메뉴 건너뛰기




Volumn 79, Issue 12, 2011, Pages 3410-3419

Histidine in continuum electrostatics protonation state calculations

Author keywords

F FDPB; Protein pK a; Redox Bohr effect; Respiratory complex I

Indexed keywords

HISTIDINE; IMIDAZOLE; MYOGLOBIN; SUPEROXIDE DISMUTASE;

EID: 81055140449     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.23114     Document Type: Article
Times cited : (8)

References (59)
  • 2
    • 0028305457 scopus 로고
    • Prediction of Ph-dependentproperties of proteins
    • Antosiewicz J, McCammon JA, Gilson MK. Prediction of Ph-dependentproperties of proteins. J Mol Biol 1994; 238: 415-436.
    • (1994) J Mol Biol , vol.238 , pp. 415-436
    • Antosiewicz, J.1    McCammon, J.A.2    Gilson, M.K.3
  • 4
    • 0026612756 scopus 로고
    • a values of ionizable groups in bacteriorhodopsin
    • a values of ionizable groups in bacteriorhodopsin. J Mol Biol 1992; 224: 473-486.
    • (1992) J Mol Biol , vol.224 , pp. 473-486
    • Bashford, D.1    Gerwert, K.2
  • 5
    • 0025197061 scopus 로고
    • as of ionizable groups in proteins-atomic detail from a continuum electrostatic model
    • as of ionizable groups in proteins-atomic detail from a continuum electrostatic model. Biochemistry 1990; 29: 10219-10225.
    • (1990) Biochemistry , vol.29 , pp. 10219-10225
    • Bashford, D.1    Karplus, M.2
  • 6
    • 0001715782 scopus 로고    scopus 로고
    • Calculation of amino acid pK's in a protein from a continuum electrostatic model: method and sensitivity analysis
    • Beroza P, Fredkin DR. Calculation of amino acid pK's in a protein from a continuum electrostatic model: method and sensitivity analysis. J Comp Chem 1996; 17: 1229-1244.
    • (1996) J Comp Chem , vol.17 , pp. 1229-1244
    • Beroza, P.1    Fredkin, D.R.2
  • 7
    • 0023779259 scopus 로고
    • Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis
    • Gilson MK, Honig B. Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis. Proteins 1988; 4: 7-18.
    • (1988) Proteins , vol.4 , pp. 7-18
    • Gilson, M.K.1    Honig, B.2
  • 8
    • 0023899747 scopus 로고
    • Energetics of charge-charge interactions in proteins
    • Gilson MK, Honig BH. Energetics of charge-charge interactions in proteins. Proteins 1988; 3: 32-52.
    • (1988) Proteins , vol.3 , pp. 32-52
    • Gilson, M.K.1    Honig, B.H.2
  • 9
    • 0023060081 scopus 로고
    • Free energy of charges in solvated proteins: microscopic calculations using a reversible charging process
    • Warshel A, Sussman F, King G. Free energy of charges in solvated proteins: microscopic calculations using a reversible charging process. Biochemistry 1986; 25: 8368-8372.
    • (1986) Biochemistry , vol.25 , pp. 8368-8372
    • Warshel, A.1    Sussman, F.2    King, G.3
  • 10
    • 0010624785 scopus 로고    scopus 로고
    • The effect of protein relaxation on charge-charge interactions and dielectric constants of proteins
    • Sham YY, Muegge I, Warshel A. The effect of protein relaxation on charge-charge interactions and dielectric constants of proteins. Biophys J 1998; 74: 1744-1753.
    • (1998) Biophys J , vol.74 , pp. 1744-1753
    • Sham, Y.Y.1    Muegge, I.2    Warshel, A.3
  • 11
    • 0030945495 scopus 로고    scopus 로고
    • Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties
    • Alexov EG, Gunner MR. Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties. Biophys J 1997; 72: 2075-2093.
    • (1997) Biophys J , vol.72 , pp. 2075-2093
    • Alexov, E.G.1    Gunner, M.R.2
  • 12
    • 33748400070 scopus 로고    scopus 로고
    • Including side chain flexibility in continuum electrostatic calculations of protein titration
    • Beroza P, Case DA. Including side chain flexibility in continuum electrostatic calculations of protein titration. J Phys Chem 1996; 100: 20156-20163.
    • (1996) J Phys Chem , vol.100 , pp. 20156-20163
    • Beroza, P.1    Case, D.A.2
  • 14
    • 42449113368 scopus 로고    scopus 로고
    • a computation in proteins with pH adapted conformations
    • a computation in proteins with pH adapted conformations. Proteins 2008; 71: 1335-1348.
    • (2008) Proteins , vol.71 , pp. 1335-1348
    • Kieseritzky, G.1    Knapp, E.W.2
  • 15
    • 0035112206 scopus 로고    scopus 로고
    • Calculated pH-dependent population and protonation of carbon-monoxy-myoglobin conformers
    • Rabenstein B, Knapp E-W. Calculated pH-dependent population and protonation of carbon-monoxy-myoglobin conformers. Biophys J 2001; 80: 1141-1150.
    • (2001) Biophys J , vol.80 , pp. 1141-1150
    • Rabenstein, B.1    Knapp, E.-W.2
  • 16
    • 0031719963 scopus 로고    scopus 로고
    • Calculation of protonation patterns in proteins with structural relaxation and molecular ensembles-application to the photosynthetic reaction center
    • Rabenstein B, Ullmann GM, Knapp EW. Calculation of protonation patterns in proteins with structural relaxation and molecular ensembles-application to the photosynthetic reaction center. Eur Biophys J 1998; 27: 626-637.
    • (1998) Eur Biophys J , vol.27 , pp. 626-637
    • Rabenstein, B.1    Ullmann, G.M.2    Knapp, E.W.3
  • 17
    • 0028859420 scopus 로고
    • Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility
    • You TJ, Bashford D. Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility. Biophys J 1995; 69: 1721-1733.
    • (1995) Biophys J , vol.69 , pp. 1721-1733
    • You, T.J.1    Bashford, D.2
  • 18
    • 0034640465 scopus 로고    scopus 로고
    • A pragmatic approach to structure based calculation of coupled proton and electron transfer in proteins
    • Gunner MR, Alexov E. A pragmatic approach to structure based calculation of coupled proton and electron transfer in proteins. Bioenergetics 2000; 1458: 63-87.
    • (2000) Bioenergetics , vol.1458 , pp. 63-87
    • Gunner, M.R.1    Alexov, E.2
  • 19
    • 28644438898 scopus 로고    scopus 로고
    • Continuum electrostatics of proteins: experimental test with model solvents and the method of the proteins pK calculations
    • Krishtalik LI. Continuum electrostatics of proteins: experimental test with model solvents and the method of the proteins pK calculations. Chem Phys 2005; 319: 316-329.
    • (2005) Chem Phys , vol.319 , pp. 316-329
    • Krishtalik, L.I.1
  • 21
    • 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
    • Beroza P, Fredkin DR, Okamura MY, Feher G. 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 1991; 88: 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
  • 22
    • 84912964993 scopus 로고
    • Refinement of triclinic lysozyme. II. The method of stereochemically restrained least squares
    • Ramanadham M, Sieker LC, Jensen LH. Refinement of triclinic lysozyme. II. The method of stereochemically restrained least squares. Acta Crystallogr B 1990; 46(Pt 1): 63-69.
    • (1990) Acta Crystallogr B , vol.46 , Issue.PART 1 , pp. 63-69
    • Ramanadham, M.1    Sieker, L.C.2    Jensen, L.H.3
  • 23
    • 84944815380 scopus 로고
    • Segmented anisotropic refinement of bovine ribonuclease A by the application of the rigid-body TLS model
    • Howlin B, Moss DS, Harris GW. Segmented anisotropic refinement of bovine ribonuclease A by the application of the rigid-body TLS model. Acta Crystallogr A 1989; 45(Pt 12): 851-861.
    • (1989) Acta Crystallogr A , vol.45 , Issue.PART 12 , pp. 851-861
    • Howlin, B.1    Moss, D.S.2    Harris, G.W.3
  • 26
    • 0029918951 scopus 로고    scopus 로고
    • Solution structure of bromelain inhibitor IV from pineapple stem: structural similarity with Bowman-Birk trypsin/chymotrypsin inhibitor from soybean
    • Hatano K, Kojima M, Tanokura M, Takahashi K. Solution structure of bromelain inhibitor IV from pineapple stem: structural similarity with Bowman-Birk trypsin/chymotrypsin inhibitor from soybean. Biochemistry 1996; 35: 5379-5384.
    • (1996) Biochemistry , vol.35 , pp. 5379-5384
    • Hatano, K.1    Kojima, M.2    Tanokura, M.3    Takahashi, K.4
  • 28
    • 84977303841 scopus 로고
    • The geometry of the reactive site and of the peptide groups in trypsin, trypsinogen and its complexes with inhibitors
    • Marquart M, Walter J, Deisenhofer J, Bode W, Huber R. The geometry of the reactive site and of the peptide groups in trypsin, trypsinogen and its complexes with inhibitors. Acta Crystallogr Sect B: Struct Sci 1983; 39: 480-490.
    • (1983) Acta Crystallogr Sect B: Struct Sci , vol.39 , pp. 480-490
    • Marquart, M.1    Walter, J.2    Deisenhofer, J.3    Bode, W.4    Huber, R.5
  • 29
    • 0026357217 scopus 로고
    • Ribonuclease T1 with free recognition and catalytic site: crystal structure analysis at 1.5 A resolution
    • Martinez-Oyanedel J, Choe HW, Heinemann U, Saenger W. Ribonuclease T1 with free recognition and catalytic site: crystal structure analysis at 1.5 A resolution. J Mol Biol 1991; 222: 335-352.
    • (1991) J Mol Biol , vol.222 , pp. 335-352
    • Martinez-Oyanedel, J.1    Choe, H.W.2    Heinemann, U.3    Saenger, W.4
  • 31
    • 28644432877 scopus 로고    scopus 로고
    • Very fast empirical prediction and rationalization of protein pKa values
    • Li H, Robertson AD, Jensen JH. Very fast empirical prediction and rationalization of protein pKa values. Proteins 2005; 61: 704-721.
    • (2005) Proteins , vol.61 , pp. 704-721
    • Li, H.1    Robertson, A.D.2    Jensen, J.H.3
  • 32
    • 0036231449 scopus 로고    scopus 로고
    • The solution structure of reduced dimeric copper zinc superoxide dismutase-the structural effects of dimerization
    • Banci L, Bertini I, Cramaro F, Del Conte R, Viezzoli MS. The solution structure of reduced dimeric copper zinc superoxide dismutase-the structural effects of dimerization. Eur J Biochem 2002; 269: 1905-1915.
    • (2002) Eur J Biochem , vol.269 , pp. 1905-1915
    • Banci, L.1    Bertini, I.2    Cramaro, F.3    Del Conte, R.4    Viezzoli, M.S.5
  • 33
    • 33644872938 scopus 로고    scopus 로고
    • Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus
    • Sazanov LA, Hinchliffe P. Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus. Science 2006; 311: 1430-1436.
    • (2006) Science , vol.311 , pp. 1430-1436
    • Sazanov, L.A.1    Hinchliffe, P.2
  • 35
    • 34547559704 scopus 로고    scopus 로고
    • PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations
    • Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 2007; 35( Suppl 2): W522-W525.
    • (2007) Nucleic Acids Res , vol.35 , Issue.SUPPL. 2
    • Dolinsky, T.J.1    Czodrowski, P.2    Li, H.3    Nielsen, J.E.4    Jensen, J.H.5    Klebe, G.6    Baker, N.A.7
  • 36
    • 3242886771 scopus 로고    scopus 로고
    • PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
    • Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res 2004; 32( Suppl 2): W665-W667.
    • (2004) Nucleic Acids Res , vol.32 , Issue.SUPPL. 2
    • Dolinsky, T.J.1    Nielsen, J.E.2    McCammon, J.A.3    Baker, N.A.4
  • 38
    • 0037188507 scopus 로고    scopus 로고
    • Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction
    • Xiang Z, Soto CS, Honig B. Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction. Proc Natl Acad Sci USA 2002; 99: 7432-7437.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 7432-7437
    • Xiang, Z.1    Soto, C.S.2    Honig, B.3
  • 39
    • 84957665033 scopus 로고    scopus 로고
    • An object-oriented programming suite for electrostatic effects in biological molecules
    • Bashford D. An object-oriented programming suite for electrostatic effects in biological molecules. Sci Comput Object-Orient Parallel Environ 1997; 1343: 233-240.
    • (1997) Sci Comput Object-Orient Parallel Environ , vol.1343 , pp. 233-240
    • Bashford, D.1
  • 41
    • 0001135382 scopus 로고
    • Redox chemistry of superoxide-dismutase-cyclic voltammetry of wild-type enzymes and mutants on functionally relevant residues
    • Azab HA, Banci L, Borsari M, Luchinat C, Sola M, Viezzoli MS. Redox chemistry of superoxide-dismutase-cyclic voltammetry of wild-type enzymes and mutants on functionally relevant residues. Inorg Chem 1992; 31: 4649-4655.
    • (1992) Inorg Chem , vol.31 , pp. 4649-4655
    • Azab, H.A.1    Banci, L.2    Borsari, M.3    Luchinat, C.4    Sola, M.5    Viezzoli, M.S.6
  • 42
    • 0001430625 scopus 로고    scopus 로고
    • CuZn superoxide dismutase geometry optimization, energetics, and redox potential calculations by density functional and electrostatic methods
    • Konecny R, Li J, Fisher CL, Dillet V, Bashford D, Noodleman L. CuZn superoxide dismutase geometry optimization, energetics, and redox potential calculations by density functional and electrostatic methods. Inorg Chem 1999; 38: 940-950.
    • (1999) Inorg Chem , vol.38 , pp. 940-950
    • Konecny, R.1    Li, J.2    Fisher, C.L.3    Dillet, V.4    Bashford, D.5    Noodleman, L.6
  • 43
    • 49649108879 scopus 로고    scopus 로고
    • Influence of nonlinear electrostatics on transfer energies between liquid phases: charge burial is far less expensive than Born model
    • Gong HP, Hocky G, Freed KF. Influence of nonlinear electrostatics on transfer energies between liquid phases: charge burial is far less expensive than Born model. Proc Natl Acad Sci USA 2008; 105: 11146-11151.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 11146-11151
    • Gong, H.P.1    Hocky, G.2    Freed, K.F.3
  • 44
    • 66349114495 scopus 로고    scopus 로고
    • Computing ion solvation free energies using the dipolar Poisson model
    • Koehl P, Orland H, Delarue M. Computing ion solvation free energies using the dipolar Poisson model. J Phys Chem B 2009; 113: 5694-5697.
    • (2009) J Phys Chem B , vol.113 , pp. 5694-5697
    • Koehl, P.1    Orland, H.2    Delarue, M.3
  • 45
    • 77952979824 scopus 로고    scopus 로고
    • The architecture of respiratory complex I
    • Efremov RG, Baradaran R, Sazanov LA. The architecture of respiratory complex I. Nature 2010; 465: 441-445.
    • (2010) Nature , vol.465 , pp. 441-445
    • Efremov, R.G.1    Baradaran, R.2    Sazanov, L.A.3
  • 46
    • 78650606712 scopus 로고    scopus 로고
    • Electron tunneling in respiratory complex I
    • Hayashi T, Stuchebrukhov AA. Electron tunneling in respiratory complex I. Proc Natl Acad Sci USA 2010; 107: 19157-19162.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 19157-19162
    • Hayashi, T.1    Stuchebrukhov, A.A.2
  • 47
    • 77954848120 scopus 로고    scopus 로고
    • Functional modules and structural basis of conformational coupling in mitochondrial complex I
    • Hunte C, Zickermann V, Brandt U. Functional modules and structural basis of conformational coupling in mitochondrial complex I. Science 2010; 329: 448-451.
    • (2010) Science , vol.329 , pp. 448-451
    • Hunte, C.1    Zickermann, V.2    Brandt, U.3
  • 48
    • 73849114263 scopus 로고    scopus 로고
    • Towards the molecular mechanism of respiratory complex I
    • Hirst J. Towards the molecular mechanism of respiratory complex I. Biochem J 2010; 425: 327-339.
    • (2010) Biochem J , vol.425 , pp. 327-339
    • Hirst, J.1
  • 50
    • 0019324533 scopus 로고
    • An analysis of some thermodynamic properties of iron-sulphur centres in site I of mitochondria
    • Ingledew WJ, Ohnishi T. An analysis of some thermodynamic properties of iron-sulphur centres in site I of mitochondria. Biochem J 1980; 186: 111-117.
    • (1980) Biochem J , vol.186 , pp. 111-117
    • Ingledew, W.J.1    Ohnishi, T.2
  • 51
    • 33747370385 scopus 로고    scopus 로고
    • The Redox-Bohr group associated with iron-sulfur cluster N2 of complex I
    • Zwicker K, Galkin A, Drose S, Grgic L, Kerscher S, Brandt U. The Redox-Bohr group associated with iron-sulfur cluster N2 of complex I. J Biol Chem 2006; 281: 23013-23017.
    • (2006) J Biol Chem , vol.281 , pp. 23013-23017
    • Zwicker, K.1    Galkin, A.2    Drose, S.3    Grgic, L.4    Kerscher, S.5    Brandt, U.6
  • 53
    • 0034227794 scopus 로고    scopus 로고
    • The coupling of protonation and reduction in proteins with multiple redox centers: theory, computational method, and application to cytochrome c3
    • Ullmann GM. The coupling of protonation and reduction in proteins with multiple redox centers: theory, computational method, and application to cytochrome c3. J Phys Chem B 2000; 104: 6293-6301.
    • (2000) J Phys Chem B , vol.104 , pp. 6293-6301
    • Ullmann, G.M.1
  • 54
    • 0000000699 scopus 로고    scopus 로고
    • Electrostatic models for computing protonation and redox equilibria in proteins
    • Ullmann GM, Knapp E-W. Electrostatic models for computing protonation and redox equilibria in proteins. Eur Biophys J 1999; 28: 533-551.
    • (1999) Eur Biophys J , vol.28 , pp. 533-551
    • Ullmann, G.M.1    Knapp, E.-W.2
  • 55
    • 40549126917 scopus 로고    scopus 로고
    • Electrostatic interactions between FeS clusters in NADH:ubiquinone oxidoreductase (complex I) from Escherichia coli
    • Euro L, Bloch DA, Wikström M, Verkhovsky MI, Verkhovskaya M. Electrostatic interactions between FeS clusters in NADH:ubiquinone oxidoreductase (complex I) from Escherichia coli. Biochemistry 2008; 47: 3185-3193.
    • (2008) Biochemistry , vol.47 , pp. 3185-3193
    • Euro, L.1    Bloch, D.A.2    Wikström, M.3    Verkhovsky, M.I.4    Verkhovskaya, M.5
  • 56
    • 77954761571 scopus 로고    scopus 로고
    • Determination of the intrinsic redox potentials of FeS centers of respiratory complex I from experimental titration curves
    • Medvedev ES, Couch VA, Stuchebrukhov AA. Determination of the intrinsic redox potentials of FeS centers of respiratory complex I from experimental titration curves. Bioenergetics 2010; 1797: 1665-1671.
    • (2010) Bioenergetics , vol.1797 , pp. 1665-1671
    • Medvedev, E.S.1    Couch, V.A.2    Stuchebrukhov, A.A.3
  • 57
    • 81055154369 scopus 로고    scopus 로고
    • Langevin dipoles model for ab initio calculations of chemical processes in solution: parametrization and application to phosphate ester hydrolysis and conformational analysis in aqueous solution
    • Florian J, Warshel A. Langevin dipoles model for ab initio calculations of chemical processes in solution: parametrization and application to phosphate ester hydrolysis and conformational analysis in aqueous solution. Abstr Pap Am Chem Soc 1997; 214: 85.
    • (1997) Abstr Pap Am Chem Soc , vol.214 , pp. 85
    • Florian, J.1    Warshel, A.2
  • 58
    • 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 B 1997; 101: 4458-4472.
    • (1997) J Phys Chem B , vol.101 , pp. 4458-4472
    • Sham, Y.Y.1    Chu, Z.T.2    Warshel, A.3
  • 59
    • 0030910225 scopus 로고    scopus 로고
    • Electrostatics of proteins: description in terms of two dielectric constants simultaneously
    • Krishtalik LI, Kuznetsov AM, Mertz EL. Electrostatics of proteins: description in terms of two dielectric constants simultaneously. Proteins-Struct Funct Genet 1997; 28: 174-182.
    • (1997) Proteins-Struct Funct Genet , vol.28 , pp. 174-182
    • Krishtalik, L.I.1    Kuznetsov, A.M.2    Mertz, E.L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.