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Vikas Nanda
Address: 679 Hoes Lane
  Department of Biochemistry - CABM
Room: 206
Phone: 732-235-5328
Email: nanda AT cabm.rutgers.edu
 
The goal of our research is to understand the molecular underpinnings of mutational tolerance and apply them to problems in protein and drug design. De novo designed proteins with significant sequence plasticity are optimal starting points for engineering functional active sites. Additionally. understanding how mutations accumulate helps predict how pathogens evolve drug-resistance. giving us the opportunity to anticipate viral evolution. We will study sequence malleability in three ways - (1) develop de novo design methods that computationally search the accessible sequences of a given fold for those that are optimally tolerant to mutations. (2) map the mutational tolerance of the small protein signaling domains through high throughput screening of large libraries of mutations and (3) explore the existing sequence variability of HIV protease for estimating the extent of possible mutations in order to abet drug design efforts.Additionally. we plan to explore the rules of capping interactions in heterochiral peptides. In natural proteins. capping interactions stabilize helices and prevent fraying of the termini. A novel bent-helix structure predicted from simulations will be designed and synthesized. Based on modeling studies. a series of hinge capping residues that bridge the bent helix ends will be engineered and evaluated for stability and structural specificity. Finally. we will focus on the design of novel tertiary folds using our simulation methods. A heterochiral bundle consisting of alpha left and alpha right-helices will be designed and characterized. The design will be extended to the molecular recognition of the Lac-repressor tetramerization domain. with the intention of disrupting the protein-protein interface by competing heterochiral interactions.
Recent Papers:

1.   Nanda V, Zahid S, Xu F, Levine D. (2011) Computational design of intermolecular stability and specificity in protein self-assembly. Methods Enzymol. 487:575-93.

2.   Nanda V, Koder RL. (2010) Designing artificial enzymes by intuition and computation. Nat Chem. Jan;2(1):15-24. Epub 2009 Dec 17. Review.

3.   Braun P, Goldberg E, Negron C, von Jan M, Xu F, Nanda V, Koder RL, Noy D.(2011) Design principles for chlorophyll-binding sites in helical proteins. Proteins. Feb;79(2):463-76.

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