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Volumn 117, Issue 41, 2013, Pages 12360-12374

Specific and non-specific protein association in solution: Computation of solvent effects and prediction of first-encounter modes for efficient configurational bias monte carlo simulations

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENTHALPIES; CONFIGURATIONAL-BIAS MONTE CARLO; CONTINUUM MODELING; LONG RANGE EFFECTS; MULTI-PROTEIN COMPLEX; PROTEIN ASSOCIATIONS; PROTEIN-PROTEIN ASSOCIATIONS; PROTEIN-PROTEIN BINDING;

EID: 84886907111     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp4050594     Document Type: Article
Times cited : (18)

References (99)
  • 4
    • 63749132353 scopus 로고    scopus 로고
    • Transglutaminase-1 (TGM1) Gene Mutations in Autosomal Recessive Congenital Ichthyosis: Summary of Mutations (Including 23 Novel) and Modeling of TGase-1
    • Herman, M. L.; Farasat, S.; Steinbach, P. J.; Wei, M. H.; Toure, O.; Fleckman, P.; Blake, P.; Bale, S. J.; Toro, J. R. Transglutaminase-1 (TGM1) Gene Mutations in Autosomal Recessive Congenital Ichthyosis: Summary of Mutations (Including 23 Novel) and Modeling of TGase-1 Hum. Mutat. 2009, 30, 537-547
    • (2009) Hum. Mutat. , vol.30 , pp. 537-547
    • Herman, M.L.1    Farasat, S.2    Steinbach, P.J.3    Wei, M.H.4    Toure, O.5    Fleckman, P.6    Blake, P.7    Bale, S.J.8    Toro, J.R.9
  • 9
    • 35548943472 scopus 로고    scopus 로고
    • Elucidating Transient Macromolecular Interactions using Paramagnetic Relaxation Enhancement
    • Clore, G. M.; Tang, C.; Iwahara, J. Elucidating Transient Macromolecular Interactions using Paramagnetic Relaxation Enhancement Curr. Opin. Struct. Biol. 2007, 17, 603-616
    • (2007) Curr. Opin. Struct. Biol. , vol.17 , pp. 603-616
    • Clore, G.M.1    Tang, C.2    Iwahara, J.3
  • 10
    • 33751086423 scopus 로고    scopus 로고
    • Visualization of Transient Encounter Complexes in Protein-Protein Association
    • Tang, C.; Iwahara, J.; Clore, G. M. Visualization of Transient Encounter Complexes in Protein-Protein Association Nature 2006, 444, 383-386
    • (2006) Nature , vol.444 , pp. 383-386
    • Tang, C.1    Iwahara, J.2    Clore, G.M.3
  • 11
    • 41149167049 scopus 로고    scopus 로고
    • Visualization of Transient Ultra-Weak Protein Self-Association in Solution using Paramagnetic Relaxation Enhancement
    • Tang, C.; Ghirlando, R.; Clore, G. Visualization of Transient Ultra-Weak Protein Self-Association in Solution using Paramagnetic Relaxation Enhancement J. Am. Chem. Soc. 2008, 130, 4048-4056
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 4048-4056
    • Tang, C.1    Ghirlando, R.2    Clore, G.3
  • 12
    • 0035478585 scopus 로고    scopus 로고
    • Macromolecular Crowding: Obvious but Underappreciated
    • Ellis, R. J. Macromolecular Crowding: Obvious but Underappreciated Trends Biochem. Sci. 2001, 26, 597-604
    • (2001) Trends Biochem. Sci. , vol.26 , pp. 597-604
    • Ellis, R.J.1
  • 13
    • 0033991590 scopus 로고    scopus 로고
    • Cytoarchitecture and Physical Properties of Cytoplasm: Volume, Viscosity, Diffusion, Intracellular Surface Area
    • Luby-Phelps, K. Cytoarchitecture and Physical Properties of Cytoplasm: Volume, Viscosity, Diffusion, Intracellular Surface Area Int. Rev. Cytol. 2000, 192, 189-221
    • (2000) Int. Rev. Cytol. , vol.192 , pp. 189-221
    • Luby-Phelps, K.1
  • 14
    • 84855460321 scopus 로고    scopus 로고
    • Flexibility and Binding Affinity in Protein-Ligand, Protein-Protein and Multi-Component Protein Interactions: Limitations of Current Computational Approaches
    • Tuffery, P.; Derremaux, P. Flexibility and Binding Affinity in Protein-Ligand, Protein-Protein and Multi-Component Protein Interactions: Limitations of Current Computational Approaches J. R. Soc., Interface 2012, 9, 20-33
    • (2012) J. R. Soc., Interface , vol.9 , pp. 20-33
    • Tuffery, P.1    Derremaux, P.2
  • 15
    • 33750056673 scopus 로고    scopus 로고
    • Rosetaligand: Protein-Small Molecule Docking with Full Side-Chain Flexibility
    • Meiler, J.; Baker, D. Rosetaligand: Protein-Small Molecule Docking with Full Side-Chain Flexibility Proteins 2006, 65, 538-548
    • (2006) Proteins , vol.65 , pp. 538-548
    • Meiler, J.1    Baker, D.2
  • 16
    • 83455162896 scopus 로고    scopus 로고
    • Water-Exclusion and Liquid-Structure Forces in Implicit Solvation
    • Hassan, S. A.; Steinbach, P. J. Water-Exclusion and Liquid-Structure Forces in Implicit Solvation J. Phys. Chem. B 2011, 115, 14668-14682
    • (2011) J. Phys. Chem. B , vol.115 , pp. 14668-14682
    • Hassan, S.A.1    Steinbach, P.J.2
  • 17
    • 84868097085 scopus 로고    scopus 로고
    • Role of Specific Cations and Water Entropy on the Stability of Branched DNA Motif Structures
    • Pascal, T. A.; Goddard, W. A., III; Maiti, P. K.; Vaidehi, N. Role of Specific Cations and Water Entropy on the Stability of Branched DNA Motif Structures J. Phys. Chem. B 2012, 116, 12159-12167
    • (2012) J. Phys. Chem. B , vol.116 , pp. 12159-12167
    • Pascal, T.A.1    Goddard III, W.A.2    Maiti, P.K.3    Vaidehi, N.4
  • 18
    • 3042685233 scopus 로고    scopus 로고
    • What can really be Learned from Dielectric Spectroscopy of Protein Solutions? A Case Study of Ribonuclease A
    • Oleinikova, A.; Sasisanker, P.; Weingartner, H. What can really be Learned from Dielectric Spectroscopy of Protein Solutions? A Case Study of Ribonuclease A J. Phys. Chem. B 2004, 108, 8467-8474
    • (2004) J. Phys. Chem. B , vol.108 , pp. 8467-8474
    • Oleinikova, A.1    Sasisanker, P.2    Weingartner, H.3
  • 19
    • 33745326750 scopus 로고    scopus 로고
    • Simulation Studies of the Protein-Water Interface: I. Properties at the Molecular Resolution
    • Schroder, C.; Rudas, T.; Boresch, S.; Steinhauser, O. Simulation Studies of the Protein-Water Interface: I. Properties at the Molecular Resolution J. Chem. Phys. 2006, 124, 234907
    • (2006) J. Chem. Phys. , vol.124 , pp. 234907
    • Schroder, C.1    Rudas, T.2    Boresch, S.3    Steinhauser, O.4
  • 20
    • 33745293234 scopus 로고    scopus 로고
    • Simulation Studies of the Protein-Water Interface. II. Properties at the Mesoscopic Resolution
    • Rudas, T.; Schroder, C.; Boresch, S.; Steinhauser, O. Simulation Studies of the Protein-Water Interface. II. Properties at the Mesoscopic Resolution J. Chem. Phys. 2006, 124, 234908
    • (2006) J. Chem. Phys. , vol.124 , pp. 234908
    • Rudas, T.1    Schroder, C.2    Boresch, S.3    Steinhauser, O.4
  • 21
    • 0037117502 scopus 로고    scopus 로고
    • Is the First Hydration Shell of Lysozyme of Higher Density than Bulk Water?
    • Merzel, F.; Smith, J. C. Is the First Hydration Shell of Lysozyme of Higher Density than Bulk Water? Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 5378-5383
    • (2002) Proc. Natl. Acad. Sci. U.S.A. , vol.99 , pp. 5378-5383
    • Merzel, F.1    Smith, J.C.2
  • 22
    • 0031577320 scopus 로고    scopus 로고
    • Calculation of the Dielectric Properties of a Protein and its Solvent: Theory and a Case Study
    • Loffler, G.; Schreiber, H.; Steinhauser, O. Calculation of the Dielectric Properties of a Protein and its Solvent: Theory and a Case Study J. Mol. Biol. 1997, 270, 520-534
    • (1997) J. Mol. Biol. , vol.270 , pp. 520-534
    • Loffler, G.1    Schreiber, H.2    Steinhauser, O.3
  • 23
    • 0037007485 scopus 로고    scopus 로고
    • Fifty Years of Solvent Denaturation
    • Schellman, J. A. Fifty Years of Solvent Denaturation Biophys. Chem. 2002, 96, 91-101
    • (2002) Biophys. Chem. , vol.96 , pp. 91-101
    • Schellman, J.A.1
  • 24
    • 0027310845 scopus 로고
    • The Control of Protein Stability and Association by Weak Interactions with Water: How Do Solvents Affect These Processes?
    • Timasheff, S. M. The Control of Protein Stability and Association by Weak Interactions with Water: How Do Solvents Affect These Processes? Annu. Rev. Biophys. Biomol. Struct. 1993, 22, 67-97
    • (1993) Annu. Rev. Biophys. Biomol. Struct. , vol.22 , pp. 67-97
    • Timasheff, S.M.1
  • 25
    • 0022032982 scopus 로고
    • The Stability of Proteins by Osmolytes
    • Arakawa, K.; Timasheff, S. M. The Stability of Proteins by Osmolytes Biophys. J. 1985, 47, 411-414
    • (1985) Biophys. J. , vol.47 , pp. 411-414
    • Arakawa, K.1    Timasheff, S.M.2
  • 27
    • 0036204260 scopus 로고    scopus 로고
    • Protein-Water Interactions
    • Parsegian, V. A. Protein-Water Interactions Int. Rev. Cytol. 2002, 215, 1-31
    • (2002) Int. Rev. Cytol. , vol.215 , pp. 1-31
    • Parsegian, V.A.1
  • 28
    • 0021205796 scopus 로고
    • Water near Intracellular Surfaces
    • Parsegian, V. A.; Rau, D. C. Water near Intracellular Surfaces J. Cell Biol. 1984, 99, 196-200
    • (1984) J. Cell Biol. , vol.99 , pp. 196-200
    • Parsegian, V.A.1    Rau, D.C.2
  • 29
    • 0242662357 scopus 로고    scopus 로고
    • Long-range Forces Extending from Polymer-Gel Surfaces
    • Zheng, J.-M.; Pollack, G. H. Long-range Forces Extending from Polymer-Gel Surfaces Phys. Rev. E 2003, 68, 031408
    • (2003) Phys. Rev. e , vol.68 , pp. 031408
    • Zheng, J.-M.1    Pollack, G.H.2
  • 30
    • 0031020268 scopus 로고    scopus 로고
    • Like-Charge Attractions in Metastable Colloidal Crystallites
    • Larsen, A. E.; Grier, D. G. Like-Charge Attractions in Metastable Colloidal Crystallites Nature 1997, 385, 230-233
    • (1997) Nature , vol.385 , pp. 230-233
    • Larsen, A.E.1    Grier, D.G.2
  • 31
    • 5244364958 scopus 로고    scopus 로고
    • When Like Charges Attract: The Effect of Geometrical Confinement on Long-Range Colloidal Interactions
    • Crocker, J. C.; Grier, D. G. When Like Charges Attract: The Effect of Geometrical Confinement on Long-Range Colloidal Interactions Phys. Rev. Lett. 1996, 77, 1897-1900
    • (1996) Phys. Rev. Lett. , vol.77 , pp. 1897-1900
    • Crocker, J.C.1    Grier, D.G.2
  • 32
    • 84882756808 scopus 로고    scopus 로고
    • In Silico Approaches to Structure and Function of Cell Components and their Assemblies: Molecular Electrostatics and Solvent Effects
    • Egelman, E. Academic Press: Oxford, U.K. Vol. - 228
    • Hassan, S. A.; Mehler, E. L. In Silico Approaches to Structure and Function of Cell Components and their Assemblies: Molecular Electrostatics and Solvent Effects. In Comprehensive Biophysics; Egelman, E., Ed.; Academic Press: Oxford, U.K., 2012; Vol. 9, pp 190-228.
    • (2012) Comprehensive Biophysics , vol.9 , pp. 190
    • Hassan, S.A.1    Mehler, E.L.2
  • 33
    • 4344602172 scopus 로고    scopus 로고
    • Protein Hydration Dynamics in Solution: A Critical Survey
    • Halle, B. Protein Hydration Dynamics in Solution: a Critical Survey Philos. Trans. R. Soc. London, Ser. B 2004, 359, 1207-1223
    • (2004) Philos. Trans. R. Soc. London, Ser. B , vol.359 , pp. 1207-1223
    • Halle, B.1
  • 36
    • 0000414612 scopus 로고
    • Configurational-bias Monte Carlo: Background and Selected Applications
    • van Gunsteren, W. F. Weiner, P. K. Wilkinson, A. J. ESCOM: Leiden, The Netherlands
    • Siepmann, J. I. Configurational-bias Monte Carlo: Background and Selected Applications. In Computer Simulations of Biomolecular Systems: Theoretical and Experimental Applications; van Gunsteren, W. F.; Weiner, P. K.; Wilkinson, A. J., Eds.; ESCOM: Leiden, The Netherlands, 1993; Vol. 2, pp 249-264.
    • (1993) Computer Simulations of Biomolecular Systems: Theoretical and Experimental Applications , vol.2 , pp. 249-264
    • Siepmann, J.I.1
  • 37
    • 78650612270 scopus 로고
    • Configurational Bias Monte Carlo: A New Sampling Scheme for Flexible Chains
    • Siepmann, J. I.; Frenkel, D. Configurational Bias Monte Carlo: A New Sampling Scheme for Flexible Chains Mol. Phys. 1992, 75, 59-70
    • (1992) Mol. Phys. , vol.75 , pp. 59-70
    • Siepmann, J.I.1    Frenkel, D.2
  • 38
    • 0037156141 scopus 로고    scopus 로고
    • A biased Monte Carlo Technique for Calculation of the Density of States of Polymer Films
    • de Pablo, J. J.; Jain, T. S. A biased Monte Carlo Technique for Calculation of the Density of States of Polymer Films J. Chem. Phys. 2002, 116, 7238-7244
    • (2002) J. Chem. Phys. , vol.116 , pp. 7238-7244
    • De Pablo, J.J.1    Jain, T.S.2
  • 39
    • 0042656263 scopus 로고    scopus 로고
    • A biased Monte Carlo Scheme for Zeolite Structure Solution
    • Falcioni, M.; Deem, M. W. A biased Monte Carlo Scheme for Zeolite Structure Solution J. Chem. Phys. 1999, 110, 1754-1767
    • (1999) J. Chem. Phys. , vol.110 , pp. 1754-1767
    • Falcioni, M.1    Deem, M.W.2
  • 40
    • 10344264957 scopus 로고    scopus 로고
    • Exploring Peptide Energy Landscapes: A Test of Force Fields and Implicit Solvent Models
    • Steinbach, P. J. Exploring Peptide Energy Landscapes: A Test of Force Fields and Implicit Solvent Models Proteins 2004, 57, 665-677
    • (2004) Proteins , vol.57 , pp. 665-677
    • Steinbach, P.J.1
  • 41
    • 0030055923 scopus 로고    scopus 로고
    • Conformational Memories and the Exploration of Biologically Relevant Peptide Conformations: An Illustration for the Gonadotropin-releasing Hormone
    • Guarnieri, F.; Weinstein, H. Conformational Memories and the Exploration of Biologically Relevant Peptide Conformations: An Illustration for the Gonadotropin-releasing Hormone J. Am. Chem. Soc. 1996, 118, 5580-5589
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 5580-5589
    • Guarnieri, F.1    Weinstein, H.2
  • 42
    • 33746268446 scopus 로고    scopus 로고
    • Ab initio Computer Modeling of Loops in G-Protein Coupled Receptors: Lessons from the Crystal Structure of Rhodopsin
    • Mehler, E. L.; Hassan, S. A.; Kortagere, S.; Weinstein, H. Ab initio Computer Modeling of Loops in G-Protein Coupled Receptors: Lessons from the Crystal Structure of Rhodopsin Proteins 2006, 64, 673-690
    • (2006) Proteins , vol.64 , pp. 673-690
    • Mehler, E.L.1    Hassan, S.A.2    Kortagere, S.3    Weinstein, H.4
  • 43
    • 0035811239 scopus 로고    scopus 로고
    • A General Screened Coulomb Potential Based Implicit Solvent Model: Calculation of Secondary Structure of Small Peptides
    • Hassan, S. A.; Mehler, E. L. A General Screened Coulomb Potential Based Implicit Solvent Model: Calculation of Secondary Structure of Small Peptides Int. J. Quantum Chem. 2001, 83, 193-202
    • (2001) Int. J. Quantum Chem. , vol.83 , pp. 193-202
    • Hassan, S.A.1    Mehler, E.L.2
  • 44
    • 0034228977 scopus 로고    scopus 로고
    • Characterization of Hydrogen Bonding in a Continuum Solvent Model
    • Hassan, S. A.; Guarnieri, F.; Mehler, E. L. Characterization of Hydrogen Bonding in a Continuum Solvent Model J. Phys. Chem. B 2000, 104, 6490-6498
    • (2000) J. Phys. Chem. B , vol.104 , pp. 6490-6498
    • Hassan, S.A.1    Guarnieri, F.2    Mehler, E.L.3
  • 45
    • 0034227821 scopus 로고    scopus 로고
    • A General Treatment of Solvent Effects Based on Screened Coulomb Potentials
    • Hassan, S. A.; Guarnieri, F.; Mehler, E. L. A General Treatment of Solvent Effects Based on Screened Coulomb Potentials J. Phys. Chem. B 2000, 104, 6478-6489
    • (2000) J. Phys. Chem. B , vol.104 , pp. 6478-6489
    • Hassan, S.A.1    Guarnieri, F.2    Mehler, E.L.3
  • 46
    • 0037375367 scopus 로고    scopus 로고
    • Molecular Dynamics Simulations of Peptides and Proteins with a Continuum Electrostatic Model Based on Screened Coulomb Potentials
    • Hassan, S. A.; Mehler, E. L.; Zhang, D.; Weinstein, H. Molecular Dynamics Simulations of Peptides and Proteins with a Continuum Electrostatic Model Based on Screened Coulomb Potentials Proteins 2003, 51, 109-125
    • (2003) Proteins , vol.51 , pp. 109-125
    • Hassan, S.A.1    Mehler, E.L.2    Zhang, D.3    Weinstein, H.4
  • 47
    • 33847114898 scopus 로고    scopus 로고
    • Liquid-structure Forces and Electrostatic Modulation of Biomolecular Interactions in Solution
    • Hassan, S. A. Liquid-structure Forces and Electrostatic Modulation of Biomolecular Interactions in Solution J. Phys. Chem. B 2007, 111, 227-241
    • (2007) J. Phys. Chem. B , vol.111 , pp. 227-241
    • Hassan, S.A.1
  • 49
    • 84872143248 scopus 로고    scopus 로고
    • Implicit Solvent Models and Stabilizing Effects of Mutations and Ligand on the Unfolding of the Amyloid β-Peptide Central Helix
    • Juneja, A.; Ito, M.; Nilsson, L. Implicit Solvent Models and Stabilizing Effects of Mutations and Ligand on the Unfolding of the Amyloid β-Peptide Central Helix J. Chem. Theory Comput. 2013, 9, 834-846
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 834-846
    • Juneja, A.1    Ito, M.2    Nilsson, L.3
  • 50
    • 0029873697 scopus 로고    scopus 로고
    • Rapid Electrostatically Assisted Association of Proteins
    • Schreiber, G.; Fersht, A. R. Rapid Electrostatically Assisted Association of Proteins Nature 1996, 3, 427-431
    • (1996) Nature , vol.3 , pp. 427-431
    • Schreiber, G.1    Fersht, A.R.2
  • 51
    • 0032508498 scopus 로고    scopus 로고
    • Long-range Electrostatic Trapping of Single-Protein Molecules at a Liquid-Solid Interface
    • Xu, X.-H. N.; Yeung, E. S. Long-range Electrostatic Trapping of Single-Protein Molecules at a Liquid-Solid Interface Science 1998, 281, 1650-1653
    • (1998) Science , vol.281 , pp. 1650-1653
    • Xu, X.-H.N.1    Yeung, E.S.2
  • 52
    • 1342302795 scopus 로고    scopus 로고
    • The Interaction of Proteins with Solid Surfaces
    • Gray, J. J. The Interaction of Proteins with Solid Surfaces Curr. Opin. Struct. Biol. 2004, 14, 110-115
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 110-115
    • Gray, J.J.1
  • 53
    • 10944256336 scopus 로고    scopus 로고
    • Intermolecular Potentials of Mean Force of Amino Acid Side Chain Interactions in Aqueous Medium
    • Hassan, S. A. Intermolecular Potentials of Mean Force of Amino Acid Side Chain Interactions in Aqueous Medium J. Phys. Chem. B 2004, 108, 19501-19509
    • (2004) J. Phys. Chem. B , vol.108 , pp. 19501-19509
    • Hassan, S.A.1
  • 54
    • 84873620390 scopus 로고    scopus 로고
    • Generating Reservoir Conformations for Replica Exchange through the Use of the Conformational Space Annealing Method
    • Okur, A.; Miller, B. T.; Joo, K.; Lee, J. A.; Brooks, B. R. Generating Reservoir Conformations for Replica Exchange through the Use of the Conformational Space Annealing Method J. Chem. Theory Comput. 2013, 9, 1115-1124
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 1115-1124
    • Okur, A.1    Miller, B.T.2    Joo, K.3    Lee, J.A.4    Brooks, B.R.5
  • 55
    • 0035160537 scopus 로고    scopus 로고
    • Barstar is Electrostatically Optimized for Tight Binding to Barnase
    • Lee, L. P.; Tidor, B. Barstar is Electrostatically Optimized for Tight Binding to Barnase Nature 2001, 8, 73-76
    • (2001) Nature , vol.8 , pp. 73-76
    • Lee, L.P.1    Tidor, B.2
  • 56
    • 0031552366 scopus 로고    scopus 로고
    • Thermodynamics of the Interaction of Barnase and Barstar: Changes in Free Energy versus Changes in Enthalpy on Mutation
    • Frisch, C.; Schreiber, G.; Johnson, C. M.; Fersht, A. R. Thermodynamics of the Interaction of Barnase and Barstar: Changes in Free Energy versus Changes in Enthalpy on Mutation J. Mol. Biol. 1997, 267, 696-706
    • (1997) J. Mol. Biol. , vol.267 , pp. 696-706
    • Frisch, C.1    Schreiber, G.2    Johnson, C.M.3    Fersht, A.R.4
  • 57
    • 0028102849 scopus 로고
    • Effect of Conformational Flexibility and Solvation on Receptor-Ligand Binding Free Energies
    • Vajda, S.; Weng, Z. P.; Rosenfeld, R.; DeLisi, C. Effect of Conformational Flexibility and Solvation on Receptor-Ligand Binding Free Energies Biochemistry 1994, 33, 13977-13988
    • (1994) Biochemistry , vol.33 , pp. 13977-13988
    • Vajda, S.1    Weng, Z.P.2    Rosenfeld, R.3    Delisi, C.4
  • 59
    • 84988074929 scopus 로고
    • Evaluation of the Dispersion Contribution to the Solvation Energy: A Simple Computational Model in the Continuum Approximation
    • Floris, F.; Tomasi, J. Evaluation of the Dispersion Contribution to the Solvation Energy: A Simple Computational Model in the Continuum Approximation J. Comput. Chem. 1989, 10, 616-627
    • (1989) J. Comput. Chem. , vol.10 , pp. 616-627
    • Floris, F.1    Tomasi, J.2
  • 60
    • 0347787914 scopus 로고    scopus 로고
    • Continuum Solvent Modeling of Nonpolar Solvation: Improvement by Separating Surface Area dependent Cavity and Dispersion Contributions
    • Zacharias, M. Continuum Solvent Modeling of Nonpolar Solvation: Improvement by Separating Surface Area dependent Cavity and Dispersion Contributions J. Phys. Chem. A 2003, 107, 3000-3004
    • (2003) J. Phys. Chem. A , vol.107 , pp. 3000-3004
    • Zacharias, M.1
  • 61
    • 33744822783 scopus 로고    scopus 로고
    • Assessing Implicit Models for Nonpolar Mean Solvation Forces: The Importance of Dispersion and Volume Terms
    • Wagoner, J. A.; Baker, N. A. Assessing Implicit Models for Nonpolar Mean Solvation Forces: The Importance of Dispersion and Volume Terms Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 8331-8336
    • (2006) Proc. Natl. Acad. Sci. U.S.A. , vol.103 , pp. 8331-8336
    • Wagoner, J.A.1    Baker, N.A.2
  • 62
    • 33751157933 scopus 로고
    • Solvent-Induced Forces between Two Hydrophilic Groups
    • Durell, S. R.; Brooks, B. R.; Ben-Naim, A. Solvent-Induced Forces Between Two Hydrophilic Groups J. Phys. Chem. 1994, 98, 2198-2202
    • (1994) J. Phys. Chem. , vol.98 , pp. 2198-2202
    • Durell, S.R.1    Brooks, B.R.2    Ben-Naim, A.3
  • 63
    • 0009623707 scopus 로고
    • Solvent-Induced Forces in Protein Folding
    • Ben-Naim, A. Solvent-Induced Forces in Protein Folding J. Phys. Chem. 1990, 94, 6893-6895
    • (1990) J. Phys. Chem. , vol.94 , pp. 6893-6895
    • Ben-Naim, A.1
  • 64
    • 0030607946 scopus 로고    scopus 로고
    • Solvent-Induced Forces on a Molecular Scale: Non-Additivity, Modulation and Causal Relation to Hydration
    • Bruge, F.; Fornilli, S. L.; Malenkov, G. G.; Palma-Vittorelli, M. B.; Palma, M. U. Solvent-Induced Forces on a Molecular Scale: Non-Additivity, Modulation and Causal Relation to Hydration Chem. Phys. Lett. 1996, 254, 283-291
    • (1996) Chem. Phys. Lett. , vol.254 , pp. 283-291
    • Bruge, F.1    Fornilli, S.L.2    Malenkov, G.G.3    Palma-Vittorelli, M.B.4    Palma, M.U.5
  • 65
    • 0018318966 scopus 로고
    • Interfacial Free Energy and the Hydrophobic Effect
    • Tanford, C. Interfacial Free Energy and the Hydrophobic Effect Proc. Natl. Acad. Sci. U.S.A. 1979, 76, 4175-4176
    • (1979) Proc. Natl. Acad. Sci. U.S.A. , vol.76 , pp. 4175-4176
    • Tanford, C.1
  • 66
    • 0011930746 scopus 로고
    • Theory of Hydrophobic Bonding. II. Correlation of Hydrocarbon Solubility in Water with Solvent Cavity Surface-Area
    • Hermann, R. B. Theory of Hydrophobic Bonding. II. Correlation of Hydrocarbon Solubility in Water with Solvent Cavity Surface-Area J. Phys. Chem. 1972, 76, 2754-2759
    • (1972) J. Phys. Chem. , vol.76 , pp. 2754-2759
    • Hermann, R.B.1
  • 67
    • 33744761434 scopus 로고    scopus 로고
    • Hierarchical Clustering via Joint Between-Within Distances: Extending Ward's Minimum Variance Method
    • Szekely, G. J.; Rizzo, M. L. Hierarchical Clustering via Joint Between-Within Distances: Extending Ward's Minimum Variance Method J. Classif. 2005, 22, 151-183
    • (2005) J. Classif. , vol.22 , pp. 151-183
    • Szekely, G.J.1    Rizzo, M.L.2
  • 69
    • 0035830963 scopus 로고    scopus 로고
    • Protein-Protein Association: Investigation of Factors Influencing Association Rates by Brownian Dynamics Simulations
    • Gabdoulline, R. R.; Wade, R. C. Protein-Protein Association: Investigation of Factors Influencing Association Rates by Brownian Dynamics Simulations J. Mol. Biol. 2001, 306, 1139-1155
    • (2001) J. Mol. Biol. , vol.306 , pp. 1139-1155
    • Gabdoulline, R.R.1    Wade, R.C.2
  • 70
    • 77953621551 scopus 로고    scopus 로고
    • Barnase-Barstar: From First Encounter to Final Complex
    • Hoefling, M.; Gottschalk, K. E. Barnase-Barstar: From First Encounter to Final Complex J. Struct. Biol. 2010, 171, 52-63
    • (2010) J. Struct. Biol. , vol.171 , pp. 52-63
    • Hoefling, M.1    Gottschalk, K.E.2
  • 71
    • 81055157980 scopus 로고    scopus 로고
    • Calculation of pKa in Proteins with the Microenvironment Modulated-Screened Coulomb Potential (MM-SCP)
    • Shan, J.; Mehler, E. L. Calculation of pKa in Proteins with the Microenvironment Modulated-Screened Coulomb Potential (MM-SCP) Proteins 2011, 79, 3346-3355
    • (2011) Proteins , vol.79 , pp. 3346-3355
    • Shan, J.1    Mehler, E.L.2
  • 72
    • 84865454330 scopus 로고    scopus 로고
    • Self-Consistent Treatment of the Local Dielectric Permittivity and Electrostatic Potential in Solution for Polarizable Macromolecular Force Fields
    • Hassan, S. A. Self-Consistent Treatment of the Local Dielectric Permittivity and Electrostatic Potential in Solution for Polarizable Macromolecular Force Fields J. Chem. Phys. 2012, 137, 074102
    • (2012) J. Chem. Phys. , vol.137 , pp. 074102
    • Hassan, S.A.1
  • 73
    • 28944450948 scopus 로고    scopus 로고
    • Amino Acid Side Chain Interactions in the Presence of Salts
    • Hassan, S. A. Amino Acid Side Chain Interactions in the Presence of Salts J. Phys. Chem. B 2005, 109, 21989-21996
    • (2005) J. Phys. Chem. B , vol.109 , pp. 21989-21996
    • Hassan, S.A.1
  • 74
    • 84876058834 scopus 로고    scopus 로고
    • A Multiscale Coarse-Grained Polarizable Solvent Model for Handling Long Tail Bulk Electrostatics
    • Masella, M.; Borgis, D.; Cuniasse, P. A Multiscale Coarse-Grained Polarizable Solvent Model for Handling Long Tail Bulk Electrostatics J. Comput. Chem. 2013, 34, 1112-1124
    • (2013) J. Comput. Chem. , vol.34 , pp. 1112-1124
    • Masella, M.1    Borgis, D.2    Cuniasse, P.3
  • 76
    • 26944481188 scopus 로고    scopus 로고
    • Interfaces and the Driving Force of Hydrophobic Assembly
    • Chandler, D. Interfaces and the Driving Force of Hydrophobic Assembly Nature 2005, 437, 640-647
    • (2005) Nature , vol.437 , pp. 640-647
    • Chandler, D.1
  • 78
    • 0036423588 scopus 로고    scopus 로고
    • Molecular theory of Hydrophobic Effects: She is too Mean to have her Name Repeated
    • Pratt, L. R. Molecular theory of Hydrophobic Effects: She is too Mean to have her Name Repeated Annu. Rev. Phys. Chem. 2002, 53, 409-436
    • (2002) Annu. Rev. Phys. Chem. , vol.53 , pp. 409-436
    • Pratt, L.R.1
  • 80
    • 0011960339 scopus 로고    scopus 로고
    • Hydrophobicity at Small and Large Length Scales
    • Lum, K.; Chandler, D.; Weeks, J. D. Hydrophobicity at Small and Large Length Scales J. Phys. Chem. B 1999, 103, 4570-4577
    • (1999) J. Phys. Chem. B , vol.103 , pp. 4570-4577
    • Lum, K.1    Chandler, D.2    Weeks, J.D.3
  • 81
    • 0032867608 scopus 로고    scopus 로고
    • A "universal" Surface Area Correlation for Molecular Hydrophobic Phenomena
    • Ashbaugh, H. S.; Kaler, E. W.; Paulaitis, M. E. A "Universal" Surface Area Correlation for Molecular Hydrophobic Phenomena J. Am. Chem. Soc. 1999, 121, 9243-9244
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 9243-9244
    • Ashbaugh, H.S.1    Kaler, E.W.2    Paulaitis, M.E.3
  • 82
    • 0035913512 scopus 로고    scopus 로고
    • A Model for Studying Drying at Hydrophobic Interfaces: Structural and Thermodynamic Properties
    • Wallqvist, A.; Gallicchio, E.; Levy, R. M. A Model for Studying Drying at Hydrophobic Interfaces: Structural and Thermodynamic Properties J. Phys. Chem. B 2001, 105, 6745-6753
    • (2001) J. Phys. Chem. B , vol.105 , pp. 6745-6753
    • Wallqvist, A.1    Gallicchio, E.2    Levy, R.M.3
  • 83
    • 3342936878 scopus 로고
    • An SCF Solvation Model for the Hydrophobic Effect and Absolute Free Energies of Aqueous Solvation
    • Cramer, C. J.; Truhlar, D. G. An SCF Solvation Model for the Hydrophobic Effect and Absolute Free Energies of Aqueous Solvation Science 1992, 256, 213-217
    • (1992) Science , vol.256 , pp. 213-217
    • Cramer, C.J.1    Truhlar, D.G.2
  • 84
    • 0001444020 scopus 로고    scopus 로고
    • Implicit Solvent Models: Combining an Analytical Formulation of Continuum Electrostatics with Simple Models of the Hydrophobic Effect
    • Wagner, F.; Simonson, T. Implicit Solvent Models: Combining an Analytical Formulation of Continuum Electrostatics with Simple Models of the Hydrophobic Effect J. Comput. Chem. 1999, 20, 322-335
    • (1999) J. Comput. Chem. , vol.20 , pp. 322-335
    • Wagner, F.1    Simonson, T.2
  • 85
    • 84875764850 scopus 로고    scopus 로고
    • Effects of Microcomplexity on Hydrophobic hydration in Amphiphiles
    • Tan, M. L.; Cendagorta, J. R.; Ichiye, T. Effects of Microcomplexity on Hydrophobic hydration in Amphiphiles J. Am. Chem. Soc. 2013, 135, 4918-4921
    • (2013) J. Am. Chem. Soc. , vol.135 , pp. 4918-4921
    • Tan, M.L.1    Cendagorta, J.R.2    Ichiye, T.3
  • 90
    • 36749006579 scopus 로고    scopus 로고
    • Docking and scoring protein complexes: Capri 3rd Edition
    • Lensink, M. F.; Mendez, R.; Wodak, S. J. Docking and scoring protein complexes: Capri 3rd Edition Proteins 2007, 69, 704-718
    • (2007) Proteins , vol.69 , pp. 704-718
    • Lensink, M.F.1    Mendez, R.2    Wodak, S.J.3
  • 91
    • 41949111630 scopus 로고    scopus 로고
    • Recent Progress and Future Directions in Protein-Protein Docking
    • Ritchie, D. W. Recent Progress and Future Directions in Protein-Protein Docking Curr. Protein Pept. Sci. 2008, 9, 1-15
    • (2008) Curr. Protein Pept. Sci. , vol.9 , pp. 1-15
    • Ritchie, D.W.1
  • 92
    • 41949102408 scopus 로고    scopus 로고
    • Predicting 3D Structures of Protein-Protein Complexes
    • Vakser, J. A.; Kundrotas, P. Predicting 3D Structures of Protein-Protein Complexes Curr. Pharm. Biotechnol. 2008, 9, 57-66
    • (2008) Curr. Pharm. Biotechnol. , vol.9 , pp. 57-66
    • Vakser, J.A.1    Kundrotas, P.2
  • 93
    • 18444383371 scopus 로고    scopus 로고
    • Protein Families and RNA Recognition
    • Chen, Y.; Varani, G. Protein Families and RNA Recognition FEBS J. 2005, 272, 2088-2097
    • (2005) FEBS J. , vol.272 , pp. 2088-2097
    • Chen, Y.1    Varani, G.2
  • 95
    • 23044465669 scopus 로고    scopus 로고
    • Long Dynamics Simulations of Proteins using Atomistic Force Fields and a Continuum Representation of Solvent Effects: Calculation of Structural and Dynamic Properties
    • Li, X.; Hassan, S. A.; Mehler, E. L. Long Dynamics Simulations of Proteins using Atomistic Force Fields and a Continuum Representation of Solvent Effects: Calculation of Structural and Dynamic Properties Proteins 2005, 60, 464-484
    • (2005) Proteins , vol.60 , pp. 464-484
    • Li, X.1    Hassan, S.A.2    Mehler, E.L.3
  • 96
    • 0020771265 scopus 로고
    • Dynamics of a Small Globular Protein in terms of Low-Frequency Vibrational Modes
    • Go, N.; Noguti, T.; Nishikawa, T. Dynamics of a Small Globular Protein in terms of Low-Frequency Vibrational Modes Proc. Natl. Acad. Sci. U.S.A. 1983, 80, 3696-3700
    • (1983) Proc. Natl. Acad. Sci. U.S.A. , vol.80 , pp. 3696-3700
    • Go, N.1    Noguti, T.2    Nishikawa, T.3
  • 97
    • 0022036264 scopus 로고
    • Efficient Monte Carlo Method for Simulation of Fluctuating Conformations of Native Proteins
    • Noguti, T.; Go, N. Efficient Monte Carlo Method for Simulation of Fluctuating Conformations of Native Proteins Biopolymers 1985, 24, 527-546
    • (1985) Biopolymers , vol.24 , pp. 527-546
    • Noguti, T.1    Go, N.2
  • 98
    • 0012280704 scopus 로고    scopus 로고
    • Structure Calculations of Protein Segments Connecting Domains with Defined Secondary Structure: A Simulated Annealing Monte Carlo Combined with Biased Scaled Collective Variables Technique
    • Hark, K. Schlick, T. Springer: New York
    • Hassan, S. A.; Mehler, E. L.; Weinstein, H. Structure Calculations of Protein Segments Connecting Domains with Defined Secondary Structure: A Simulated Annealing Monte Carlo Combined with Biased Scaled Collective Variables Technique. In Lecture Notes in Computational Science and Engineering; Hark, K.; Schlick, T., Eds.; Springer: New York, 2002; Vol. 24, pp 197-231.
    • (2002) Lecture Notes in Computational Science and Engineering , vol.24 , pp. 197-231
    • Hassan, S.A.1    Mehler, E.L.2    Weinstein, H.3
  • 99
    • 77955276088 scopus 로고    scopus 로고
    • Structural and Dynamic Determinants of Ligand Binding and Regulation of Cyclin-Dependent Kinase 5 by Pathological Activator p25 and Inhibitory Peptide CIP
    • Cardone, A.; Hassan, S. A.; Albers, R. W.; Sriram, R. D.; Pant, H. C. Structural and Dynamic Determinants of Ligand Binding and Regulation of Cyclin-Dependent Kinase 5 by Pathological Activator p25 and Inhibitory Peptide CIP J. Mol. Biol. 2010, 401, 478-492
    • (2010) J. Mol. Biol. , vol.401 , pp. 478-492
    • Cardone, A.1    Hassan, S.A.2    Albers, R.W.3    Sriram, R.D.4    Pant, H.C.5


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