Water-mediated interactions between DNA and PhoB DNA-binding/ transactivation domain: NMR-restrained molecular dynamics in explicit water environment

Proteins: Structure, Function and Genetics

Volumn 71, Issue 4, 2008, Pages 1970-1983

  Yamane, Tsutomu ^a   Okamura, Hideyasu ^a   Ikeguchi, Mitsunori ^a   Nishimura, Yoshifumi ^a   Kidera, Akinori ^a  

^a YOKOHAMA CITY UNIVERSITY   (Japan)

Author keywords

DNA recognition; Explicit water refinement; Molecular dynamics simulation; PhoB; Solution structure; Water mediated interactions

Indexed keywords

DNA; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR PHOB; WATER;

AQUEOUS SOLUTION; ARTICLE; COMPARATIVE STUDY; COMPLEX FORMATION; CRYSTAL STRUCTURE; DNA BINDING MOTIF; DNA STRUCTURE; ELECTRICITY; GEOMETRY; HYDRATION; HYDROGEN BOND; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; NUCLEAR MAGNETIC RESONANCE; PARTICULATE MATTER; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN DOMAIN; PROTEIN INTERACTION; TRANSACTIVATION; VACUUM;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BINDING SITES; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; DNA; ELECTROSTATICS; ESCHERICHIA COLI; HYDROGEN BONDING; HYDROPHOBICITY; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; TEMPERATURE; TRANS-ACTIVATION (GENETICS); WATER;

EID: 44349089769     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21874     Document Type: Article

References (36)

1. Lejeune D, Delsaux N, Charloteaux B, Thomas A, Brasseur R. Protein-nucleic acid recognition: statistical analysis of atomic interactions and Influence of DNA structure. Proteins 2005;61:258-271.
2. Jayaram B, Jain T. The role of water in protein-DNA recognition. Annu Rev Biophys Biomol Struct 2004;33:343-361.
3. Nilges M, Gronenborm AM, Brünger AT, Clore GM. Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints. Application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2. Protein Eng 1988;2:27-38.
4. Linge JP, Williams MA, Spronk CA, Bonvin AM, Nilges M. Refinement of protein structures in explicit solvent. Proteins 2003;50:496-506.
5. Chen J, Im W, Brooks CL, III. Refinement of NMR structures using implicit solvent and advanced sampling techniques. J Am Chem Soc 2004;126:16038-16047.
6. Chen J, Won H, Im W, Dyson HJ, Brooks CL, III. Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling. J Biomol NMR 2005;31:59-64.
7. Nabuurs SB, Nederveen AJ, Vranken W, Doreleijers JF, Bonvin AM, Vuister GW, Vriend G, Spronk CA. DRESS: a database of refined solution NMR structures. Proteins 2004;55:483-486.
8. Nederveen AJ, Doreleijers JF, Vranken W, Miller Z, Spronk CA, Nabuurs SB, Güntert P, Livny M, Markley JL, Nilges M, Ulrich EL, Kaptein R, Bonvin AM. RECOORD: a recalculated coordinate data-base of 500+ proteins from the PDB using restraints from the Bio-MagResBank. Proteins 2005;59:662-672.
9. Xia B, Tsui V, Case DA, Dyson HJ, Wright PE. Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water. J Biomol NMR 2002;22:317-331.
10. Otwinowski Z, Schevitz RW, Zhang R-G, Lawson CL, Joachimiak A, Marmorstein RQ, Luisi BF, Sigler PB. Crystal structure of trp represser/operator complex at atomic resolution. Nature 1988;335:321-329.
11. Wilson DS, Guenther B, Desplan C, Kuriyan J. High resolution crystal structure of a paired (Pax) class cooperative homeodomain dimer on DNA. Cell 1995;82:709-719.
12. Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ. Solvent-mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution. J Mol Biol 2002;319:1097-1113.
13. Chiu TK, Sohn C, Dickerson RE, Johnson RC. Testing water-mediated DNA recognition by the Hin recombinase. EMBO J 2002;21:801-814.
14. Chai J, Wu J-W, Yan N, Massagué J, Pavletich NP, Shi Y. Features of a Smad3 MH1-DNA complex. J Biol Chem 2003;278:20327-20331.
15. Wanner BL. Phosphorus assimilation and control of the phosphate regulon. In: Neidhardt FC, Curtiss RJ, Ingraham JL, Lin EC, Low KBJ, Magasanik B, Reznikoff W, Riley M, Schaechter M, Umbarger HE, editors. Escherichia coli and Salmonella typhimurium cellular and molecular biology. Washington, DC: American Society for Microbiology; 1996. pp 1357-1381.
16. Kim SK, Kimura S, Shinagawa H, Nakata A, Lee KS, Wanner BL, Makino K. Dual transcriptional regulation of the Escherichia coli phosphate-starvation-inducible psiE gene of the phosphate regulon by PhoB and cyclic AMP (cAMP)-cAMP receptor protein complex. J Bacteriol 2000;182:5596-5599.
17. Blanco AG, Sola M, Gomis-Rüth FX, Coll M. Tandem DNA recognition by PhoB, a two-component signal transduction transcriptional activator. Structure 2002;10:701-713.
18. Wanner BL. Gene regulation by phosphate in enteric bacteria. J Cell Biochem 1993;51:47-54.
19. Makino K, Shinagawa H, Amemura M, Nakata A. Nucleotide sequence of the PhoB gene, the positive regulatory gene for the phosphate regulon of Escherichia coli K-12. J Mol Biol 1986;190:37-44.
20. Okamura H, Hanaoka S, Nagadoi A, Makino K, Nishimura Y. Structural comparison of the PhoB and OmpR DNA-binding transactivation domains and the arrangement of PhoB molecules on the Phosphate box.. J Mol Biol 2000;259:1225-1236.
21. Makino K, Amemura M, Kawamoto T, Kimura S, Shinagawa H, Nakata A, Suzuki M. DNA binding of PhoB and its interaction with RNA polymerase. J Mol Biol 1996;259:15-26.
22. Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A. NMRPipe: a multidimensional spectral processing system based on UNIX PIPES. J Biomol NMR 1995;6:277-293.
23. Garret DS, Powers R, Gronenborm AM, Clore GM. A common sense approach to peak picking in two-, three-, and four-dimensional spectra using automatic computer analysis of contour diagrams. J Magn Reson 1991;99:214-220.
24. Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang J-S, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL. Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D 1998;54:905-921.
25. Ikeguchi M. Partial rigid-body dynamics in NPT. NPAT and NPγT ensembles for proteins and membranes J Comput Chem 2004;25:529-541.
26. Clore GM, Nilges M, Sukumaran DK, Brünger AT, Karplus M, Gronenborn AM. The three-dimensional structure of a 1-purothionin in solution: combined use of nuclear magnetic resonance, distance geometry, and restrained molecular dynamics. EMBO J 1986;104:2729-2735.
27. Schomaker V, Waser J, Marsh RE, Bergman G. To fit a plane or a line to a set of points by least squares. Acta Crystallogr 1959;12:600-604.
28. MacKerell ADJ, Feig M, Brooks CLI. Extending the treatment of backbone energetics in protein force fields: limitation of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem 2004;25:1400-1415.
29. Feller SE, Yin D, Pastor RW, MacKerell ADJ. Molecular dynamics simulation of unsaturated lipid bilayers at low hydration: parameterization and comparison with diffraction studies. Biophys J 1997;73:2269-2279.
30. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;79:926-935.
31. Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG. A smooth particle mesh Ewald method. J Chem Phys 1995;103:8577-8593.
32. Pelton JG, Torchia DA, Meadow ND, Roseman S. Tautomeric states of the active-site histidines of phosphorylated and unphosphorylated IIIG1c, a signal-transducing protein from Escherichia coli, using two-dimensional heteronuclear NMR techniques. Protein Sci 1993;2:543-558.
33. a values of ionizable groups in bacteriorhodopsin. J Mol Biol 1992;224:473-486.
34. Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 1993;26:283-291.
35. McDonald IK, Thornton JM. Satisfying hydrogen bonding potential in proteins. J Mol Biol 1994;238:777-793.
36. Tsui V, Radhakrishnan I, Wright PE, Case DA. NMR and molecular dynamics studies of the hydration of zinc finger-DNA complex. J Mol Biol 2000;302:1101-1117.