메뉴 건너뛰기




Volumn 98, Issue 5, 2010, Pages 872-880

Statistics and physical origins of pK and ionization state changes upon protein-ligand binding

Author keywords

[No Author keywords available]

Indexed keywords


EID: 77749292431     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2009.11.016     Document Type: Article
Times cited : (42)

References (54)
  • 1
    • 0004053611 scopus 로고
    • 2nd Ed. John Wiley & Sons, New York
    • Voet, D., and J. G. Voet. 1995. Biochemistry, 2nd Ed. John Wiley & Sons, New York.
    • (1995) Biochemistry
    • Voet, D.1    Voet, J.G.2
  • 2
    • 0031191655 scopus 로고    scopus 로고
    • Signaling recognition events with fluorescent sensors and switches
    • de Silva,A. P.,H.Q.Gunaratne, ..., T. E. Rice. 1997. Signaling recognition events with fluorescent sensors and switches. Chem. Rev. 97:1515-1566.
    • (1997) Chem. Rev , vol.97 , pp. 1515-1566
    • de Silva, A.P.1    Gunaratne, H.Q.2    Rice, T.E.3
  • 3
    • 1642357706 scopus 로고    scopus 로고
    • The many roles of computation in drug discovery
    • Jorgensen, W. L. 2004. The many roles of computation in drug discovery. Science. 303:1813-1818.
    • (2004) Science , vol.303 , pp. 1813-1818
    • Jorgensen, W.L.1
  • 4
    • 1342302339 scopus 로고    scopus 로고
    • Conformational changes associated with protein-protein interactions
    • Goh, C.-S., D. Milburn, and M. Gerstein. 2004. Conformational changes associated with protein-protein interactions. Curr. Opin. Struct. Biol. 14:104-109.
    • (2004) Curr. Opin. Struct. Biol , vol.14 , pp. 104-109
    • Goh, C.-S.1    Milburn, D.2    Gerstein, M.3
  • 5
    • 0141843643 scopus 로고    scopus 로고
    • Electron cryomicroscopy shows how strong binding of myosin to actin releases nucleotide
    • Holmes, K. C., I. Angert, ..., R. R. Schröder. 2003. Electron cryomicroscopy shows how strong binding of myosin to actin releases nucleotide. Nature. 425:423-427.
    • (2003) Nature , vol.425 , pp. 423-427
    • Holmes, K.C.1    Angert, I.2    Schröder, R.R.3
  • 6
    • 45849095234 scopus 로고    scopus 로고
    • Biochemistry: How do proteins interact?
    • Boehr, D. D., and P. E. Wright. 2008. Biochemistry: How do proteins interact? Science. 320:1429-1430.
    • (2008) Science , vol.320 , pp. 1429-1430
    • Boehr, D.D.1    Wright, P.E.2
  • 7
    • 0036306236 scopus 로고    scopus 로고
    • On the role of electrostatic interactions in the design of protein-protein interfaces
    • Sheinerman, F. B., and B. Honig. 2002. On the role of electrostatic interactions in the design of protein-protein interfaces. J. Mol. Biol. 318:161-177.
    • (2002) J. Mol. Biol , vol.318 , pp. 161-177
    • Sheinerman, F.B.1    Honig, B.2
  • 8
    • 0035281357 scopus 로고    scopus 로고
    • Computer simulation of protein-protein interactions
    • Elcock, A. H., D. Sept, and J. A. McCammon. 2001. Computer simulation of protein-protein interactions. J. Phys. Chem. B. 105:1504-1518.
    • (2001) J. Phys. Chem. B , vol.105 , pp. 1504-1518
    • Elcock, A.H.1    Sept, D.2    McCammon, J.A.3
  • 9
    • 23044487169 scopus 로고    scopus 로고
    • Statistical analysis and prediction of protein-protein interfaces
    • Bordner, A. J., and R. Abagyan. 2005. Statistical analysis and prediction of protein-protein interfaces. Proteins. 60:353-366.
    • (2005) Proteins , vol.60 , pp. 353-366
    • Bordner, A.J.1    Abagyan, R.2
  • 10
    • 0038356582 scopus 로고    scopus 로고
    • Predicted protein-protein interaction sites from local sequence information
    • Ofran, Y., and B. Rost. 2003. Predicted protein-protein interaction sites from local sequence information. FEBS Lett. 544:236-239.
    • (2003) FEBS Lett , vol.544 , pp. 236-239
    • Ofran, Y.1    Rost, B.2
  • 11
    • 0028916599 scopus 로고
    • A hot spot of binding energy in a hormone-receptor interface
    • Clackson, T., and J. A. Wells. 1995. A hot spot of binding energy in a hormone-receptor interface. Science. 267:383-386.
    • (1995) Science , vol.267 , pp. 383-386
    • Clackson, T.1    Wells, J.A.2
  • 12
    • 0025831781 scopus 로고
    • Mutational analysis and protein engineering of receptor-binding determinants in human placental lactogen
    • Lowman, H. B., B. C. Cunningham, and J. A. Wells. 1991. Mutational analysis and protein engineering of receptor-binding determinants in human placental lactogen. J. Biol. Chem. 266:10982-10988.
    • (1991) J. Biol. Chem , vol.266 , pp. 10982-10988
    • Lowman, H.B.1    Cunningham, B.C.2    Wells, J.A.3
  • 13
    • 0042710087 scopus 로고    scopus 로고
    • Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies
    • Massova, I., and P. A. Kollman. 1999. Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies. J. Am. Chem. Soc. 121:8133-8143.
    • (1999) J. Am. Chem. Soc , vol.121 , pp. 8133-8143
    • Massova, I.1    Kollman, P.A.2
  • 15
    • 24644518008 scopus 로고    scopus 로고
    • Design of improved protein inhibitors of HIV-1 cell entry: Optimization of electrostatic interactions at the binding interface
    • Green, D. F., and B. Tidor. 2005. Design of improved protein inhibitors of HIV-1 cell entry: optimization of electrostatic interactions at the binding interface. Proteins. 60:644-657.
    • (2005) Proteins , vol.60 , pp. 644-657
    • Green, D.F.1    Tidor, B.2
  • 16
    • 20344403522 scopus 로고    scopus 로고
    • Importance of accurate charges in molecular docking: Quantum mechanical/molecular mechanical (QM/MM) approach
    • Cho, A. E., V. Guallar, ..., R. Friesner. 2005. Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach. J. Comput. Chem. 26:915-931.
    • (2005) J. Comput. Chem , vol.26 , pp. 915-931
    • Cho, A.E.1    Guallar, V.2    Friesner, R.3
  • 17
    • 84962343568 scopus 로고    scopus 로고
    • Inclusion of ionization states of ligands in affinity calculations
    • Donnini, S., A. Villa, ..., A. H. Juffer. 2009. Inclusion of ionization states of ligands in affinity calculations. Proteins. 76:138-150.
    • (2009) Proteins , vol.76 , pp. 138-150
    • Donnini, S.1    Villa, A.2    Juffer, A.H.3
  • 18
    • 40549107752 scopus 로고    scopus 로고
    • Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors
    • Wittayanarakul, K., S. Hannongbua, and M. Feig. 2008. Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors. J. Comput. Chem. 29:673-685.
    • (2008) J. Comput. Chem , vol.29 , pp. 673-685
    • Wittayanarakul, K.1    Hannongbua, S.2    Feig, M.3
  • 19
    • 0041347814 scopus 로고    scopus 로고
    • Structure and energetics of protein-protein interactions: The role of conformational heterogeneity in OMTKY3 binding to serine proteases
    • Horn, J. R., S. Ramaswamy, and K. P. Murphy. 2003. Structure and energetics of protein-protein interactions: the role of conformational heterogeneity in OMTKY3 binding to serine proteases. J. Mol. Biol. 331:497-508.
    • (2003) J. Mol. Biol , vol.331 , pp. 497-508
    • Horn, J.R.1    Ramaswamy, S.2    Murphy, K.P.3
  • 20
    • 0036129394 scopus 로고    scopus 로고
    • a shifts and changes of tautomeric states induced by the binding of galliumprotoporphyrin IXin the hemophore HasA(SM)
    • a shifts and changes of tautomeric states induced by the binding of galliumprotoporphyrin IXin the hemophore HasA(SM). Protein Sci. 11:757-765.
    • (2002) Protein Sci , vol.11 , pp. 757-765
    • Wolff, N.1    Deniau, C.2    Lecroisey, A.3
  • 21
    • 32344437202 scopus 로고    scopus 로고
    • a values in the Pol-λ lyase domain: Mechanistic implications
    • a values in the Pol-λ lyase domain: mechanistic implications. Biochemistry. 45:1785-1794.
    • (2006) Biochemistry , vol.45 , pp. 1785-1794
    • Gao, G.1    DeRose, E.F.2    London, R.E.3
  • 22
    • 41149167073 scopus 로고    scopus 로고
    • Structural identification of the pathway of long-range communication in an allosteric enzyme
    • Gandhi, P. S., Z. Chen, ..., E. Di Cera. 2008. Structural identification of the pathway of long-range communication in an allosteric enzyme. Proc. Natl. Acad. Sci. USA. 105:1832-1837.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 1832-1837
    • Gandhi, P.S.1    Chen, Z.2    Di Cera, E.3
  • 26
    • 3142661052 scopus 로고    scopus 로고
    • Charge optimization of the interface between protein kinases and their ligands
    • Sims, P. A., C. F. Wong, and J. A. McCammon. 2004. Charge optimization of the interface between protein kinases and their ligands. J. Comput. Chem. 25:1416-1429.
    • (2004) J. Comput. Chem , vol.25 , pp. 1416-1429
    • Sims, P.A.1    Wong, C.F.2    McCammon, J.A.3
  • 27
    • 0032898499 scopus 로고    scopus 로고
    • Thermodynamic linkage between the binding of protons and inhibitors to HIV-1 protease
    • Trylska, J., J. Antosiewicz, ..., M. K. Gilson. 1999. Thermodynamic linkage between the binding of protons and inhibitors to HIV-1 protease. Protein Sci. 8:180-195.
    • (1999) Protein Sci , vol.8 , pp. 180-195
    • Trylska, J.1    Antosiewicz, J.2    Gilson, M.K.3
  • 28
    • 33748476481 scopus 로고    scopus 로고
    • Electrostatic properties of protein-protein complexes
    • Kundrotas, P. J., and E. Alexov. 2006. Electrostatic properties of protein-protein complexes. Biophys. J. 91:1724-1736.
    • (2006) Biophys. J , vol.91 , pp. 1724-1736
    • Kundrotas, P.J.1    Alexov, E.2
  • 29
    • 40549144041 scopus 로고    scopus 로고
    • Protein-protein binding is often associated with changes in protonation state
    • Mason, A. C., and J. H. Jensen. 2008. Protein-protein binding is often associated with changes in protonation state. Proteins. 71:81-91.
    • (2008) Proteins , vol.71 , pp. 81-91
    • Mason, A.C.1    Jensen, J.H.2
  • 30
    • 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. 29:10219-10225.
    • (1990) Biochemistry , vol.29 , pp. 10219-10225
    • Bashford, D.1    Karplus, M.2
  • 31
    • 0028305457 scopus 로고
    • Prediction of pH-dependent properties of proteins
    • Antosiewicz, J., J. A. McCammon, and M. K. Gilson. 1994. Prediction of pH-dependent properties of proteins. J. Mol. Biol. 238:415-436.
    • (1994) J. Mol. Biol , vol.238 , pp. 415-436
    • Antosiewicz, J.1    McCammon, J.A.2    Gilson, M.K.3
  • 34
    • 0037529067 scopus 로고    scopus 로고
    • Electrostatics and dynamics of proteins
    • Simonson, T. 2003. Electrostatics and dynamics of proteins. Rep. Prog. Phys. 66:737-787.
    • (2003) Rep. Prog. Phys , vol.66 , pp. 737-787
    • Simonson, T.1
  • 35
    • 21644480883 scopus 로고    scopus 로고
    • Protein-Protein Docking Benchmark 2.0: An update
    • Mintseris, J., K. Wiehe, ..., Z. Weng. 2005. Protein-Protein Docking Benchmark 2.0: an update. Proteins. 60:214-216.
    • (2005) Proteins , vol.60 , pp. 214-216
    • Mintseris, J.1    Wiehe, K.2    Weng, Z.3
  • 36
    • 0035950051 scopus 로고    scopus 로고
    • Ligand-protein database: Linking protein-ligand complex structures to binding data
    • Roche, O., R. Kiyama, and C. L. Brooks, 3rd. 2001. Ligand-protein database: linking protein-ligand complex structures to binding data. J. Med. Chem. 44:3592-3598.
    • (2001) J. Med. Chem , vol.44 , pp. 3592-3598
    • Roche, O.1    Kiyama, R.2    Brooks 3rd, C.L.3
  • 37
    • 36549064679 scopus 로고    scopus 로고
    • NPIDB: A database of nucleic acids-protein interactions
    • Spirin, S., M. Titov, ..., A. Alexeevski. 2007. NPIDB: a database of nucleic acids-protein interactions. Bioinformatics. 23:3247-3248.
    • (2007) Bioinformatics , vol.23 , pp. 3247-3248
    • Spirin, S.1    Titov, M.2    Alexeevski, A.3
  • 39
    • 23444454552 scopus 로고    scopus 로고
    • The AMBER biomolecular simulation programs
    • Case, D. A., T. E. Cheatham, 3rd, ..., R. J. Woods. 2005. The AMBER biomolecular simulation programs. J. Comput. Chem. 26:1668-1688.
    • (2005) J. Comput. Chem , vol.26 , pp. 1668-1688
    • Case, D.A.1    Cheatham 3rd, T.E.2    Woods, R.J.3
  • 41
    • 2942532422 scopus 로고    scopus 로고
    • Development and testing of a general amber force field
    • Wang, J., R. M. Wolf, ..., D. A. Case. 2004. Development and testing of a general amber force field. J. Comput. Chem. 25:1157-1174.
    • (2004) J. Comput. Chem , vol.25 , pp. 1157-1174
    • Wang, J.1    Wolf, R.M.2    Case, D.A.3
  • 42
    • 33748538349 scopus 로고    scopus 로고
    • Automatic atom type and bond type perception in molecular mechanical calculations
    • Wang, J., W. Wang, ..., D. A. Case. 2006. Automatic atom type and bond type perception in molecular mechanical calculations. J. Mol. Graph. Model. 25:247-260.
    • (2006) J. Mol. Graph. Mode , vol.50 , Issue.25 , pp. 247-260
    • Wang, J.1    Wang, W.2    Case, D.A.3
  • 43
    • 0001858251 scopus 로고
    • Application of a theory of enzyme specificity to protein synthesis
    • Koshland, D. E. 1958. Application of a theory of enzyme specificity to protein synthesis. Proc. Natl. Acad. Sci. USA. 44:98-104.
    • (1958) Proc. Natl. Acad. Sci. USA , vol.44 , pp. 98-104
    • Koshland, D.E.1
  • 44
    • 0037305552 scopus 로고    scopus 로고
    • On the evaluation and optimization of protein x-ray structures for pKa calculations
    • Nielsen, J. E., and J. A. McCammon. 2003. On the evaluation and optimization of protein x-ray structures for pKa calculations. Protein Sci. 12:313-326.
    • (2003) Protein Sci , vol.12 , pp. 313-326
    • Nielsen, J.E.1    McCammon, J.A.2
  • 45
    • 0042386423 scopus 로고    scopus 로고
    • Proton affinity changes driving unidirectional proton transport in the bacteriorhodopsin photocycle
    • Onufriev, A., A. Smondyrev, and D. Bashford. 2003. Proton affinity changes driving unidirectional proton transport in the bacteriorhodopsin photocycle. J. Mol. Biol. 332:1183-1193.
    • (2003) J. Mol. Biol , vol.332 , pp. 1183-1193
    • Onufriev, A.1    Smondyrev, A.2    Bashford, D.3
  • 46
    • 33748593093 scopus 로고    scopus 로고
    • Improving the continuum dielectric approach to calculating pKas of ionizable groups in proteins
    • Demchuk, E., and R. C. Wade. 1996. Improving the continuum dielectric approach to calculating pKas of ionizable groups in proteins. J. Phys. Chem. 100:17373-17387.
    • (1996) J. Phys. Chem , vol.100 , pp. 17373-17387
    • Demchuk, E.1    Wade, R.C.2
  • 47
    • 55549111898 scopus 로고    scopus 로고
    • A fast and accurate computational approach to protein ionization
    • Spassov, V. Z., and L. Yan. 2008. A fast and accurate computational approach to protein ionization. Protein Sci. 17:1955-1970.
    • (2008) Protein Sci , vol.17 , pp. 1955-1970
    • Spassov, V.Z.1    Yan, L.2
  • 48
    • 0028335096 scopus 로고
    • Structural mechanisms for domain movements in proteins
    • Gerstein, M., A. M. Lesk, and C. Chothia. 1994. Structural mechanisms for domain movements in proteins. Biochemistry. 33:6739-6749.
    • (1994) Biochemistry , vol.33 , pp. 6739-6749
    • Gerstein, M.1    Lesk, A.M.2    Chothia, C.3
  • 49
    • 77749241906 scopus 로고    scopus 로고
    • Large-scale analysis of secondary structure changes in proteins suggests a role for disorder-to-order transitions in nucleotide binding proteins
    • in press
    • Dan, A., Y. Ofran, and Y. Kliger. 2009. Large-scale analysis of secondary structure changes in proteins suggests a role for disorder-to-order transitions in nucleotide binding proteins. Proteins. in press.
    • (2009) Proteins
    • Dan, A.1    Ofran, Y.2    Kliger, Y.3
  • 50
    • 0032897494 scopus 로고    scopus 로고
    • An analysis of conformational changes on protein-protein association: Implications for predictive docking
    • Betts, M. J., and M. J. E. Sternberg. 1999. An analysis of conformational changes on protein-protein association: implications for predictive docking. Protein Eng. 12:271-283.
    • (1999) Protein Eng , vol.12 , pp. 271-283
    • Betts, M.J.1    Sternberg, M.J.E.2
  • 51
    • 0027477251 scopus 로고
    • Multiple-site titration and molecular modeling: Two rapid methods for computing energies and forces for ionizable groups in proteins
    • Gilson, M. K. 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
  • 52
    • 33646794930 scopus 로고    scopus 로고
    • A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules
    • Myers, J., G. Grothaus, ..., A. Onufriev. 2006. A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules. Proteins. 63:928-938.
    • (2006) Proteins , vol.63 , pp. 928-938
    • Myers, J.1    Grothaus, G.2    Onufriev, A.3
  • 53
    • 40049098280 scopus 로고    scopus 로고
    • Analysis of basic clustering algorithms for numerical estimation of statistical averages in biomolecules
    • Anandakrishnan, R., and A. Onufriev. 2008. Analysis of basic clustering algorithms for numerical estimation of statistical averages in biomolecules. J. Comput. Biol. 15:165-184.
    • (2008) J. Comput. Biol , vol.15 , pp. 165-184
    • Anandakrishnan, R.1    Onufriev, A.2
  • 54
    • 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., D. R. Fredkin, ..., G. Feher. 1991. 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. 88:5804-5808.
    • (1991) Proc. Natl. Acad. Sci. USA , vol.88 , pp. 5804-5808
    • Beroza, P.1    Fredkin, D.R.2    Feher, G.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.