Configurational entropy change of netropsin and distamycin upon DNA minor-groove binding.
暂无分享,去创建一个
Wilfred F van Gunsteren | Chris Oostenbrink | Joze Koller | Riccardo Baron | Jozica Dolenc | R. Baron | W. V. van Gunsteren | C. Oostenbrink | J. Dolenc | J. Koller
[1] H. Berendsen,et al. Free energy determination of polypeptide conformations generated by molecular dynamics , 1984 .
[2] Mark A. Miller,et al. Why is it so difficult to simulate entropies, free energies, and their differences? , 2001, Accounts of chemical research.
[3] P. Kollman,et al. Relative binding affinities of distamycin and its analog to d(CGCAAGTTGGC).d(GCCAACTTGCG): comparison of simulation results with experiment. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[4] Andrew E. Torda,et al. The GROMOS biomolecular simulation program package , 1999 .
[5] J G Pelton,et al. Structural characterization of a 2:1 distamycin A.d(CGCAAATTGGC) complex by two-dimensional NMR. , 1989, Proceedings of the National Academy of Sciences of the United States of America.
[6] J. Chaires,et al. Sequence and structural selectivity of nucleic acid binding ligands. , 1999, Biochemistry.
[7] D. Beveridge,et al. Structure and axis curvature in two dA6·dT6 DNA oligonucleotides: Comparison of molecular dynamics simulations with results from crystallography and NMR spectroscopy , 2004 .
[8] A V Finkelstein,et al. The price of lost freedom: entropy of bimolecular complex formation. , 1989, Protein engineering.
[9] X. Daura,et al. Entropy calculations on a reversibly folding peptide: Changes in solute free energy cannot explain folding behavior , 2001, Proteins.
[10] M. Orozco,et al. Cooperativity in drug-DNA recognition: a molecular dynamics study. , 2001, Journal of the American Chemical Society.
[11] R. Hertzberg,et al. Map of distamycin, netropsin, and actinomycin binding sites on heterogeneous DNA: DNA cleavage-inhibition patterns with methidiumpropyl-EDTA.Fe(II). , 1982, Proceedings of the National Academy of Sciences of the United States of America.
[12] Michael K Gilson,et al. Evaluating the Accuracy of the Quasiharmonic Approximation. , 2005, Journal of chemical theory and computation.
[13] J. Lah,et al. Binding of distamycin A and netropsin to the 12mer DNA duplexes containing mixed AT.GC sequences with at most five or three successive AT base pairs. , 2000, Biochemistry.
[14] D. Goodsell,et al. The molecular origin of DNA-drug specificity in netropsin and distamycin. , 1985, Proceedings of the National Academy of Sciences of the United States of America.
[15] W. V. van Gunsteren,et al. Estimating entropies from molecular dynamics simulations. , 2004, The Journal of chemical physics.
[16] J. Chaires,et al. Specific binding of hoechst 33258 to the d(CGCAAATTTGCG)2 duplex: calorimetric and spectroscopic studies. , 1997, Journal of molecular biology.
[17] H. Berendsen,et al. Interaction Models for Water in Relation to Protein Hydration , 1981 .
[18] J. Berg,et al. Molecular dynamics simulations of biomolecules , 2002, Nature Structural Biology.
[19] M. Searle,et al. Sequence-dependent variation in DNA minor groove width dictates orientational preference of Hoechst 33258 in A-tract recognition: solution NMR structure of the 2:1 complex with d(CTTTTGCAAAAG)(2). , 2000, Nucleic acids research.
[20] Adam R. Urbach,et al. Structure of a beta-alanine-linked polyamide bound to a full helical turn of purine tract DNA in the 1:1 motif. , 2002, Journal of molecular biology.
[21] William A. Goddard,et al. The two-phase model for calculating thermodynamic properties of liquids from molecular dynamics: Validation for the phase diagram of Lennard-Jones fluids , 2003 .
[22] J. Chaires,et al. Energetics of drug-DNA interactions. , 1997, Biopolymers.
[23] D. Goodsell,et al. Binding of an antitumor drug to DNA, Netropsin and C-G-C-G-A-A-T-T-BrC-G-C-G. , 1984, Journal of molecular biology.
[24] M. Karplus,et al. Method for estimating the configurational entropy of macromolecules , 1981 .
[25] K. Breslauer,et al. Enthalpy-entropy compensations in drug-DNA binding studies. , 1987, Proceedings of the National Academy of Sciences of the United States of America.
[26] A. Mclachlan. Gene duplications in the structural evolution of chymotrypsin. , 1979, Journal of molecular biology.
[27] D. Beveridge,et al. Free energy via molecular simulation: applications to chemical and biomolecular systems. , 1989, Annual review of biophysics and biophysical chemistry.
[28] S. Mackay,et al. Short lexitropsin that recognizes the DNA minor groove at 5'-ACTAGT-3': understanding the role of isopropyl-thiazole. , 2004, Journal of the American Chemical Society.
[29] B. Ramakrishnan,et al. Binding of two distamycin A molecules in the minor groove of an alternating B–DNA duplex , 1994, Nature Structural Biology.
[30] V. Sasisekharan,et al. Interaction of synthetic analogues of distamycin with poly(dA-dT): role of the conjugated N-methylpyrrole system. , 1987, Biochemistry.
[31] D. Wemmer,et al. Interaction of minor groove ligands to an AAATT/AATTT site: correlation of thermodynamic characterization and solution structure. , 1995, Biochemistry.
[32] H. Berendsen,et al. Molecular dynamics with coupling to an external bath , 1984 .
[33] Peter A. Kollman,et al. FREE ENERGY CALCULATIONS : APPLICATIONS TO CHEMICAL AND BIOCHEMICAL PHENOMENA , 1993 .
[34] Chris Oostenbrink,et al. Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site , 2005, Nucleic acids research.
[35] Wilfred F van Gunsteren,et al. Comparison of atomic-level and coarse-grained models for liquid hydrocarbons from molecular dynamics configurational entropy estimates. , 2006, The journal of physical chemistry. B.
[36] Wilfred F. van Gunsteren,et al. Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications , 1989 .
[37] Christophe Chipot,et al. Free Energy Calculations. The Long and Winding Gilded Road , 2002 .
[38] Wilma K Olson,et al. Knowledge-based elastic potentials for docking drugs or proteins with nucleic acids. , 2005, Biophysical journal.
[39] A. Cooper,et al. Thermodynamic analysis of biomolecular interactions. , 1999, Current opinion in chemical biology.
[40] W. Wilson,et al. Intercalation binding of 6‐substituted naphthothiopheneamides to DNA: Enthalpy and entropy components , 1991, Biopolymers.
[41] H. Dyson,et al. Intrinsically unstructured proteins and their functions , 2005, Nature Reviews Molecular Cell Biology.
[42] R. S. Spolar,et al. Coupling of local folding to site-specific binding of proteins to DNA. , 1994, Science.
[43] Thomas E Cheatham,et al. Simulation and modeling of nucleic acid structure, dynamics and interactions. , 2004, Current opinion in structural biology.
[44] A. Lyubartsev,et al. Molecular dynamics simulation study of oriented polyamine‐ and Na‐DNA: Sequence specific interactions and effects on DNA structure , 2004, Biopolymers.
[45] U. Pindur,et al. DNA Complexing Minor Groove-Binding Ligands: Perspectives in Antitumour and Antimicrobial Drug Design , 1999, Current Medicinal Chemistry.
[46] J. Šponer,et al. Crystal structure of d(GGCCAATTGG) complexed with DAPI reveals novel binding mode. , 1999, Biochemistry.
[47] J M Briggs,et al. Electrostatic and non-electrostatic contributions to the binding free energies of anthracycline antibiotics to DNA. , 1997, Journal of molecular biology.
[48] Kirk W. Johnson,et al. DNA binding ligands targeting drug-resistant bacteria: structure, activity, and pharmacology. , 2003, Journal of medicinal chemistry.
[49] Lukas D. Schuler,et al. On the Choice of Dihedral Angle Potential Energy Functions for n-Alkanes , 2000 .
[50] R. Wells,et al. Netropsin. A specific probe for A-T regions of duplex deoxyribonucleic acid. , 1974, The Journal of biological chemistry.
[51] T. P. Straatsma,et al. Free Energy by Molecular Simulation , 2007 .
[52] Wilfred F. van Gunsteren,et al. Absolute entropies from molecular dynamics simulation trajectories , 2000 .
[53] B. Tidor. Molecular dynamics simulations , 1997, Current Biology.
[54] Chris Oostenbrink,et al. An improved nucleic acid parameter set for the GROMOS force field , 2005, J. Comput. Chem..
[55] Christian Bailly,et al. Targeting DNA with novel diphenylcarbazoles. , 2004, Biochemistry.
[56] R. Hockney. The potential calculation and some applications , 1970 .
[57] A. Amadei,et al. A Theoretical Model for the Folding/Unfolding Thermodynamics of Single-Domain Proteins, Based on the Quasi-Gaussian Entropy Theory , 2004 .
[58] Luc Van Meervelt,et al. Two 1 : 1 binding modes for distamycin in the minor groove of d(GGCCAATTGG). , 2002, European journal of biochemistry.
[59] G. Ciccotti,et al. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .
[60] Mika A. Kastenholz,et al. Influence of artificial periodicity and ionic strength in molecular dynamics simulations of charged biomolecules employing lattice-sum methods , 2004 .
[61] Ronald M. Levy,et al. Entropy−Enthalpy Compensation in Solvation and Ligand Binding Revisited , 1998 .
[62] D. Goodsell,et al. Refinement of netropsin bound to DNA: bias and feedback in electron density map interpretation. , 1995, Biochemistry.
[63] H. Berendsen,et al. ENTROPY ESTIMATION FROM SIMULATIONS OF NON-DIFFUSIVE SYSTEMS , 1984 .
[64] Pavel Hobza,et al. Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. Minor groove binding between 4',6-diamidino-2-phenylindole and DNA duplexes in solution. , 2003, Journal of the American Chemical Society.
[65] P. Schleyer. Encyclopedia of computational chemistry , 1998 .
[66] J. Lah,et al. Energetic diversity of DNA minor-groove recognition by small molecules displayed through some model ligand-DNA systems. , 2004, Journal of molecular biology.
[67] D. Beveridge,et al. Assessment of the molecular dynamics structure of DNA in solution based on calculated and observed NMR NOESY volumes and dihedral angles from scalar coupling constants. , 2003, Biopolymers.
[68] Ioan Andricioaei,et al. On the calculation of entropy from covariance matrices of the atomic fluctuations , 2001 .
[69] Tim N. Heinz,et al. Comparison of four methods to compute the dielectric permittivity of liquids from molecular dynamics simulations , 2001 .
[70] D. Wemmer,et al. Binding modes of distamycin A with d(CGCAAATTTGCG)2 determined by two-dimensional NMR , 1990 .
[71] J. Schlitter. Estimation of absolute and relative entropies of macromolecules using the covariance matrix , 1993 .
[72] K. Liedl,et al. Significance of ligand tails for interaction with the minor groove of B-DNA. , 2001, Biophysical journal.
[73] C. Bailly,et al. Comparative thermodynamics for monomer and dimer sequence-dependent binding of a heterocyclic dication in the DNA minor groove. , 2002, Journal of molecular biology.
[74] T. Cheatham,et al. Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise * , 2000, Biopolymers.
[75] Peter A. Kollman,et al. CALCULATING THE ABSOLUTE FREE ENERGY OF ASSOCIATION OF NETROPSIN AND DNA , 1999 .
[76] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[77] R. Baron,et al. Configurational entropies of lipids in pure and mixed bilayers from atomic-level and coarse-grained molecular dynamics simulations. , 2006, The journal of physical chemistry. B.
[78] M. Waring,et al. Energetics of echinomycin binding to DNA. , 2003, Nucleic acids research.
[79] Jens Carlsson,et al. Absolute and relative entropies from computer simulation with applications to ligand binding. , 2005, The journal of physical chemistry. B.
[80] J. Chaires,et al. Energetics of DNA intercalation reactions. , 2000, Biochemistry.
[81] K. Liedl,et al. Simulation of EcoRI Dodecamer Netropsin Complex Confirms Class I Complexation Mode , 2000 .
[82] Wilfred F. van Gunsteren,et al. A generalized reaction field method for molecular dynamics simulations , 1995 .
[83] Mark A. Williams,et al. The extended interface: measuring non-local effects in biomolecular interactions. , 2004, Current opinion in structural biology.