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Volumn 348, Issue 5, 2005, Pages 1283-1298

Are acidic and basic groups in buried proteins predicted to be ionized?

Author keywords

Buried charges; Continuum electrostatics; Multi conformation; pKa; Structural genomics

Indexed keywords

ANION; ARGININE; ASPARTIC ACID; CATION; GLUTAMIC ACID; HYDROGEN; HYDROXYL GROUP; LYSINE; PROTEIN; SERINE; THREONINE; TYROSINE;

EID: 18144394277     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.03.051     Document Type: Article
Times cited : (95)

References (111)
  • 2
    • 0027243893 scopus 로고
    • Electron transfer kinetics and electrostatic properties of the Rhodobacter sphaeroides reaction center and soluble c-cytochromes
    • D.M. Tiede, A.-C. Vashishta, and M.R. Gunner Electron transfer kinetics and electrostatic properties of the Rhodobacter sphaeroides reaction center and soluble c-cytochromes Biochemistry 32 1993 4515 4531
    • (1993) Biochemistry , vol.32 , pp. 4515-4531
    • Tiede, D.M.1    Vashishta, A.-C.2    Gunner, M.R.3
  • 3
    • 3142661052 scopus 로고    scopus 로고
    • Charge optimization of the interface between protein kinases and their ligands
    • P.A. Sims, C.F. Wong, and J.A. McCammon Charge optimization of the interface between protein kinases and their ligands J. Comp. Chem. 25 2004 1416 1429
    • (2004) J. Comp. Chem. , vol.25 , pp. 1416-1429
    • Sims, P.A.1    Wong, C.F.2    McCammon, J.A.3
  • 4
    • 0000414723 scopus 로고    scopus 로고
    • Electrostatic potentials in Rhodopseudomonas viridis reaction center: Implications for the driving force and directionality of electron transfer
    • M.R. Gunner, A. Nicholls, and B. Honig Electrostatic potentials in Rhodopseudomonas viridis reaction center: implications for the driving force and directionality of electron transfer J. Phys. Chem. 100 1996 4277 4291
    • (1996) J. Phys. Chem. , vol.100 , pp. 4277-4291
    • Gunner, M.R.1    Nicholls, A.2    Honig, B.3
  • 5
  • 6
    • 0344418714 scopus 로고    scopus 로고
    • Simulating proton translocations in proteins: Probing proton transfer pathways in the Rhodobacter sphaeroides reaction center
    • Y. Sham, I. Muegge, and A. Warshel Simulating proton translocations in proteins: probing proton transfer pathways in the Rhodobacter sphaeroides reaction center Proteins: Struct. Funct. Genet. 36 1999 484 500
    • (1999) Proteins: Struct. Funct. Genet. , vol.36 , pp. 484-500
    • Sham, Y.1    Muegge, I.2    Warshel, A.3
  • 7
    • 1542320003 scopus 로고    scopus 로고
    • Structural interpretation of pH and salt-dependent processes in proteins with computational methods
    • E.B. Garcia-Moreno, and C.A. Fitch Structural interpretation of pH and salt-dependent processes in proteins with computational methods Methods Enzymol. 380 2004 20 51
    • (2004) Methods Enzymol. , vol.380 , pp. 20-51
    • Garcia-Moreno, E.B.1    Fitch, C.A.2
  • 11
    • 0029761027 scopus 로고    scopus 로고
    • A pH-dependent polarity at the binuclear center of reduced cytochrome c oxidase detected by FTIR difference spectroscopy of the CO adduct
    • D.M. Mitchell, J.P. Shapleigh, A.M. Archer, J.O. Alben, and B. G.R. A pH-dependent polarity at the binuclear center of reduced cytochrome c oxidase detected by FTIR difference spectroscopy of the CO adduct Biochemistry 35 1996 9446 9450
    • (1996) Biochemistry , vol.35 , pp. 9446-9450
    • Mitchell, D.M.1    Shapleigh, J.P.2    Archer, A.M.3    Alben, J.O.4
  • 12
    • 0242657394 scopus 로고    scopus 로고
    • Some recent contributions of FTIR difference spectroscopy to the study of cytochrome oxidas
    • R.B. Gennis Some recent contributions of FTIR difference spectroscopy to the study of cytochrome oxidas FEBS Letters 555 2003 2 7
    • (2003) FEBS Letters , vol.555 , pp. 2-7
    • Gennis, R.B.1
  • 13
    • 0025005525 scopus 로고
    • Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease
    • D. Shortle, W.E. Stites, and A.K. Meeker Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease Biochemistry 29 1990 8033 8041
    • (1990) Biochemistry , vol.29 , pp. 8033-8041
    • Shortle, D.1    Stites, W.E.2    Meeker, A.K.3
  • 15
  • 16
    • 0000671518 scopus 로고    scopus 로고
    • a's of ionizable residues in proteins: Semi-microscopic and microscopic approaches
    • a's of ionizable residues in proteins: Semi-microscopic and microscopic approaches J. Phys. Chem. 101 1997 4458 4472
    • (1997) J. Phys. Chem. , vol.101 , pp. 4458-4472
    • Sham, Y.Y.1    Chu, Z.T.2    Warshel, A.3
  • 17
    • 0035811239 scopus 로고    scopus 로고
    • A general screened coulomb potential based implicit solvent model: Calculation of secondary structure of small peptides
    • S.A. Hassan, and E.L. Mehler A general screened coulomb potential based implicit solvent model: calculation of secondary structure of small peptides Int. J. Quant. Chem. 83 2001 193 202
    • (2001) Int. J. Quant. Chem. , vol.83 , pp. 193-202
    • Hassan, S.A.1    Mehler, E.L.2
  • 18
    • 0035312551 scopus 로고    scopus 로고
    • Macromolecular electrostatics: Continuum models and their growing pains
    • T. Simonson Macromolecular electrostatics: continuum models and their growing pains Curr. Opin. Struct. Biol. 11 2001 243 252
    • (2001) Curr. Opin. Struct. Biol. , vol.11 , pp. 243-252
    • Simonson, T.1
  • 20
    • 2442693239 scopus 로고    scopus 로고
    • Macroscopic electrostatic models for protonation states in proteins
    • D. Bashford Macroscopic electrostatic models for protonation states in proteins Front Biosci. 9 2004 1082 1099
    • (2004) Front Biosci. , vol.9 , pp. 1082-1099
    • Bashford, D.1
  • 21
    • 0021476470 scopus 로고
    • Calculations of electrostatic interactions in biological systems and in solutions
    • A. Warshel, and S.T. Russell Calculations of electrostatic interactions in biological systems and in solutions Quant. Rev. Biophys. 17 1984 283 422
    • (1984) Quant. Rev. Biophys. , vol.17 , pp. 283-422
    • Warshel, A.1    Russell, S.T.2
  • 22
    • 0028929583 scopus 로고
    • Free energy balance in protein folding
    • B. Honig, and A.-S. Yang Free energy balance in protein folding Advan. Protein Chem. 46 1995 27 58
    • (1995) Advan. Protein Chem. , vol.46 , pp. 27-58
    • Honig, B.1    Yang, A.-S.2
  • 23
    • 0021763134 scopus 로고
    • On the environment of ionizable groups in globular proteins
    • A.A. Rashin, and B. Honig On the environment of ionizable groups in globular proteins J. Mol. Biol. 173 1984 515 521
    • (1984) J. Mol. Biol. , vol.173 , pp. 515-521
    • Rashin, A.A.1    Honig, B.2
  • 24
    • 0022777523 scopus 로고
    • The distribution of charged groups in proteins
    • D.J. Barlow, and J.M. Thornton The distribution of charged groups in proteins Biopolymers 25 1986 1717 1733
    • (1986) Biopolymers , vol.25 , pp. 1717-1733
    • Barlow, D.J.1    Thornton, J.M.2
  • 26
    • 0033550299 scopus 로고    scopus 로고
    • Salt bridge stability in monomeric proteins
    • S. Kumar, and R. Nussinov Salt bridge stability in monomeric proteins J. Mol. Biol. 293 1999 1241 1255
    • (1999) J. Mol. Biol. , vol.293 , pp. 1241-1255
    • Kumar, S.1    Nussinov, R.2
  • 27
    • 0034091669 scopus 로고    scopus 로고
    • Backbone dipoles generate positive potentials in all proteins: Origins and implications of the effect
    • M.R. Gunner, M.A. Saleh, E. Cross, A. ud-Doula, and M. Wise Backbone dipoles generate positive potentials in all proteins: origins and implications of the effect Biophys. J. 78 2000 1126 1144
    • (2000) Biophys. J. , vol.78 , pp. 1126-1144
    • Gunner, M.R.1    Saleh, M.A.2    Cross, E.3    Ud-Doula, A.4    Wise, M.5
  • 28
    • 0029864591 scopus 로고    scopus 로고
    • Direct measurement of salt-bridge solvation energies using a peptide model system: Implications for protein stability
    • W.C. Wimley, K. Gawrisch, T.P. Creamer, and S.H. White Direct measurement of salt-bridge solvation energies using a peptide model system: implications for protein stability Proc. Natl Acad. Sci. USA 93 1996 2985 2990
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 2985-2990
    • Wimley, W.C.1    Gawrisch, K.2    Creamer, T.P.3    White, S.H.4
  • 29
    • 0021828928 scopus 로고
    • Hydrogen bonding and biological specificity analysed by protein engineering
    • A.R. Fersht, J. Shi, J. Knill-Jones, D.M. Lowe, A.J. Wilkinson, and D.M. Blow Hydrogen bonding and biological specificity analysed by protein engineering Nature 314 1985 235 238
    • (1985) Nature , vol.314 , pp. 235-238
    • Fersht, A.R.1    Shi, J.2    Knill-Jones, J.3    Lowe, D.M.4    Wilkinson, A.J.5    Blow, D.M.6
  • 30
    • 0029121068 scopus 로고
    • Free energy determinants of secondary structure formation: I. α-helices
    • A. Yang, and B. Honig Free energy determinants of secondary structure formation: I. α-helices J. Mol. Biol. 252 1995 351 365
    • (1995) J. Mol. Biol. , vol.252 , pp. 351-365
    • Yang, A.1    Honig, B.2
  • 31
    • 0029150955 scopus 로고
    • Free energy determinants of secondary structure formation: II. Antiparallel β-sheet
    • A. Yang, and B. Honig Free energy determinants of secondary structure formation: II. Antiparallel β-sheet J. Mol. Biol. 252 1995 366 376
    • (1995) J. Mol. Biol. , vol.252 , pp. 366-376
    • Yang, A.1    Honig, B.2
  • 32
    • 0021049880 scopus 로고
    • Waterlogged molecules
    • R. Wolfenden Waterlogged molecules Science 222 1983 1087 1093
    • (1983) Science , vol.222 , pp. 1087-1093
    • Wolfenden, R.1
  • 33
    • 0028093141 scopus 로고
    • On the probability of finding a water molecule in a non-polar cavity
    • R. Wolfenden, and A. Radzicka On the probability of finding a water molecule in a non-polar cavity Science 265 1994 936 937
    • (1994) Science , vol.265 , pp. 936-937
    • Wolfenden, R.1    Radzicka, A.2
  • 34
    • 0034640465 scopus 로고    scopus 로고
    • A pragmatic approach to structure based calculation of coupled proton and electron transfer in proteins
    • M.R. Gunner, and E. Alexov A pragmatic approach to structure based calculation of coupled proton and electron transfer in proteins Biochim. Biophys. Acta 1458 2000 63 87
    • (2000) Biochim. Biophys. Acta , vol.1458 , pp. 63-87
    • Gunner, M.R.1    Alexov, E.2
  • 35
    • 0000176654 scopus 로고
    • Stablilty of "salt bridges' in membrane proteins
    • B.H. Honig, and W.L. Hubble Stablilty of "salt bridges' in membrane proteins Proc. Natl Acad. Sci. USA 81 1984 5412 5416
    • (1984) Proc. Natl Acad. Sci. USA , vol.81 , pp. 5412-5416
    • Honig, B.H.1    Hubble, W.L.2
  • 36
    • 0025234587 scopus 로고
    • PH-induced denaturation of proteins: A single salt bridge contrubutes 3-5 kcal/mol to the free energy of folding of T-4 lysozyme
    • D.E. Anderson, W.J. Becktel, and F.W. Dahlquist pH-induced denaturation of proteins: A single salt bridge contrubutes 3-5 kcal/mol to the free energy of folding of T-4 lysozyme Biochemistry 29 1990 2403 2408
    • (1990) Biochemistry , vol.29 , pp. 2403-2408
    • Anderson, D.E.1    Becktel, W.J.2    Dahlquist, F.W.3
  • 37
    • 0028277521 scopus 로고
    • Spatial optimization of electrostatic interactions between the ionized groups in globular proteins
    • V.Z. Spassov, and B.P. Atanasov Spatial optimization of electrostatic interactions between the ionized groups in globular proteins Proteins: Struct. Funct. Genet. 19 1994 222 229
    • (1994) Proteins: Struct. Funct. Genet. , vol.19 , pp. 222-229
    • Spassov, V.Z.1    Atanasov, B.P.2
  • 38
    • 0029564595 scopus 로고
    • Are buried salt-bridges imporant for protein stability and conformational specificity?
    • C.D. Waldburger, J.F. Schildbach, and R.T. Sauer Are buried salt-bridges imporant 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
  • 39
    • 0026438116 scopus 로고
    • Electrostatic fields in antibodies and antibody/antigen complexes
    • J. Novotny, and K. Sharp Electrostatic fields in antibodies and antibody/antigen complexes Prog. Biophys. Molec. Biol. 58 1992 203 224
    • (1992) Prog. Biophys. Molec. Biol. , vol.58 , pp. 203-224
    • Novotny, J.1    Sharp, K.2
  • 40
    • 0028204490 scopus 로고
    • Do salt bridges stabilize proteins? a continuum electrostatic analysis
    • Z. Hendsch, and B. Tidor 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.1    Tidor, B.2
  • 41
    • 0032563113 scopus 로고    scopus 로고
    • Electrostatic contributions to the stability of halophilic proteins
    • A.H. Elcock, and J.A. McCammon Electrostatic contributions to the stability of halophilic proteins J. Mol. Biol. 280 1998 731 748
    • (1998) J. Mol. Biol. , vol.280 , pp. 731-748
    • Elcock, A.H.1    McCammon, J.A.2
  • 43
    • 0035107570 scopus 로고    scopus 로고
    • Optimization of binding electrostatics: Charge complementarity in the barnase-barstar protein complex
    • L.P. Lee, and B. Tidor Optimization of binding electrostatics: charge complementarity in the barnase-barstar protein complex Protein Sci. 10 2001 362 377
    • (2001) Protein Sci. , vol.10 , pp. 362-377
    • Lee, L.P.1    Tidor, B.2
  • 44
    • 0032856161 scopus 로고    scopus 로고
    • Buried, charged, non-ion-paired aspartic acid 76 contributes favorably to the conformational stability of ribonuclease T1
    • A. Giletto, and C.N. Pace Buried, charged, non-ion-paired aspartic acid 76 contributes favorably to the conformational stability of ribonuclease T1 Biochemistry 38 1999 13379 13384
    • (1999) Biochemistry , vol.38 , pp. 13379-13384
    • Giletto, A.1    Pace, C.N.2
  • 45
    • 0035448574 scopus 로고    scopus 로고
    • Ion pairs and the thermotolerance of proteins from hyperthermophiles: A "traffic rule" for hot roads
    • A. Karshikoff, and R. Ladenstein Ion pairs and the thermotolerance of proteins from hyperthermophiles: a "traffic rule" for hot roads TIBS 26 2001 550 556
    • (2001) TIBS , vol.26 , pp. 550-556
    • Karshikoff, A.1    Ladenstein, R.2
  • 46
    • 0032514762 scopus 로고    scopus 로고
    • From ab initio quantum mechanics to molecular neurobiology: A cation-π binding site in the nicotinic receptor
    • W. Zhong, J.P. Gallivan, Y. Zhang, L. Li, H.A. Lester, and D.A. Dougherty From ab initio quantum mechanics to molecular neurobiology: A cation-π binding site in the nicotinic receptor PNAS 95 1998 12088 12093
    • (1998) PNAS , vol.95 , pp. 12088-12093
    • Zhong, W.1    Gallivan, J.P.2    Zhang, Y.3    Li, L.4    Lester, H.A.5    Dougherty, D.A.6
  • 47
    • 0027125907 scopus 로고
    • A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations
    • J. Gao, and X. Xia A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations Science 258 1992 631 635
    • (1992) Science , vol.258 , pp. 631-635
    • Gao, J.1    Xia, X.2
  • 48
    • 0001664118 scopus 로고    scopus 로고
    • A mixed quantum mechanics/molecular mechanics (QM/MM) method for large-scale modeling of chemistry in protein environments
    • R.B. Murphy, D.M. Philipp, and R.A. Friesner A mixed quantum mechanics/molecular mechanics (QM/MM) method for large-scale modeling of chemistry in protein environments J. Comput. Chem. 21 2000 1442 1457
    • (2000) J. Comput. Chem. , vol.21 , pp. 1442-1457
    • Murphy, R.B.1    Philipp, D.M.2    Friesner, R.A.3
  • 50
    • 9244223045 scopus 로고    scopus 로고
    • Constant pH molecular dynamics in generalized Born implicit solvent
    • J. Mongan, D.A. Case, and J.A. McCammon Constant pH molecular dynamics in generalized Born implicit solvent J. Comput. Chem. 25 2004 2038 2048
    • (2004) J. Comput. Chem. , vol.25 , pp. 2038-2048
    • Mongan, J.1    Case, D.A.2    McCammon, J.A.3
  • 51
    • 8444247565 scopus 로고    scopus 로고
    • a shifts in proteins using a combination of molecular mechanical and continuum solvent calculations
    • a shifts in proteins using a combination of molecular mechanical and continuum solvent calculations J. Comput. Chem. 25 2004 1865 1872
    • (2004) J. Comput. Chem. , vol.25 , pp. 1865-1872
    • Kuhn, B.1    Kollman, P.A.2    Stahl, M.3
  • 52
    • 0026095641 scopus 로고
    • Protonation of interacting residues in a protein by a Monte Carlo method: Application to Lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides
    • P. Beroza, D.R. Fredkin, M.Y. Okamura, and G. Feher Protonation of interacting residues in a protein by a Monte Carlo method: application to Lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides Proc. Natl Acad. Sci. USA 88 1991 5804 5808
    • (1991) Proc. Natl Acad. Sci. USA , vol.88 , pp. 5804-5808
    • Beroza, P.1    Fredkin, D.R.2    Okamura, M.Y.3    Feher, G.4
  • 54
    • 0025197061 scopus 로고
    • a's of ionizable groups in proteins: Atomic detail from a continuum electrostatic model
    • a's of ionizable groups in proteins: atomic detail from a continuum electrostatic model Biochemistry 29 1990 10219 10225
    • (1990) Biochemistry , vol.29 , pp. 10219-10225
    • Bashford, D.1    Karplus, M.2
  • 55
    • 0028305457 scopus 로고
    • Prediction of pH-dependent properties in proteins
    • J. Antosiewicz, J.A. McCammon, and M.K. Gilson Prediction of pH-dependent properties in proteins J. Mol. Biol. 238 1994 415 436
    • (1994) J. Mol. Biol. , vol.238 , pp. 415-436
    • Antosiewicz, J.1    McCammon, J.A.2    Gilson, M.K.3
  • 56
    • 0035451052 scopus 로고    scopus 로고
    • What are the "dielectric constants" of proteins and how to validate electrostatic models?
    • C.N. Schutz, and A. Warshel What are the "dielectric constants" of proteins and how to validate electrostatic models? Proteins: Struct. Funct. Genet. 44 2001 400 417
    • (2001) Proteins: Struct. Funct. Genet. , vol.44 , pp. 400-417
    • Schutz, C.N.1    Warshel, A.2
  • 57
    • 0000703443 scopus 로고    scopus 로고
    • Self-consistent, free energy based approximation to calulate pH dependent electrostatic effects in proteins
    • E.L. Mehler Self-consistent, free energy based approximation to calulate pH dependent electrostatic effects in proteins J. Phys. Chem. 100 1996 16006 16018
    • (1996) J. Phys. Chem. , vol.100 , pp. 16006-16018
    • Mehler, E.L.1
  • 58
    • 0033012333 scopus 로고    scopus 로고
    • A self-consistent, microenvironment modulated screened Coulomb potential approximation to calculate pH-dependent electrostatic effects in proteins
    • E.L. Mehler, and F. Guarnieri A self-consistent, microenvironment modulated screened Coulomb potential approximation to calculate pH-dependent electrostatic effects in proteins Biophys. J. 77 1999 3 22
    • (1999) Biophys. J. , vol.77 , pp. 3-22
    • Mehler, E.L.1    Guarnieri, F.2
  • 59
    • 33748593093 scopus 로고    scopus 로고
    • a's of ionizable groups in protein
    • a's of ionizable groups in protein J. Phys. Chem. 100 1996 17373 17387
    • (1996) J. Phys. Chem. , vol.100 , pp. 17373-17387
    • Demchuk, E.1    Wade, R.C.2
  • 60
    • 0030910225 scopus 로고    scopus 로고
    • Electrostatics for proteins: Description in terms of two dielectric constants simultaneously
    • L.I. Krishtalik, A.M. Kuznetsov, and E.L. Mertz Electrostatics for proteins: description in terms of two dielectric constants simultaneously Proteins: Struct. Funct. Genet. 28 1997 174 182
    • (1997) Proteins: Struct. Funct. Genet. , vol.28 , pp. 174-182
    • Krishtalik, L.I.1    Kuznetsov, A.M.2    Mertz, E.L.3
  • 61
    • 0001315749 scopus 로고    scopus 로고
    • A model of a local dielectric constant in proteins
    • D. Voges, and A. Karshikoff A model of a local dielectric constant in proteins J.Chem.Phys. 108 1998 2219 2227
    • (1998) J.Chem.Phys. , vol.108 , pp. 2219-2227
    • Voges, D.1    Karshikoff, A.2
  • 62
    • 0035913537 scopus 로고    scopus 로고
    • Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions
    • W. Rocchia, E. Alexov, and B. Honig Extending the applicability of the nonlinear Poisson-Boltzmann equation: multiple dielectric constants and multivalent ions J. Phys. Chem. B 105 2001 6507 6514
    • (2001) J. Phys. Chem. B , vol.105 , pp. 6507-6514
    • Rocchia, W.1    Alexov, E.2    Honig, B.3
  • 63
    • 0030582736 scopus 로고    scopus 로고
    • Coupling between folding and ionization equilibria: Effects of pH on the conformational preferences of polypeptides
    • D.R. Ripoll, Y.N. Vorobjev, A. Liwo, J.A. Vila, and H.A. Scheraga Coupling between folding and ionization equilibria: Effects of pH on the conformational preferences of polypeptides J. Mol. Biol. 264 1996 770 783
    • (1996) J. Mol. Biol. , vol.264 , pp. 770-783
    • Ripoll, D.R.1    Vorobjev, Y.N.2    Liwo, A.3    Vila, J.A.4    Scheraga, H.A.5
  • 65
    • 33748400070 scopus 로고    scopus 로고
    • Including side chain flexibility in continuum electrostatic calculations of protein titration
    • P. Beroza, and D. Case Including side chain flexibility in continuum electrostatic calculations of protein titration J. Phys. Chem. 100 1996 20156 20163
    • (1996) J. Phys. Chem. , vol.100 , pp. 20156-20163
    • Beroza, P.1    Case, D.2
  • 66
    • 0030945495 scopus 로고    scopus 로고
    • Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties
    • E.G. Alexov, and M.R. Gunner Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties Biophys. J. 72 1997 2075 2093
    • (1997) Biophys. J. , vol.72 , pp. 2075-2093
    • Alexov, E.G.1    Gunner, M.R.2
  • 67
    • 0028859420 scopus 로고
    • Conformation and hydrogen ion titration of proteins: A continuum electrostatic model with conformational flexibility
    • T.J. You, and D. Bashford Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility Biophys. J. 69 1995 1721 1733
    • (1995) Biophys. J. , vol.69 , pp. 1721-1733
    • You, T.J.1    Bashford, D.2
  • 69
    • 0036140443 scopus 로고    scopus 로고
    • Continuum electrostatic analysis of irregular ionization and proton allocation in proteins
    • A. Koumanov, H. Ruterjans, and A. Karshikoff Continuum electrostatic analysis of irregular ionization and proton allocation in proteins Proteins: Struct. Funct. Genet. 46 2002 85 96
    • (2002) Proteins: Struct. Funct. Genet. , vol.46 , pp. 85-96
    • Koumanov, A.1    Ruterjans, H.2    Karshikoff, A.3
  • 70
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • A.G. Murzin, S.E. Brenner, T. Hubbard, and C. Chothia SCOP: a structural classification of proteins database for the investigation of sequences and structures J. Mol. Biol. 247 1995 536 540
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 71
    • 0033565815 scopus 로고    scopus 로고
    • Residue depth: A novel parameter for the analysis of protein structure and stability
    • S. Chakravatry, and R. Varadarajan Residue depth: a novel parameter for the analysis of protein structure and stability Structure 7 1999 723 732
    • (1999) Structure , vol.7 , pp. 723-732
    • Chakravatry, S.1    Varadarajan, R.2
  • 72
    • 0017429069 scopus 로고
    • Areas, volumes, packing, and protein structure
    • F.M. Richards Areas, volumes, packing, and protein structure Annu. Rev. Biophys. Bioengng. 6 1977 151 176
    • (1977) Annu. Rev. Biophys. Bioengng. , vol.6 , pp. 151-176
    • Richards, F.M.1
  • 73
    • 0021755764 scopus 로고
    • Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect
    • T.J. Richmond Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect J. Mol. Biol. 178 1984 63 89
    • (1984) J. Mol. Biol. , vol.178 , pp. 63-89
    • Richmond, T.J.1
  • 74
    • 0017876485 scopus 로고
    • Packing of a-helices: Geometrical constraints and contact areas
    • T.J. Richmond, and F.M. Richards Packing of a-helices: geometrical constraints and contact areas J. Mol. Biol. 119 1978 537 555
    • (1978) J. Mol. Biol. , vol.119 , pp. 537-555
    • Richmond, T.J.1    Richards, F.M.2
  • 75
    • 84986486656 scopus 로고
    • A rapid finite difference algorithm utilizing successive over-relaxation to solve the Poisson-Boltzmann equation
    • A. Nicholls, and B. Honig A rapid finite difference algorithm utilizing successive over-relaxation to solve the Poisson-Boltzmann equation J. Comput. Chem. 12 1991 435 445
    • (1991) J. Comput. Chem. , vol.12 , pp. 435-445
    • Nicholls, A.1    Honig, B.2
  • 76
    • 0026030641 scopus 로고
    • Database of homology-derived protein structures and the structural meaning of sequence alignment
    • C. Sander, and R. Schneider Database of homology-derived protein structures and the structural meaning of sequence alignment Proteins: Struct. Funct. Genet. 9 1991 56 68
    • (1991) Proteins: Struct. Funct. Genet. , vol.9 , pp. 56-68
    • Sander, C.1    Schneider, R.2
  • 77
    • 0036805481 scopus 로고    scopus 로고
    • Intramolecular interactions at protein surfaces and thier impact on protein function
    • A.D. Robertson Intramolecular interactions at protein surfaces and thier impact on protein function TIBS 27 2002 521 526
    • (2002) TIBS , vol.27 , pp. 521-526
    • Robertson, A.D.1
  • 78
    • 0041972670 scopus 로고    scopus 로고
    • How cytochromes with different folds control heme redox potentials
    • J. Mao, K. Hauser, and M.R. Gunner How cytochromes with different folds control heme redox potentials Biochemistry 42 2003 9829 9840
    • (2003) Biochemistry , vol.42 , pp. 9829-9840
    • Mao, J.1    Hauser, K.2    Gunner, M.R.3
  • 79
    • 0033614791 scopus 로고    scopus 로고
    • B in bacterial photosynthetic reaction centers
    • B in bacterial photosynthetic reaction centers Biochemistry 38 1999 8253 8270
    • (1999) Biochemistry , vol.38 , pp. 8253-8270
    • Alexov, E.G.1    Gunner, M.R.2
  • 80
    • 0034730115 scopus 로고    scopus 로고
    • Electron transfer between the quinones in the photosynthetic reaction center and its coupling to conformational changes
    • B. Rabenstein, G.M. Ullmann, and E.W. Knapp Electron transfer between the quinones in the photosynthetic reaction center and its coupling to conformational changes Biochemistry 39 2000 10487 10496
    • (2000) Biochemistry , vol.39 , pp. 10487-10496
    • Rabenstein, B.1    Ullmann, G.M.2    Knapp, E.W.3
  • 81
    • 11844302809 scopus 로고    scopus 로고
    • Energetics of quinone-dependent electron and proton transfers in Rhodobacter sphaeroides photosynthetic reaction centers
    • Z. Zhu, and M.R. Gunner Energetics of quinone-dependent electron and proton transfers in Rhodobacter sphaeroides photosynthetic reaction centers Biochemistry 44 2005 82 96
    • (2005) Biochemistry , vol.44 , pp. 82-96
    • Zhu, Z.1    Gunner, M.R.2
  • 82
    • 0035823064 scopus 로고    scopus 로고
    • a alculations suggest storage of an excess proton in a hydrogen-bonded water network in bacteriorhodopsin
    • a alculations suggest storage of an excess proton in a hydrogen-bonded water network in bacteriorhodopsin J. Mol. Biol. 312 2001 203 219
    • (2001) J. Mol. Biol. , vol.312 , pp. 203-219
    • Spassov, V.Z.1    Luecke, H.2    Gerwert, K.3    Bashford, D.4
  • 83
    • 0041471589 scopus 로고    scopus 로고
    • Calculation of proton transfers in Bacteriorhodopsin bR and M intermediates
    • Y. Song, J. Mao, and M.R. Gunner Calculation of proton transfers in Bacteriorhodopsin bR and M intermediates Biochemistry 42 2003 9875 9888
    • (2003) Biochemistry , vol.42 , pp. 9875-9888
    • Song, Y.1    Mao, J.2    Gunner, M.R.3
  • 85
    • 10044230751 scopus 로고    scopus 로고
    • Calculated coupling of transmembrane electron and proton transfer in dihemic quinol:fumarate reductase
    • A.H. Haas, and C.R. Lancaster Calculated coupling of transmembrane electron and proton transfer in dihemic quinol:fumarate reductase Biophys. J. 87 2004 4298 4315
    • (2004) Biophys. J. , vol.87 , pp. 4298-4315
    • Haas, A.H.1    Lancaster, C.R.2
  • 86
    • 0028126676 scopus 로고
    • Optimization of the electrostatic interactions between ionized groups and peptide dipoles in proteins
    • V. Spassov, A. Karshokoff, and R. Ladenstein Optimization of the electrostatic interactions between ionized groups and peptide dipoles in proteins Protein Sci. 3 1994 1556 1569
    • (1994) Protein Sci. , vol.3 , pp. 1556-1569
    • Spassov, V.1    Karshokoff, A.2    Ladenstein, R.3
  • 88
    • 0030926503 scopus 로고    scopus 로고
    • Optimization of the electrostatic interactions between ionized groups and peptide dipoles in proteins
    • V.Z. Spassov, R. Ladenstein, and A.D. Karshikoff Optimization of the electrostatic interactions between ionized groups and peptide dipoles in proteins Protein Sci. 6 1997 1190 1196
    • (1997) Protein Sci. , vol.6 , pp. 1190-1196
    • Spassov, V.Z.1    Ladenstein, R.2    Karshikoff, A.D.3
  • 89
    • 0034620528 scopus 로고    scopus 로고
    • Rational modification of protein stability by the mutation of charged surface residues
    • S. Spector, M. Wang, S.A. Carp, J. Robblee, Z. Hendsch, and R. Fairman Rational modification of protein stability by the mutation of charged surface residues Biochemistry 39 2000 872 879
    • (2000) Biochemistry , vol.39 , pp. 872-879
    • Spector, S.1    Wang, M.2    Carp, S.A.3    Robblee, J.4    Hendsch, Z.5    Fairman, R.6
  • 90
    • 0034062925 scopus 로고    scopus 로고
    • Deterministic features of side-chain main-chain hydrogen bonds in globular protein structures
    • N. Eswar, and C. Ramakrishnan Deterministic features of side-chain main-chain hydrogen bonds in globular protein structures Protein Engng. 13 2000 227 238
    • (2000) Protein Engng. , vol.13 , pp. 227-238
    • Eswar, N.1    Ramakrishnan, C.2
  • 91
    • 0028304962 scopus 로고
    • Satisfying hydrogen bonding potential in proteins
    • I.K. McDonald, and J.M. Thorton 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    Thorton, J.M.2
  • 92
    • 18144373253 scopus 로고    scopus 로고
    • Polar group burial contributes more to protein stability than nonpolar group burial
    • C.N. Pace Polar group burial contributes more to protein stability than nonpolar group burial J. Am. Chem. Soc. 39 2000 A D
    • (2000) J. Am. Chem. Soc. , vol.39
    • Pace, C.N.1
  • 94
    • 0035965145 scopus 로고    scopus 로고
    • Prediction of functionally important residues based solely on the computed energetics of protein structure
    • A.H. Elcock Prediction of functionally important residues based solely on the computed energetics of protein structure J. Mol. Biol. 312 2001 885 896
    • (2001) J. Mol. Biol. , vol.312 , pp. 885-896
    • Elcock, A.H.1
  • 95
    • 2942517681 scopus 로고    scopus 로고
    • Enzyme/non-enzyme discrimination and prediction of enzyme active site location using charge-based methods
    • P. Bate, and J. Warwicker Enzyme/non-enzyme discrimination and prediction of enzyme active site location using charge-based methods J. Mol. Biol. 340 2004 263 276
    • (2004) J. Mol. Biol. , vol.340 , pp. 263-276
    • Bate, P.1    Warwicker, J.2
  • 96
    • 0032562210 scopus 로고    scopus 로고
    • Energetics of electron-transfer and protonation reactions of the quinones in the photosynthetic reaction center of Rhodopseudonas viridis
    • B. Rabenstein, G.M. Ullmann, and E.-W. Knapp Energetics of electron-transfer and protonation reactions of the quinones in the photosynthetic reaction center of Rhodopseudonas viridis Biochemistry 37 1998 2488 2495
    • (1998) Biochemistry , vol.37 , pp. 2488-2495
    • Rabenstein, B.1    Ullmann, G.M.2    Knapp, E.-W.3
  • 97
    • 0035957234 scopus 로고    scopus 로고
    • A novel view of pH titration in biomolecules
    • A. Onufriev, D.A. Case, and G.M. Ullmann A novel view of pH titration in biomolecules Biochemistry 40 2001 3413 3419
    • (2001) Biochemistry , vol.40 , pp. 3413-3419
    • Onufriev, A.1    Case, D.A.2    Ullmann, G.M.3
  • 98
    • 0035940421 scopus 로고    scopus 로고
    • THEMATICS: A simple computational predictor of enzyme function from structure
    • M. Ondrechen, J. Clifton, and D. Ringe THEMATICS: a simple computational predictor of enzyme function from structure Proc. Natl Acad. Sci. USA 98 2001 12473 12478
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 12473-12478
    • Ondrechen, M.1    Clifton, J.2    Ringe, D.3
  • 99
    • 0033613164 scopus 로고    scopus 로고
    • Tanford-Kirkwood electrostatics for protein modeling
    • J.J. Havranek, and P.B. Harbury Tanford-Kirkwood electrostatics for protein modeling Proc. Natl Acad. Sci. USA 96 1999 11145 11150
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 11145-11150
    • Havranek, J.J.1    Harbury, P.B.2
  • 101
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: A protein sequence culling server
    • G. Wang, and R.L. Dunbrack PISCES: a protein sequence culling server Bioinformatics 19 2003 1589 1591
    • (2003) Bioinformatics , vol.19 , pp. 1589-1591
    • Wang, G.1    Dunbrack, R.L.2
  • 102
    • 0032169688 scopus 로고    scopus 로고
    • PQS: A protein quaternary structure file server
    • K. Henrick, and J.M. Thornton PQS: a protein quaternary structure file server Trends Biochem. Sci. 23 1998 358 361
    • (1998) Trends Biochem. Sci. , vol.23 , pp. 358-361
    • Henrick, K.1    Thornton, J.M.2
  • 103
    • 0026319199 scopus 로고
    • Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbonds
    • A. Nicholls, K.A. Sharp, and B. Honig Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbonds Proteins: Struct. Funct. Genet. 11 1991 281 296
    • (1991) Proteins: Struct. Funct. Genet. , vol.11 , pp. 281-296
    • Nicholls, A.1    Sharp, K.A.2    Honig, B.3
  • 104
    • 84986452939 scopus 로고
    • The fast multipole boundary element method for molecular electrostatics: An optimal approach for large systems
    • R. Bharadwaj, A. Windemuth, S. Sridharan, B. Honig, and A. Nicholls The fast multipole boundary element method for molecular electrostatics: an optimal approach for large systems J. Comp. Chem. 16 1995 898 913
    • (1995) J. Comp. Chem. , vol.16 , pp. 898-913
    • Bharadwaj, R.1    Windemuth, A.2    Sridharan, S.3    Honig, B.4    Nicholls, A.5
  • 105
    • 0000328844 scopus 로고
    • A new vertex algorithm to calculate solvent accessible surface areas
    • S. Sridharan, A. Nicholls, and B. Honig A new vertex algorithm to calculate solvent accessible surface areas Biophys. J. 61 1992 A174
    • (1992) Biophys. J. , vol.61 , pp. 174
    • Sridharan, S.1    Nicholls, A.2    Honig, B.3
  • 107
    • 32844457567 scopus 로고
    • Accurate calculation of hydration free energies using macroscopic solvent models
    • D. Sitkoff, K.A. Sharp, and B. Honig Accurate calculation of hydration free energies using macroscopic solvent models J. Phys. Chem. 98 1994 1978 1988
    • (1994) J. Phys. Chem. , vol.98 , pp. 1978-1988
    • Sitkoff, D.1    Sharp, K.A.2    Honig, B.3
  • 111
    • 2442488799 scopus 로고    scopus 로고
    • PH dependence of heme electrochemistry in cytochromes investigated by multiconformation continuum electrostatic calculations
    • K. Hauser, J. Mao, and M.R. Gunner pH dependence of heme electrochemistry in cytochromes investigated by multiconformation continuum electrostatic calculations Biopolymers 74 2004 51 54
    • (2004) Biopolymers , vol.74 , pp. 51-54
    • Hauser, K.1    Mao, J.2    Gunner, M.R.3


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