Electrostatics and hydration at the homeodomain-DNA interface: chemical probes of an interfacial water cavity.
Electrostatics and hydration of a homeodomain-DNA complex are dissected by chemical modification. Selective neutralization of phosphate charges by methylphosphonate substitution demonstrates the differential importance of short- and long-range electrostatic interactions. Whereas the footprint of direct contacts is in accord with crystal structures, interference is also observed at non-contacted sites. Such sites adjoin a novel interfacial water cavity in the major groove. Non-contacted phosphodiester groups in the cavity are proposed to contribute to long-range ordering of an extended protein-water-DNA interface. Use of isolated S(p) and R(p) methylphosphonate diastereomers demonstrates that interference at this extended interface is stereoselective and charge-independent. Attenuation of protein binding presumably reflects groove-specific reorganization of bound water. Surprisingly, such attenuation can exceed that due to neutralization of a direct phosphate-side-chain salt bridge. These results support the hypothesis that hydration of an interfacial cavity functions as a non-covalent extension of the DNA surface. Stereo-specific interrogation of bound water by chemical synthesis provides a general method to assess the coupling between solvation and DNA recognition.
Labeots
L A
LA
Department of Biochemistry and Molecular Biology and Center for Molecular Oncology, The University of Chicago, IL 60637-5419, USA.
Weiss
M A
MA
D001426:Bacterial Proteins; D001482:Base Composition; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D018398:Homeodomain Proteins / Q000737:chemistry* / Q000378:metabolism*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009943:Organophosphorus Compounds / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D012097:Repressor Proteins / Q000737:chemistry / Q000378:metabolism; D055672:Static Electricity; D014867:Water / Q000737:chemistry / Q000378:metabolism; D029968:Escherichia coli Proteins
D001426:Bacterial Proteins; D004247:DNA; D018398:Homeodomain Proteins; D009943:Organophosphorus Compounds; D012097:Repressor Proteins; D014867:Water; C027190:TRPR protein, E coli; D029968:Escherichia coli Proteins; C032627:methylphosphonic acid