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Volumn 35, Issue 6, 2002, Pages 430-437

Free energy simulations come of age: Protein-ligand recognition

Author keywords

[No Author keywords available]

Indexed keywords

ASPARTIC ACID TRANSFER RNA; LIGAND; PROTEIN; SYNTHETASE;

EID: 0036286654     PISSN: 00014842     EISSN: None     Source Type: Journal    
DOI: 10.1021/ar010030m     Document Type: Article
Times cited : (353)

References (86)
  • 1
    • 0027321958 scopus 로고
    • Absolute and relative binding free energy calculations of the interaction of biotin and its analogues with streptavidin using molecular dynamics/free energy perturbation approaches
    • (1993) Proteins , vol.16 , pp. 226-245
    • Miyamoto, S.1    Kollman, P.2
  • 6
    • 0029151245 scopus 로고
    • First principles calculation of the folding free energy of a three helix bundle protein
    • (1995) Science , vol.269 , pp. 393-396
    • Boczko, E.M.1    Brooks, C.L.2
  • 11
    • 7044239742 scopus 로고
    • Free energy calculations: Applications to chemical and biochemical phenomena
    • (1993) Chem. Rev. , vol.93 , pp. 2395
    • Kollman, P.1
  • 18
    • 0028354926 scopus 로고
    • Molecular recognition in proteins. Simulation analysis of substrate binding by a tyrosyl-tRNA synthetase mutant
    • (1994) J. Mol. Biol. , vol.236 , pp. 1049-1066
    • Lau, F.1    Karplus, M.2
  • 21
    • 0029757992 scopus 로고    scopus 로고
    • Thermodynamic stability of water molecules in the Bacteriorhodopsin proton channel: A molecular dynamics and free energy perturbation study
    • (1996) Biophys. J. , vol.71 , pp. 670-681
    • Roux, B.1    Nina, M.2    Pomes, R.3    Smith, J.4
  • 22
    • 0030887944 scopus 로고    scopus 로고
    • Inclusion of loss of translational and rotational freedom in theoretical estimates of free energies of binding. Application to a complex of benzene and mutant T4 lysozyme
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 2702-2714
    • Hermans, J.1    Wang, L.2
  • 26
    • 0029623184 scopus 로고
    • Computational methods to predict binding free energy in ligand-receptor complexes
    • (1995) J. Med. Chem. , vol.38 , pp. 49534967
    • Ajai1    Murcko, M.2
  • 31
    • 0032189032 scopus 로고    scopus 로고
    • Calculation of HyHel10-lysozyme binding free energy changes: Effect of ten point mutations
    • (1998) Proteins , vol.33 , pp. 39-48
    • Sharp, K.1
  • 32
    • 0032789936 scopus 로고    scopus 로고
    • Electrostatic interactions in the GCN4 leucine zipper: Substantial contributions arise from intramolecular interactions enhanced on binding
    • (1999) Protein Sci. , vol.8 , pp. 1381-1392
    • Hendsch, Z.1    Tidor, B.2
  • 35
    • 0034225199 scopus 로고    scopus 로고
    • Electrostatic free energy calculations for macromolecule: A hybrid molecular dynamics/continuum electrostatics approach
    • (2000) J. Phys. Chem. B , vol.104 , pp. 6509-6513
    • Simonson, T.1
  • 36
    • 0035895423 scopus 로고    scopus 로고
    • Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase
    • (2001) J. Mol. Biol. , vol.306 , pp. 307-327
    • Archontis, G.1    Simonson, T.2    Karplus, M.3
  • 42
    • 0034320964 scopus 로고    scopus 로고
    • Free energy perturbation calculations of DNA destabilization by base substitutions: The effect of neutral guanine-thymine, adenine-cytosine, and adenine-difluorotoluene mismatches
    • (2000) J. Phys. Chem. B , vol.104 , pp. 10092-10099
    • Florian, J.1    Goodman, M.2    Warshel, A.3
  • 45
    • 0000115004 scopus 로고
    • A local reaction field method for fast evaluation of long range interactions in molecular simulations
    • (1992) J. Chem. Phys. , vol.95 , pp. 4366-4377
    • Lee, F.1    Warshel, A.2
  • 49
    • 0035823823 scopus 로고    scopus 로고
    • Dielectric relaxation in an enzyme active site: Molecular dynamics simulations intepreted with a macroscopic continuum model
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 11047-11056
    • Archontis, G.1    Simonson, T.2
  • 52
    • 84872607890 scopus 로고
    • Free energy of particle insertion an exact analysis of the origin singularity for simple liquids
    • (1993) Mol. Phys. , vol.80 , pp. 441-447
    • Simonson, T.1
  • 57
    • 0029584358 scopus 로고
    • The meaning of component analysis: Decomposition of the free energy in terms of specific interactions
    • (1995) J. Mol. Biol. , vol.254 , pp. 801-807
    • Boresch, S.1    Karplus, M.2
  • 60
    • 16444377080 scopus 로고    scopus 로고
    • The role of bonded terms in free energy simulations. 2. Calculation of their in influence on free energy differences of solvation
    • (1999) J. Phys. Chem. A , vol.103 , pp. 119-136
    • Boresch, S.1    Karplus, M.2
  • 61
    • 0032958585 scopus 로고    scopus 로고
    • Energetic analysis of an antibody/antigeninterface: Alanine scanning mutagenesis and double mutant cycles on the HyHEL-10/lysozyme interaction
    • (1999) Protein Sci. , vol.8 , pp. 958-968
    • Pons, J.1    Rajpal, A.2    Kirsch, J.3
  • 62
    • 0030322783 scopus 로고    scopus 로고
    • Double-mutant cycles: A powerful tool for analyzing protein structure and function
    • (1996) Folding Des. , vol.1
    • Horovitz, A.1
  • 63
    • 0034868445 scopus 로고    scopus 로고
    • NMR relaxation studies of the role of conformational entropy on protein stability and ligand binding
    • (2001) Acc. Chem. Res. , vol.34 , pp. 379-388
    • Stone, M.1
  • 64
    • 0034703701 scopus 로고    scopus 로고
    • Dissection of binding energy with native and ligand-bound protein stabilities: Determining the affinity of ultratight-binding inhibitors of HIV-1 protease and its drug-resistant mutants
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 11533-11534
    • Xie, D.1    Gulnick, S.2    Erickson, J.3
  • 66
    • 0026641163 scopus 로고
    • Thermodynamics of protein-peptide binding in the ribonuclease s system studied by molecular dynamics and free energy calculations
    • (1992) Biochemistry , vol.31 , pp. 8661-8674
    • Simonson, T.1    Brünger, A.T.2
  • 68
    • 0009517080 scopus 로고    scopus 로고
    • What are the dielectric "constants" of proteins and how to validate electrostatic models?
    • (2001) Proteins , vol.8 , pp. 211-217
    • Schutz, C.1    Warshel, A.2
  • 71
    • 0033568644 scopus 로고    scopus 로고
    • Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 8133-8143
    • Massova, I.1    Kollman, P.2
  • 72
    • 0028916760 scopus 로고
    • pH dependence of binding reactions from free energy simulations and macroscopic continuum electrostatics calculations: Application to the 2′GMP/3′GMP binding to Ribonuclease T1 and implications for catalysis
    • (1995) J. Mol. Biol. , vol.247 , pp. 774-807
    • Mackerell, A.1    Sommer, M.2    Karplus, M.3
  • 73
    • 0000174762 scopus 로고    scopus 로고
    • Multiple-site ligand binding to flexible macromolecules: Separation of global and local conformational change and an iterativemobile clustering approach
    • (1999) J. Comput. Chem. , vol.20 , pp. 1091-1111
    • Spassov, V.1    Bashford, D.2
  • 76
    • 0031872292 scopus 로고    scopus 로고
    • Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with explicit solvent and an implicit solvent continuum model
    • (1998) Proteins , vol.32 , pp. 399-413
    • Vorobjev, Y.1    Almagro, J.2    Hermans, J.3
  • 81
    • 0033532905 scopus 로고    scopus 로고
    • Hydrophobic force field as a molecular alternative to surface area models
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 6299-6305
    • Hummer, G.1


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