Structure‐based prediction of DNA target sites by regulatory proteins

Prediction of DNA Target Sites by Regulatory Proteins Based on Structure-Derived Potential

Gene expression in higher organisms is controlled by a variety of regulatory proteins. Structural analysis of protein-DNA complexes has revealed that the same amino acids often interact with di erent bases and vice versa. Thus, no general rules yet exist to explain how proteins discriminate among DNA sequences or that predict their target sites. On the other hand, the amount of structural infor...

Prediction of Epigenetic Target Sites by Using Genomic DNA Sequence

Epigenetic regulation provides an extra layer of gene control in addition to the genomic sequence and is critical for the maintenance of cell-type specific gene expression programs. Significant changes of epigenetic patterns have been linked to developmental stages, environmental exposure, ageing, and diet. However, the regulatory mechanisms for epigenetic recruitment, maintenance, and switch a...

Searching target sites on DNA by proteins: Role of DNA dynamics under confinement

DNA-binding proteins (DBPs) rapidly search and specifically bind to their target sites on genomic DNA in order to trigger many cellular regulatory processes. It has been suggested that the facilitation of search dynamics is achieved by combining 3D diffusion with one-dimensional sliding and hopping dynamics of interacting proteins. Although, recent studies have advanced the knowledge of molecul...

Systematic prediction of control proteins and their DNA binding sites

We present here the results of a systematic bioinformatics analysis of control (C) proteins, a class of DNA-binding regulators that control time-delayed transcription of their own genes as well as restriction endonuclease genes in many type II restriction-modification systems. More than 290 C protein homologs were identified and DNA-binding sites for approximately 70% of new and previously know...

Prediction of DNA-binding sites in proteins using evolutionary profiles