메뉴 건너뛰기




Volumn 79, Issue 3, 2011, Pages 925-936

In silico modeling of pH-optimum of protein-protein binding

Author keywords

Electrostatics; PH dependent effects; PH optimum; PKa's; Protein binding

Indexed keywords

AMINO ACID; BARNASE; BARSTAR; MONOMER;

EID: 79551474943     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22931     Document Type: Article
Times cited : (42)

References (82)
  • 2
    • 33745779229 scopus 로고    scopus 로고
    • Diabetes-associated mitochondrial DNA mutation A3243G impairs cellular metabolic pathways necessary for beta cell function
    • de Andrade PB, Rubi B, Frigerio F, van den Ouweland JM, Maassen JA, Maechler P. Diabetes-associated mitochondrial DNA mutation A3243G impairs cellular metabolic pathways necessary for beta cell function. Diabetologia 2006; 49: 1816-1826.
    • (2006) Diabetologia , vol.49 , pp. 1816-1826
    • de Andrade, P.B.1    Rubi, B.2    Frigerio, F.3    van den Ouweland, J.M.4    Maassen, J.A.5    Maechler, P.6
  • 3
    • 46349091157 scopus 로고    scopus 로고
    • Tissue specificity of mitochondrial glutamate pathways and the control of metabolic homeostasis
    • Frigerio F, Casimir M, Carobbio S, Maechler P. Tissue specificity of mitochondrial glutamate pathways and the control of metabolic homeostasis. Biochim Biophys Acta 2008; 1777(7-8): 965-972.
    • (2008) Biochim Biophys Acta , vol.1777 , Issue.7-8 , pp. 965-972
    • Frigerio, F.1    Casimir, M.2    Carobbio, S.3    Maechler, P.4
  • 5
    • 59649103113 scopus 로고    scopus 로고
    • Mechanisms of inhibition of zinc-finger transcription factors by selenium compounds ebselen and selenite
    • Larabee JL, Hocker JR, Hanas JS. Mechanisms of inhibition of zinc-finger transcription factors by selenium compounds ebselen and selenite. J Inorg Biochem 2009; 103: 419-426.
    • (2009) J Inorg Biochem , vol.103 , pp. 419-426
    • Larabee, J.L.1    Hocker, J.R.2    Hanas, J.S.3
  • 6
    • 64049083918 scopus 로고    scopus 로고
    • Protein-protein interaction as a predictor of subcellular location
    • Shin CJ, Wong S, Davis MJ, Ragan MA. Protein-protein interaction as a predictor of subcellular location. BMC Syst Biol 2009; 3: 28.
    • (2009) BMC Syst Biol , vol.3 , pp. 28
    • Shin, C.J.1    Wong, S.2    Davis, M.J.3    Ragan, M.A.4
  • 10
    • 37049028145 scopus 로고    scopus 로고
    • Structural analysis of the synaptic protein neuroligin and its beta-neurexin complex: determinants for folding and cell adhesion
    • Fabrichny IP, Leone P, Sulzenbacher G, Comoletti D, Miller MT, Taylor P, Bourne Y, Marchot P. Structural analysis of the synaptic protein neuroligin and its beta-neurexin complex: determinants for folding and cell adhesion. Neuron 2007; 56: 979-991.
    • (2007) Neuron , vol.56 , pp. 979-991
    • Fabrichny, I.P.1    Leone, P.2    Sulzenbacher, G.3    Comoletti, D.4    Miller, M.T.5    Taylor, P.6    Bourne, Y.7    Marchot, P.8
  • 11
    • 4844228689 scopus 로고    scopus 로고
    • Association of hormone replacement therapy to estrogen and progesterone receptor status in invasive breast carcinoma
    • Chen WY, Hankinson SE, Schnitt SJ, Rosner BA, Holmes MD, Colditz GA. Association of hormone replacement therapy to estrogen and progesterone receptor status in invasive breast carcinoma. Cancer 2004; 101: 1490-1500.
    • (2004) Cancer , vol.101 , pp. 1490-1500
    • Chen, W.Y.1    Hankinson, S.E.2    Schnitt, S.J.3    Rosner, B.A.4    Holmes, M.D.5    Colditz, G.A.6
  • 12
    • 0036923836 scopus 로고    scopus 로고
    • Differences in electrostatic properties at antibody-antigen binding sites: implications for specificity and cross-reactivity
    • Sinha N, Mohan S, Lipschultz CA, Smith-Gill SJ. Differences in electrostatic properties at antibody-antigen binding sites: implications for specificity and cross-reactivity. Biophys J 2002; 83: 2946-2968.
    • (2002) Biophys J , vol.83 , pp. 2946-2968
    • Sinha, N.1    Mohan, S.2    Lipschultz, C.A.3    Smith-Gill, S.J.4
  • 13
    • 37849015433 scopus 로고    scopus 로고
    • The regulation of the B-cell gene expression programme by Pax5
    • Holmes ML, Pridans C, Nutt SL. The regulation of the B-cell gene expression programme by Pax5. Immunol Cell Biol 2008; 86: 47-53.
    • (2008) Immunol Cell Biol , vol.86 , pp. 47-53
    • Holmes, M.L.1    Pridans, C.2    Nutt, S.L.3
  • 16
    • 0034628508 scopus 로고    scopus 로고
    • A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
    • Uetz P. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000; 403: 623.
    • (2000) Nature , vol.403 , pp. 623
    • Uetz, P.1
  • 17
    • 22244465254 scopus 로고    scopus 로고
    • Protein-protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach
    • Keskin O, Ma BY, Rogale K, Gunasekaran K, Nussinov R. Protein-protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach. Phys Biol 2005; 2: S24-S35.
    • (2005) Phys Biol , vol.2
    • Keskin, O.1    Ma, B.Y.2    Rogale, K.3    Gunasekaran, K.4    Nussinov, R.5
  • 18
    • 0030028728 scopus 로고    scopus 로고
    • Principles of protein-protein interactions
    • Jones S, Thornton J. Principles of protein-protein interactions. Proc Natl Acad Sci USA 1996; 93: 13-20.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 13-20
    • Jones, S.1    Thornton, J.2
  • 19
    • 0037474541 scopus 로고    scopus 로고
    • Structural characterisation and functional significance of transient protein-protein interactions
    • Nooren IMA, Thornton JM. Structural characterisation and functional significance of transient protein-protein interactions. J Mol Biol 2003; 325: 991-1018.
    • (2003) J Mol Biol , vol.325 , pp. 991-1018
    • Nooren, I.M.A.1    Thornton, J.M.2
  • 20
    • 2942553723 scopus 로고    scopus 로고
    • Protein-protein interactions: coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking
    • Halperin I, Wolfson H, Nussinov R. Protein-protein interactions: coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking. Structure 2004; 12: 1027-1038.
    • (2004) Structure , vol.12 , pp. 1027-1038
    • Halperin, I.1    Wolfson, H.2    Nussinov, R.3
  • 21
    • 11844249426 scopus 로고    scopus 로고
    • Hot regions in protein-protein interactions: the organization and contribution of structurally conserved hot spot residues
    • Keskin O, Ma BY, Nussinov R. Hot regions in protein-protein interactions: the organization and contribution of structurally conserved hot spot residues. J Mol Biol 2005; 345: 1281-1294.
    • (2005) J Mol Biol , vol.345 , pp. 1281-1294
    • Keskin, O.1    Ma, B.Y.2    Nussinov, R.3
  • 22
    • 0035281357 scopus 로고    scopus 로고
    • Computer simulation of protein-protein interactions
    • Elcock AH, Sept D, McCammon JA. Computer simulation of protein-protein interactions. J Phys Chem B 2001; 105: 1504-1518.
    • (2001) J Phys Chem B , vol.105 , pp. 1504-1518
    • Elcock, A.H.1    Sept, D.2    McCammon, J.A.3
  • 23
    • 0042710087 scopus 로고    scopus 로고
    • Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies
    • Massova I, Kollman PA. Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies. J Am Chem Soc 1999; 121: 8133-8143.
    • (1999) J Am Chem Soc , vol.121 , pp. 8133-8143
    • Massova, I.1    Kollman, P.A.2
  • 24
    • 22344435988 scopus 로고    scopus 로고
    • Prediction of physical protein-protein interactions
    • Szilagyi A, Grimm V, Arakaki AK, Skolnick J. Prediction of physical protein-protein interactions. Phys Biol 2005; 2(1-2): S1-S16.
    • (2005) Phys Biol , vol.2 , Issue.1-2
    • Szilagyi, A.1    Grimm, V.2    Arakaki, A.K.3    Skolnick, J.4
  • 25
    • 0036890316 scopus 로고    scopus 로고
    • Electrostatics in protein binding and function
    • Sinha N, Smith-Gill SJ. Electrostatics in protein binding and function. Curr Protein Pept Sci 2002; 3: 601-614.
    • (2002) Curr Protein Pept Sci , vol.3 , pp. 601-614
    • Sinha, N.1    Smith-Gill, S.J.2
  • 28
    • 40549134985 scopus 로고    scopus 로고
    • Electrostatic rate enhancement and transient complex of protein-protein association
    • Alsallaq R, Zhou HX. Electrostatic rate enhancement and transient complex of protein-protein association. Proteins 2008; 71: 320-335.
    • (2008) Proteins , vol.71 , pp. 320-335
    • Alsallaq, R.1    Zhou, H.X.2
  • 31
    • 40549144041 scopus 로고    scopus 로고
    • Protein-protein binding is often associated with changes in protonation state
    • Mason AC, Jensen JH. Protein-protein binding is often associated with changes in protonation state. Proteins 2008; 71: 81-91.
    • (2008) Proteins , vol.71 , pp. 81-91
    • Mason, A.C.1    Jensen, J.H.2
  • 32
    • 0031076776 scopus 로고    scopus 로고
    • pH-Dependence of protein stability: absolute electrostatic free energy difference between conformations
    • Schaefer M, Sommer M, Karplus M. pH-Dependence of protein stability: absolute electrostatic free energy difference between conformations. J Phys Chem 1997; 101: 1663-1683.
    • (1997) J Phys Chem , vol.101 , pp. 1663-1683
    • Schaefer, M.1    Sommer, M.2    Karplus, M.3
  • 33
    • 0031423107 scopus 로고    scopus 로고
    • Dissection of the pH dependence of inhibitor binding energetics for an aspatric protease: direct measurement of the protonation states of the catalytic aspartic acid residues
    • Xie D, Gulnik S, Collins L, Gustchina E, Suvorov L, Erickson J. Dissection of the pH dependence of inhibitor binding energetics for an aspatric protease: direct measurement of the protonation states of the catalytic aspartic acid residues. Biochemistry 1997; 36: 16166-16172.
    • (1997) Biochemistry , vol.36 , pp. 16166-16172
    • Xie, D.1    Gulnik, S.2    Collins, L.3    Gustchina, E.4    Suvorov, L.5    Erickson, J.6
  • 34
    • 0028916760 scopus 로고
    • pH dependence of binding reactions from free energy simulations and macroscopic continuum electrostatic calculations: application to 2'GMP/3'GMP binding to ribonuclease T1 and implications for catalysis
    • MacKerell AD, Jr, Sommer MS, Karplus M. pH dependence of binding reactions from free energy simulations and macroscopic continuum electrostatic calculations: application to 2'GMP/3'GMP binding to ribonuclease T1 and implications for catalysis. J Mol Biol 1995; 247: 774-807.
    • (1995) J Mol Biol , vol.247 , pp. 774-807
    • MacKerell Jr, A.D.1    Sommer, M.S.2    Karplus, M.3
  • 35
    • 36749020127 scopus 로고    scopus 로고
    • Prediction and rationalization of the pH dependence of the activity and stability of family 11 xylanases
    • Kongsted J, Ryde U, Wydra J, Jensen JH. Prediction and rationalization of the pH dependence of the activity and stability of family 11 xylanases. Biochemistry 2007; 46: 13581-13592.
    • (2007) Biochemistry , vol.46 , pp. 13581-13592
    • Kongsted, J.1    Ryde, U.2    Wydra, J.3    Jensen, J.H.4
  • 36
    • 41949108433 scopus 로고    scopus 로고
    • Calculating pH and salt dependence of protein-protein binding
    • Jensen JH. Calculating pH and salt dependence of protein-protein binding. Curr Pharm Biotechnol 2008; 9: 96-102.
    • (2008) Curr Pharm Biotechnol , vol.9 , pp. 96-102
    • Jensen, J.H.1
  • 37
    • 54749089268 scopus 로고    scopus 로고
    • Calculation of the protonation states of proteins and small molecules: implications to ligand-receptor interactions
    • Mitra R, Shyam R, Mitra I, Miteva MA, Alexov E. Calculation of the protonation states of proteins and small molecules: implications to ligand-receptor interactions. Current Comput-Aided Drug Design 2008; 4: 169-179.
    • (2008) Current Comput-Aided Drug Design , vol.4 , pp. 169-179
    • Mitra, R.1    Shyam, R.2    Mitra, I.3    Miteva, M.A.4    Alexov, E.5
  • 38
    • 0034039797 scopus 로고    scopus 로고
    • Electrostatics aspects of protein-protein interactions
    • Sheinerman F, Norel R, Honig B. Electrostatics aspects of protein-protein interactions. Current Opin Struct Biol 2000; 10: 153-159.
    • (2000) Current Opin Struct Biol , vol.10 , pp. 153-159
    • Sheinerman, F.1    Norel, R.2    Honig, B.3
  • 39
    • 3142708566 scopus 로고    scopus 로고
    • Calculating proton uptake/release and the binding free energy taking into account ionization and conformation changes induced by protein-inhibitor association. Application to Plasmepsin Cathepsin D and Endothiapepsin-Pepstatin Complexes
    • Alexov E. Calculating proton uptake/release and the binding free energy taking into account ionization and conformation changes induced by protein-inhibitor association. Application to Plasmepsin Cathepsin D and Endothiapepsin-Pepstatin Complexes. Proteins 2004; 56: 572-584.
    • (2004) Proteins , vol.56 , pp. 572-584
    • Alexov, E.1
  • 40
    • 0029056922 scopus 로고
    • Energetics of protein-protein interactions: analysis of the barnase-barstar interface by single mutations and double mutant cycles
    • Schreiber G, Fersht AR. Energetics of protein-protein interactions: analysis of the barnase-barstar interface by single mutations and double mutant cycles. J Mol Biol 1995; 248: 478-486.
    • (1995) J Mol Biol , vol.248 , pp. 478-486
    • Schreiber, G.1    Fersht, A.R.2
  • 41
    • 0015818586 scopus 로고
    • Flavine-protein interactions in flavoenzymes. pH dependence of the binding of flavine mononucleotide and riboflavine to Azotobacter flavodoxin
    • MacKnight ML, Gillard JM, Tollin G. Flavine-protein interactions in flavoenzymes. pH dependence of the binding of flavine mononucleotide and riboflavine to Azotobacter flavodoxin. Biochemistry 1973; 12: 4200-4206.
    • (1973) Biochemistry , vol.12 , pp. 4200-4206
    • MacKnight, M.L.1    Gillard, J.M.2    Tollin, G.3
  • 43
    • 0027231258 scopus 로고
    • On the pH dependence of protein stability
    • Yang A-S, Honig B. On the pH dependence of protein stability. J Mol Biol 1993; 231: 459-474.
    • (1993) J Mol Biol , vol.231 , pp. 459-474
    • Yang, A.-S.1    Honig, B.2
  • 44
    • 0034700307 scopus 로고    scopus 로고
    • pH Dependence of Stability of Staphyloccocal Nuclease: evidence of substantial electrostatic interactions in the denaturated state
    • Whitten S, Garcia-Moreno B. pH Dependence of Stability of Staphyloccocal Nuclease: evidence of substantial electrostatic interactions in the denaturated state. Biochemistry 2000; 39: 14292-14304.
    • (2000) Biochemistry , vol.39 , pp. 14292-14304
    • Whitten, S.1    Garcia-Moreno, B.2
  • 45
    • 0037446852 scopus 로고    scopus 로고
    • Site-specific contributions to the pH dependence of protein stability
    • Tollinger M, Crowhurst K, Kay L, Forman-Kay J. Site-specific contributions to the pH dependence of protein stability. Proc Natl Acad Sci USA 2003; 100: 4545-4550.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 4545-4550
    • Tollinger, M.1    Crowhurst, K.2    Kay, L.3    Forman-Kay, J.4
  • 46
    • 33748775782 scopus 로고    scopus 로고
    • pH Dependence of peptidylglycine monooxygenase. Mechanistic implications of Cu-methionine binding dynamics
    • Bauman AT, Jaron S, Yukl ET, Burchfiel JR, Blackburn NJ. pH Dependence of peptidylglycine monooxygenase. Mechanistic implications of Cu-methionine binding dynamics. Biochemistry 2006; 45: 11140-11150.
    • (2006) Biochemistry , vol.45 , pp. 11140-11150
    • Bauman, A.T.1    Jaron, S.2    Yukl, E.T.3    Burchfiel, J.R.4    Blackburn, N.J.5
  • 47
    • 52949093935 scopus 로고    scopus 로고
    • pH dependence of cyanide binding to the ferric heme domain of the direct oxygen sensor from Escherichia coli and the effect of alkaline denaturation
    • Bidwai AK, Ok EY, Erman JE. pH dependence of cyanide binding to the ferric heme domain of the direct oxygen sensor from Escherichia coli and the effect of alkaline denaturation. Biochemistry 2008; 47: 10458-10470.
    • (2008) Biochemistry , vol.47 , pp. 10458-10470
    • Bidwai, A.K.1    Ok, E.Y.2    Erman, J.E.3
  • 49
    • 0025234587 scopus 로고
    • pH-induced denaturation of proteins: a single salt bridges contributes 3-5 kcal/mol to the free energy of folding of T4-lysozyme
    • Anderson DE, Becktel WJ, Dahlquist FW. pH-induced denaturation of proteins: a single salt bridges contributes 3-5 kcal/mol to the free energy of folding of T4-lysozyme. Biochem 1990; 29: 2403-2408.
    • (1990) Biochem , vol.29 , pp. 2403-2408
    • Anderson, D.E.1    Becktel, W.J.2    Dahlquist, F.W.3
  • 50
    • 0026602704 scopus 로고
    • Urea denaturation of barnase: pH dependence and characterzation of the unfolded state
    • Pace CN, Laurents DV, Erickson RE. Urea denaturation of barnase: pH dependence and characterzation of the unfolded state. Biochemistry 1992; 31: 2728-2734.
    • (1992) Biochemistry , vol.31 , pp. 2728-2734
    • Pace, C.N.1    Laurents, D.V.2    Erickson, R.E.3
  • 51
    • 0029007734 scopus 로고
    • pH dependence of the stability of barstar to chemical and thermal denaturation
    • Khurana R, Hate A, Nath U, Udgaonkar B. pH dependence of the stability of barstar to chemical and thermal denaturation. Prot Sci 1995; 4: 1133-1144.
    • (1995) Prot Sci , vol.4 , pp. 1133-1144
    • Khurana, R.1    Hate, A.2    Nath, U.3    Udgaonkar, B.4
  • 52
    • 33745711882 scopus 로고    scopus 로고
    • Subcellular pH and predicted pH-dependent features of proteins
    • Chan P, Lovric J, Warwicker J. Subcellular pH and predicted pH-dependent features of proteins. Proteomics 2006; 6: 3494-3501.
    • (2006) Proteomics , vol.6 , pp. 3494-3501
    • Chan, P.1    Lovric, J.2    Warwicker, J.3
  • 53
    • 70450248465 scopus 로고    scopus 로고
    • Evidence for the adaptation of protein pH-dependence to subcellular pH
    • Chan P, Warwicker J. Evidence for the adaptation of protein pH-dependence to subcellular pH. BMC Biol 2009; 7: 69.
    • (2009) BMC Biol , vol.7 , pp. 69
    • Chan, P.1    Warwicker, J.2
  • 54
    • 72849108234 scopus 로고    scopus 로고
    • Adaptations of proteins to cellular and subcellular pH
    • Garcia-Moreno B. Adaptations of proteins to cellular and subcellular pH. J Biol 2009; 8: 98.
    • (2009) J Biol , vol.8 , pp. 98
    • Garcia-Moreno, B.1
  • 55
    • 0030945495 scopus 로고    scopus 로고
    • Incorporating protein conformation flexibility into the calculation of pH-dependent protein properties
    • Alexov E, Gunner M. Incorporating protein conformation flexibility into the calculation of pH-dependent protein properties. Biophys J 1997; 74: 2075-2093.
    • (1997) Biophys J , vol.74 , pp. 2075-2093
    • Alexov, E.1    Gunner, M.2
  • 56
    • 0036787760 scopus 로고    scopus 로고
    • Combining conformational flexibility and continuum electrostatics for calculating residue pKa's in proteins
    • Georgescu R, Alexov E, Gunner M. Combining conformational flexibility and continuum electrostatics for calculating residue pKa's in proteins. Biophys J 2002; 83: 1731-1748.
    • (2002) Biophys J , vol.83 , pp. 1731-1748
    • Georgescu, R.1    Alexov, E.2    Gunner, M.3
  • 57
    • 1642499126 scopus 로고    scopus 로고
    • Numerical calculations of the pH of maximal protein stability. The effect of the sequence composition and 3D structure
    • Alexov E. Numerical calculations of the pH of maximal protein stability. The effect of the sequence composition and 3D structure Eur J Biochem 2004; 271: 173-185.
    • (2004) Eur J Biochem , vol.271 , pp. 173-185
    • Alexov, E.1
  • 58
    • 77955785242 scopus 로고    scopus 로고
    • On the pH-optimum of activity and stability of proteins
    • Talley K, Alexov E. On the pH-optimum of activity and stability of proteins. Proteins 2010; 78: 2699-2706.
    • (2010) Proteins , vol.78 , pp. 2699-2706
    • Talley, K.1    Alexov, E.2
  • 59
    • 33748476481 scopus 로고    scopus 로고
    • Electrostatic properties of protein-protein complexes
    • Kundrotas PJ, Alexov E. Electrostatic properties of protein-protein complexes. Biophys J 2006; 91: 1724-1736.
    • (2006) Biophys J , vol.91 , pp. 1724-1736
    • Kundrotas, P.J.1    Alexov, E.2
  • 60
    • 57349090665 scopus 로고    scopus 로고
    • Very fast prediction and rationalization of pKa values for protein-ligand complexes
    • Bas DC, Rogers DM, Jensen JH. Very fast prediction and rationalization of pKa values for protein-ligand complexes. Proteins 2008; 73: 765-783.
    • (2008) Proteins , vol.73 , pp. 765-783
    • Bas, D.C.1    Rogers, D.M.2    Jensen, J.H.3
  • 62
    • 0346122798 scopus 로고    scopus 로고
    • "GRASP2: Visualization, surface properties and electrostatic of macromolecular structures
    • Petrey D, Honig B. "GRASP2: Visualization, surface properties and electrostatic of macromolecular structures. Methods Enzymol 2003; 374: 492-509.
    • (2003) Methods Enzymol , vol.374 , pp. 492-509
    • Petrey, D.1    Honig, B.2
  • 63
    • 62749167980 scopus 로고    scopus 로고
    • MCCE2: improving protein pka calculations with extensive side chain rotamer sampling
    • Song Y, Mao J, Gunner MR. MCCE2: improving protein pka calculations with extensive side chain rotamer sampling. J Comp Chem 2009; 30: 2231-2247.
    • (2009) J Comp Chem , vol.30 , pp. 2231-2247
    • Song, Y.1    Mao, J.2    Gunner, M.R.3
  • 65
    • 0001158366 scopus 로고
    • Die Berechnung der Wasserstoffzahl des Blutes aus der freien und gebundenen Kohlensäure desselben, und die Sauerstoffbindung des Blutes als Funktion der Wasserstoffzahl
    • Hasselbalch KA. Die Berechnung der Wasserstoffzahl des Blutes aus der freien und gebundenen Kohlensäure desselben, und die Sauerstoffbindung des Blutes als Funktion der Wasserstoffzahl. Biochemische Zeitschrift 1917; 78: 112-144.
    • (1917) Biochemische Zeitschrift , vol.78 , pp. 112-144
    • Hasselbalch, K.A.1
  • 66
    • 18744382508 scopus 로고    scopus 로고
    • PIBASE: a comprehensive database of structurally defined protein interfaces
    • Davis FP, Sali A. PIBASE: a comprehensive database of structurally defined protein interfaces. Bioinformatics 2005; 21: 1901-1907.
    • (2005) Bioinformatics , vol.21 , pp. 1901-1907
    • Davis, F.P.1    Sali, A.2
  • 67
    • 0041384252 scopus 로고    scopus 로고
    • In silico identification of functional protein interfaces
    • Bell RE, Ben-Tal N. In silico identification of functional protein interfaces. Compar Funct Genom 2003; 4: 420-423.
    • (2003) Compar Funct Genom , vol.4 , pp. 420-423
    • Bell, R.E.1    Ben-Tal, N.2
  • 68
    • 23044487169 scopus 로고    scopus 로고
    • Statistical analysis and prediction of protein-protein interfaces
    • Bordner AJ, Abagyan R. Statistical analysis and prediction of protein-protein interfaces. Proteins 2005; 60: 353-366.
    • (2005) Proteins , vol.60 , pp. 353-366
    • Bordner, A.J.1    Abagyan, R.2
  • 69
    • 33748779553 scopus 로고    scopus 로고
    • Insights into protein-protein interfaces using a Bayesian network prediction method
    • Bradford JR, Needham CJ, Bulpitt AJ, Westhead DR. Insights into protein-protein interfaces using a Bayesian network prediction method. J Mol Biol 2006; 362: 365-386.
    • (2006) J Mol Biol , vol.362 , pp. 365-386
    • Bradford, J.R.1    Needham, C.J.2    Bulpitt, A.J.3    Westhead, D.R.4
  • 70
    • 19544369864 scopus 로고    scopus 로고
    • An evolution based classifier for prediction of protein interfaces without using protein structures
    • Res I, Mihalek I, Lichtarge O. An evolution based classifier for prediction of protein interfaces without using protein structures. Bioinformatics 2005; 21: 2496-2501.
    • (2005) Bioinformatics , vol.21 , pp. 2496-2501
    • Res, I.1    Mihalek, I.2    Lichtarge, O.3
  • 71
    • 20844454090 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces
    • Aytuna AS, Gursoy A, Keskin O. Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces. Bioinformatics 2005; 21: 2850-2855.
    • (2005) Bioinformatics , vol.21 , pp. 2850-2855
    • Aytuna, A.S.1    Gursoy, A.2    Keskin, O.3
  • 72
    • 0000328844 scopus 로고
    • A new vertex algorithm to calculate solvent accessible surface areas
    • Sridharan S, Nicholls A, Honig B. A new vertex algorithm to calculate solvent accessible surface areas. Biophys J 1992; 61: A174.
    • (1992) Biophys J , vol.61
    • Sridharan, S.1    Nicholls, A.2    Honig, B.3
  • 73
    • 0037133605 scopus 로고    scopus 로고
    • A Gaussian-chain model for treating residual charge-charge interactions in the unfolded state of proteins
    • Zhou H. A Gaussian-chain model for treating residual charge-charge interactions in the unfolded state of proteins. Proc Natl Acad Sci USA 2002; 99: 3569-3574.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 3569-3574
    • Zhou, H.1
  • 75
    • 0041878652 scopus 로고    scopus 로고
    • Effects of charge-charge interactions on dimensions of unfolded proteins: a Monte Carlo study
    • Kundrotas PJ, Karshikoff A. Effects of charge-charge interactions on dimensions of unfolded proteins: a Monte Carlo study. J Chem Phys 2003; 119: 3574-3581.
    • (2003) J Chem Phys , vol.119 , pp. 3574-3581
    • Kundrotas, P.J.1    Karshikoff, A.2
  • 76
    • 3142708566 scopus 로고    scopus 로고
    • Calculating proton uptake/release and binding free energy taking into account ionization and conformation changes induced by protein-inhibitor association: application to plasmepsin, cathepsin D and endothiapepsin-pepstatin complexes
    • Alexov E. Calculating proton uptake/release and binding free energy taking into account ionization and conformation changes induced by protein-inhibitor association: application to plasmepsin, cathepsin D and endothiapepsin-pepstatin complexes. Proteins 2004; 56: 572-584.
    • (2004) Proteins , vol.56 , pp. 572-584
    • Alexov, E.1
  • 77
    • 0033524394 scopus 로고    scopus 로고
    • Biophysical characterization of the interaction of the beta-lactamase TEM-1 with its protein inhibitor BLIP
    • Albeck S, Schreiber G. Biophysical characterization of the interaction of the beta-lactamase TEM-1 with its protein inhibitor BLIP. Biochemistry 1999; 38: 11-21.
    • (1999) Biochemistry , vol.38 , pp. 11-21
    • Albeck, S.1    Schreiber, G.2
  • 78
    • 0028983182 scopus 로고
    • pKa values of carboxyl groups in the native and denaturated states of barnase: the pKa of the denaturated state are on average 0.4 units lower than those of model compounds
    • Oliverberg M, Arcus V, Fersht A. pKa values of carboxyl groups in the native and denaturated states of barnase: the pKa of the denaturated state are on average 0.4 units lower than those of model compounds. Biochemistry 1995; 34: 9424-9433.
    • (1995) Biochemistry , vol.34 , pp. 9424-9433
    • Oliverberg, M.1    Arcus, V.2    Fersht, A.3
  • 79
    • 0026553768 scopus 로고
    • The folding of an enzyme. II. Structure of Barnase and the contribution of different interactions to protein stability
    • Serrano L, Kellis JT, Cann P, Matouschek A, Fersht AR. The folding of an enzyme. II. Structure of Barnase and the contribution of different interactions to protein stability. J Mol Biol 1992; 224: 783-804.
    • (1992) J Mol Biol , vol.224 , pp. 783-804
    • Serrano, L.1    Kellis, J.T.2    Cann, P.3    Matouschek, A.4    Fersht, A.R.5
  • 80
    • 0028941934 scopus 로고
    • A calorimetric study of the thermal-stability of barstar and its interaction with barnase
    • Martinez JC, Filimonov VV, Mateo PL, Schreiber G, Fersht AR. A calorimetric study of the thermal-stability of barstar and its interaction with barnase. Biochemistry 1995; 34: 5224-5233.
    • (1995) Biochemistry , vol.34 , pp. 5224-5233
    • Martinez, J.C.1    Filimonov, V.V.2    Mateo, P.L.3    Schreiber, G.4    Fersht, A.R.5
  • 81
    • 0027177102 scopus 로고
    • Interaction of barnase with its popypeptide inhibitor barstar studied by protein engineering
    • Schreiber G, Fersht AR. Interaction of barnase with its popypeptide inhibitor barstar studied by protein engineering. Biochemistry 1993; 32: 5145-5150.
    • (1993) Biochemistry , vol.32 , pp. 5145-5150
    • Schreiber, G.1    Fersht, A.R.2
  • 82
    • 44849086045 scopus 로고    scopus 로고
    • Modelling salt dependence of protein-protein association: linear vs non-linear Poisson-Bolzmann equation
    • Talley K, Alexov E. Modelling salt dependence of protein-protein association: linear vs non-linear Poisson-Bolzmann equation. Comm Computat Phys 2008; 3: 1071-1086.
    • (2008) Comm Computat Phys , vol.3 , pp. 1071-1086
    • Talley, K.1    Alexov, E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.