Protein-DNA recognition patterns and predictions.
Structural data on protein-DNA complexes provide clues for understanding the mechanism of protein-DNA recognition. Although the structures of a large number of protein-DNA complexes are known, the mechanisms underlying their specific binding are still only poorly understood. Analysis of these structures has shown that there is no simple one-to-one correspondence between bases and amino acids within protein-DNA complexes; nevertheless, the observed patterns of interaction carry important information on the mechanisms of protein-DNA recognition. In this review, we show how the patterns of interaction, either observed in known structures or derived from computer simulations, confer recognition specificity, and how they can be used to examine the relationship between structure and specificity and to predict target DNA sequences used by regulatory proteins.
Sarai
Akinori
A
Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka 820-8520, Japan. sarai@bse.kyutech.ac.jp
Kono
Hidetoshi
H
D000225:Adenine / Q000737:chemistry; D001703:Biophysics / Q000379:methods*; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry; D016681:Genome, Fungal; D023281:Genomics; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011487:Protein Conformation; D040901:Proteomics / Q000379:methods; D012680:Sensitivity and Specificity; D012984:Software; D013816:Thermodynamics; D016335:Zinc Fingers
D004268:DNA-Binding Proteins; D004247:DNA; D000225:Adenine