Nuance in the double-helix and its role in protein-DNA recognition.
It has been known for some time that the double-helix is not a uniform structure but rather exhibits sequence-specific variations that, combined with base-specific intermolecular interactions, offer the possibility of numerous modes of protein-DNA recognition. All-atom simulations have revealed mechanistic insights into the structural and energetic basis of various recognition mechanisms for a number of protein-DNA complexes while coarser grained simulations have begun to provide an understanding of the function of larger assemblies. Molecular simulations have also been applied to the prediction of transcription factor binding sites, while empirical approaches have been developed to predict nucleosome positioning. Studies that combine and integrate experimental, statistical and computational data offer the promise of rapid advances in our understanding of protein-DNA recognition mechanisms.
Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Columbia University, 1130 St. Nicholas Avenue, New York, NY 10032, USA.
Remo
R
Rohs
Sean M
SM
West
Peng
P
Liu
Barry
B
Honig
D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D014157:Transcription Factors / Q000378:metabolism
D009707:Nucleosomes; D011506:Proteins; D014157:Transcription Factors; D004247:DNA