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Volumn 326, Issue 4, 2003, Pages 1239-1259

An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes

Author keywords

Electrostatics; Free energy function; Hydrogen bond; Protein design; Protein docking

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; CRYSTAL STRUCTURE; HYDROGEN BOND; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE;

EID: 0037470581     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(03)00021-4     Document Type: Article
Times cited : (443)

References (61)
  • 2
    • 0003187567 scopus 로고    scopus 로고
    • The atomic structure of protein-protein recognition sites
    • Conte L.L., Chothia C., Janin J. The atomic structure of protein-protein recognition sites. J. Mol. Biol. 285:1999;2177-2198.
    • (1999) J. Mol. Biol. , vol.285 , pp. 2177-2198
    • Conte, L.L.1    Chothia, C.2    Janin, J.3
  • 3
    • 0028204490 scopus 로고
    • Do salt bridges stabilize proteins? A continuum electrostatic analysis
    • Hendsch Z.S., Tidor B. Do salt bridges stabilize proteins? A continuum electrostatic analysis. Protein Sci. 3:1994;211-226.
    • (1994) Protein Sci. , vol.3 , pp. 211-226
    • Hendsch, Z.S.1    Tidor, B.2
  • 4
    • 0035895356 scopus 로고    scopus 로고
    • Polar group burial contributes more to protein stability than nonpolar group burial
    • Pace C.N. Polar group burial contributes more to protein stability than nonpolar group burial. Biochemistry. 40:2001;310-313.
    • (2001) Biochemistry , vol.40 , pp. 310-313
    • Pace, C.N.1
  • 5
    • 0028304962 scopus 로고
    • Satisfying hydrogen bonding potential in proteins
    • McDonald I.K., Thornton J.M. Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 238:1994;777-793.
    • (1994) J. Mol. Biol. , vol.238 , pp. 777-793
    • McDonald, I.K.1    Thornton, J.M.2
  • 6
    • 0029564595 scopus 로고
    • Are buried salt bridges important for protein stability and conformational specificity?
    • Waldburger C.D., Schildbach J.F., Sauer R.T. Are buried salt bridges important for protein stability and conformational specificity? Nature Struct. Biol. 2:1995;122-128.
    • (1995) Nature Struct. Biol. , vol.2 , pp. 122-128
    • Waldburger, C.D.1    Schildbach, J.F.2    Sauer, R.T.3
  • 7
    • 0029121068 scopus 로고
    • Free energy determinants of secondary structure formation: I. alpha-helices
    • Yang A.S., Honig B. Free energy determinants of secondary structure formation: I. alpha-helices. J. Mol. Biol. 252:1995;351-365.
    • (1995) J. Mol. Biol. , vol.252 , pp. 351-365
    • Yang, A.S.1    Honig, B.2
  • 8
    • 4243067681 scopus 로고    scopus 로고
    • Protein stabilization by removal of unsatisfied polar groups: Computational approaches and experimental tests
    • Hendsch Z.S., Jonsson T., Sauer R.T., Tidor B. Protein stabilization by removal of unsatisfied polar groups: computational approaches and experimental tests. Biochemistry. 35:1996;7621-7625.
    • (1996) Biochemistry , vol.35 , pp. 7621-7625
    • Hendsch, Z.S.1    Jonsson, T.2    Sauer, R.T.3    Tidor, B.4
  • 9
    • 0029008590 scopus 로고
    • A buried polar interaction imparts structural uniqueness in a designed heterodimeric coiled coil
    • Lumb K.J., Kim P.S. A buried polar interaction imparts structural uniqueness in a designed heterodimeric coiled coil. Biochemistry. 34:1995;8642-8648.
    • (1995) Biochemistry , vol.34 , pp. 8642-8648
    • Lumb, K.J.1    Kim, P.S.2
  • 10
    • 0034486196 scopus 로고    scopus 로고
    • Free energy determinants of tertiary structure and the evaluation of protein models
    • Petrey D., Honig B. Free energy determinants of tertiary structure and the evaluation of protein models. Protein Sci. 9:2000;2181-2191.
    • (2000) Protein Sci. , vol.9 , pp. 2181-2191
    • Petrey, D.1    Honig, B.2
  • 11
    • 33847089778 scopus 로고
    • Why do molecules interact? The origin of electron donor-acceptor complexes, hydrogen bonding and proton affinity
    • Morokuma K. Why do molecules interact? The origin of electron donor-acceptor complexes, hydrogen bonding and proton affinity. Accts. Chem. Res. 10:1977;294-300.
    • (1977) Accts. Chem. Res. , vol.10 , pp. 294-300
    • Morokuma, K.1
  • 12
    • 0000455490 scopus 로고
    • Noncovalent interactions
    • Kollman P.A. Noncovalent interactions. Accts. Chem. Res. 10:1977;365-371.
    • (1977) Accts. Chem. Res. , vol.10 , pp. 365-371
    • Kollman, P.A.1
  • 13
    • 33845551411 scopus 로고
    • Geometry of the N-HOC hydrogen bond. 1. Lone-pair directionality
    • Taylor R., Kennard O., Versichel W. Geometry of the N-HOC hydrogen bond. 1. Lone-pair directionality. J. Am. Chem. Soc. 105:1983;5761-5766.
    • (1983) J. Am. Chem. Soc. , vol.105 , pp. 5761-5766
    • Taylor, R.1    Kennard, O.2    Versichel, W.3
  • 14
    • 21844437785 scopus 로고
    • Hydrogen-bond geometry in organic crystals
    • Taylor R., Kennard O. Hydrogen-bond geometry in organic crystals. Accts. Chem. Res. 17:1984;320-325.
    • (1984) Accts. Chem. Res. , vol.17 , pp. 320-325
    • Taylor, R.1    Kennard, O.2
  • 15
    • 0006248511 scopus 로고
    • Geometry of the intermolecular X-H́Y (X, Y=N, O) hydrogen bond and the calibration of empirical hydrogen-bond potentials
    • Gavezzotti A., Filippini G. Geometry of the intermolecular X-H́Y (X, Y=N, O) hydrogen bond and the calibration of empirical hydrogen-bond potentials. J. Phys. Chem. ser. B. 98:1994;4831-4837.
    • (1994) J. Phys. Chem. ser. B , vol.98 , pp. 4831-4837
    • Gavezzotti, A.1    Filippini, G.2
  • 16
    • 0029979565 scopus 로고    scopus 로고
    • Directionality of hydrogen bonds to sulfur and oxygen
    • Platts J.A., Howard S.T., Bracke B.R.F. Directionality of hydrogen bonds to sulfur and oxygen. J. Am. Chem. Soc. 118:1996;2726-2733.
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 2726-2733
    • Platts, J.A.1    Howard, S.T.2    Bracke, B.R.F.3
  • 17
    • 0000174195 scopus 로고    scopus 로고
    • Hydrogen bonding of carbonyl, ether, and ester oxygen atoms with alkanol hydroxyl groups
    • Lommerse J.P.M., Price S.L., Taylor R. Hydrogen bonding of carbonyl, ether, and ester oxygen atoms with alkanol hydroxyl groups. J. Comput. Chem. 18:1997;757-774.
    • (1997) J. Comput. Chem. , vol.18 , pp. 757-774
    • Lommerse, J.P.M.1    Price, S.L.2    Taylor, R.3
  • 18
    • 0034248140 scopus 로고    scopus 로고
    • Development of a knowledge-based potential for crystals of small organic molecules: Calculation of energy surfaces for ĆÓH-N hydrogen bonds
    • Grzybowski B.A., Ishchenko A.V., DeWitte R.S., Whitesides G.M., Shakhnovich E.I. Development of a knowledge-based potential for crystals of small organic molecules: calculation of energy surfaces for ĆÓH-N hydrogen bonds. J. Phys. Chem. ser. B. 104:2000;7293-7298.
    • (2000) J. Phys. Chem. ser. B , vol.104 , pp. 7293-7298
    • Grzybowski, B.A.1    Ishchenko, A.V.2    DeWitte, R.S.3    Whitesides, G.M.4    Shakhnovich, E.I.5
  • 19
    • 0025115609 scopus 로고
    • Hydrogen bond stereochemistry in protein structure and function
    • Ippolito J.A., Alexander R.S., Christianson D.W. Hydrogen bond stereochemistry in protein structure and function. J. Mol. Biol. 215:1990;457-471.
    • (1990) J. Mol. Biol. , vol.215 , pp. 457-471
    • Ippolito, J.A.1    Alexander, R.S.2    Christianson, D.W.3
  • 21
    • 0036100338 scopus 로고    scopus 로고
    • An improved hydrogen bond potential: Impact on medium resolution protein structures
    • Fabiola F., Bertram R., Korostelev A., Chapman M.S. An improved hydrogen bond potential: impact on medium resolution protein structures. Protein Sci. 11:2002;1415-1423.
    • (2002) Protein Sci. , vol.11 , pp. 1415-1423
    • Fabiola, F.1    Bertram, R.2    Korostelev, A.3    Chapman, M.S.4
  • 22
    • 0015492519 scopus 로고
    • Energy parameters in polypeptides. V. An empirical hydrogen bond function based on molecular orbital calculations
    • McGuire R.F., Momany F.A., Scheraga H.A. Energy parameters in polypeptides. V. An empirical hydrogen bond function based on molecular orbital calculations. J. Phys. Chem. 76:1972;375-393.
    • (1972) J. Phys. Chem. , vol.76 , pp. 375-393
    • McGuire, R.F.1    Momany, F.A.2    Scheraga, H.A.3
  • 23
    • 0000562558 scopus 로고
    • Lone pairs in carbonyl compounds and ethers
    • Wiberg K.B., Marquez M., Castejon H. Lone pairs in carbonyl compounds and ethers. J. Org. Chem. 59:1994;6817-6822.
    • (1994) J. Org. Chem. , vol.59 , pp. 6817-6822
    • Wiberg, K.B.1    Marquez, M.2    Castejon, H.3
  • 25
    • 0021757436 scopus 로고
    • A new force field for molecular mechanical simulation of nucleic acids and proteins
    • Weiner S.J., Kollman P.A., Case D.A., Singh U.C., Ghio C., Alagona G., et al. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106:1984;765-784.
    • (1984) J. Am. Chem. Soc. , vol.106 , pp. 765-784
    • Weiner, S.J.1    Kollman, P.A.2    Case, D.A.3    Singh, U.C.4    Ghio, C.5    Alagona, G.6
  • 26
    • 33645941402 scopus 로고
    • The OPLS potential function for proteins. Energy minimizations for crystals of cyclic peptides and crambin
    • Jorgensen W.J., Tirado-Rives J. The OPLS potential function for proteins. Energy minimizations for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110:1988;1657-1666.
    • (1988) J. Am. Chem. Soc. , vol.110 , pp. 1657-1666
    • Jorgensen, W.J.1    Tirado-Rives, J.2
  • 27
    • 0029011701 scopus 로고
    • A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
    • Cornell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz K.M.J., Ferguson D.M., et al. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:1995;5179-5197.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 5179-5197
    • Cornell, W.D.1    Cieplak, P.2    Bayly, C.I.3    Gould, I.R.4    Merz, K.M.J.5    Ferguson, D.M.6
  • 28
    • 0000036869 scopus 로고    scopus 로고
    • Simulation of activation free energies in molecular systems
    • Neria E., Fischer S., Karplus M. Simulation of activation free energies in molecular systems. J. Chem. Phys. 105:1996;1902-1921.
    • (1996) J. Chem. Phys. , vol.105 , pp. 1902-1921
    • Neria, E.1    Fischer, S.2    Karplus, M.3
  • 29
    • 0035829905 scopus 로고    scopus 로고
    • Hydrogen bond energetics: A simulation and statistical analysis of N-methyl acetamide (NMA), water and human lysozyme
    • Buck M., Karplus M. Hydrogen bond energetics: a simulation and statistical analysis of N-methyl acetamide (NMA), water and human lysozyme. J. Phys. Chem. ser. B. 105:2001;11000-11015.
    • (2001) J. Phys. Chem. ser. B , vol.105 , pp. 11000-11015
    • Buck, M.1    Karplus, M.2
  • 30
    • 9144240095 scopus 로고
    • DREIDING: A generic force field for molecular simulations
    • Mayo S.L., Olafson B.D., Goddard W.A.I. DREIDING: a generic force field for molecular simulations. J. Phys. Chem. 94:1990;8897-8909.
    • (1990) J. Phys. Chem. , vol.94 , pp. 8897-8909
    • Mayo, S.L.1    Olafson, B.D.2    Goddard, W.A.I.3
  • 31
    • 0343742614 scopus 로고    scopus 로고
    • Automated design of the surface positions of protein helices
    • Dahiyat B.I., Gordon D.B., Mayo S.L. 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
  • 32
    • 0035782661 scopus 로고    scopus 로고
    • Review: Protein design - Where we were, where we are, where we're going
    • Pokala N., Handel T.M. Review: protein design - where we were, where we are, where we're going. J. Struct. Biol. 134:2001;269-281.
    • (2001) J. Struct. Biol. , vol.134 , pp. 269-281
    • Pokala, N.1    Handel, T.M.2
  • 33
    • 0033117762 scopus 로고    scopus 로고
    • Designing potential energy functions for protein folding
    • Hao M.H., Scheraga H.A. Designing potential energy functions for protein folding. Curr. Opin. Struct. Biol. 9:1999;184-188.
    • (1999) Curr. Opin. Struct. Biol. , vol.9 , pp. 184-188
    • Hao, M.H.1    Scheraga, H.A.2
  • 35
  • 36
    • 0024250301 scopus 로고
    • Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison
    • Brunger A.T., Karplus M. Polar hydrogen positions in proteins: empirical energy placement and neutron diffraction comparison. Proteins: Struct. Funct. Genet. 4:1988;148-156.
    • (1988) Proteins: Struct. Funct. Genet. , vol.4 , pp. 148-156
    • Brunger, A.T.1    Karplus, M.2
  • 37
    • 0037019550 scopus 로고    scopus 로고
    • Hydrogen bonding in high-resolution protein structures: A new method to assess NMR protein geometry
    • Lipsitz R.S., Sharma Y., Brooks B.R., Tjandra N. Hydrogen bonding in high-resolution protein structures: a new method to assess NMR protein geometry. J. Am. Chem. Soc. 124:2002;10621-10626.
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 10621-10626
    • Lipsitz, R.S.1    Sharma, Y.2    Brooks, B.R.3    Tjandra, N.4
  • 38
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • Anfinsen C.B. Principles that govern the folding of protein chains. Science. 181:1973;223-230.
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.B.1
  • 39
    • 1842326139 scopus 로고    scopus 로고
    • Bayesian statistical analysis of protein side-chain rotamer preferences
    • Dunbrack R.L. Jr, Cohen F.E. 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., Jr.1    Cohen, F.E.2
  • 40
    • 0036468995 scopus 로고    scopus 로고
    • Kinetic studies of protein-protein interactions
    • Schreiber G. Kinetic studies of protein-protein interactions. Curr. Opin. Struct. Biol. 12:2002;41-47.
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 41-47
    • Schreiber, G.1
  • 42
    • 0035160537 scopus 로고    scopus 로고
    • Barstar is electrostatically optimized for tight binding to barnase
    • Lee L.P., Tidor B. Barstar is electrostatically optimized for tight binding to barnase. Nature Struct. Biol. 8:2001;73-76.
    • (2001) Nature Struct. Biol. , vol.8 , pp. 73-76
    • Lee, L.P.1    Tidor, B.2
  • 44
    • 0032929780 scopus 로고    scopus 로고
    • Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins
    • Simons K.T., Ruczinski I., Kooperberg C., Fox B.A., Bystroff C., Baker D. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins: Struct. Funct. Genet. 34:1999;82-95.
    • (1999) Proteins: Struct. Funct. Genet. , vol.34 , pp. 82-95
    • Simons, K.T.1    Ruczinski, I.2    Kooperberg, C.3    Fox, B.A.4    Bystroff, C.5    Baker, D.6
  • 45
    • 0034641749 scopus 로고    scopus 로고
    • Native protein sequences are close to optimal for their structures
    • Kuhlman B., Baker D. Native protein sequences are close to optimal for their structures. Proc. Natl Acad. Sci. USA. 97:2000;10383-10388.
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 10383-10388
    • Kuhlman, B.1    Baker, D.2
  • 46
    • 0037195144 scopus 로고    scopus 로고
    • A simple physical model for binding energy hot spots in protein-protein complexes
    • Kortemme T., Baker D. A simple physical model for binding energy hot spots in protein-protein complexes. Proc. Natl Acad. Sci. USA. 99:2002;14116-14121.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 14116-14121
    • Kortemme, T.1    Baker, D.2
  • 47
    • 0031557390 scopus 로고    scopus 로고
    • Factors affecting the ability of energy functions to discriminate correct from incorrect folds
    • Park B.H., Huang E.S., Levitt M. Factors affecting the ability of energy functions to discriminate correct from incorrect folds. J. Mol. Biol. 266:1997;831-846.
    • (1997) J. Mol. Biol. , vol.266 , pp. 831-846
    • Park, B.H.1    Huang, E.S.2    Levitt, M.3
  • 48
    • 0034560338 scopus 로고    scopus 로고
    • Discrimination of near-native protein structures from misfolded models by empirical free energy functions
    • Gatchell D.W., Dennis S., Vajda S. Discrimination of near-native protein structures from misfolded models by empirical free energy functions. Proteins: Struct. Funct. Genet. 41:2000;518-534.
    • (2000) Proteins: Struct. Funct. Genet. , vol.41 , pp. 518-534
    • Gatchell, D.W.1    Dennis, S.2    Vajda, S.3
  • 49
    • 0035186285 scopus 로고    scopus 로고
    • Free energies of protein decoys provide insight into determinants of protein stability
    • Vorobjev Y.N., Hermans J. Free energies of protein decoys provide insight into determinants of protein stability. Protein Sci. 10:2001;2498-2506.
    • (2001) Protein Sci. , vol.10 , pp. 2498-2506
    • Vorobjev, Y.N.1    Hermans, J.2
  • 51
    • 0027772959 scopus 로고
    • Shape complementarity at protein/protein interfaces
    • Lawrence M.C., Colman P.M. Shape complementarity at protein/protein interfaces. J. Mol. Biol. 234:1993;946-950.
    • (1993) J. Mol. Biol. , vol.234 , pp. 946-950
    • Lawrence, M.C.1    Colman, P.M.2
  • 52
    • 0035845563 scopus 로고    scopus 로고
    • Protein docking along smooth association pathways
    • Camacho C.J., Vajda S. Protein docking along smooth association pathways. Proc. Natl Acad. Sci. USA. 98:2001;10636-10641.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 10636-10641
    • Camacho, C.J.1    Vajda, S.2
  • 54
    • 0033613812 scopus 로고    scopus 로고
    • Visualizing and quantifying molecular goodness-of-fit: Small-probe contact dots with explicit hydrogen atoms
    • Word J.M., Lovell S.C., LaBean T.H., Taylor H.C., Zalis M.E., Presley B.K., et al. Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. J. Mol. Biol. 285:1999;1711-1733.
    • (1999) J. Mol. Biol. , vol.285 , pp. 1711-1733
    • Word, J.M.1    Lovell, S.C.2    LaBean, T.H.3    Taylor, H.C.4    Zalis, M.E.5    Presley, B.K.6
  • 55
    • 0030339738 scopus 로고    scopus 로고
    • AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR
    • Laskowski R.A., Rullmannn J.A., MacArthur M.W., Kaptein R., Thornton J.M. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR. 8:1996;477-486.
    • (1996) J. Biomol. NMR , vol.8 , pp. 477-486
    • Laskowski, R.A.1    Rullmannn, J.A.2    MacArthur, M.W.3    Kaptein, R.4    Thornton, J.M.5
  • 56
    • 0030602896 scopus 로고    scopus 로고
    • A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique
    • Tsai C.J., Lin S.L., Wolfson H.J., Nussinov R. A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique. J. Mol. Biol. 260:1996;604-620.
    • (1996) J. Mol. Biol. , vol.260 , pp. 604-620
    • Tsai, C.J.1    Lin, S.L.2    Wolfson, H.J.3    Nussinov, R.4
  • 58
    • 0030793767 scopus 로고    scopus 로고
    • De novo protein design: Fully automated sequence selection
    • Dahiyat B.I., Mayo S.L. De novo protein design: fully automated sequence selection. Science. 278:1997;82-87.
    • (1997) Science , vol.278 , pp. 82-87
    • Dahiyat, B.I.1    Mayo, S.L.2
  • 59
    • 0025338948 scopus 로고
    • Hydroxyl hydrogen conformations in trypsin determined by the neutron diffraction solvent difference map method: Relative importance of steric and electrostatic factors in defining hydrogen-bonding geometries
    • Kossiakoff A.A., Shpungin J., Sintchak M.D. Hydroxyl hydrogen conformations in trypsin determined by the neutron diffraction solvent difference map method: relative importance of steric and electrostatic factors in defining hydrogen-bonding geometries. Proc. Natl Acad. Sci. USA. 87:1990;4468-4472.
    • (1990) Proc. Natl Acad. Sci. USA , vol.87 , pp. 4468-4472
    • Kossiakoff, A.A.1    Shpungin, J.2    Sintchak, M.D.3
  • 61
    • 0037422359 scopus 로고    scopus 로고
    • Evaluation of models of electrostatic interactions in proteins
    • In press
    • Morozov A.V., Kortemme T., Baker D. Evaluation of models of electrostatic interactions in proteins. J. Phys. Chem. B. 2003;. In press.
    • (2003) J. Phys. Chem. B
    • Morozov, A.V.1    Kortemme, T.2    Baker, D.3


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