Counterion atmosphere and hydration patterns near a nucleosome core particle.
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Alexey Savelyev | Garegin A Papoian | G. Papoian | A. Savelyev | Christopher K Materese | C. Materese
[1] G. Papoian,et al. Electrostatic, steric, and hydration interactions favor Na(+) condensation around DNA compared with K(+). , 2006, Journal of the American Chemical Society.
[2] Karolin Luger,et al. Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions , 2001, The EMBO journal.
[3] G. S. Manning. Is a small number of charge neutralizations sufficient to bend nucleosome core DNA onto its superhelical ramp? , 2003, Journal of the American Chemical Society.
[4] T. Richmond,et al. Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. , 2002, Journal of molecular biology.
[5] Martin Zacharias,et al. Structural flexibility of the nucleosome core particle at atomic resolution studied by molecular dynamics simulation. , 2007, Biopolymers.
[6] T. Richmond,et al. Crystal structure of the nucleosome core particle at 2.8 Å resolution , 1997, Nature.
[7] A. Dobrynin,et al. Theory of polyelectrolytes in solutions and at surfaces , 2005 .
[8] Arieh Warshel,et al. Modeling electrostatic effects in proteins. , 2006, Biochimica et biophysica acta.
[9] D. Tremethick,et al. The nucleosome surface regulates chromatin compaction and couples it with transcriptional repression , 2007, Nature Structural &Molecular Biology.
[10] G. Papoian,et al. Inter-DNA electrostatics from explicit solvent molecular dynamics simulations. , 2007, Journal of the American Chemical Society.
[11] D. Durand,et al. Structure and phase diagram of nucleosome core particles aggregated by multivalent cations. , 2007, Biophysical journal.
[12] A. Wolffe,et al. Histone-DNA contacts in a nucleosome core containing a Xenopus 5S rRNA gene. , 1993, Biochemistry.
[13] Kelly M. Thayer,et al. Ion motions in molecular dynamics simulations on DNA. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[14] C. Allis,et al. Histone and chromatin cross-talk. , 2003, Current opinion in cell biology.
[15] Dieter W Heermann,et al. Computational modeling of the chromatin fiber. , 2007, Seminars in cell & developmental biology.
[16] Nathan A. Baker,et al. Electrostatics of nanosystems: Application to microtubules and the ribosome , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[17] Alexander D. MacKerell,et al. Development and current status of the CHARMM force field for nucleic acids , 2000, Biopolymers.
[18] Alexey Savelyev,et al. Molecular renormalization group coarse-graining of electrolyte solutions: application to aqueous NaCl and KCl. , 2009, The journal of physical chemistry. B.
[19] Alexey Savelyev,et al. Molecular renormalization group coarse-graining of polymer chains: application to double-stranded DNA. , 2009, Biophysical journal.
[20] M. Rubinstein,et al. Counterion phase transitions in dilute polyelectrolyte solutions. , 2001, Physical review letters.
[21] B. Pettitt,et al. Sodium and chlorine ions as part of the DNA solvation shell. , 1999, Biophysical journal.
[22] M. Berkowitz,et al. Orientational dynamics of water in phospholipid bilayers with different hydration levels. , 2009, The journal of physical chemistry. B.
[23] Mikael Lund,et al. A mesoscopic model for protein-protein interactions in solution. , 2003, Biophysical journal.
[24] D. Angelov,et al. Preferential interaction of the core histone tail domains with linker DNA , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[25] G. Papoian,et al. Polyionic charge density plays a key role in differential recognition of mobile ions by biopolymers. , 2008, The journal of physical chemistry. B.
[26] W. Gelbart,et al. DNA folding: structural and mechanical properties of the two-angle model for chromatin. , 2001, Biophysical journal.
[27] Gerald S. Manning,et al. Limiting Laws and Counterion Condensation in Polyelectrolyte Solutions I. Colligative Properties , 1969 .
[28] Changbong Hyeon,et al. Charge density of divalent metal cations determines RNA stability. , 2007, Journal of the American Chemical Society.
[29] Krystyna Zakrzewska,et al. DNA and its counterions: a molecular dynamics study. , 2004, Nucleic acids research.
[30] C. Allis,et al. The language of covalent histone modifications , 2000, Nature.
[31] S. Grigoryev,et al. A chromatin folding model that incorporates linker variability generates fibers resembling the native structures. , 1993, Proceedings of the National Academy of Sciences of the United States of America.
[32] G. Papoian,et al. Hierarchical organization of eglin c native state dynamics is shaped by competing direct and water-mediated interactions , 2008, Proceedings of the National Academy of Sciences.
[33] G. Papoian,et al. Free energy calculations of counterion partitioning between DNA and chloride solutions , 2007 .
[34] Laxmikant V. Kalé,et al. Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..
[35] Hans-Peter Lenhof,et al. BALL-rapid software prototyping in computational molecular biology , 2000, Bioinform..
[36] T. Schlick,et al. Electrostatic mechanism of nucleosomal array folding revealed by computer simulation. , 2005, Proceedings of the National Academy of Sciences of the United States of America.