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Water‐mediated interactions between DNA and PhoB DNA‐binding/transactivation domain: NMR‐restrained molecular dynamics in explicit water environment
Author(s) -
Yamane Tsutomu,
Okamura Hideyasu,
Ikeguchi Mitsunori,
Nishimura Yoshifumi,
Kidera Akinori
Publication year - 2008
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21874
Subject(s) - dna , hydrogen bond , molecular dynamics , transactivation , chemistry , crystallography , biophysics , chemical physics , crystal structure , dna binding domain , static electricity , molecule , computational chemistry , biochemistry , transcription factor , physics , biology , gene , organic chemistry , quantum mechanics
The solution structure of the complex between the transcription factor PhoB DNA‐binding/transactivation domain and DNA was determined by NMR spectroscopy and simulated annealing in a periodic boundary box of explicit water with the particle mesh Ewald method. The refined structures provided better convergence and better local geometry compared with the structures determined in vacuum. The hydrogen bond interactions between the PhoB domain and DNA in the aqueous environment were fully formed. The complex structure was found to be very similar to the crystal structure, particularly at the PhoB‐DNA interface, much more so than expected from the vacuum structure. These results indicate the importance of the proper treatment of electrostatic and hydration influences in describing protein‐DNA interactions. The hydration structures observed for the refined structures contained most of the crystal waters as a subset. We observed that various water‐mediated PhoB‐DNA interactions contributed to the molecular recognition between PhoB and DNA. Proteins 2008. © 2008 Wiley‐Liss, Inc.