메뉴 건너뛰기




Volumn 7, Issue 1, 2012, Pages

Electrostatic contribution of surface charge residues to the stability of a thermophilic protein: Benchmarking experimental and predicted pKa values

Author keywords

[No Author keywords available]

Indexed keywords

ASPARTIC ACID; GLUTAMIC ACID; RIBOSOME PROTEIN; RIBOSOME PROTEIN L30E; UNCLASSIFIED DRUG; ARCHAEAL PROTEIN; RIBOSOMAL PROTEIN L30;

EID: 84855929682     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0030296     Document Type: Article
Times cited : (35)

References (50)
  • 1
    • 0030802904 scopus 로고    scopus 로고
    • Conformational stabilities of Escherichia coli RNase HI variants with a series of amino acid substitutions at a cavity within the hydrophobic core
    • Akasako A, Haruki M, Oobatake M, Kanaya S, (1997) Conformational stabilities of Escherichia coli RNase HI variants with a series of amino acid substitutions at a cavity within the hydrophobic core. J Biol Chem 272: 18686-18693.
    • (1997) J Biol Chem , vol.272 , pp. 18686-18693
    • Akasako, A.1    Haruki, M.2    Oobatake, M.3    Kanaya, S.4
  • 4
    • 0033548543 scopus 로고    scopus 로고
    • Increased helix and protein stability through the introduction of a new tertiary hydrogen bond
    • Peterson RW, Nicholson EM, Thapar R, Klevit RE, Scholtz JM, (1999) Increased helix and protein stability through the introduction of a new tertiary hydrogen bond. J Mol Biol 286: 1609-1619.
    • (1999) J Mol Biol , vol.286 , pp. 1609-1619
    • Peterson, R.W.1    Nicholson, E.M.2    Thapar, R.3    Klevit, R.E.4    Scholtz, J.M.5
  • 5
    • 0033135227 scopus 로고    scopus 로고
    • Computational protein design
    • Street AG, Mayo SL, (1999) Computational protein design. Structure 7: R105-109.
    • (1999) Structure , vol.7
    • Street, A.G.1    Mayo, S.L.2
  • 6
    • 0035782661 scopus 로고    scopus 로고
    • Protein design-where we were, where we are, where we're going
    • Pokala N, Handel TM, (2001) Protein design-where we were, where we are, where we're going. J Struct Biol 134: 269-281.
    • (2001) J Struct Biol , vol.134 , pp. 269-281
    • Pokala, N.1    Handel, T.M.2
  • 7
    • 0041387567 scopus 로고    scopus 로고
    • A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins
    • Dantas G, Kuhlman B, Callender D, Wong M, Baker D, (2003) A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins. J Mol Biol 332: 449-460.
    • (2003) J Mol Biol , vol.332 , pp. 449-460
    • Dantas, G.1    Kuhlman, B.2    Callender, D.3    Wong, M.4    Baker, D.5
  • 8
    • 33749055081 scopus 로고    scopus 로고
    • Consensus design as a tool for engineering repeat proteins
    • Kajander T, Cortajarena AL, Regan L, (2006) Consensus design as a tool for engineering repeat proteins. Methods Mol Biol 340: 151-170.
    • (2006) Methods Mol Biol , vol.340 , pp. 151-170
    • Kajander, T.1    Cortajarena, A.L.2    Regan, L.3
  • 9
    • 36448996957 scopus 로고    scopus 로고
    • Computational design of the Fyn SH3 domain with increased stability through optimization of surface charge charge interactions
    • Schweiker KL, Zarrine-Afsar A, Davidson AR, Makhatadze GI, (2007) Computational design of the Fyn SH3 domain with increased stability through optimization of surface charge charge interactions. Protein Sci 16: 2694-2702.
    • (2007) Protein Sci , vol.16 , pp. 2694-2702
    • Schweiker, K.L.1    Zarrine-Afsar, A.2    Davidson, A.R.3    Makhatadze, G.I.4
  • 10
    • 0033554840 scopus 로고    scopus 로고
    • Engineering a thermostable protein via optimization of charge-charge interactions on the protein surface
    • Loladze VV, Ibarra-Molero B, Sanchez-Ruiz JM, Makhatadze GI, (1999) Engineering a thermostable protein via optimization of charge-charge interactions on the protein surface. Biochemistry 38: 16419-16423.
    • (1999) Biochemistry , vol.38 , pp. 16419-16423
    • Loladze, V.V.1    Ibarra-Molero, B.2    Sanchez-Ruiz, J.M.3    Makhatadze, G.I.4
  • 12
    • 59649107985 scopus 로고    scopus 로고
    • A computational approach for the rational design of stable proteins and enzymes: optimization of surface charge-charge interactions
    • Schweiker KL, Makhatadze GI, (2009) A computational approach for the rational design of stable proteins and enzymes: optimization of surface charge-charge interactions. Methods Enzymol 454: 175-211.
    • (2009) Methods Enzymol , vol.454 , pp. 175-211
    • Schweiker, K.L.1    Makhatadze, G.I.2
  • 13
    • 62449335519 scopus 로고    scopus 로고
    • Protein stabilization by the rational design of surface charge-charge interactions
    • Schweiker KL, Makhatadze GI, (2009) Protein stabilization by the rational design of surface charge-charge interactions. Methods Mol Biol 490: 261-283.
    • (2009) Methods Mol Biol , vol.490 , pp. 261-283
    • Schweiker, K.L.1    Makhatadze, G.I.2
  • 14
    • 62449293337 scopus 로고    scopus 로고
    • Rational stabilization of enzymes by computational redesign of surface charge-charge interactions
    • Gribenko AV, Patel MM, Liu J, McCallum SA, Wang C, et al. (2009) Rational stabilization of enzymes by computational redesign of surface charge-charge interactions. Proc Natl Acad Sci U S A 106: 2601-2606.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 2601-2606
    • Gribenko, A.V.1    Patel, M.M.2    Liu, J.3    McCallum, S.A.4    Wang, C.5
  • 16
    • 0000449960 scopus 로고    scopus 로고
    • Response: how much solar radiation do clouds absorb?
    • Lumb KJ, Kim PS, (1996) Response: how much solar radiation do clouds absorb? Science 271: 1137-1138.
    • (1996) Science , vol.271 , pp. 1137-1138
    • Lumb, K.J.1    Kim, P.S.2
  • 17
    • 0026800672 scopus 로고
    • Analysis of the heat capacity dependence of protein folding
    • Yang AS, Sharp KA, Honig B, (1992) Analysis of the heat capacity dependence of protein folding. J Mol Biol 227: 889-900.
    • (1992) J Mol Biol , vol.227 , pp. 889-900
    • Yang, A.S.1    Sharp, K.A.2    Honig, B.3
  • 18
    • 1242299059 scopus 로고    scopus 로고
    • Protein stabilization by salt bridges: concepts, experimental approaches and clarification of some misunderstandings
    • Bosshard HR, Marti DN, Jelesarov I, (2004) Protein stabilization by salt bridges: concepts, experimental approaches and clarification of some misunderstandings. J Mol Recognit 17: 1-16.
    • (2004) J Mol Recognit , vol.17 , pp. 1-16
    • Bosshard, H.R.1    Marti, D.N.2    Jelesarov, I.3
  • 19
    • 0033850087 scopus 로고    scopus 로고
    • High apparent dielectric constants in the interior of a protein reflect water penetration
    • Dwyer JJ, Gittis AG, Karp DA, Lattman EE, Spencer DS, et al. (2000) High apparent dielectric constants in the interior of a protein reflect water penetration. Biophysical Journal 79: 1610-1620.
    • (2000) Biophysical Journal , vol.79 , pp. 1610-1620
    • Dwyer, J.J.1    Gittis, A.G.2    Karp, D.A.3    Lattman, E.E.4    Spencer, D.S.5
  • 20
    • 0036099192 scopus 로고    scopus 로고
    • Experimental pK(a) values of buried residues: analysis with continuum methods and role of water penetration
    • Fitch CA, Karp DA, Lee KK, Stites WE, Lattman EE, et al. (2002) Experimental pK(a) values of buried residues: analysis with continuum methods and role of water penetration. Biophys J 82: 3289-3304.
    • (2002) Biophys J , vol.82 , pp. 3289-3304
    • Fitch, C.A.1    Karp, D.A.2    Lee, K.K.3    Stites, W.E.4    Lattman, E.E.5
  • 21
    • 0034700307 scopus 로고    scopus 로고
    • pH dependence of stability of staphylococcal nuclease: Evidence of substantial electrostatic interactions in the denatured state
    • Whitten ST, Garcia-Moreno B, (2000) pH dependence of stability of staphylococcal nuclease: Evidence of substantial electrostatic interactions in the denatured state. Biochemistry 39: 14292-14304.
    • (2000) Biochemistry , vol.39 , pp. 14292-14304
    • Whitten, S.T.1    Garcia-Moreno, B.2
  • 24
    • 23144457576 scopus 로고    scopus 로고
    • H++: a server for estimating pK(a)s and adding missing hydrogens to macromolecules
    • Gordon JC, Myers JB, Folta T, Shoja V, Heath LS, et al. (2005) H++: a server for estimating pK(a)s and adding missing hydrogens to macromolecules. Nucleic Acids Research 33: W368-W371.
    • (2005) Nucleic Acids Research , vol.33
    • Gordon, J.C.1    Myers, J.B.2    Folta, T.3    Shoja, V.4    Heath, L.S.5
  • 26
    • 84986486656 scopus 로고
    • A Rapid Finite-Difference Algorithm, Utilizing Successive over-Relaxation to Solve the Poisson-Boltzmann Equation
    • Nicholls A, Honig B, (1991) A Rapid Finite-Difference Algorithm, Utilizing Successive over-Relaxation to Solve the Poisson-Boltzmann Equation. Journal of Computational Chemistry 12: 435-445.
    • (1991) Journal of Computational Chemistry , vol.12 , pp. 435-445
    • Nicholls, A.1    Honig, B.2
  • 27
    • 0025398721 scopus 로고
    • What If - a Molecular Modeling and Drug Design Program
    • Vriend G, (1990) What If- a Molecular Modeling and Drug Design Program. Journal of Molecular Graphics 8: 52-56.
    • (1990) Journal of Molecular Graphics , vol.8 , pp. 52-56
    • Vriend, G.1
  • 31
    • 0027477251 scopus 로고
    • Multiple-site titration and molecular modeling: two rapid methods for computing energies and forces for ionizable groups in proteins
    • Gilson MK, (1993) Multiple-site titration and molecular modeling: two rapid methods for computing energies and forces for ionizable groups in proteins. Proteins 15: 266-282.
    • (1993) Proteins , vol.15 , pp. 266-282
    • Gilson, M.K.1
  • 32
    • 81055157735 scopus 로고    scopus 로고
    • MCCE analysis of the pK(a) s of introduced buried acids and bases in staphylococcal nuclease
    • Gunner MR, Zhu X, Klein MC, (2011) MCCE analysis of the pK(a) s of introduced buried acids and bases in staphylococcal nuclease. Proteins 79: 3306-3319.
    • (2011) Proteins , vol.79 , pp. 3306-3319
    • Gunner, M.R.1    Zhu, X.2    Klein, M.C.3
  • 33
    • 81055157980 scopus 로고    scopus 로고
    • Calculation of pK(a) in proteins with the microenvironment modulated-screened coulomb potential
    • Shan J, Mehler EL, (2011) Calculation of pK(a) in proteins with the microenvironment modulated-screened coulomb potential. Proteins 79: 3346-3355.
    • (2011) Proteins , vol.79 , pp. 3346-3355
    • Shan, J.1    Mehler, E.L.2
  • 34
    • 81055140448 scopus 로고    scopus 로고
    • Is the prediction of pK(a) values by constant-pH molecular dynamics being hindered by inherited problems?
    • Machuqueiro M, Baptista AM, (2011) Is the prediction of pK(a) values by constant-pH molecular dynamics being hindered by inherited problems? Proteins 79: 3437-3447.
    • (2011) Proteins , vol.79 , pp. 3437-3447
    • Machuqueiro, M.1    Baptista, A.M.2
  • 35
    • 23244440384 scopus 로고    scopus 로고
    • Constant pH molecular dynamics with proton tautomerism
    • Khandogin J, Brooks CL III, (2005) Constant pH molecular dynamics with proton tautomerism. Biophys J 89: 141-157.
    • (2005) Biophys J , vol.89 , pp. 141-157
    • Khandogin, J.1    Brooks III, C.L.2
  • 38
    • 33846614924 scopus 로고    scopus 로고
    • Analysing the pH-dependent properties of proteins using pKa calculations
    • Nielsen JE, (2007) Analysing the pH-dependent properties of proteins using pKa calculations. J Mol Graph Model 25: 691-699.
    • (2007) J Mol Graph Model , vol.25 , pp. 691-699
    • Nielsen, J.E.1
  • 39
    • 59649095261 scopus 로고    scopus 로고
    • Analyzing Enzymatic Ph Activity Profiles and Protein Titration Curves Using Structure-Based Pk(a) Calculations and Titration Curve Fitting
    • Nielsen JE, (2009) Analyzing Enzymatic Ph Activity Profiles and Protein Titration Curves Using Structure-Based Pk(a) Calculations and Titration Curve Fitting. Methods in Enzymology: Computer Methods Vol 454, Pt A 454: 233-258.
    • (2009) Methods in Enzymology: Computer Methods , vol.454 , Issue.Pt A454 , pp. 233-258
    • Nielsen, J.E.1
  • 40
    • 16244366490 scopus 로고    scopus 로고
    • Electrostatic interactions contribute to reduced heat capacity change of unfolding in a thermophilic ribosomal protein l30e
    • Lee CF, Allen MD, Bycroft M, Wong KB, (2005) Electrostatic interactions contribute to reduced heat capacity change of unfolding in a thermophilic ribosomal protein l30e. J Mol Biol 348: 419-431.
    • (2005) J Mol Biol , vol.348 , pp. 419-431
    • Lee, C.F.1    Allen, M.D.2    Bycroft, M.3    Wong, K.B.4
  • 41
    • 0037972269 scopus 로고    scopus 로고
    • Solution structure and thermal stability of ribosomal protein L30e from hyperthermophilic archaeon Thermococcus celer
    • Wong KB, Lee CF, Chan SH, Leung TY, Chen YW, et al. (2003) Solution structure and thermal stability of ribosomal protein L30e from hyperthermophilic archaeon Thermococcus celer. Protein Sci 12: 1483-1495.
    • (2003) Protein Sci , vol.12 , pp. 1483-1495
    • Wong, K.B.1    Lee, C.F.2    Chan, S.H.3    Leung, T.Y.4    Chen, Y.W.5
  • 42
    • 79959612799 scopus 로고    scopus 로고
    • Stabilizing salt-bridge enhances protein thermostability by reducing the heat capacity change of unfolding
    • Chan CH, Yu TH, Wong KB, (2011) Stabilizing salt-bridge enhances protein thermostability by reducing the heat capacity change of unfolding. PLoS One 6: e21624.
    • (2011) PLoS One , vol.6
    • Chan, C.H.1    Yu, T.H.2    Wong, K.B.3
  • 43
    • 29344472867 scopus 로고    scopus 로고
    • Effects of charge-to-alanine substitutions on the stability of ribosomal protein L30e from Thermococcus celer
    • Lee CF, Makhatadze GI, Wong KB, (2005) Effects of charge-to-alanine substitutions on the stability of ribosomal protein L30e from Thermococcus celer. Biochemistry 44: 16817-16825.
    • (2005) Biochemistry , vol.44 , pp. 16817-16825
    • Lee, C.F.1    Makhatadze, G.I.2    Wong, K.B.3
  • 44
    • 0003187567 scopus 로고    scopus 로고
    • The atomic structure of protein-protein recognition sites
    • Lo Conte L, Chothia C, Janin J, (1999) The atomic structure of protein-protein recognition sites. J Mol Biol 285: 2177-2198.
    • (1999) J Mol Biol , vol.285 , pp. 2177-2198
    • Lo Conte, L.1    Chothia, C.2    Janin, J.3
  • 46
    • 0015507243 scopus 로고
    • Mathematical models for interacting groups in nuclear magnetic resonance titration curves
    • Shrager RI, Cohen JS, Heller SR, Sachs DH, Schechter AN, (1972) Mathematical models for interacting groups in nuclear magnetic resonance titration curves. Biochemistry 11: 541-547.
    • (1972) Biochemistry , vol.11 , pp. 541-547
    • Shrager, R.I.1    Cohen, J.S.2    Heller, S.R.3    Sachs, D.H.4    Schechter, A.N.5
  • 47
    • 38048998514 scopus 로고    scopus 로고
    • Determination of electrostatic interaction energies and protonation state populations in enzyme active sites
    • Sondergaard CR, McIntosh LP, Pollastri G, Nielsen JE, (2008) Determination of electrostatic interaction energies and protonation state populations in enzyme active sites. J Mol Biol 376: 269-287.
    • (2008) J Mol Biol , vol.376 , pp. 269-287
    • Sondergaard, C.R.1    McIntosh, L.P.2    Pollastri, G.3    Nielsen, J.E.4
  • 48
    • 84855968560 scopus 로고
    • NMR and X-ray Evidence That the HIV Protease Catalytic Aspartyl Groups Are Protonated in the Complex Formed by the Protease and a Non-Peptide Cyclic Urea-Based Inhibitor
    • Yamazaki T, Nicholson LK, Wingfield P, Stahl SJ, Kaufman JD, et al. (1994) NMR and X-ray Evidence That the HIV Protease Catalytic Aspartyl Groups Are Protonated in the Complex Formed by the Protease and a Non-Peptide Cyclic Urea-Based Inhibitor.
    • (1994)
    • Yamazaki, T.1    Nicholson, L.K.2    Wingfield, P.3    Stahl, S.J.4    Kaufman, J.D.5
  • 49
    • 0030596513 scopus 로고    scopus 로고
    • Cold denaturation of barstar: 1H, 15N and 13C NMR assignment and characterisation of residual structure
    • Wong KB, Freund SM, Fersht AR, (1996) Cold denaturation of barstar: 1H, 15N and 13C NMR assignment and characterisation of residual structure. J Mol Biol 259: 805-818.
    • (1996) J Mol Biol , vol.259 , pp. 805-818
    • Wong, K.B.1    Freund, S.M.2    Fersht, A.R.3
  • 50
    • 0347383758 scopus 로고    scopus 로고
    • Modeller: generation and refinement of homology-based protein structure models
    • Fiser A, Sali A, (2003) Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol 374: 461-491.
    • (2003) Methods Enzymol , vol.374 , pp. 461-491
    • Fiser, A.1    Sali, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.