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Volumn 24, Issue 1, 2016, Pages 187-199

New Dynamic Rotamer Libraries: Data-Driven Analysis of Side-Chain Conformational Propensities

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; MOLECULAR DYNAMICS; MOLECULAR LIBRARY; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DATA BANK; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; ANIMAL; CHEMISTRY; HUMAN; ISOMERISM; PEPTIDE LIBRARY; SOFTWARE;

EID: 84953222037     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2015.10.017     Document Type: Article
Times cited : (43)

References (81)
  • 1
    • 27444434259 scopus 로고    scopus 로고
    • Directed evolution of highly homologous proteins with different folds by phage display: Implications for the protein folding code
    • P.A. Alexander, D.A. Rozak, J. Orban, and P.N. Bryan Directed evolution of highly homologous proteins with different folds by phage display: implications for the protein folding code Biochemistry 44 2005 14045 14054
    • (2005) Biochemistry , vol.44 , pp. 14045-14054
    • Alexander, P.A.1    Rozak, D.A.2    Orban, J.3    Bryan, P.N.4
  • 3
    • 26444534036 scopus 로고    scopus 로고
    • Characterization of a possible amyloidogenic precursor in glutamine-repeat neurodegenerative diseases
    • R.S. Armen, B.M. Bernard, R. Day, D.O.V. Alonso, and V. Daggett Characterization of a possible amyloidogenic precursor in glutamine-repeat neurodegenerative diseases Proc. Natl. Acad. Sci. USA 102 2005 13433 13438
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 13433-13438
    • Armen, R.S.1    Bernard, B.M.2    Day, R.3    Alonso, D.O.V.4    Daggett, V.5
  • 4
    • 0032488638 scopus 로고    scopus 로고
    • The solution structure of oxidized rat microsomal cytochrome b5
    • F. Arnesano, L. Banci, I. Bertini, and I.C. Felli The solution structure of oxidized rat microsomal cytochrome b5 Biochemistry 37 1998 173 184
    • (1998) Biochemistry , vol.37 , pp. 173-184
    • Arnesano, F.1    Banci, L.2    Bertini, I.3    Felli, I.C.4
  • 6
    • 0030324869 scopus 로고    scopus 로고
    • Coordination geometry of nonbonded residues in globular proteins
    • I. Bahar, and R.L. Jernigan Coordination geometry of nonbonded residues in globular proteins Fold. Des. 1 1996 357 370
    • (1996) Fold. Des. , vol.1 , pp. 357-370
    • Bahar, I.1    Jernigan, R.L.2
  • 7
    • 3342918929 scopus 로고    scopus 로고
    • Methods for molecular dynamics simulations of protein folding/unfolding in solution
    • D.A.C. Beck, and V. Daggett Methods for molecular dynamics simulations of protein folding/unfolding in solution Methods 34 2004 112 120
    • (2004) Methods , vol.34 , pp. 112-120
    • Beck, D.A.C.1    Daggett, V.2
  • 8
    • 0037438967 scopus 로고    scopus 로고
    • A microscopic view of peptide and protein solvation
    • D.A.C. Beck, D.O.V. Alonso, and V. Daggett A microscopic view of peptide and protein solvation Biophys. Chem. 100 2003 221 237
    • (2003) Biophys. Chem. , vol.100 , pp. 221-237
    • Beck, D.A.C.1    Alonso, D.O.V.2    Daggett, V.3
  • 9
    • 12144275299 scopus 로고    scopus 로고
    • Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides
    • D.A.C. Beck, R.S. Armen, and V. Daggett Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides Biochemistry 44 2005 609 616
    • (2005) Biochemistry , vol.44 , pp. 609-616
    • Beck, D.A.C.1    Armen, R.S.2    Daggett, V.3
  • 14
    • 3042639229 scopus 로고    scopus 로고
    • The origin of protein sidechain order parameter distributions
    • R.B. Best, J. Clarke, and M. Karplus The origin of protein sidechain order parameter distributions J. Am. Chem. Soc. 126 2004 7734 7735
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 7734-7735
    • Best, R.B.1    Clarke, J.2    Karplus, M.3
  • 15
    • 46749127364 scopus 로고    scopus 로고
    • Are current molecular dynamics force fields too helical?
    • R.B. Best, N.-V. Buchete, and G. Hummer Are current molecular dynamics force fields too helical? Biophys. J. 95 2008 L07 L09
    • (2008) Biophys. J. , vol.95 , pp. L07-L09
    • Best, R.B.1    Buchete, N.-V.2    Hummer, G.3
  • 16
    • 0030983386 scopus 로고    scopus 로고
    • Population statistics of protein structures: Lessons from structural classifications
    • S.E. Brenner, C. Chothia, and T.J. Hubbard Population statistics of protein structures: lessons from structural classifications Curr. Opin. Struct. Biol. 7 1997 369 376
    • (1997) Curr. Opin. Struct. Biol. , vol.7 , pp. 369-376
    • Brenner, S.E.1    Chothia, C.2    Hubbard, T.J.3
  • 17
    • 84878370261 scopus 로고    scopus 로고
    • A proteomic Ramachandran plot (PRplot)
    • O. Carugo, and K. Djinović-Carugo A proteomic Ramachandran plot (PRplot) Amino Acids 44 2013 781 790
    • (2013) Amino Acids , vol.44 , pp. 781-790
    • Carugo, O.1    Djinović-Carugo, K.2
  • 18
    • 0014885326 scopus 로고
    • Studies on the conformation of amino acids. XI. Analysis of the observed side group conformation in proteins
    • R. Chandrasekaran, and G.N. Ramachandran Studies on the conformation of amino acids. XI. Analysis of the observed side group conformation in proteins Int. J. Protein Res. 2 1970 223 233
    • (1970) Int. J. Protein Res. , vol.2 , pp. 223-233
    • Chandrasekaran, R.1    Ramachandran, G.N.2
  • 22
    • 0141524060 scopus 로고    scopus 로고
    • A consensus view of fold space: Combining SCOP, CATH, and the Dali domain dictionary
    • R. Day, D.A.C. Beck, R.S. Armen, and V. Daggett A consensus view of fold space: combining SCOP, CATH, and the Dali domain dictionary Protein Sci. 12 2003 2150 2160
    • (2003) Protein Sci. , vol.12 , pp. 2150-2160
    • Day, R.1    Beck, D.A.C.2    Armen, R.S.3    Daggett, V.4
  • 24
    • 0027160197 scopus 로고
    • Backbone-dependent rotamer library for proteins. Application to side-chain prediction
    • R.L. Dunbrack, and M. Karplus Backbone-dependent rotamer library for proteins. Application to side-chain prediction J. Mol. Biol. 230 1993 543 574
    • (1993) J. Mol. Biol. , vol.230 , pp. 543-574
    • Dunbrack, R.L.1    Karplus, M.2
  • 25
    • 0028429178 scopus 로고
    • Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains
    • R.L. Dunbrack, and M. Karplus Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains Nat. Struct. Mol. Biol. 1 1994 334 340
    • (1994) Nat. Struct. Mol. Biol. , vol.1 , pp. 334-340
    • Dunbrack, R.L.1    Karplus, M.2
  • 26
    • 1842326139 scopus 로고    scopus 로고
    • Bayesian statistical analysis of protein side-chain rotamer preferences
    • R.L. Dunbrack, and F.E. Cohen Bayesian statistical analysis of protein side-chain rotamer preferences Protein Sci. 6 1997 1661 1681
    • (1997) Protein Sci. , vol.6 , pp. 1661-1681
    • Dunbrack, R.L.1    Cohen, F.E.2
  • 28
    • 84891811692 scopus 로고    scopus 로고
    • SCOPe: Structural classification of proteins-extended, integrating SCOP and ASTRAL data and classification of new structures
    • N.K. Fox, S.E. Brenner, and J.-M. Chandonia SCOPe: structural classification of proteins-extended, integrating SCOP and ASTRAL data and classification of new structures Nucleic Acids Res. 42 2014 D304 D309
    • (2014) Nucleic Acids Res. , vol.42 , pp. D304-D309
    • Fox, N.K.1    Brenner, S.E.2    Chandonia, J.-M.3
  • 32
    • 79957936173 scopus 로고    scopus 로고
    • Amino acids with hydrogen-bonding side chains have an intrinsic tendency to sample various turn conformations in aqueous solution
    • A. Hagarman, D. Mathieu, S. Toal, T.J. Measey, H. Schwalbe, and R. Schweitzer-Stenner Amino acids with hydrogen-bonding side chains have an intrinsic tendency to sample various turn conformations in aqueous solution Chem. Eur. J. 17 2011 6789 6797
    • (2011) Chem. Eur. J. , vol.17 , pp. 6789-6797
    • Hagarman, A.1    Mathieu, D.2    Toal, S.3    Measey, T.J.4    Schwalbe, H.5    Schweitzer-Stenner, R.6
  • 36
    • 0036310711 scopus 로고    scopus 로고
    • On the role of the crystal environment in determining protein side-chain conformations
    • M.P. Jacobson, R.A. Friesner, Z. Xiang, and B. Honig On the role of the crystal environment in determining protein side-chain conformations J. Mol. Biol. 320 2002 597 608
    • (2002) J. Mol. Biol. , vol.320 , pp. 597-608
    • Jacobson, M.P.1    Friesner, R.A.2    Xiang, Z.3    Honig, B.4
  • 37
    • 0018115846 scopus 로고
    • Conformation of amino acid side-chains in proteins
    • J. Janin, S. Wodak, M. Levitt, and B. Maigret Conformation of amino acid side-chains in proteins J. Mol. Biol. 125 1978 357 386
    • (1978) J. Mol. Biol. , vol.125 , pp. 357-386
    • Janin, J.1    Wodak, S.2    Levitt, M.3    Maigret, B.4
  • 38
    • 84874072440 scopus 로고    scopus 로고
    • The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development
    • F. Jiang, W. Han, and Y.-D. Wu The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development Phys. Chem. Chem. Phys. 15 2013 3413 3428
    • (2013) Phys. Chem. Chem. Phys. , vol.15 , pp. 3413-3428
    • Jiang, F.1    Han, W.2    Wu, Y.-D.3
  • 40
    • 84892968997 scopus 로고    scopus 로고
    • CASP10 results compared to those of previous CASP experiments
    • A. Kryshtafovych, K. Fidelis, and J. Moult CASP10 results compared to those of previous CASP experiments Proteins 82 Suppl 2 2014 164 174
    • (2014) Proteins , vol.82 , pp. 164-174
    • Kryshtafovych, A.1    Fidelis, K.2    Moult, J.3
  • 41
    • 84893398413 scopus 로고    scopus 로고
    • Design of a rotamer library for coarse-grained models in protein-folding simulations
    • M. Larriva, and A. Rey Design of a rotamer library for coarse-grained models in protein-folding simulations J. Chem. Inf. Model. 54 2014 302 313
    • (2014) J. Chem. Inf. Model. , vol.54 , pp. 302-313
    • Larriva, M.1    Rey, A.2
  • 42
    • 33847616971 scopus 로고    scopus 로고
    • Growth of novel protein structural data
    • M. Levitt Growth of novel protein structural data Proc. Natl. Acad. Sci. USA 104 2007 3183 3188
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 3183-3188
    • Levitt, M.1
  • 43
    • 0029633167 scopus 로고
    • Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution
    • M. Levitt, M. Hirshberg, R. Sharon, and V. Daggett Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution Comput. Phys. Commun. 91 1995 215 231
    • (1995) Comput. Phys. Commun. , vol.91 , pp. 215-231
    • Levitt, M.1    Hirshberg, M.2    Sharon, R.3    Daggett, V.4
  • 44
    • 0000125216 scopus 로고    scopus 로고
    • Calibration and testing of a water model for simulation of the molecular dynamics of proteins and nucleic acids in solution
    • M. Levitt, M. Hirshberg, R. Sharon, K.E. Laidig, and V. Daggett Calibration and testing of a water model for simulation of the molecular dynamics of proteins and nucleic acids in solution J. Phys. Chem. B 101 1997 5051 5061
    • (1997) J. Phys. Chem. B , vol.101 , pp. 5051-5061
    • Levitt, M.1    Hirshberg, M.2    Sharon, R.3    Laidig, K.E.4    Daggett, V.5
  • 45
    • 0029586380 scopus 로고
    • Investigation of the solution structure of chymotrypsin inhibitor 2 using molecular dynamics: Comparison to X-ray crystallographic and NMR data
    • A. Li, and V. Daggett Investigation of the solution structure of chymotrypsin inhibitor 2 using molecular dynamics: comparison to X-ray crystallographic and NMR data Protein Eng. Des. Sel. 8 1995 1117 1128
    • (1995) Protein Eng. Des. Sel. , vol.8 , pp. 1117-1128
    • Li, A.1    Daggett, V.2
  • 47
    • 0034610360 scopus 로고    scopus 로고
    • Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation
    • U. Mayor, C.M. Johnson, V. Daggett, and A.R. Fersht Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation Proc. Natl. Acad. Sci. USA 97 2000 13518 13522
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 13518-13522
    • Mayor, U.1    Johnson, C.M.2    Daggett, V.3    Fersht, A.R.4
  • 49
    • 0023521842 scopus 로고
    • Analysis of the relationship between side-chain conformation and secondary structure in globular proteins
    • M.J. McGregor, S.A. Islam, and M.J. Sternberg Analysis of the relationship between side-chain conformation and secondary structure in globular proteins J. Mol. Biol. 198 1987 295 310
    • (1987) J. Mol. Biol. , vol.198 , pp. 295-310
    • McGregor, M.J.1    Islam, S.A.2    Sternberg, M.J.3
  • 51
    • 0028988836 scopus 로고
    • Side-chain determinants of β-sheet stability
    • D.E. Otzen, and A.R. Fersht Side-chain determinants of β-sheet stability Biochemistry 34 1995 5718 5724
    • (1995) Biochemistry , vol.34 , pp. 5718-5724
    • Otzen, D.E.1    Fersht, A.R.2
  • 53
    • 0023155210 scopus 로고
    • Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes
    • J.W. Ponder, and F.M. Richards Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes J. Mol. Biol. 193 1987 775 791
    • (1987) J. Mol. Biol. , vol.193 , pp. 775-791
    • Ponder, J.W.1    Richards, F.M.2
  • 55
    • 27144532135 scopus 로고    scopus 로고
    • Solution structure of a protein denatured state and folding intermediate
    • T.L. Religa, J.S. Markson, U. Mayor, S.M.V. Freund, and A.R. Fersht Solution structure of a protein denatured state and folding intermediate Nature 437 2005 1053 1056
    • (2005) Nature , vol.437 , pp. 1053-1056
    • Religa, T.L.1    Markson, J.S.2    Mayor, U.3    Freund, S.M.V.4    Fersht, A.R.5
  • 56
    • 0019443447 scopus 로고
    • The anatomy and taxonomy of protein structure
    • J.S. Richardson The anatomy and taxonomy of protein structure Adv. Protein Chem. 34 1981 339
    • (1981) Adv. Protein Chem. , vol.34 , pp. 339
    • Richardson, J.S.1
  • 57
    • 84876543070 scopus 로고    scopus 로고
    • Using simulations to provide the framework for experimental protein folding studies
    • B. Rizzuti, and V. Daggett Using simulations to provide the framework for experimental protein folding studies Arch. Biochem. Biophys. 531 2013 128 135
    • (2013) Arch. Biochem. Biophys. , vol.531 , pp. 128-135
    • Rizzuti, B.1    Daggett, V.2
  • 58
    • 77957224813 scopus 로고    scopus 로고
    • Polymorphisms and disease: Hotspots of inactivation in methyltransferases
    • K. Rutherford, and V. Daggett Polymorphisms and disease: hotspots of inactivation in methyltransferases Trends Biochem. Sci. 35 2010 531 538
    • (2010) Trends Biochem. Sci. , vol.35 , pp. 531-538
    • Rutherford, K.1    Daggett, V.2
  • 59
    • 33144471940 scopus 로고    scopus 로고
    • The 108M Polymorph of human catechol O-methyltransferase is prone to deformation at physiological temperatures
    • K. Rutherford, B.J. Bennion, W.W. Parson, and V. Daggett The 108M Polymorph of human catechol O-methyltransferase is prone to deformation at physiological temperatures Biochemistry 45 2006 2178 2188
    • (2006) Biochemistry , vol.45 , pp. 2178-2188
    • Rutherford, K.1    Bennion, B.J.2    Parson, W.W.3    Daggett, V.4
  • 62
    • 39149104002 scopus 로고    scopus 로고
    • Combining experiment and simulation in protein folding: Closing the gap for small model systems
    • R.D. Schaeffer, A. Fersht, and V. Daggett Combining experiment and simulation in protein folding: closing the gap for small model systems Curr. Opin. Struct. Biol. 18 2008 4 9
    • (2008) Curr. Opin. Struct. Biol. , vol.18 , pp. 4-9
    • Schaeffer, R.D.1    Fersht, A.2    Daggett, V.3
  • 64
    • 0027208112 scopus 로고
    • Rotamers: To be or not to be? An analysis of amino acid side-chain conformations in globular proteins
    • H. Schrauber, F. Eisenhaber, and P. Argos Rotamers: to be or not to be? an analysis of amino acid side-chain conformations in globular proteins J. Mol. Biol. 230 1993 592 612
    • (1993) J. Mol. Biol. , vol.230 , pp. 592-612
    • Schrauber, H.1    Eisenhaber, F.2    Argos, P.3
  • 65
    • 79956204828 scopus 로고    scopus 로고
    • Stereochemical errors and their implications for molecular dynamics simulations
    • E. Schreiner, L.G. Trabuco, P.L. Freddolino, and K. Schulten Stereochemical errors and their implications for molecular dynamics simulations BMC Bioinformatics 12 2011 190
    • (2011) BMC Bioinformatics , vol.12 , pp. 190
    • Schreiner, E.1    Trabuco, L.G.2    Freddolino, P.L.3    Schulten, K.4
  • 66
    • 79251565520 scopus 로고    scopus 로고
    • The dynameomics rotamer library: Amino acid side chain conformations and dynamics from comprehensive molecular dynamics simulations in water
    • A.D. Scouras, and V. Daggett The dynameomics rotamer library: amino acid side chain conformations and dynamics from comprehensive molecular dynamics simulations in water Protein Sci. 20 2011 341 352
    • (2011) Protein Sci. , vol.20 , pp. 341-352
    • Scouras, A.D.1    Daggett, V.2
  • 67
  • 68
    • 79958079887 scopus 로고    scopus 로고
    • A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions
    • M.V. Shapovalov, and R.L. Dunbrack A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions Structure 19 2011 844 858
    • (2011) Structure , vol.19 , pp. 844-858
    • Shapovalov, M.V.1    Dunbrack, R.L.2
  • 71
    • 84865662866 scopus 로고    scopus 로고
    • Protein simulation data in the relational model
    • A.M. Simms, and V. Daggett Protein simulation data in the relational model J. Supercomput. 62 2012 150 173
    • (2012) J. Supercomput. , vol.62 , pp. 150-173
    • Simms, A.M.1    Daggett, V.2
  • 72
    • 44649195146 scopus 로고    scopus 로고
    • Dynameomics: Design of a computational lab workflow and scientific data repository for protein simulations
    • A.M. Simms, R. Toofanny, C. Kehl, N.C. Benson, and V. Daggett Dynameomics: design of a computational lab workflow and scientific data repository for protein simulations Protein Eng. Des. Sel. 21 2008 369 377
    • (2008) Protein Eng. Des. Sel. , vol.21 , pp. 369-377
    • Simms, A.M.1    Toofanny, R.2    Kehl, C.3    Benson, N.C.4    Daggett, V.5
  • 73
    • 0029094684 scopus 로고
    • Molecular dynamics simulation of cytochrome b5: Implications for protein-protein recognition
    • E.M. Storch, and V. Daggett Molecular dynamics simulation of cytochrome b5: implications for protein-protein recognition Biochemistry 34 1995 9682 9693
    • (1995) Biochemistry , vol.34 , pp. 9682-9693
    • Storch, E.M.1    Daggett, V.2
  • 74
    • 0033586716 scopus 로고    scopus 로고
    • Engineering out motion: Introduction of a de novo disulfide bond and a salt bridge designed to close a dynamic cleft on the surface of cytochrome b5
    • E.M. Storch, V. Daggett, and W.M. Atkins Engineering out motion: introduction of a de novo disulfide bond and a salt bridge designed to close a dynamic cleft on the surface of cytochrome b5 Biochemistry 38 1999 5054 5064
    • (1999) Biochemistry , vol.38 , pp. 5054-5064
    • Storch, E.M.1    Daggett, V.2    Atkins, W.M.3
  • 76
    • 84869123655 scopus 로고    scopus 로고
    • When a domain is not a domain, and why it is important to properly filter proteins in databases
    • C.-L. Towse, and V. Daggett When a domain is not a domain, and why it is important to properly filter proteins in databases Bioessays 34 2012 1060 1069
    • (2012) Bioessays , vol.34 , pp. 1060-1069
    • Towse, C.-L.1    Daggett, V.2
  • 78
    • 84953276310 scopus 로고    scopus 로고
    • Insights into unfolded proteins from the intrinsic φ/ψ properties of the AAXAA host-guest series
    • in press
    • C.-L. Towse, J. Vymetal, J. Vondrasek, and V. Daggett Insights into unfolded proteins from the intrinsic φ/ψ properties of the AAXAA host-guest series Biophys. J. 2015 in press
    • (2015) Biophys. J.
    • Towse, C.-L.1    Vymetal, J.2    Vondrasek, J.3    Daggett, V.4
  • 80
    • 0026651557 scopus 로고
    • NMR structure determination in solution: A critique and comparison with X-ray crystallography
    • G. Wagner, S.G. Hyberts, and T.F. Havel NMR structure determination in solution: a critique and comparison with X-ray crystallography Annu. Rev. Biophys. Biomol. Struct. 21 1992 167 198
    • (1992) Annu. Rev. Biophys. Biomol. Struct. , vol.21 , pp. 167-198
    • Wagner, G.1    Hyberts, S.G.2    Havel, T.F.3
  • 81
    • 0035838974 scopus 로고    scopus 로고
    • Extending the accuracy limits of prediction for side-chain conformations
    • Z. Xiang, and B. Honig Extending the accuracy limits of prediction for side-chain conformations J. Mol. Biol. 311 2001 421 430
    • (2001) J. Mol. Biol. , vol.311 , pp. 421-430
    • Xiang, Z.1    Honig, B.2


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