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Volumn 90, Issue 2, 2006, Pages 433-442

Probing the effect of point mutations at protein-protein interfaces with free energy calculations

Author keywords

[No Author keywords available]

Indexed keywords

APROTININ; CHYMOTRYPSIN; ELASTASE; OVOMUCOID; PROTEIN; TRYPSIN;

EID: 33646166928     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.105.073239     Document Type: Article
Times cited : (56)

References (41)
  • 1
    • 0036606483 scopus 로고    scopus 로고
    • Principles of docking: An overview of search algorithms and a guide to scoring functions
    • Halperin, I., B. Y. Ma, H. Wolfson, and R. Nussinov. 2002. Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins. 47:409-443.
    • (2002) Proteins , vol.47 , pp. 409-443
    • Halperin, I.1    Ma, B.Y.2    Wolfson, H.3    Nussinov, R.4
  • 2
    • 0036468385 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions by docking methods
    • Smith, G. R., and M. J. E. Sternberg. 2002. Prediction of protein-protein interactions by docking methods. Curr. Opin. Struct. Biol. 12: 28-35.
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 28-35
    • Smith, G.R.1    Sternberg, M.J.E.2
  • 3
    • 0032479179 scopus 로고    scopus 로고
    • Anatomy of hot spots in protein interfaces
    • Bogan, A. A., and K. S. Thorn. 1998. Anatomy of hot spots in protein interfaces. J. Mol. Biol. 280:1-9.
    • (1998) J. Mol. Biol. , vol.280 , pp. 1-9
    • Bogan, A.A.1    Thorn, K.S.2
  • 5
    • 7044239742 scopus 로고
    • Free energy calculations: Applications to chemical and biochemical phenomena
    • Kollman, P. 1993. Free energy calculations: applications to chemical and biochemical phenomena. Chem. Rev. 93:2395-2417.
    • (1993) Chem. Rev. , vol.93 , pp. 2395-2417
    • Kollman, P.1
  • 6
    • 0028155689 scopus 로고
    • A new method for predicting binding affinity in computer-aided drug design
    • Åqvist, J., C. Medina, and J. E. Samuelsson. 1994. A new method for predicting binding affinity in computer-aided drug design. Protein Eng. 7:385-391.
    • (1994) Protein Eng. , vol.7 , pp. 385-391
    • Åqvist, J.1    Medina, C.2    Samuelsson, J.E.3
  • 7
    • 0036280661 scopus 로고    scopus 로고
    • Ligand binding affinities from MD simulations
    • Åqvist, J., V. B. Luzhkov, and B. O. Brandsdal. 2002. Ligand binding affinities from MD simulations. Acc. Chem. Res. 35:358-365.
    • (2002) Acc. Chem. Res. , vol.35 , pp. 358-365
    • Åqvist, J.1    Luzhkov, V.B.2    Brandsdal, B.O.3
  • 8
    • 0032560959 scopus 로고    scopus 로고
    • Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate - DNA helices
    • Srinivasan, J., T. E. Cheatham, P. Cieplak, P. A. Kollman, and D. A. Case. 1998. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate - DNA helices. J. Am. Chem. Soc. 120:9401-9409.
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 9401-9409
    • Srinivasan, J.1    Cheatham, T.E.2    Cieplak, P.3    Kollman, P.A.4    Case, D.A.5
  • 9
    • 0027087369 scopus 로고
    • Calculation of the free-energy of association for protein complexes
    • Horton, N., and M. Lewis. 1992. Calculation of the free-energy of association for protein complexes. Protein Sci. 1:169-181.
    • (1992) Protein Sci. , vol.1 , pp. 169-181
    • Horton, N.1    Lewis, M.2
  • 10
    • 0033568644 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
  • 12
    • 0347602124 scopus 로고    scopus 로고
    • Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf
    • Gohlke, H., and D. A. Case. 2004. Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. J. Comput. Chem. 25:238-250.
    • (2004) J. Comput. Chem. , vol.25 , pp. 238-250
    • Gohlke, H.1    Case, D.A.2
  • 13
    • 0030134110 scopus 로고    scopus 로고
    • On the validity of electrostatic linear response in polar solvents
    • Åqvist, J., and T. Hansson. 1996. On the validity of electrostatic linear response in polar solvents. J. Phys. Chem. 100:9512-9521.
    • (1996) J. Phys. Chem. , vol.100 , pp. 9512-9521
    • Åqvist, J.1    Hansson, T.2
  • 14
    • 3042549928 scopus 로고    scopus 로고
    • Binding affinity prediction with different force fields: Examination of the linear interaction energy method
    • Almlöf, M., B. O. Brandsdal, and J. Åqvist. 2004. Binding affinity prediction with different force fields: examination of the linear interaction energy method. J. Comput. Chem. 25:1242-1254.
    • (2004) J. Comput. Chem. , vol.25 , pp. 1242-1254
    • Almlöf, M.1    Brandsdal, B.O.2    Åqvist, J.3
  • 15
    • 0026596911 scopus 로고
    • Calculations of antibody-antigen interactions: Microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603
    • Lee, F. S., Z. T. Chu, M. B. Bolger, and A. Warshel. 1992. Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603. Protein Eng. 5:215-228.
    • (1992) Protein Eng. , vol.5 , pp. 215-228
    • Lee, F.S.1    Chu, Z.T.2    Bolger, M.B.3    Warshel, A.4
  • 16
    • 0034925093 scopus 로고    scopus 로고
    • Computational analysis of binding of P1 variants to trypsin
    • Brandsdal, B. O., J. Åqvist, and A. O. Smalås. 2001. Computational analysis of binding of P1 variants to trypsin. Protein Sci. 10:1584-1595.
    • (2001) Protein Sci. , vol.10 , pp. 1584-1595
    • Brandsdal, B.O.1    Åqvist, J.2    Smalås, A.O.3
  • 17
    • 0033612211 scopus 로고    scopus 로고
    • Interscaffolding additivity: Binding of P1 variants of bovine pancreatic trypsin inhibitor to four serine proteases
    • Krowarsch, D., M. Dadlez, O. Buczek, I. Krokoszynska, A. O. Smalås, and J. Otlewski. 1999. Interscaffolding additivity: binding of P1 variants of bovine pancreatic trypsin inhibitor to four serine proteases. J. Mol. Biol. 289:175-186.
    • (1999) J. Mol. Biol. , vol.289 , pp. 175-186
    • Krowarsch, D.1    Dadlez, M.2    Buczek, O.3    Krokoszynska, I.4    Smalås, A.O.5    Otlewski, J.6
  • 18
    • 0032232405 scopus 로고    scopus 로고
    • Q: A molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems
    • Marelius, J., K. Kolmodin, I. Feierberg, and J. Åqvist. 1998. Q: a molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems. J. Mol. Graph. Model. 16:213-225, 261.
    • (1998) J. Mol. Graph. Model. , vol.16
    • Marelius, J.1    Kolmodin, K.2    Feierberg, I.3    Åqvist, J.4
  • 19
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
    • Jorgensen, W. L., D. S. Maxwell, and J. Tirado-Rives. 1996. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 118:11225-11236.
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 20
    • 0032923399 scopus 로고    scopus 로고
    • High-resolution structures of three new trypsin-squash-inhibitor complexes: A detailed comparison with other trypsins and their complexes
    • Helland, R., G. I. Berglund, J. Otlewski, W. Apostoluk, O. A. Andersen, N. P. Willassen, and A. O. Smalås. 1999. High-resolution structures of three new trypsin-squash-inhibitor complexes: a detailed comparison with other trypsins and their complexes. Acta Crystallogr. D. 55:139-148.
    • (1999) Acta Crystallogr. D , vol.55 , pp. 139-148
    • Helland, R.1    Berglund, G.I.2    Otlewski, J.3    Apostoluk, W.4    Andersen, O.A.5    Willassen, N.P.6    Smalås, A.O.7
  • 21
    • 84889120137 scopus 로고
    • Improved methods for building protein models in electron-density maps and the location of errors in these models
    • Jones, T. A., J. Y. Zou, S. W. Cowan, and M. Kjeldgaard. 1991. Improved methods for building protein models in electron-density maps and the location of errors in these models. Acta Crystallogr. A. 47:110-119.
    • (1991) Acta Crystallogr. A , vol.47 , pp. 110-119
    • Jones, T.A.1    Zou, J.Y.2    Cowan, S.W.3    Kjeldgaard, M.4
  • 22
    • 0022801412 scopus 로고
    • X-ray crystal-structure of the complex of human-leukocyte elastase (PMN elastase) and the third domain of the turkey ovomucoid inhibitor
    • Bode, W., A. Z. Wei, R. Huber, E. Meyer, J. Travis, and S. Neumann. 1986. X-ray crystal-structure of the complex of human-leukocyte elastase (PMN elastase) and the third domain of the turkey ovomucoid inhibitor. EMBO J. 5:2453-2458.
    • (1986) EMBO J. , vol.5 , pp. 2453-2458
    • Bode, W.1    Wei, A.Z.2    Huber, R.3    Meyer, E.4    Travis, J.5    Neumann, S.6
  • 23
    • 0023198896 scopus 로고
    • Crystal and molecular structures of the complex of alpha-chymotrypsin with its inhibitor turkey ovomucoid third domain at 1.8 Å resolution
    • Fujinaga, M., A. R. Sielecki, R. J. Read, W. Ardelt, M. Laskowski, Jr., and M. N. James. 1987. Crystal and molecular structures of the complex of alpha-chymotrypsin with its inhibitor turkey ovomucoid third domain at 1.8 Å resolution. J. Mol. Biol. 195:397-418.
    • (1987) J. Mol. Biol. , vol.195 , pp. 397-418
    • Fujinaga, M.1    Sielecki, A.R.2    Read, R.J.3    Ardelt, W.4    Laskowski Jr., M.5    James, M.N.6
  • 24
    • 0000115003 scopus 로고
    • A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations
    • Lee, F. S., and A. Warshel. 1992. A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations. J. Chem. Phys. 97:3100-3107.
    • (1992) J. Chem. Phys. , vol.97 , pp. 3100-3107
    • Lee, F.S.1    Warshel, A.2
  • 26
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of the Cartesian equations of motion of system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23: 327-341.
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 27
    • 0035875953 scopus 로고    scopus 로고
    • Electrostatic effects play a central role in cold adaptation of trypsin
    • Brandsdal, B. O., A. O. Smalås, and J. Åqvist. 2001. Electrostatic effects play a central role in cold adaptation of trypsin. FEBS Lett. 499:171-175.
    • (2001) FEBS Lett. , vol.499 , pp. 171-175
    • Brandsdal, B.O.1    Smalås, A.O.2    Åqvist, J.3
  • 28
    • 0001205818 scopus 로고
    • Electrostatic effects in water-accessible regions of proteins
    • Mehler, E. I., and G. Eichele. 1984. Electrostatic effects in water-accessible regions of proteins. Biochemistry. 23:3887-3891.
    • (1984) Biochemistry , vol.23 , pp. 3887-3891
    • Mehler, E.I.1    Eichele, G.2
  • 29
    • 0028856716 scopus 로고
    • Water molecules participate in proteinase-inhibitor interactions: Crystal structures of Leu18, Ala18, and Gly18 variants of turkey ovomucoid inhibitor third domain complexed with Streptomyces griseus proteinase B
    • Huang, K., W. Lu, S. Anderson, M. Laskowski, Jr., and M. N. James. 1995. Water molecules participate in proteinase-inhibitor interactions: crystal structures of Leu18, Ala18, and Gly18 variants of turkey ovomucoid inhibitor third domain complexed with Streptomyces griseus proteinase B. Protein Sci. 4:1985-1997.
    • (1995) Protein Sci. , vol.4 , pp. 1985-1997
    • Huang, K.1    Lu, W.2    Anderson, S.3    Laskowski Jr., M.4    James, M.N.5
  • 31
    • 0031637651 scopus 로고    scopus 로고
    • Ligand binding affinity prediction by linear interaction energy methods
    • Hansson, T., J. Marelius, and J. Åqvist. 1998. Ligand binding affinity prediction by linear interaction energy methods. J. Comput. Aided Mol. Des. 12:27-35.
    • (1998) J. Comput. Aided Mol. Des. , vol.12 , pp. 27-35
    • Hansson, T.1    Marelius, J.2    Åqvist, J.3
  • 32
    • 0032014129 scopus 로고    scopus 로고
    • Computation of affinity and selectivity: Binding of 2,4-diaminopteridine and 2,4-diaminoquinazoline inhibitors to dihydrofolate reductases
    • Marelius, J., M. Graffner-Nordberg, T. Hansson, A. Hallberg, and J. Åqvist. 1998. Computation of affinity and selectivity: binding of 2,4-diaminopteridine and 2,4-diaminoquinazoline inhibitors to dihydrofolate reductases. J. Comput. Aided Mol. Des. 12:119-131.
    • (1998) J. Comput. Aided Mol. Des. , vol.12 , pp. 119-131
    • Marelius, J.1    Graffner-Nordberg, M.2    Hansson, T.3    Hallberg, A.4    Åqvist, J.5
  • 34
    • 0035913056 scopus 로고    scopus 로고
    • Design, synthesis, computational prediction, and biological evaluation of ester soft drugs as inhibitors of dihydrofolate reductase from Pneumocystis carinii
    • Graffner-Nordberg, M., K. Kolmodin, J. Åqvist, S. F. Queener, and A. Hallberg. 2001. Design, synthesis, computational prediction, and biological evaluation of ester soft drugs as inhibitors of dihydrofolate reductase from Pneumocystis carinii. J. Med. Chem. 44:2391-2402.
    • (2001) J. Med. Chem. , vol.44 , pp. 2391-2402
    • Graffner-Nordberg, M.1    Kolmodin, K.2    Åqvist, J.3    Queener, S.F.4    Hallberg, A.5
  • 36
    • 0035957732 scopus 로고    scopus 로고
    • Mechanisms of tetraethylammonium ion block in the KcsA potassium channel
    • Luzhkov, V. B., and J. Åqvist. 2001. Mechanisms of tetraethylammonium ion block in the KcsA potassium channel. FEBS Lett. 495:191-196.
    • (2001) FEBS Lett. , vol.495 , pp. 191-196
    • Luzhkov, V.B.1    Åqvist, J.2
  • 37
    • 0034257240 scopus 로고    scopus 로고
    • Electrostatics of mesophilic and psychrophilic trypsin isoenzymes: Qualitative evaluation of electrostatic differences at the substrate binding site
    • Gorfe, A. A., B. O. Brandsdal, H. K. Leiros, R. Helland, and A. O. Smalås. 2000. Electrostatics of mesophilic and psychrophilic trypsin isoenzymes: qualitative evaluation of electrostatic differences at the substrate binding site. Proteins. 40:207-217.
    • (2000) Proteins , vol.40 , pp. 207-217
    • Gorfe, A.A.1    Brandsdal, B.O.2    Leiros, H.K.3    Helland, R.4    Smalås, A.O.5
  • 39
    • 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
  • 40
    • 0028810673 scopus 로고
    • Ionizable P1 residues in serine proteinase inhibitors undergo large pK shifts on complex formation
    • Qasim, M. A., M. R. Ranjbar, R. Wynn, S. Anderson, and M. J. Laskowski. 1995. Ionizable P1 residues in serine proteinase inhibitors undergo large pK shifts on complex formation. J. Biol. Chem. 270: 27419-27422.
    • (1995) J. Biol. Chem. , vol.270 , pp. 27419-27422
    • Qasim, M.A.1    Ranjbar, M.R.2    Wynn, R.3    Anderson, S.4    Laskowski, M.J.5
  • 41
    • 0342321950 scopus 로고    scopus 로고
    • Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease
    • Sham, Y. Y., Z. T. Chu, H. Tao, and A. Warshel. 2000. Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease. Proteins. 39:393-407.
    • (2000) Proteins , vol.39 , pp. 393-407
    • Sham, Y.Y.1    Chu, Z.T.2    Tao, H.3    Warshel, A.4


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