메뉴 건너뛰기




Volumn 117, Issue 25, 2013, Pages 7535-7545

Dissociation free-energy profiles of specific and nonspecific DNA-protein complexes

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; DNA; FREE ENERGY; MOLECULAR DYNAMICS; PROTEINS;

EID: 84879579060     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp402664w     Document Type: Article
Times cited : (17)

References (62)
  • 2
    • 65549171477 scopus 로고    scopus 로고
    • An End to 40 Years of Mistakes in DNA-Protein Association Kinetics?
    • Halford, S. E. An End to 40 Years of Mistakes in DNA-Protein Association Kinetics? Biochem. Soc. Trans. 2009, 37, 343-348
    • (2009) Biochem. Soc. Trans. , vol.37 , pp. 343-348
    • Halford, S.E.1
  • 3
    • 3042579602 scopus 로고    scopus 로고
    • How Do Site-Specific DNA-Binding Proteins Find Their Targets?
    • Halford, S. E.; Marko, J. F. How Do Site-Specific DNA-Binding Proteins Find Their Targets? Nucleic Acids Res. 2004, 32, 3040-3052
    • (2004) Nucleic Acids Res. , vol.32 , pp. 3040-3052
    • Halford, S.E.1    Marko, J.F.2
  • 4
    • 84861775142 scopus 로고    scopus 로고
    • Towards a Molecular View of Transcriptional Control
    • Zakrzewska, K.; Lavery, R. Towards a Molecular View of Transcriptional Control Curr. Opin. Struct. Biol. 2012, 22, 160-167
    • (2012) Curr. Opin. Struct. Biol. , vol.22 , pp. 160-167
    • Zakrzewska, K.1    Lavery, R.2
  • 5
    • 0014945567 scopus 로고
    • The Lac Repressor-Operator Interaction. 3. Kinetic Studies
    • Riggs, A. D.; Bourgeois, S.; Cohn, M. The Lac Repressor-Operator Interaction. 3. Kinetic Studies J. Mol. Biol. 1970, 53, 401-417
    • (1970) J. Mol. Biol. , vol.53 , pp. 401-417
    • Riggs, A.D.1    Bourgeois, S.2    Cohn, M.3
  • 6
    • 0024531901 scopus 로고
    • Facilitated Target Location in Biological Systems
    • von Hippel, P. H.; Berg, O. G. Facilitated Target Location in Biological Systems J. Biol. Chem. 1989, 264, 675-678
    • (1989) J. Biol. Chem. , vol.264 , pp. 675-678
    • Von Hippel, P.H.1    Berg, O.G.2
  • 8
    • 4344581629 scopus 로고    scopus 로고
    • Toward an Integrated Model of Protein-DNA Recognition as Inferred from NMR Studies on the Lac Repressor System
    • Kalodimos, C. G.; Boelens, R.; Kaptein, R. Toward an Integrated Model of Protein-DNA Recognition as Inferred from NMR Studies on the Lac Repressor System Chem. Rev. 2004, 104, 3567-3586
    • (2004) Chem. Rev. , vol.104 , pp. 3567-3586
    • Kalodimos, C.G.1    Boelens, R.2    Kaptein, R.3
  • 9
    • 0037124326 scopus 로고    scopus 로고
    • Plasticity in Protein-DNA Recognition: Lac Repressor Interacts with Its Natural Operator O1 Through Alternative Conformations of Its DNA-Binding Domain
    • Kalodimos, C. G.; Bonvin, A. M. J. J.; Salinas, R. K.; Wechselberger, R.; Boelens, R.; Kaptein, R. Plasticity in Protein-DNA Recognition: Lac Repressor Interacts with Its Natural Operator O1 Through Alternative Conformations of Its DNA-Binding Domain EMBO J. 2002, 21, 2866-2876
    • (2002) EMBO J. , vol.21 , pp. 2866-2876
    • Kalodimos, C.G.1    Bonvin, A.M.J.J.2    Salinas, R.K.3    Wechselberger, R.4    Boelens, R.5    Kaptein, R.6
  • 11
    • 0033634983 scopus 로고    scopus 로고
    • Structure of BamHI Bound to Nonspecific DNA: A Model for DNA Sliding
    • Viadiu, H.; Aggarwal, A. K. Structure of BamHI Bound to Nonspecific DNA: A Model for DNA Sliding Mol. Cell 2000, 5, 889-895
    • (2000) Mol. Cell , vol.5 , pp. 889-895
    • Viadiu, H.1    Aggarwal, A.K.2
  • 12
    • 33646356250 scopus 로고    scopus 로고
    • Detecting Transient Intermediates in Macromolecular Binding by Paramagnetic NMR
    • Iwahara, J.; Clore, G. M. Detecting Transient Intermediates in Macromolecular Binding by Paramagnetic NMR Nature 2006, 440, 1227-1230
    • (2006) Nature , vol.440 , pp. 1227-1230
    • Iwahara, J.1    Clore, G.M.2
  • 13
    • 33750078971 scopus 로고    scopus 로고
    • NMR Structural and Kinetic Characterization of a Homeodomain Diffusing and Hopping on Nonspecific DNA
    • Iwahara, J.; Zweckstetter, M.; Clore, G. M. NMR Structural and Kinetic Characterization of a Homeodomain Diffusing and Hopping on Nonspecific DNA Proc. Natl. Acad. Sci. U. S. A. 2006, 103, 15062-15067
    • (2006) Proc. Natl. Acad. Sci. U. S. A. , vol.103 , pp. 15062-15067
    • Iwahara, J.1    Zweckstetter, M.2    Clore, G.M.3
  • 15
    • 0036182617 scopus 로고    scopus 로고
    • A Residue-Specific View of the Association and Dissociation Pathway in Protein-DNA Recognition
    • Kalodimos, C. G.; Boelens, R.; Kaptein, R. A Residue-Specific View of the Association and Dissociation Pathway in Protein-DNA Recognition Nat. Struct. Biol. 2002, 9, 193-197
    • (2002) Nat. Struct. Biol. , vol.9 , pp. 193-197
    • Kalodimos, C.G.1    Boelens, R.2    Kaptein, R.3
  • 17
    • 10044223573 scopus 로고    scopus 로고
    • Kinetics of Protein-DNA Interaction: Facilitated Target Location in Sequence-Dependent Potential
    • Slutsky, M.; Mirny, L. A. Kinetics of Protein-DNA Interaction: Facilitated Target Location in Sequence-Dependent Potential Biophys. J. 2004, 87, 4021-4035
    • (2004) Biophys. J. , vol.87 , pp. 4021-4035
    • Slutsky, M.1    Mirny, L.A.2
  • 18
    • 77649111696 scopus 로고    scopus 로고
    • Insights into the Sliding Movement of the Lac Repressor Nonspecifically Bound to DNA
    • Furini, S.; Domene, C.; Cavalcanti, S. Insights into the Sliding Movement of the Lac Repressor Nonspecifically Bound to DNA J. Phys. Chem. B 2010, 114, 2238-2245
    • (2010) J. Phys. Chem. B , vol.114 , pp. 2238-2245
    • Furini, S.1    Domene, C.2    Cavalcanti, S.3
  • 19
    • 67651232308 scopus 로고    scopus 로고
    • A Free Energy Pathway for the Interaction of the SRY Protein with Its Binding Site on DNA from Atomistic Simulations
    • Bouvier, B.; Lavery, R. A Free Energy Pathway for the Interaction of the SRY Protein with Its Binding Site on DNA from Atomistic Simulations J. Am. Chem. Soc. 2009, 131, 9864-9865
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 9864-9865
    • Bouvier, B.1    Lavery, R.2
  • 20
    • 54549100470 scopus 로고    scopus 로고
    • Dissociation of Minor Groove Binders from DNA: Insights from Metadynamics Simulations
    • Vargiu, A. V.; Ruggerone, P.; Magistrato, A.; Carloni, P. Dissociation of Minor Groove Binders from DNA: Insights from Metadynamics Simulations Nucleic Acids Res. 2008, 36, 5910-5921
    • (2008) Nucleic Acids Res. , vol.36 , pp. 5910-5921
    • Vargiu, A.V.1    Ruggerone, P.2    Magistrato, A.3    Carloni, P.4
  • 21
    • 48249123805 scopus 로고    scopus 로고
    • On the Molecular Mechanism of Drug Intercalation into DNA: A Simulation Study of the Intercalation Pathway, Free Energy, and DNA Structural Changes
    • Mukherjee, A.; Lavery, R.; Bagchi, B.; Hynes, J. T. On the Molecular Mechanism of Drug Intercalation into DNA: A Simulation Study of the Intercalation Pathway, Free Energy, and DNA Structural Changes J. Am. Chem. Soc. 2008, 130, 9747-9755
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 9747-9755
    • Mukherjee, A.1    Lavery, R.2    Bagchi, B.3    Hynes, J.T.4
  • 22
    • 18744391399 scopus 로고    scopus 로고
    • Structural Dynamics of the Lac Repressor-DNA Complex Revealed by a Multiscale Simulation
    • Villa, E.; Balaeff, A.; Schulten, K. Structural Dynamics of the Lac Repressor-DNA Complex Revealed by a Multiscale Simulation Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 6783-6788
    • (2005) Proc. Natl. Acad. Sci. U. S. A. , vol.102 , pp. 6783-6788
    • Villa, E.1    Balaeff, A.2    Schulten, K.3
  • 24
    • 0035935802 scopus 로고    scopus 로고
    • Calculating Free Energies Using Average Force
    • Darve, E.; Pohorille, A. Calculating Free Energies Using Average Force J. Chem. Phys. 2001, 115, 9169-9183
    • (2001) J. Chem. Phys. , vol.115 , pp. 9169-9183
    • Darve, E.1    Pohorille, A.2
  • 25
    • 42149194240 scopus 로고    scopus 로고
    • Adaptive Biasing Force Method for Scalar and Vector Free Energy Calculations
    • Darve, E.; Rodríguez-Gómez, D.; Pohorille, A. Adaptive Biasing Force Method for Scalar and Vector Free Energy Calculations J. Chem. Phys. 2008, 128, 144120
    • (2008) J. Chem. Phys. , vol.128 , pp. 144120
    • Darve, E.1    Rodríguez-Gómez, D.2    Pohorille, A.3
  • 26
    • 0035933104 scopus 로고    scopus 로고
    • Strong DNA Binding by Covalently Linked Dimeric Lac Headpiece: Evidence for the Crucial Role of the Hinge Helices
    • Kalodimos, C. G.; Folkers, G. E.; Boelens, R.; Kaptein, R. Strong DNA Binding by Covalently Linked Dimeric Lac Headpiece: Evidence for the Crucial Role of the Hinge Helices Proc. Natl. Acad. Sci. U. S. A. 2001, 98, 6039-6044
    • (2001) Proc. Natl. Acad. Sci. U. S. A. , vol.98 , pp. 6039-6044
    • Kalodimos, C.G.1    Folkers, G.E.2    Boelens, R.3    Kaptein, R.4
  • 27
    • 33748518255 scopus 로고    scopus 로고
    • Comparison of Multiple Amber Force Fields and Development of Improved Protein Backbone Parameters
    • Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of Multiple Amber Force Fields and Development of Improved Protein Backbone Parameters Proteins 2006, 65, 712-725
    • (2006) Proteins , vol.65 , pp. 712-725
    • Hornak, V.1    Abel, R.2    Okur, A.3    Strockbine, B.4    Roitberg, A.5    Simmerling, C.6
  • 28
    • 34250318638 scopus 로고    scopus 로고
    • Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers
    • Pérez, A.; Marchán, I.; Svozil, D.; Sponer, J.; Cheatham, T. E., III; Laughton, C. A.; Orozco, M. Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers Biophys. J. 2007, 92, 3817-3829
    • (2007) Biophys. J. , vol.92 , pp. 3817-3829
    • Pérez, A.1    Marchán, I.2    Svozil, D.3    Sponer, J.4    Cheatham Iii, T.E.5    Laughton, C.A.6    Orozco, M.7
  • 32
    • 33846823909 scopus 로고
    • Particle Mesh Ewald-An N·log(N) Method for Ewald Sums in Large Systems
    • Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald-an N·log(N) Method for Ewald Sums in Large Systems J. Chem. Phys. 1993, 98, 10089-10092
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 33
    • 79960041673 scopus 로고    scopus 로고
    • A Free-Energy Landscape for Coupled Folding and Binding of an Intrinsically Disordered Protein in Explicit Solvent from Detailed All-Atom Computations
    • Higo, J.; Nishimura, Y.; Nakamura, H. A Free-Energy Landscape for Coupled Folding and Binding of an Intrinsically Disordered Protein in Explicit Solvent from Detailed All-Atom Computations J. Am. Chem. Soc. 2011, 133, 10448-10458
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 10448-10458
    • Higo, J.1    Nishimura, Y.2    Nakamura, H.3
  • 34
    • 77950102787 scopus 로고    scopus 로고
    • Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables
    • Hénin, J.; Fiorin, G.; Chipot, C.; Klein, M. L. Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables J. Chem. Theory Comput. 2010, 6, 35-47
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 35-47
    • Hénin, J.1    Fiorin, G.2    Chipot, C.3    Klein, M.L.4
  • 35
    • 34548645722 scopus 로고    scopus 로고
    • Secondary and Tertiary Structure Elasticity of Titin Z1Z2 and a Titin Chain Model
    • Lee, E. H.; Hsin, J.; Mayans, O.; Schulten, K. Secondary and Tertiary Structure Elasticity of Titin Z1Z2 and a Titin Chain Model Biophys. J. 2007, 93, 1719-1735
    • (2007) Biophys. J. , vol.93 , pp. 1719-1735
    • Lee, E.H.1    Hsin, J.2    Mayans, O.3    Schulten, K.4
  • 36
    • 20444499328 scopus 로고    scopus 로고
    • Insights into the Recognition and Association of Transmembrane α-Helices. The Free Energy of α-Helix Dimerization in Glycophorin A
    • Hénin, J.; Pohorille, A.; Chipot, C. Insights into the Recognition and Association of Transmembrane α-Helices. The Free Energy of α-Helix Dimerization in Glycophorin A J. Am. Chem. Soc. 2005, 127, 8478-8484
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 8478-8484
    • Hénin, J.1    Pohorille, A.2    Chipot, C.3
  • 37
    • 65649099114 scopus 로고    scopus 로고
    • Building a Foundation for Structure-Based Cellulosome Design for Cellulosic Ethanol: Insight into Cohesin-Dockerin Complexation from Computer Simulation
    • Xu, J.; Crowley, M. F.; Smith, J. C. Building a Foundation for Structure-Based Cellulosome Design for Cellulosic Ethanol: Insight into Cohesin-Dockerin Complexation from Computer Simulation Protein Sci. 2009, 18, 949-959
    • (2009) Protein Sci. , vol.18 , pp. 949-959
    • Xu, J.1    Crowley, M.F.2    Smith, J.C.3
  • 39
    • 0029910813 scopus 로고    scopus 로고
    • Differences in Water Release for the Binding of EcoRI to Specific and Nonspecific DNA Sequences
    • Sidorova, N. Y.; Rau, D. C. Differences in Water Release for the Binding of EcoRI to Specific and Nonspecific DNA Sequences Proc. Natl. Acad. Sci. U. S. A. 1996, 93, 12272-12277
    • (1996) Proc. Natl. Acad. Sci. U. S. A. , vol.93 , pp. 12272-12277
    • Sidorova, N.Y.1    Rau, D.C.2
  • 40
    • 0027338124 scopus 로고
    • 31P Nuclear Magnetic Resonance Spectra and Dissociation Constants of Lac Repressor Headpiece Duplex Operator Complexes: The Importance of Phosphate Ester Backbone Flexibility in Protein-DNA Recognition
    • Botuyan, M. V.; Keire, D. A.; Kroen, C.; Gorenstein, D. G. 31P Nuclear Magnetic Resonance Spectra and Dissociation Constants of Lac Repressor Headpiece Duplex Operator Complexes: The Importance of Phosphate Ester Backbone Flexibility in Protein-DNA Recognition Biochemistry 1993, 32, 6863-6874
    • (1993) Biochemistry , vol.32 , pp. 6863-6874
    • Botuyan, M.V.1    Keire, D.A.2    Kroen, C.3    Gorenstein, D.G.4
  • 41
    • 0026498015 scopus 로고
    • Thermodynamic Stoichiometries of Participation of Water, Cations and Anions in Specific and Non-Specific Binding of Lac Repressor to DNA
    • Ha, J.-H.; Capp, M. W.; Hohenwalter, M. D.; Baskerville, M.; Record, M. T., Jr. Thermodynamic Stoichiometries of Participation of Water, Cations and Anions in Specific and Non-Specific Binding of Lac Repressor to DNA J. Mol. Biol. 1992, 228, 252-264
    • (1992) J. Mol. Biol. , vol.228 , pp. 252-264
    • Ha, J.-H.1    Capp, M.W.2    Hohenwalter, M.D.3    Baskerville, M.4    Record, Jr.M.T.5
  • 42
    • 2042475515 scopus 로고
    • Nonspecific DNA Binding of Genome-Regulating Proteins as a Biological Control Mechanism: Measurement of DNA-Bound Escherichia Coli Lac Repressor in Vivo
    • Kao-Huang, Y.; Revzin, A.; Butler, A. P.; O'Conner, P.; Noble, D. W.; von Hippel, P. H. Nonspecific DNA Binding of Genome-Regulating Proteins as a Biological Control Mechanism: Measurement of DNA-Bound Escherichia Coli Lac Repressor in Vivo Proc. Natl. Acad. Sci. U. S. A. 1977, 74, 4228-4232
    • (1977) Proc. Natl. Acad. Sci. U. S. A. , vol.74 , pp. 4228-4232
    • Kao-Huang, Y.1    Revzin, A.2    Butler, A.P.3    O'Conner, P.4    Noble, D.W.5    Von Hippel, P.H.6
  • 43
    • 0031576995 scopus 로고    scopus 로고
    • Thermodynamics of the Interactions of Lac Repressor with Variants of the Symmetric Lac Operator: Effects of Converting a Consensus Site to a Nonspecific Site
    • Frank, D. E.; Saecker, R. M.; Bond, J. P.; Capp, M. W.; Tsodikov, O. V.; Melcher, S. E.; Levandoski, M. M.; Record, M. T., Jr. Thermodynamics of the Interactions of Lac Repressor with Variants of the Symmetric Lac Operator: Effects of Converting a Consensus Site to a Nonspecific Site J. Mol. Biol. 1997, 267, 1186-1206
    • (1997) J. Mol. Biol. , vol.267 , pp. 1186-1206
    • Frank, D.E.1    Saecker, R.M.2    Bond, J.P.3    Capp, M.W.4    Tsodikov, O.V.5    Melcher, S.E.6    Levandoski, M.M.7    Record, Jr.M.T.8
  • 45
    • 77949320402 scopus 로고    scopus 로고
    • Searching DNA via a "monkey Bar" Mechanism: The Significance of Disordered Tails
    • Vuzman, D.; Azia, A.; Levy, Y. Searching DNA via a "Monkey Bar" Mechanism: The Significance of Disordered Tails J. Mol. Biol. 2010, 396, 674-684
    • (2010) J. Mol. Biol. , vol.396 , pp. 674-684
    • Vuzman, D.1    Azia, A.2    Levy, Y.3
  • 46
    • 84876554311 scopus 로고    scopus 로고
    • DNA-Recognition Process Described by MD Simulations of the Lactose Repressor Protein on a Specific and a Non-Specific DNA Sequence
    • Furini, S.; Barbini, P.; Domene, C. DNA-Recognition Process Described by MD Simulations of the Lactose Repressor Protein on a Specific and a Non-Specific DNA Sequence Nucleic Acids Res. 2013, 41, 3963-3972
    • (2013) Nucleic Acids Res. , vol.41 , pp. 3963-3972
    • Furini, S.1    Barbini, P.2    Domene, C.3
  • 47
    • 34249932435 scopus 로고    scopus 로고
    • Probing Transcription Factor Dynamics at the Single-Molecule Level in a Living Cell
    • Elf, J.; Li, G.-W.; Xie, X. S. Probing Transcription Factor Dynamics at the Single-Molecule Level in a Living Cell Science 2007, 316, 1191-1194
    • (2007) Science , vol.316 , pp. 1191-1194
    • Elf, J.1    Li, G.-W.2    Xie, X.S.3
  • 48
    • 80052467650 scopus 로고    scopus 로고
    • The Binding Process of a Nonspecific Enzyme with DNA
    • Chen, C.; Pettitt, B. M. The Binding Process of a Nonspecific Enzyme with DNA Biophys. J. 2011, 101, 1139-1147
    • (2011) Biophys. J. , vol.101 , pp. 1139-1147
    • Chen, C.1    Pettitt, B.M.2
  • 49
    • 49449107340 scopus 로고    scopus 로고
    • Visualizing One-Dimensional Diffusion of Proteins Along DNA
    • Gorman, J.; Greene, E. C. Visualizing One-Dimensional Diffusion of Proteins Along DNA Nat. Struct. Mol. Biol. 2008, 15, 768-774
    • (2008) Nat. Struct. Mol. Biol. , vol.15 , pp. 768-774
    • Gorman, J.1    Greene, E.C.2
  • 50
    • 33746649820 scopus 로고    scopus 로고
    • Single Molecule Measurements of Repressor Protein 1D Diffusion on DNA
    • Wang, Y. M.; Austin, R. H.; Cox, E. C. Single Molecule Measurements of Repressor Protein 1D Diffusion on DNA Phys. Rev. Lett. 2006, 97, 048302
    • (2006) Phys. Rev. Lett. , vol.97 , pp. 048302
    • Wang, Y.M.1    Austin, R.H.2    Cox, E.C.3
  • 51
    • 27644460480 scopus 로고    scopus 로고
    • Measurement of the Contributions of 1D and 3D Pathways to the Translocation of a Protein Along DNA
    • Gowers, D. M.; Wilson, G. G.; Halford, S. E. Measurement of the Contributions of 1D and 3D Pathways to the Translocation of a Protein Along DNA Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 15883-15888
    • (2005) Proc. Natl. Acad. Sci. U. S. A. , vol.102 , pp. 15883-15888
    • Gowers, D.M.1    Wilson, G.G.2    Halford, S.E.3
  • 52
    • 77955416347 scopus 로고    scopus 로고
    • Visualizing One-Dimensional Diffusion of Eukaryotic DNA Repair Factors Along a Chromatin Lattice
    • Gorman, J.; Plys, A. J.; Visnapuu, M.-L.; Alani, E.; Greene, E. C. Visualizing One-Dimensional Diffusion of Eukaryotic DNA Repair Factors Along a Chromatin Lattice Nat. Struct. Mol. Biol. 2010, 17, 932-938
    • (2010) Nat. Struct. Mol. Biol. , vol.17 , pp. 932-938
    • Gorman, J.1    Plys, A.J.2    Visnapuu, M.-L.3    Alani, E.4    Greene, E.C.5
  • 54
    • 0019886912 scopus 로고
    • Ion Effects on the Lac Repressor-Operator Equilibrium
    • Barkley, M. D.; Lewis, P. A.; Sullivan, G. E. Ion Effects on the Lac Repressor-Operator Equilibrium Biochemistry 1981, 20, 3842-3851
    • (1981) Biochemistry , vol.20 , pp. 3842-3851
    • Barkley, M.D.1    Lewis, P.A.2    Sullivan, G.E.3
  • 55
    • 0031058541 scopus 로고    scopus 로고
    • The Statistical-Thermodynamic Basis for Computation of Binding Affinities: A Critical Review
    • Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A. The Statistical-Thermodynamic Basis for Computation of Binding Affinities: A Critical Review Biophys. J. 1997, 72, 1047-1069
    • (1997) Biophys. J. , vol.72 , pp. 1047-1069
    • Gilson, M.K.1    Given, J.A.2    Bush, B.L.3    McCammon, J.A.4
  • 56
    • 0347949637 scopus 로고    scopus 로고
    • Revisiting Free Energy Calculations: A Theoretical Connection to MM/PBSA and Direct Calculation of the Association Free Energy
    • Swanson, J. M. J.; Henchman, R. H.; McCammon, J. A. Revisiting Free Energy Calculations: A Theoretical Connection to MM/PBSA and Direct Calculation of the Association Free Energy Biophys. J. 2004, 86, 67-74
    • (2004) Biophys. J. , vol.86 , pp. 67-74
    • Swanson, J.M.J.1    Henchman, R.H.2    McCammon, J.A.3
  • 57
    • 18744372751 scopus 로고    scopus 로고
    • Calculation of Absolute Protein-Ligand Binding Free Energy from Computer Simulations
    • Woo, H.-J.; Roux, B. Calculation of Absolute Protein-Ligand Binding Free Energy from Computer Simulations Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 6825-6830
    • (2005) Proc. Natl. Acad. Sci. U. S. A. , vol.102 , pp. 6825-6830
    • Woo, H.-J.1    Roux, B.2
  • 58
    • 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, 2234-2246
    • (2009) J. Phys. Chem. B , vol.113 , pp. 2234-2246
    • Deng, Y.1    Roux, B.2
  • 59
    • 67449102263 scopus 로고    scopus 로고
    • Specificity and Affinity of Lac Repressor for the Auxiliary Operators O2 and O3 Are Explained by the Structures of Their Protein-DNA Complexes
    • Romanuka, J.; Folkers, G. E.; Biris, N.; Tishchenko, E.; Wienk, H.; Bonvin, A. M. J. J.; Kaptein, R.; Boelens, R. Specificity and Affinity of Lac Repressor for the Auxiliary Operators O2 and O3 Are Explained by the Structures of Their Protein-DNA Complexes J. Mol. Biol. 2009, 390, 478-489
    • (2009) J. Mol. Biol. , vol.390 , pp. 478-489
    • Romanuka, J.1    Folkers, G.E.2    Biris, N.3    Tishchenko, E.4    Wienk, H.5    Bonvin, A.M.J.J.6    Kaptein, R.7    Boelens, R.8
  • 60
    • 0030596509 scopus 로고    scopus 로고
    • Refined Structure of Lac Repressor Headpiece (1-56) Determined by Relaxation Matrix Calculations form 2D and 3D NOE Data: Change of Tertiary Structure upon Binding to the Lac Operator
    • Slijper, M.; Bonvin, A. M. J. J.; Boelens, R.; Kaptein, R. Refined Structure of Lac Repressor Headpiece (1-56) Determined by Relaxation Matrix Calculations form 2D and 3D NOE Data: Change of Tertiary Structure upon Binding to the Lac Operator J. Mol. Biol. 1996, 259, 761-773
    • (1996) J. Mol. Biol. , vol.259 , pp. 761-773
    • Slijper, M.1    Bonvin, A.M.J.J.2    Boelens, R.3    Kaptein, R.4
  • 61
    • 84865714640 scopus 로고    scopus 로고
    • P53 Searches on DNA by Rotation-Uncoupled Sliding at C-Terminal Tails and Restricted Hopping of Core Domains
    • Terakawa, T.; Kenzaki, H.; Takada, S. p53 Searches on DNA by Rotation-Uncoupled Sliding at C-Terminal Tails and Restricted Hopping of Core Domains J. Am. Chem. Soc. 2012, 134, 14555-14562
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 14555-14562
    • Terakawa, T.1    Kenzaki, H.2    Takada, S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.