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Group: baker-group - with tag protein-nucleic_acid_interactions [93 articles]

Neue Artikel von Mitliedern der Gruppe baker-group Gruppe with tag protein-nucleic_acid_interactions
  • Salt-Mediated Electrostatics in the Association of TATA Binding Proteins to DNA: A Combined Molecular Mechanics/Poisson-Boltzmann Study
    Biophys. J., Vol. 94, No. 12. (15 June 2008), pp. 4634-4645.
    by Johan H Bredenberg, Cristina Russo, Marcia O Fenley
    posted to electrostatics protein-nucleic_acid_interactions solvation by sobolevnrm to the group baker-group on 2008-07-25 11:56:28 as read along with 1 person and 2 groups barry McCammon structural_bioinformatics
  • DNA Binding and Bending by HMG Boxes: Energetic Determinants of Specificity
    Journal of Molecular Biology, Vol. 343, No. 2. (15 October 2004), pp. 371-393.
    by Anatoly I Dragan, Christopher M Read, Elena N Makeyeva, Ekaterina I Milgotina, Mair E Churchill, Colyn Crane-Robinson, Peter L Privalov
    posted to electrostatics protein-nucleic_acid_interactions solvation by sobolevnrm to the group baker-group on 2008-06-30 15:33:24 as read
  • RNA recognition motifs: boring? Not quite
    Current Opinion in Structural Biology, Vol. 18, No. 3. (June 2008), pp. 290-298.
    by Antoine Cléry, Markus Blatter, Frédéric H Allain
    posted to protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2008-06-17 12:11:28 as read
  • Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry
    Nucl. Acids Res. (14 February 2008), gkn008.
    by Yao C Chen, Carmay Lim
    posted to bioinformatics electrostatics nucleic_acids protein-nucleic_acid_interactions structure by sobolevnrm to the group baker-group on 2008-04-29 11:22:51 as read along with 3 people kaarsinogen sunhwan marck
  • Do water molecules mediate protein-DNA recognition?
    J Mol Biol, Vol. 314, No. 3. (30 November 2001), pp. 619-632.
    by CK Reddy, A Das, B Jayaram
    posted to electrostatics protein-nucleic_acid_interactions solvation by sobolevnrm to the group baker-group on 2008-04-25 16:07:15 as read along with 2 people yoonk medic0747
  • Hydration and DNA Recognition by Homeodomains
    Cell, Vol. 85, No. 7. (28 June 1996), pp. 1057-1065.
    by Martin Billeter, Peter Güntert, Peter Luginbühl, Kurt Wüthrich
    posted to electrostatics protein-nucleic_acid_interactions solvation by sobolevnrm to the group baker-group on 2008-04-25 15:57:42 as read
  • Water molecules in DNA recognition II: a molecular dynamics view of the structure and hydration of the trp operator
    Journal of Molecular Biology, Vol. 282, No. 4. (2 October 1998), pp. 859-873.
    by Alexandre M Bonvin, Maria Sunnerhagen, Gottfried Otting, Wilfred F van Gunsteren
    posted to electrostatics nucleic_acids protein-nucleic_acid_interactions solvation by sobolevnrm to the group baker-group on 2008-04-25 15:52:31 as read
  • Structural basis for gate-DNA recognition and bending by type IIA topoisomerases
    Nature, Vol. 450, No. 7173., pp. 1201-1205.
    by Ken C Dong, James M Berger
    posted to apbs protein-nucleic_acid_interactions structure by sobolevnrm to the group baker-group on 2008-04-18 14:02:38 as read along with 1 person cactus
  • Dynamics of Recognition between tRNA and Elongation Factor Tu
    Journal of Molecular Biology, Vol. 377, No. 5. (11 April 2008), pp. 1382-1405.
    by John Eargle, Alexis A Black, Anurag Sethi, Leonardo G Trabuco, Zaida Luthey-Schulten
    posted to allostery electrostatics nucleic_acids protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2008-03-25 11:14:58 as read
  • Molecular dynamics simulations of nucleic acid-protein complexes
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Mackerell, Lennart Nilsson
    posted to molecular_dynamics molecular_simulation protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2008-03-14 11:15:30 as read along with 3 people ruvido zwang phoenixzxl
  • Formation of a Wrapped DNA-Protein Interface: Experimental Characterization and Analysis of the Large Contributions of Ions and Water to the Thermodynamics of Binding IHF to H' DNA
    Journal of Molecular Biology, Vol. 377, No. 1. (14 March 2008), pp. 9-27.
    by Vander, Ruth M Saecker, Record
    posted to electrostatics protein-nucleic_acid_interactions solvation by sobolevnrm to the group baker-group on 2008-03-03 12:04:18 as read
  • Prediction of Salt and Mutational Effects on the Association Rate of U1A Protein and U1 Small Nuclear RNA Stem/Loop II
    J. Phys. Chem. B (22 December 2007)
    by S Qin, HX Zhou
    posted to diffusion kinetics protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2008-01-30 12:33:48 as read
  • From “Simple” DNA-Protein Interactions to the Macromolecular Machines of Gene Expression
    Annual Review of Biophysics and Biomolecular Structure, Vol. 36 (2007), pp. 79-105.
    by PH von Hippel
    posted to protein-nucleic_acid_interactions nucleic_acids by sobolevnrm to the group baker-group on 2007-08-06 14:33:02 as read
  • Dynamic Structural Rearrangements Between DNA Binding Modes of E. coli SSB Protein
    Journal of Molecular Biology, Vol. 369, No. 5. (2007), pp. 1244-57.
    by R Roy, AG Kozlov, TM Lohman, T Ha
    posted to protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2007-07-23 13:34:53 as read
  • Linkage of pH, Anion and Cation Effects in Protein-Nucleic Acid Equilibria
    Journal of Molecular Biology, Vol. 236, No. 1. (1994), pp. 165-78.
    by LB Overman, TM Lohman
    posted to solvation protein-nucleic_acid_interactions electrostatics by sobolevnrm to the group baker-group on 2007-06-13 01:34:48 as read
  • A Highly Salt-Dependent Enthalpy Change for Escherichia coli SSB Protein-Nucleic Acid Binding Due to Ion-Protein Interactions
    Biochemistry, Vol. 35, No. 16. (1996), pp. 5272-9.
    by TM Lohman, LB Overman, ME Ferrari, AG Kozlov
    posted to solvation protein-nucleic_acid_interactions electrostatics by sobolevnrm to the group baker-group on 2007-06-13 01:34:48 as read
  • Calorimetric studies of E. coli SSB protein-single-stranded DNA interactions. Effects of monovalent salts on binding enthalpy
    Journal of Molecular Biology, Vol. 278, No. 5. (1998), pp. 999-1014.
    by AG Kozlov, TM Lohman
    posted to solvation protein-nucleic_acid_interactions electrostatics by sobolevnrm to the group baker-group on 2007-06-13 01:34:48 as read
  • The Importance of Coulombic End Effects: Experimental Characterization of the Effects of Oligonucleotide Flanking Charges on the Strength and Salt Dependence of Oligocation (L8+) Binding to Single-Stranded DNA Oligomers
    Biophysical Journal, Vol. 76, No. 2. (1999), pp. 1008-17.
    by W Zhang, H Ni, MW Capp, CF Anderson, TM Lohman, MT Record
    posted to solvation protein-nucleic_acid_interactions nucleic_acids electrostatics by sobolevnrm to the group baker-group on 2007-06-13 01:34:48 as read
  • RNA-binding proteins: modular design for efficient function
    Nature Reviews Molecular Cell Biology, Vol. 8, No. 6. (2007), pp. 479-90.
    by BM Lunde, C Moore, G Varani
    posted to structure protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2007-06-05 13:06:49 as read
  • Water mediated protein-DNA interactions: The relationship of thermodynamics to structural detail
    Protein Science, Vol. 5, No. 10. (1996), pp. 2115-8.
    by CJ Morton, JE Ladbury
    posted to solvation protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2007-05-25 14:37:06 as read
  • Do electrostatic interactions destabilize protein-nucleic acid binding?
    Biopolymers (in press)
    by S Qin, HX Zhou
    posted to protein-nucleic_acid_interactions nucleic_acids electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:36:29 as read
  • Mechanisms of nucleic acid translocases: lessons from structural biology and single-molecule biophysics
    Current Opinion in Structural Biology, Vol. 17, No. 1. (2007), pp. 87-95.
    by KP Hopfner, J Michaelis
    posted to protein-nucleic_acid_interactions nucleic_acids helicase by sobolevnrm to the group baker-group on 2007-05-25 14:36:29 as read
  • DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces
    Nucleic Acids Research (in press)
    by H Tjong, HX Zhou
    posted to protein-nucleic_acid_interactions bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:36:28 as read
  • A Systems Approach to Measuring the Binding Energy Landscapes of Transcription Factors
    Science, Vol. 315, No. 5809. (2007), pp. 233-7.
    by SJ Maerkl, SR Quake
    posted to systems_biology protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2007-05-25 14:36:04 as read
  • Fly-Casting in Protein-DNA Binding: Frustration between Protein Folding and Electrostatics Facilitates Target Recognition
    Journal of the American Chemical Society (in press)
    by Y Levy, JN Onuchic, PG Wolynes
    posted to protein-nucleic_acid_interactions electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:36:04 as read
  • Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 103, No. 44. (2006), pp. 16236-41.
    by G Arya, T Schlick
    posted to protein-nucleic_acid_interactions multiscale by sobolevnrm to the group baker-group on 2007-05-25 14:24:56 as read
  • Probing 3'-ssDNA loop formation in E. coli RecBCD/RecBC-DNA complexes using non-natural DNA: a model for "Chi" recognition complexes
    Journal of Molecular Biology, Vol. 362, No. 1. (2006), pp. 26-43.
    by CJ Wong, RL Rice, T Ju, TM Lohman
    posted to protein-nucleic_acid_interactions nucleic_acids by sobolevnrm to the group baker-group on 2007-05-25 14:23:17 as read
  • Do Collective Atomic Fluctuations Account for Cooperative Effects? Molecular Dynamics Studies of the U1A-RNA Complex
    Journal of the American Chemical Society, Vol. 128, No. 28. (2006), pp. 8992-3.
    by BL Kormos, AM Baranger, DL Beveridge
    posted to protein-nucleic_acid_interactions nucleic_acids molecular_dynamics allostery by sobolevnrm to the group baker-group on 2007-05-25 14:23:17 as read
  • Modeling the Lac repressor-operator assembly: The influence of DNA looping on Lac repressor conformation
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 103, No. 26. (2006), pp. 9879-84.
    by D Swigon, BD Coleman, WK Olson
    posted to protein-nucleic_acid_interactions multiscale by sobolevnrm to the group baker-group on 2007-05-25 14:23:17 as read
  • Computational redesign of endonuclease DNA binding and cleavage specificity
    Nature, Vol. 441, No. 7093. (2006), pp. 656-9.
    by J Ashworth, JJ Havranek, CM Duarte, D Sussman, Jr, BL Stoddard, D Baker
    posted to protein_engineering protein-nucleic_acid_interactions nucleic_acids by sobolevnrm to the group baker-group on 2007-05-25 14:22:46 as read
  • Kinetic mechanism of adenine nucleotide binding to and hydrolysis by the Escherichia coli Rep monomer. 2. Application of a kinetic competition approach
    Biochemistry, Vol. 33, No. 48. (1994), pp. 14565-78.
    by KJM Moore, TM Lohman
    posted to protein-nucleic_acid_interactions nucleic_acids electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:22:46 as read
  • Microsecond Dynamics of ProteinâDNA Interactions: Direct Observation of the Wrapping/Unwrapping Kinetics of Single-stranded DNA around the E. coli SSB Tetramer
    Journal of Molecular Biology, Vol. 359, No. 1. (2006), pp. 55-65.
    by SV Kuznetsov, AG Kozlov, TM Lohman, A Ansari
    posted to protein-nucleic_acid_interactions diffusion by sobolevnrm to the group baker-group on 2007-05-25 14:22:46 as read
  • Effects of Monovalent Anions on a Temperature-Dependent Heat Capacity Change for Escherichia coli SSB Tetramer Binding to Single-Stranded DNA
    Biochemistry, Vol. 45, No. 16. (2006), pp. 5190-205.
    by AG Kozlov, TM Lohman
    posted to solvation protein-nucleic_acid_interactions electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:22:45 as read
  • Exploring Assembly Energetics of the 30S Ribosomal Subunit Using an Implicit Solvent Approach
    Journal of the American Chemical Society, Vol. 127, No. 31. (2005), pp. 11125-31.
    by J Trylska, JA Mccammon, Iii
    posted to ribosome protein-nucleic_acid_interactions electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:19:28 as read
  • The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA
    Nucleic Acids Research, Vol. 34, No. 1. (2006), pp. 275-85.
    by MJ Law, ME Linde, EJ Chambers, C Oubridge, PS Katsamba, L Nilsson, IS Haworth, Laird IA Offringa
    posted to protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2007-05-25 14:19:28 as read
  • Kernel-based machine learning protocol for predicting DNA-binding proteins
    Nucleic Acids Research, Vol. 33, No. 20. (2005), pp. 6486-93.
    by N Bhardwaj, RE Langlois, H Lu
    posted to protein-nucleic_acid_interactions electrostatics bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:19:26 as read
  • Repetitive shuttling of a motor protein on DNA
    Nature, Vol. 437, No. 7063. (2005), pp. 1321-5.
    by S Myong, I Rasnik, C Joo, TM Lohman, T Ha
    posted to protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2007-05-25 14:19:03 as read
  • Coupled dynamics of DNA breathing and of proteins that selectively bind to single-stranded DNA
    Physical Review E, Vol. 72 (2005)
    by T Ambjã¶rnsson, R Metzler
    posted to statistical_mechanics protein-nucleic_acid_interactions nucleic_acids diffusion by sobolevnrm to the group baker-group on 2007-05-25 14:18:44 as read
  • Energetics of DNA End Binding by E. coli RecBC and RecBCD Helicases Indicate Loop Formation in the 3â²-Single-stranded DNA Tail
    Journal of Molecular Biology, Vol. 352, No. 4. (2005), pp. 765-82.
    by CJ Wong, AL Lucius, TM Lohman
    posted to protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2007-05-25 14:18:25 as read
  • Exploring Assembly Energetics of the 30S Ribosomal Subunit Using an Implicit Solvent Approach
    Journal of the American Chemical Society, Vol. 127, No. 31. (2005), pp. 11125-33.
    by J Trylska, JA Mccammon, Iii
    posted to ribosome protein-nucleic_acid_interactions electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:18:24 as read
  • Docking kinetics and equilibrium of a GAAA tetraloop-receptor motif probed by single-molecule FRET
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 30. (2005), pp. 10505-10.
    by JH Hodak, JL Fiore, DJ Nesbitt, CD Downey, A Pardi
    posted to protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2007-05-25 14:18:24 as read
  • Autoinhibition of Escherichia coli Rep monomer helicase activity by its 2B subdomain
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 29. (2005), pp. 10076-81.
    by KM Brendza, W Cheng, CJ Fischer, MA Chesnik, Niedziela A Majka, TM Lohman
    posted to protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2007-05-25 14:18:24 as read
  • Correlated Motions in the U1 snRNA Stem/Loop 2: U1A RBD1 Complex
    Biophysical Journal, Vol. 89, No. 3. (2005), pp. 2046-58.
    by SA Showalter, KB Hall
    posted to protein-nucleic_acid_interactions nucleic_acids molecular_dynamics by sobolevnrm to the group baker-group on 2007-05-25 14:18:04 as read
  • Regulation of transcription: from lambda to eukaryotes
    Trends in Biochemical Sciences, Vol. 30, No. 6. (2005), pp. 275-9.
    by M Ptashne
    posted to protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2007-05-25 14:17:41 as read
  • Electrostatic mechanism of nucleosomal array folding revealed by computer simulation
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 23. (2005), pp. 8180-5.
    by J Sun, Q Zhang, T Schlick
    posted to protein-nucleic_acid_interactions multiscale electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:17:41 as read
  • Interfacial water as a "hydration fingerprint" in the non-cognate complex of BamHI
    Biophysical Journal (2005)
    by M Fuxreiter, M Mezei, I Simon, R Osman
    posted to solvation protein-nucleic_acid_interactions nucleic_acids by sobolevnrm to the group baker-group on 2007-05-25 14:17:41 as read
  • Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 19. (2005), pp. 6783-8.
    by E Villa, A Balaeff, K Schulten
    posted to protein-nucleic_acid_interactions multiscale molecular_dynamics by sobolevnrm to the group baker-group on 2007-05-25 14:17:41 as read
  • Strongly coupled polyelectrolyteâmacroion complexes
    Journal of Physics: Condensed Matter, Vol. 17, No. 14. (2005), pp. S1137-S1151.
    by H Boroudjerdi, RR Netz
    posted to statistical_mechanics protein-nucleic_acid_interactions electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:16:05 as read
  • A binding mechanism in proteinânucleotide interactions: Implication for U1A RNA binding
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 11. (2005), pp. 3954-9.
    by V Guallar, KW Borrelli
    posted to protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2007-05-25 14:16:05 as read
  • DNA twisting flexibility and the formation of sharply looped proteinâDNA complexes
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 10. (2005), pp. 3645-50.
    by TE Cloutier, J Widom
    posted to protein-nucleic_acid_interactions nucleic_acids by sobolevnrm to the group baker-group on 2007-05-25 14:15:43 as read
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