메뉴 건너뛰기




Volumn 10, Issue 7, 2014, Pages 2759-2768

Relative binding enthalpies from molecular dynamics simulations using a direct method

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84904110938     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct500200n     Document Type: Article
Times cited : (18)

References (42)
  • 1
    • 77955567116 scopus 로고    scopus 로고
    • Constraining Binding Hot Spots: NMR and Molecular Dynamics Simulations Provide a Structural Explanation for Enthalpy-Entropy Compensation in SH2-Ligand Binding
    • Ward, J. M.; Gorenstein, N. M.; Tian, J.; Martin, S. F.; Post, C. B. Constraining Binding Hot Spots: NMR and Molecular Dynamics Simulations Provide a Structural Explanation for Enthalpy-Entropy Compensation in SH2-Ligand Binding J. Am. Chem. Soc. 2010, 132 (32) 11058-11070
    • (2010) J. Am. Chem. Soc. , vol.132 , Issue.32 , pp. 11058-11070
    • Ward, J.M.1    Gorenstein, N.M.2    Tian, J.3    Martin, S.F.4    Post, C.B.5
  • 3
    • 70349731747 scopus 로고    scopus 로고
    • A Thermodynamic Approach to the Affinity Optimization of Drug Candidates
    • Freire, E. A Thermodynamic Approach to the Affinity Optimization of Drug Candidates Chem. Biol. Drug Des. 2009, 74 (5) 468-472
    • (2009) Chem. Biol. Drug Des. , vol.74 , Issue.5 , pp. 468-472
    • Freire, E.1
  • 4
    • 48249102785 scopus 로고    scopus 로고
    • Calorimetry and Thermodynamics in Drug Design
    • Chaires, J. B. Calorimetry and Thermodynamics in Drug Design Annu. Rev. Biophys. 2008, 37 (1) 135-151
    • (2008) Annu. Rev. Biophys. , vol.37 , Issue.1 , pp. 135-151
    • Chaires, J.B.1
  • 6
    • 84877768087 scopus 로고    scopus 로고
    • Entropy-Enthalpy Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design
    • Chodera, J. D.; Mobley, D. L. Entropy-Enthalpy Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design Annu. Rev. Biophys. 2013, 42 (1) 121-142
    • (2013) Annu. Rev. Biophys. , vol.42 , Issue.1 , pp. 121-142
    • Chodera, J.D.1    Mobley, D.L.2
  • 7
    • 79959243001 scopus 로고    scopus 로고
    • Thermodynamics of Ligand Binding and Efficiency
    • Reynolds, C. H.; Holloway, M. K. Thermodynamics of Ligand Binding and Efficiency ACS Med. Chem. Lett. 2011, 2 (6) 433-437
    • (2011) ACS Med. Chem. Lett. , vol.2 , Issue.6 , pp. 433-437
    • Reynolds, C.H.1    Holloway, M.K.2
  • 8
    • 84870579518 scopus 로고    scopus 로고
    • Entropy-Enthalpy Transduction Caused by Conformational Shifts Can Obscure the Forces Driving Protein-Ligand Binding
    • Fenley, A. T.; Muddana, H. S.; Gilson, M. K. Entropy-Enthalpy Transduction Caused by Conformational Shifts Can Obscure the Forces Driving Protein-Ligand Binding Proc. Natl. Acad. Sci. U.S.A. 2012, 109 (49) 20006-20011
    • (2012) Proc. Natl. Acad. Sci. U.S.A. , vol.109 , Issue.49 , pp. 20006-20011
    • Fenley, A.T.1    Muddana, H.S.2    Gilson, M.K.3
  • 9
    • 0001594721 scopus 로고    scopus 로고
    • Entropy-Enthalpy Compensation in Solvation and Ligand Binding Revisited
    • Gallicchio, E.; Kubo, M. M.; Levy, R. M. Entropy-Enthalpy Compensation in Solvation and Ligand Binding Revisited J. Am. Chem. Soc. 1998, 120 (18) 4526-4527
    • (1998) J. Am. Chem. Soc. , vol.120 , Issue.18 , pp. 4526-4527
    • Gallicchio, E.1    Kubo, M.M.2    Levy, R.M.3
  • 10
    • 28044466911 scopus 로고    scopus 로고
    • Enthalpy-Entropy Compensation is Not a General Feature of Weak Association
    • Ford, D. M. Enthalpy-Entropy Compensation is Not a General Feature of Weak Association J. Am. Chem. Soc. 2005, 127 (46) 16167-16170
    • (2005) J. Am. Chem. Soc. , vol.127 , Issue.46 , pp. 16167-16170
    • Ford, D.M.1
  • 11
    • 70450194691 scopus 로고    scopus 로고
    • Thermodynamic and Structural Effects of Conformational Constraints in Protein-Ligand Interactions. Entropic Paradoxy Associated with Ligand Preorganization
    • DeLorbe, J. E.; Clements, J. H.; Teresk, M. G.; Benfield, A. P.; Plake, H. R.; Millspaugh, L. E.; Martin, S. F. Thermodynamic and Structural Effects of Conformational Constraints in Protein-Ligand Interactions. Entropic Paradoxy Associated with Ligand Preorganization J. Am. Chem. Soc. 2009, 131 (46) 16758-16770
    • (2009) J. Am. Chem. Soc. , vol.131 , Issue.46 , pp. 16758-16770
    • Delorbe, J.E.1    Clements, J.H.2    Teresk, M.G.3    Benfield, A.P.4    Plake, H.R.5    Millspaugh, L.E.6    Martin, S.F.7
  • 12
    • 0036286654 scopus 로고    scopus 로고
    • Free Energy Simulations Come of Age: Protein-Ligand Recognition
    • Simonson, T.; Archontis, G.; Karplus, M. Free Energy Simulations Come of Age: Protein-Ligand Recognition Acc. Chem. Res. 2002, 35 (6) 430-437
    • (2002) Acc. Chem. Res. , vol.35 , Issue.6 , pp. 430-437
    • Simonson, T.1    Archontis, G.2    Karplus, M.3
  • 13
    • 0037008160 scopus 로고    scopus 로고
    • Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors
    • Gohlke, H.; Klebe, G. Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors Angew. Chem., Int. Ed. 2002, 41 (15) 2644-2676
    • (2002) Angew. Chem., Int. Ed. , vol.41 , Issue.15 , pp. 2644-2676
    • Gohlke, H.1    Klebe, G.2
  • 14
    • 0037438567 scopus 로고    scopus 로고
    • Thermodynamics of Protein Folding: A Microscopic View
    • Lazaridis, T.; Karplus, M. Thermodynamics of Protein Folding: A Microscopic View Biophys. Chem. 2003, 100 (1-3) 367-395
    • (2003) Biophys. Chem. , vol.100 , Issue.13 , pp. 367-395
    • Lazaridis, T.1    Karplus, M.2
  • 16
    • 77952390528 scopus 로고    scopus 로고
    • Basic Ingredients of Free Energy Calculations: A Review
    • Christ, C. D.; Mark, A. E.; van Gunsteren, W. F. Basic Ingredients of Free Energy Calculations: A Review J. Comput. Chem. 2010, 31 (8) 1569-1582
    • (2010) J. Comput. Chem. , vol.31 , Issue.8 , pp. 1569-1582
    • Christ, C.D.1    Mark, A.E.2    Van Gunsteren, W.F.3
  • 17
    • 65249124122 scopus 로고    scopus 로고
    • Computations of Standard Binding Free Energies with Molecular Dynamics Simulations
    • Deng, Y.; Roux, B. Computations of Standard Binding Free Energies with Molecular Dynamics Simulations J. Phys. Chem. B 2009, 113 (8) 2234-2246
    • (2009) J. Phys. Chem. B , vol.113 , Issue.8 , pp. 2234-2246
    • Deng, Y.1    Roux, B.2
  • 18
    • 79953109635 scopus 로고    scopus 로고
    • Advances in All Atom Sampling Methods for Modeling Protein-Ligand Binding Affinities
    • Gallicchio, E.; Levy, R. M. Advances in All Atom Sampling Methods for Modeling Protein-Ligand Binding Affinities Curr. Opin. Struct. Biol. 2011, 21 (2) 161-166
    • (2011) Curr. Opin. Struct. Biol. , vol.21 , Issue.2 , pp. 161-166
    • Gallicchio, E.1    Levy, R.M.2
  • 19
    • 84857537331 scopus 로고    scopus 로고
    • Statistical Mechanics and Molecular Dynamics in Evaluating Thermodynamic Properties of Biomolecular Recognition
    • Wereszczynski, J.; McCammon, J. A. Statistical Mechanics and Molecular Dynamics in Evaluating Thermodynamic Properties of Biomolecular Recognition Q. Rev. Biophys. 2012, 45 (01) 1-25
    • (2012) Q. Rev. Biophys. , vol.45 , Issue.1 , pp. 1-25
    • Wereszczynski, J.1    McCammon, J.A.2
  • 20
    • 76649121530 scopus 로고    scopus 로고
    • Dynamical Aspects of Molecular Recognition
    • Karplus, M. Dynamical Aspects of Molecular Recognition J. Mol. Recog. 2010, 23 (2) 102-104
    • (2010) J. Mol. Recog. , vol.23 , Issue.2 , pp. 102-104
    • Karplus, M.1
  • 21
    • 84864261290 scopus 로고    scopus 로고
    • Will Molecular Dynamics Simulations of Proteins Ever Reach Equilibrium?
    • Genheden, S.; Ryde, U. Will Molecular Dynamics Simulations of Proteins Ever Reach Equilibrium? Phys. Chem. Chem. Phys. 2012, 14 (24) 8662-8677
    • (2012) Phys. Chem. Chem. Phys. , vol.14 , Issue.24 , pp. 8662-8677
    • Genheden, S.1    Ryde, U.2
  • 22
    • 0032233055 scopus 로고    scopus 로고
    • Computer Simulations with Explicit Solvent: Recent Progress in the Thermodynamic Decomposition of Free Energies and in Modeling Electrostatic Effects
    • Levy, R. M.; Gallicchio, E. Computer Simulations with Explicit Solvent: Recent Progress in the Thermodynamic Decomposition of Free Energies and in Modeling Electrostatic Effects Annu. Rev. Phys. Chem. 1998, 49, 531-567
    • (1998) Annu. Rev. Phys. Chem. , vol.49 , pp. 531-567
    • Levy, R.M.1    Gallicchio, E.2
  • 23
    • 0038001529 scopus 로고    scopus 로고
    • Staging Is More Important than Perturbation Method for Computation of Enthalpy and Entropy Changes in Complex Systems
    • Lu, N.; Kofke, D. A.; Woolf, T. B. Staging Is More Important than Perturbation Method for Computation of Enthalpy and Entropy Changes in Complex Systems J. Phys. Chem. B 2003, 107 (23) 5598-5611
    • (2003) J. Phys. Chem. B , vol.107 , Issue.23 , pp. 5598-5611
    • Lu, N.1    Kofke, D.A.2    Woolf, T.B.3
  • 24
    • 77956583186 scopus 로고    scopus 로고
    • How Can Hydrophobic Association Be Enthalpy Driven?
    • Setny, P.; Baron, R.; McCammon, J. A. How Can Hydrophobic Association Be Enthalpy Driven? J. Chem. Theory Comput. 2010, 6 (9) 2866-2871
    • (2010) J. Chem. Theory Comput. , vol.6 , Issue.9 , pp. 2866-2871
    • Setny, P.1    Baron, R.2    McCammon, J.A.3
  • 25
    • 84856860496 scopus 로고    scopus 로고
    • Probing the Effect of Conformational Constraint on Phosphorylated Ligand Binding to an SH2 Domain Using Polarizable Force Field Simulations
    • Shi, Y.; Zhu, C. Z.; Martin, S. F.; Ren, P. Probing the Effect of Conformational Constraint on Phosphorylated Ligand Binding to an SH2 Domain Using Polarizable Force Field Simulations J. Phys. Chem. B 2012, 116 (5) 1716-1727
    • (2012) J. Phys. Chem. B , vol.116 , Issue.5 , pp. 1716-1727
    • Shi, Y.1    Zhu, C.Z.2    Martin, S.F.3    Ren, P.4
  • 26
    • 10844229225 scopus 로고    scopus 로고
    • Calculation of the Aqueous Solvation Energy and Entropy, as Well as Free Energy, of Simple Polar Solutes
    • Wan, S.; Stote, R. H.; Karplus, M. Calculation of the Aqueous Solvation Energy and Entropy, as Well as Free Energy, Of Simple Polar Solutes J. Chem. Phys. 2004, 121 (19) 9539-9548
    • (2004) J. Chem. Phys. , vol.121 , Issue.19 , pp. 9539-9548
    • Wan, S.1    Stote, R.H.2    Karplus, M.3
  • 27
    • 0031553195 scopus 로고    scopus 로고
    • Thermodynamic Decomposition of Hydration Free Energies by Computer Simulation: Application to Amines, Oxides, and Sulfides
    • Kubo, M. M.; Gallicchio, E.; Levy, R. M. Thermodynamic Decomposition of Hydration Free Energies by Computer Simulation: Application to Amines, Oxides, and Sulfides J. Phys. Chem. B 1997, 101 (49) 10527-10534
    • (1997) J. Phys. Chem. B , vol.101 , Issue.49 , pp. 10527-10534
    • Kubo, M.M.1    Gallicchio, E.2    Levy, R.M.3
  • 28
    • 0034598017 scopus 로고    scopus 로고
    • Use of 1,2,3-Trisubstituted Cyclopropanes As Conformationally Constrained Peptide Mimics in SH2 Antagonists
    • Davidson, J. P.; Martin, S. F. Use of 1,2,3-Trisubstituted Cyclopropanes As Conformationally Constrained Peptide Mimics in SH2 Antagonists Tetrahedron Lett. 2000, 41 (49) 9459-9464
    • (2000) Tetrahedron Lett. , vol.41 , Issue.49 , pp. 9459-9464
    • Davidson, J.P.1    Martin, S.F.2
  • 29
    • 0037116524 scopus 로고    scopus 로고
    • Calorimetric and Structural Studies of 1,2,3-Trisubstituted Cyclopropanes As Conformationally Constrained Peptide Inhibitors of Src SH2 Domain Binding
    • Davidson, J. P.; Lubman, O.; Rose, T.; Waksman, G.; Martin, S. F. Calorimetric and Structural Studies of 1,2,3-Trisubstituted Cyclopropanes As Conformationally Constrained Peptide Inhibitors of Src SH2 Domain Binding J. Am. Chem. Soc. 2002, 124 (2) 205-215
    • (2002) J. Am. Chem. Soc. , vol.124 , Issue.2 , pp. 205-215
    • Davidson, J.P.1    Lubman, O.2    Rose, T.3    Waksman, G.4    Martin, S.F.5
  • 30
    • 0027409064 scopus 로고
    • Binding of a High Affinity Phosphotyrosyl Peptide to the Src SH2 Domain: Crystal Structures of the Complexed and Peptide-Free Forms
    • Waksman, G.; Shoelson, S. E.; Pant, N.; Cowburn, D.; Kuriyan, J. Binding of a High Affinity Phosphotyrosyl Peptide to the Src SH2 Domain: Crystal Structures of the Complexed and Peptide-Free Forms Cell 1993, 72 (5) 779-790
    • (1993) Cell , vol.72 , Issue.5 , pp. 779-790
    • Waksman, G.1    Shoelson, S.E.2    Pant, N.3    Cowburn, D.4    Kuriyan, J.5
  • 34
    • 1642576012 scopus 로고    scopus 로고
    • Improved Treatment of the Protein Backbone in Empirical Force Fields
    • MacKerell, A. D.; Feig, M.; Brooks, C. L. Improved Treatment of the Protein Backbone in Empirical Force Fields J. Am. Chem. Soc. 2004, 126 (3) 698-699
    • (2004) J. Am. Chem. Soc. , vol.126 , Issue.3 , pp. 698-699
    • MacKerell, A.D.1    Feig, M.2    Brooks, C.L.3
  • 35
    • 0031910020 scopus 로고    scopus 로고
    • Locally Accessible Conformations of Proteins: Multiple Molecular Dynamics Simulations of Crambin
    • Caves, L. S. D.; Evanseck, J. D.; Karplus, M. Locally Accessible Conformations of Proteins: Multiple Molecular Dynamics Simulations of Crambin Protein Sci. 1998, 7 (3) 649-666
    • (1998) Protein Sci. , vol.7 , Issue.3 , pp. 649-666
    • Caves, L.S.D.1    Evanseck, J.D.2    Karplus, M.3
  • 36
    • 47149107224 scopus 로고    scopus 로고
    • Molecular Simulation of Multistate Peptide Dynamics: A Comparison between Microsecond Timescale Sampling and Multiple Shorter Trajectories
    • Monticelli, L.; Sorin, E. J.; Tieleman, D. P.; Pande, V. S.; Colombo, G. Molecular Simulation of Multistate Peptide Dynamics: A Comparison between Microsecond Timescale Sampling and Multiple Shorter Trajectories J. Comput. Chem. 2008, 29 (11) 1740-1752
    • (2008) J. Comput. Chem. , vol.29 , Issue.11 , pp. 1740-1752
    • Monticelli, L.1    Sorin, E.J.2    Tieleman, D.P.3    Pande, V.S.4    Colombo, G.5
  • 37
    • 76249085850 scopus 로고    scopus 로고
    • How to Obtain Statistically Converged MM/GBSA Results
    • Genheden, S.; Ryde, U. How to Obtain Statistically Converged MM/GBSA Results J. Comput. Chem. 2010, 31 (4) 837-846
    • (2010) J. Comput. Chem. , vol.31 , Issue.4 , pp. 837-846
    • Genheden, S.1    Ryde, U.2
  • 38
    • 69349101503 scopus 로고    scopus 로고
    • Quantifying Uncertainty and Sampling Quality in Biomolecular Simulations
    • Ralph, A. W. Elsevier: New York, Ch. 2
    • Grossfield, A.; Zuckerman, D. M. Quantifying Uncertainty and Sampling Quality in Biomolecular Simulations. In Ann. Rep. Comput. Chem., Ralph, A. W., Ed.; Elsevier: New York, 2009; Vol. 5, Ch. 2, pp 23-48.
    • (2009) Ann. Rep. Comput. Chem. , vol.5 , pp. 23-48
    • Grossfield, A.1    Zuckerman, D.M.2
  • 39
    • 0001616080 scopus 로고    scopus 로고
    • Replica-Exchange Molecular Dynamics Method for Protein Folding
    • Sugita, Y.; Okamoto, Y. Replica-Exchange Molecular Dynamics Method for Protein Folding Chem. Phys. Lett. 1999, 314 (1-2) 141-151
    • (1999) Chem. Phys. Lett. , vol.314 , Issue.12 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 40
    • 37649014404 scopus 로고    scopus 로고
    • On Searching in, Sampling of, and Dynamically Moving through Conformational Space of Biomolecular Systems: A Review
    • Christen, M.; van Gunsteren, W. F. On Searching in, Sampling of, and Dynamically Moving through Conformational Space of Biomolecular Systems: A Review J. Comput. Chem. 2008, 29 (2) 157-166
    • (2008) J. Comput. Chem. , vol.29 , Issue.2 , pp. 157-166
    • Christen, M.1    Van Gunsteren, W.F.2
  • 41
    • 84964203940 scopus 로고
    • Bootstrap Methods for Standard Errors, Confidence Intervals, and Other Measures of Statistical Accuracy
    • Efron, B.; Tibshirani, R. Bootstrap Methods for Standard Errors, Confidence Intervals, and Other Measures of Statistical Accuracy Stat. Sci. 1986, 1 (1) 54-75
    • (1986) Stat. Sci. , vol.1 , Issue.1 , pp. 54-75
    • Efron, B.1    Tibshirani, R.2
  • 42
    • 0027972206 scopus 로고
    • Dynamics in Rugged Energy Landscapes with Applications to the S-Peptide and Ribonuclease A
    • Straub, J. E.; Rashkin, A. B.; Thirumalai, D. Dynamics in Rugged Energy Landscapes with Applications to the S-Peptide and Ribonuclease A J. Am. Chem. Soc. 1994, 116 (5) 2049-2063
    • (1994) J. Am. Chem. Soc. , vol.116 , Issue.5 , pp. 2049
    • Straub, J.E.1    Rashkin, A.B.2    Thirumalai, D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.