Investigators and Program Directors

Research Interests

Biological systems exist through complex interplay of a diverse range of macromolecules performing specific functions. For each macromolecule, the gap between visualizing its atomic-level crystal structure and understanding its functional properties needs to be traversed by a description of the conformational free energy landscape governing its activity. The primary goal of our research is to use computational techniques of varying complexity along with refined analysis techniques to optimally extract free energy landscapes describing biologically relevant macromolecular conformational change. This research is primarily targeted to two areas:

RNA-protein interaction:
Recognition of small interfering RNA (siRNA) by proteins involved in RNA interference (RNAi) depends on their ability to identify the presence of specific features like phosphorylation at the 5'-end, symmetric 3'-dinucleotide overhangs, and a narrow end-to-end length range in siRNA. Our goal is to delineate the quantitative determinants of these structural and protein interaction properties of the RNAi machinery.

Nucleotide-dependent Protein Conformational Change:
A ubiquitous biological mechanism involves protein conformational changes caused by binding and cleavage of the terminal phosphate of specific nucleotides (e.g. ATP, GTP). We aim to probe the details of this specific mechanism by determination of effects of presence or absence of this terminal phosphate on the free energy landscapes of the nucleotides and nucleotide-binding proteins in their various ligand-bound conformational combinations.

Our long range goals are to incorporate such detailed atomic-scale understanding of conformational change into simplified models to scrutinize how macromolecular components interact and coordinate their activity to form functional nanoscale cellular machinery.

Contact Information

Telephone: (518) 474-0569
Fax: (518) 402-4623
E-mail: banavali@wadsworth.org