Water molecules in DNA recognition I: hydration lifetimes of trp operator DNA in solution measured by NMR spectroscopy.
The present NMR study investigates the residence times of the hydration water molecules associated with uncomplexed trp operator DNA in solution by measuring intermolecular nuclear Overhauser effects (NOE) between water and DNA protons, and the nuclear magnetic relaxation dispersion (NMRD) of the water 2H and 17O resonances. Both methods indicate that the hydration water molecules exchange with bulk water on the sub-nanosecond time scale at 4 degreesC. No evidence was obtained for water molecules bound with longer residence times. In particular, the water molecules at the sites of interfacial hydration in the trp repressor/operator complex do not seem kinetically stabilized in the uncomplexed DNA. Analysis of the crystal structures of two different trp repressor/operator complexes shows very similar structural environments for the water molecules mediating specific contacts between the protein and the DNA, whereas much larger variations are observed for the location of corresponding water molecules detected in the crystal structure of an uncomplexed trp operator DNA duplex. Therefore, it appears unlikely that the hydration characteristics of the uncomplexed DNA target would be a major determinant of trp repressor/operator recognition.
Sunnerhagen
M
M
Department of Medical Biochemistry and Biophysics, Karolinska Institute, Doktorsringen 9A1, Stockholm, S-171 77, Sweden.
Denisov
V P
VP
Venu
K
K
Bonvin
A M
AM
Carey
J
J
Halle
B
B
Otting
G
G
D001426:Bacterial Proteins; D001483:Base Sequence; D001665:Binding Sites; D003460:Crystallization; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D005798:Genes, Bacterial / Q000235:genetics; D006860:Hydrogen Bonding; D007700:Kinetics; D008958:Models, Molecular; D009429:Netropsin / Q000378:metabolism; D019906:Nuclear Magnetic Resonance, Biomolecular; D009875:Operator Regions, Genetic / Q000235:genetics*; D011522:Protons; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism; D012997:Solvents; D014364:Tryptophan / Q000235:genetics*; D014867:Water / Q000737:chemistry / Q000378:metabolism*; D029968:Escherichia coli Proteins
D001426:Bacterial Proteins; D004247:DNA; D004268:DNA-Binding Proteins; D009429:Netropsin; D011522:Protons; D012097:Repressor Proteins; D012997:Solvents; D014364:Tryptophan; D014867:Water; C027190:TRPR protein, E coli; D029968:Escherichia coli Proteins