Essentially, most of the biological functions of DNA require the binding of specific proteins to specific DNA sequences. For binding to occur, the protein has to discriminate between many similar and competing binding sites. It must not only recognize the DNA site, but also find the appropriate target rapidly, and tightly bind to one having the special features and corresponding biological function that distinguishes it from the millions of competing and overlapping non-specific sites.
We focus on deciphering the mechanisms and kinetics of DNA recognition by monomeric and multimeric proteins with the ultimate goal of understanding cellular communication from physical and molecular viewpoints using theoretical and computational tools. Quantifying the molecular and physical principles of the mechanisms of protein-DNA assembly is key to cracking down the protein-DNA recognition code and improving the prediction of specificity and binding affinity.
Computer-based models will aid in understanding the movement and mechanisms of protein assembly on DNA. Advancing the molecular mechanism of DNA search by proteins is not only vital to understanding the cellular machinery and the products of the information stored on the genome sequence, but it can also yield many practical applications. Computational model can aid in investigating how mutations in the p53 protein lead to cancerous growths by directly or indirectly affecting the assembly of the protein subunits and their interactions with DNA. Theoretical studies of such key events in cellular life and death may suggest approaches for designing drugs that will restore the network of interactions of p53 that allow it to act as a guardian of the genome and prevent the malignancies.