Water organization between oppositely charged surfaces: implications for protein sliding along DNA.
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[1] Jeremy L. England,et al. Chemical denaturants inhibit the onset of dewetting. , 2008, Journal of the American Chemical Society.
[2] Janet M Thornton,et al. Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity. , 2002, Journal of molecular biology.
[3] P. Bradley,et al. Probing the role of interfacial waters in protein–DNA recognition using a hybrid implicit/explicit solvation model , 2013, Proteins.
[4] R. Lavery,et al. Protein-DNA recognition triggered by a DNA conformational switch. , 2011, Angewandte Chemie.
[5] B. Luisi,et al. A recipe for specificity , 1995, Nature Structural Biology.
[6] Alexey Savelyev,et al. Counterion atmosphere and hydration patterns near a nucleosome core particle. , 2009, Journal of the American Chemical Society.
[7] Peter G Wolynes,et al. Role of water mediated interactions in protein-protein recognition landscapes. , 2003, Journal of the American Chemical Society.
[8] V A Parsegian,et al. On the electrostatic interaction across a salt solution between two bodies bearing unequal charges. , 1972, Biophysical journal.
[9] Eric J. Sorin,et al. Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. , 2005, Biophysical journal.
[10] G. Papoian,et al. Inter-DNA electrostatics from explicit solvent molecular dynamics simulations. , 2007, Journal of the American Chemical Society.
[11] N. Khazanov,et al. Asymmetric DNA-search dynamics by symmetric dimeric proteins. , 2013, Biochemistry.
[12] L. Mirny,et al. Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential. , 2004, Biophysical journal.
[13] V. Dahirel,et al. Nonspecific DNA-protein interaction: why proteins can diffuse along DNA. , 2009, Physical review letters.
[14] M Levitt,et al. Water: now you see it, now you don't. , 1993, Structure.
[15] Alexey Savelyev,et al. Chemically accurate coarse graining of double-stranded DNA , 2010, Proceedings of the National Academy of Sciences.
[16] J. Janin,et al. Wet and dry interfaces: the role of solvent in protein-protein and protein-DNA recognition. , 1999, Structure.
[17] Gerrit Groenhof,et al. GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..
[18] S. Safran,et al. Direct measurement of sub-Debye-length attraction between oppositely charged surfaces. , 2009, Physical review letters.
[19] P. Ball. Water as an active constituent in cell biology. , 2008, Chemical reviews.
[20] Yaakov Levy,et al. DNA search efficiency is modulated by charge composition and distribution in the intrinsically disordered tail , 2010, Proceedings of the National Academy of Sciences.
[21] D. Rau,et al. Water release associated with specific binding of gal repressor. , 1995, The EMBO journal.
[22] X. Xie,et al. Nonspecifically bound proteins spin while diffusing along DNA , 2009, Nature Structural &Molecular Biology.
[23] Y. Levy,et al. Asymmetrical roles of zinc fingers in dynamic DNA-scanning process by the inducible transcription factor Egr-1 , 2012, Proceedings of the National Academy of Sciences.
[24] B Montgomery Pettitt,et al. The binding process of a nonspecific enzyme with DNA. , 2011, Biophysical journal.
[25] Richard Lavery,et al. A free energy pathway for the interaction of the SRY protein with its binding site on DNA from atomistic simulations. , 2009, Journal of the American Chemical Society.
[26] Yaakov Levy,et al. Protein sliding along DNA: dynamics and structural characterization. , 2009, Journal of molecular biology.
[27] J. Onuchic,et al. Water mediation in protein folding and molecular recognition. , 2006, Annual review of biophysics and biomolecular structure.
[28] J. Leroy,et al. Hydration and solution structure of nucleic acids. , 1995, Current opinion in structural biology.
[29] Y. Levy,et al. Searching DNA via a "Monkey Bar" mechanism: the significance of disordered tails. , 2010, Journal of molecular biology.
[30] Tarun Jain,et al. The role of water in protein-DNA recognition. , 2004, Annual review of biophysics and biomolecular structure.
[31] T. Härd,et al. Sequence-specific DNA-binding dominated by dehydration. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[32] Kumar,et al. Efficient Monte Carlo methods for the computer simulation of biological molecules. , 1992, Physical review. A, Atomic, molecular, and optical physics.
[33] R. Zwanzig,et al. Diffusion in a rough potential. , 1988, Proceedings of the National Academy of Sciences of the United States of America.
[34] C. Garvie,et al. Recognition of specific DNA sequences. , 2001, Molecular cell.
[35] G. Papoian,et al. Electrostatic, steric, and hydration interactions favor Na(+) condensation around DNA compared with K(+). , 2006, Journal of the American Chemical Society.
[36] Yaakov Levy,et al. Water and proteins: a love-hate relationship. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[37] M. Record,et al. Ions as regulators of protein-nucleic acid interactions in vitro and in vivo. , 1985, Advances in biophysics.
[38] V. Dahirel,et al. Ion-mediated interactions between charged and neutral nanoparticles. , 2008, Physical chemistry chemical physics : PCCP.
[39] Yaakov Levy,et al. Weak frustration regulates sliding and binding kinetics on rugged protein-DNA landscapes. , 2013, The journal of physical chemistry. B.
[40] Yaakov Levy,et al. Frustration in protein–DNA binding influences conformational switching and target search kinetics , 2011, Proceedings of the National Academy of Sciences.