Protein surface salt bridges and paths for DNA wrapping.
The organization of large regions of DNA on the surface of proteins is critical to many DNA 'transactions', including replication, transcription, recombination and repair, as well as the packaging of chromosomal DNA. Recent thermodynamic and structural studies of DNA binding by integration host factor indicate that the disruption of protein surface salt bridges (dehydrated ion pairs) dominates the observed thermodynamics of integration host factor binding and, more generally, allows the wrapping of DNA on protein surfaces. The proposed thermodynamic signature of wrapping with coupled salt bridge disruption includes large negative salt-concentration-dependent enthalpy, entropy and heat capacity changes and smaller than expected magnitudes of the observed binding constant and its power dependence on salt concentration. Examination of the free structures of proteins recently shown to wrap DNA leads us to hypothesize that a pattern of surface salt bridges interspersed with cationic sidechains provides a structural signature for wrapping and that the number and organization of salt bridges and cationic groups dictate the thermodynamics and topology of DNA wrapping, which in turn are critical to function.
Saecker
Ruth M
RM
Department of Chemistry, University of Wisconsin-Madison, 1101University Avenue, Madison, WI 53706, USA. saecker@monte.biochem.wisc.edu
Record
M Thomas
MT
D001426:Bacterial Proteins; D004247:DNA / Q000737:chemistry*; D027081:DNA Gyrase / Q000378:metabolism; D004265:DNA Helicases / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry*; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000378:metabolism; D034982:Integration Host Factors / Q000378:metabolism; D056968:Lac Repressors; D008958:Models, Molecular; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D012097:Repressor Proteins / Q000378:metabolism; D012492:Salts / Q000737:chemistry*; D013816:Thermodynamics
D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D034982:Integration Host Factors; D056968:Lac Repressors; D012097:Repressor Proteins; D012492:Salts; C058093:UvrB protein, E coli; D004247:DNA; D012321:DNA-Directed RNA Polymerases; D004265:DNA Helicases; D027081:DNA Gyrase