1    Kern, D.2
  • 23
    • 0025789054 scopus 로고
    • Side-chain clusters in protein structures and their role in protein folding
    • J. Heringa, and P. Argos Side-chain clusters in protein structures and their role in protein folding J. Mol. Biol. 220 1991 151 171
    • (1991) J. Mol. Biol. , vol.220 , pp. 151-171
    • Heringa, J.1    Argos, P.2
  • 24
    • 0036888379 scopus 로고    scopus 로고
    • Identifying protein folding cores from the evolution of flexible regions during unfolding
    • B.M. Hespenheide, A.J. Rader, M.F. Thorpe, and L.A. Kuhn Identifying protein folding cores from the evolution of flexible regions during unfolding J. Mol. Graph. Model. 21 2002 195 207
    • (2002) J. Mol. Graph. Model. , vol.21 , pp. 195-207
    • Hespenheide, B.M.1    Rader, A.J.2    Thorpe, M.F.3    Kuhn, L.A.4
  • 25
    • 33947716119 scopus 로고    scopus 로고
    • A semiempirical free energy force field with charge-based desolvation
    • R. Huey, G.M. Morris, A.J. Olson, and D.S. Goodsell A semiempirical free energy force field with charge-based desolvation J. Comput. Chem. 28 2007 1145 1152
    • (2007) J. Comput. Chem. , vol.28 , pp. 1145-1152
    • Huey, R.1    Morris, G.M.2    Olson, A.J.3    Goodsell, D.S.4
  • 26
    • 0000785338 scopus 로고
    • Generic rigidity percolation: The pebble game
    • D.J. Jacobs, and M.F. Thorpe Generic rigidity percolation: The pebble game Phys. Rev. Lett. 75 1995 4051 4054
    • (1995) Phys. Rev. Lett. , vol.75 , pp. 4051-4054
    • Jacobs, D.J.1    Thorpe, M.F.2
  • 27
    • 21244483843 scopus 로고    scopus 로고
    • Elucidating protein thermodynamics from the three-dimensional structure of the native state using network rigidity
    • D.J. Jacobs, and S. Dallakyan Elucidating protein thermodynamics from the three-dimensional structure of the native state using network rigidity Biophys. J. 88 2005 903 915
    • (2005) Biophys. J. , vol.88 , pp. 903-915
    • Jacobs, D.J.1    Dallakyan, S.2
  • 28
    • 0035427398 scopus 로고    scopus 로고
    • Protein flexibility predictions using graph theory
    • D.J. Jacobs, A.J. Rader, L.A. Kuhn, and M.F. Thorpe Protein flexibility predictions using graph theory Proteins 44 2001 150 165
    • (2001) Proteins , vol.44 , pp. 150-165
    • Jacobs, D.J.1    Rader, A.J.2    Kuhn, L.A.3    Thorpe, M.F.4
  • 29
    • 1542285840 scopus 로고    scopus 로고
    • Network rigidity at finite temperature: Relationships between thermodynamic stability, the nonadditivity of entropy, and cooperativity in molecular systems
    • D.J. Jacobs, S. Dallakyan, G.G. Wood, and A. Heckathorne Network rigidity at finite temperature: Relationships between thermodynamic stability, the nonadditivity of entropy, and cooperativity in molecular systems Phys. Rev. E. Stat. Nonlin. Soft Matter Phys. 68 2003
    • (2003) Phys. Rev. E. Stat. Nonlin. Soft Matter Phys. , vol.68
    • Jacobs, D.J.1    Dallakyan, S.2    Wood, G.G.3    Heckathorne, A.4
  • 31
    • 79954629700 scopus 로고    scopus 로고
    • A proof of the molecular conjecture
    • N. Katoh, and S. Tanigawa A proof of the molecular conjecture Discrete Comput. Geom. 45 2011 647 700
    • (2011) Discrete Comput. Geom. , vol.45 , pp. 647-700
    • Katoh, N.1    Tanigawa, S.2
  • 32
    • 29544432479 scopus 로고    scopus 로고
    • Stability and fluctuations of amide hydrogen bonds in a bacterial cytochrome c: A molecular dynamics study
    • G. Kieseritzky, G. Morra, and E.W. Knapp Stability and fluctuations of amide hydrogen bonds in a bacterial cytochrome c: a molecular dynamics study J. Biol. Inorg. Chem. 11 2006 26 40
    • (2006) J. Biol. Inorg. Chem. , vol.11 , pp. 26-40
    • Kieseritzky, G.1    Morra, G.2    Knapp, E.W.3
  • 33
    • 79958837339 scopus 로고    scopus 로고
    • An introduction to NMR-based approaches for measuring protein dynamics
    • I.R. Kleckner, and M.P. Foster An introduction to NMR-based approaches for measuring protein dynamics Biochim. Biophys. Acta 1814 2011 942 968
    • (2011) Biochim. Biophys. Acta , vol.1814 , pp. 942-968
    • Kleckner, I.R.1    Foster, M.P.2
  • 34
    • 46749096337 scopus 로고    scopus 로고
    • Starting structure dependence of NMR order parameters derived from MD simulations: Implications for judging force-field quality
    • A.N. Koller, H. Schwalbe, and H. Gohlke Starting structure dependence of NMR order parameters derived from MD simulations: implications for judging force-field quality Biophys. J. 95 2008 L04 L06
    • (2008) Biophys. J. , vol.95
    • Koller, A.N.1    Schwalbe, H.2    Gohlke, H.3
  • 35
    • 84876532652 scopus 로고    scopus 로고
    • CNA web server: Rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo)stability, and function
    • D.M. Krüger, P.C. Rathi, C. Pfleger, and H. Gohlke CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo)stability, and function Nucleic Acids Res. 41 2013 W340 W348
    • (2013) Nucleic Acids Res. , vol.41
    • Krüger, D.M.1    Rathi, P.C.2    Pfleger, C.3    Gohlke, H.4
  • 37
    • 84985649741 scopus 로고
    • Vibrational approach to the dynamics of an alpha-helix
    • R.M. Levy, and M. Karplus Vibrational approach to the dynamics of an alpha-helix Biopolymers 18 1979 2465 2495
    • (1979) Biopolymers , vol.18 , pp. 2465-2495
    • Levy, R.M.1    Karplus, M.2
  • 38
    • 30344476409 scopus 로고    scopus 로고
    • Conserved quantitative stability/flexibility relationships (QSFR) in an orthologous RNase H pair
    • D.R. Livesay, and D.J. Jacobs Conserved quantitative stability/ flexibility relationships (QSFR) in an orthologous RNase H pair Proteins 62 2006 130 143
    • (2006) Proteins , vol.62 , pp. 130-143
    • Livesay, D.R.1    Jacobs, D.J.2
  • 39
    • 6344223617 scopus 로고    scopus 로고
    • A flexible approach for understanding protein stability
    • D.R. Livesay, S. Dallakyan, G.G. Wood, and D.J. Jacobs A flexible approach for understanding protein stability FEBS Lett. 576 2004 468 476
    • (2004) FEBS Lett. , vol.576 , pp. 468-476
    • Livesay, D.R.1    Dallakyan, S.2    Wood, G.G.3    Jacobs, D.J.4
  • 41
    • 84876551539 scopus 로고    scopus 로고
    • Constraint Network Analysis (CNA): A Python software package for efficiently linking biomacromolecular structure, flexibility, (thermo-)stability, and function
    • C. Pfleger, P.C. Rathi, D.L. Klein, S. Radestock, and H. Gohlke Constraint Network Analysis (CNA): a Python software package for efficiently linking biomacromolecular structure, flexibility, (thermo-)stability, and function J. Chem. Inf. Model. 53 2013 1007 1015
    • (2013) J. Chem. Inf. Model. , vol.53 , pp. 1007-1015
    • Pfleger, C.1    Rathi, P.C.2    Klein, D.L.3    Radestock, S.4    Gohlke, H.5
  • 42
    • 84872307122 scopus 로고    scopus 로고
    • Global and local indices for characterizing biomolecular flexibility and rigidity
    • C. Pfleger, S. Radestock, E. Schmidt, and H. Gohlke Global and local indices for characterizing biomolecular flexibility and rigidity J. Comput. Chem. 34 2013 220 233
    • (2013) J. Comput. Chem. , vol.34 , pp. 220-233
    • Pfleger, C.1    Radestock, S.2    Schmidt, E.3    Gohlke, H.4
  • 43
    • 36749120002 scopus 로고
    • Theory of hydrophobic effect
    • L.R. Pratt, and D. Chandler Theory of hydrophobic effect J. Chem. Phys. 67 1977 3683 3704
    • (1977) J. Chem. Phys. , vol.67 , pp. 3683-3704
    • Pratt, L.R.1    Chandler, D.2
  • 44
    • 75449086680 scopus 로고    scopus 로고
    • Thermostability in rubredoxin and its relationship to mechanical rigidity
    • A.J. Rader Thermostability in rubredoxin and its relationship to mechanical rigidity Phys. Biol. 7 2009 16002
    • (2009) Phys. Biol. , vol.7 , pp. 16002
    • Rader, A.J.1
  • 45
    • 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 Polymer (Guildf.) 45 2004 659 668
    • (2004) Polymer (Guildf.) , vol.45 , pp. 659-668
    • Rader, A.J.1    Bahar, I.2
  • 47
    • 61649103550 scopus 로고    scopus 로고
    • Exploiting the link between protein rigidity and thermostability for data-driven protein engineering
    • S. Radestock, and H. Gohlke Exploiting the link between protein rigidity and thermostability for data-driven protein engineering Eng. Life Sci. 8 2008 507 522
    • (2008) Eng. Life Sci. , vol.8 , pp. 507-522
    • Radestock, S.1    Gohlke, H.2
  • 48
    • 79952487469 scopus 로고    scopus 로고
    • Protein rigidity and thermophilic adaptation
    • S. Radestock, and H. Gohlke Protein rigidity and thermophilic adaptation Proteins 79 2011 1089 1108
    • (2011) Proteins , vol.79 , pp. 1089-1108
    • Radestock, S.1    Gohlke, H.2
  • 49
    • 0026731991 scopus 로고
    • Hydrogen exchange in native and denatured states of hen egg-white lysozyme
    • S.E. Radford, M. Buck, K.D. Topping, C.M. Dobson, and P.A. Evans Hydrogen exchange in native and denatured states of hen egg-white lysozyme Proteins 14 1992 237 248
    • (1992) Proteins , vol.14 , pp. 237-248
    • Radford, S.E.1    Buck, M.2    Topping, K.D.3    Dobson, C.M.4    Evans, P.A.5
  • 50
    • 84860835198 scopus 로고    scopus 로고
    • Thermostabilizing mutations preferentially occur at structural weak spots with a high mutation ratio
    • P.C. Rathi, S. Radestock, and H. Gohlke Thermostabilizing mutations preferentially occur at structural weak spots with a high mutation ratio J. Biotechnol. 159 2012 135 144
    • (2012) J. Biotechnol. , vol.159 , pp. 135-144
    • Rathi, P.C.1    Radestock, S.2    Gohlke, H.3
  • 51
    • 0027256739 scopus 로고
    • Hydrogen bonding, hydrophobicity, packing, and protein folding
    • G.D. Rose, and R. Wolfenden Hydrogen bonding, hydrophobicity, packing, and protein folding Annu. Rev. Biophys. Biomol. Struct. 22 1993 381 415
    • (1993) Annu. Rev. Biophys. Biomol. Struct. , vol.22 , pp. 381-415
    • Rose, G.D.1    Wolfenden, R.2
  • 52
    • 84872301054 scopus 로고    scopus 로고
    • The relationship between catalytic activity, structural flexibility and conformational stability as deduced from the analysis of mesophilic-thermophilic enzyme pairs and protein engineering studies
    • F. Robb, G. Antranikian, D. Grogan, A. Driessen, CRC Press London, New York
    • R. Sterner, and E. Brunner The relationship between catalytic activity, structural flexibility and conformational stability as deduced from the analysis of mesophilic-thermophilic enzyme pairs and protein engineering studies F. Robb, G. Antranikian, D. Grogan, A. Driessen, Thermophiles: Biology and Technology at High Temperatures 2008 CRC Press London, New York 25 38
    • (2008) Thermophiles: Biology and Technology at High Temperatures , pp. 25-38
    • Sterner, R.1    Brunner, E.2
  • 54
    • 0036139093 scopus 로고    scopus 로고
    • Why are proteins marginally stable?
    • D.M. Taverna, and R.A. Goldstein Why are proteins marginally stable? Proteins 46 2002 105 109
    • (2002) Proteins , vol.46 , pp. 105-109
    • Taverna, D.M.1    Goldstein, R.A.2
  • 55
    • 0037666888 scopus 로고    scopus 로고
    • Implications of protein flexibility for drug discovery
    • S.J. Teague Implications of protein flexibility for drug discovery Nat. Rev. Drug Discov. 2 2003 527 541
    • (2003) Nat. Rev. Drug Discov. , vol.2 , pp. 527-541
    • Teague, S.J.1
  • 56
    • 0021093473 scopus 로고
    • Continuous deformations in random networks
    • M.F. Thorpe Continuous deformations in random networks J. Non-Cryst. Solids 57 1983 355 370
    • (1983) J. Non-Cryst. Solids , vol.57 , pp. 355-370
    • Thorpe, M.F.1
  • 57
    • 41349118690 scopus 로고    scopus 로고
    • Small-world view of the amino acids that play a key role in protein folding. Phys. Rev. E: Stat.; Nonlinear
    • M. Vendruscolo, N.V. Dokholyan, E. Paci, and M. Karplus Small-world view of the amino acids that play a key role in protein folding. Phys. Rev. E: Stat.; Nonlinear Soft Matter Physiol. 65 2002 1 4
    • (2002) Soft Matter Physiol. , vol.65 , pp. 1-4
    • Vendruscolo, M.1    Dokholyan, N.V.2    Paci, E.3    Karplus, M.4
  • 58
    • 27744521303 scopus 로고    scopus 로고
    • Counting out to the flexibility of molecules
    • W. Whiteley Counting out to the flexibility of molecules Phys. Biol. 2 2005 S116 S126
    • (2005) Phys. Biol. , vol.2
    • Whiteley, W.1
  • 59
    • 0035815288 scopus 로고    scopus 로고
    • Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation
    • M.A. Young, S. Gonfloni, G. Superti-Furga, B. Roux, and J. Kuriyan Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation Cell 105 2001 115 126
    • (2001) Cell , vol.105 , pp. 115-126
    • Young, M.A.1    Gonfloni, S.2    Superti-Furga, G.3    Roux, B.4    Kuriyan, J.5
  • 60
    • 0034595671 scopus 로고    scopus 로고
    • How soft is a protein? A protein dynamics force constant measured by neutron scattering
    • G. Zaccai How soft is a protein? A protein dynamics force constant measured by neutron scattering Science 288 2000 1604 1607
    • (2000) Science , vol.288 , pp. 1604-1607
    • Zaccai, G.1


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