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| Vikas Nanda |
| Address: |
679 Hoes Lane |
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Department of Biochemistry - CABM |
| Room: |
206 |
| Phone: |
732-235-5328 |
| Email: |
nanda AT cabm.rutgers.edu
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| 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. |
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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.
Website
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BME Graduate Alumni PhD Student Wins SoE Award
May 14, 2013
PhD alumni Dr. Shirley Masand is one of 3 who has been awarded the SoE Outstanding Student Award. The award will be given to outstanding Ph.D. students in engineering graduate programs at Rutgers....
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BME-UMDNJ Researchers Test Potentially Lifesaving Tool for Detecting Schizophrenia
May 10, 2013
Thomas Papathomas, a professor in the Department of Biomedical Engineering and director of the university's Laboratory for Vision Research, and his colleague Prof. Steven Silverstein from UMDNJ...
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BME Student wins 2013 Aresty Best Poster Award
May 06, 2013
BME junior Srivathsan Babu Prabu won the best poster award for STEM (Science, Technology, Engineering, and Mathematics) fields for his poster entitled, "A Novel Method to Quantify Levels of Macrosteatosis...
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BME Faculty wins grant from NJCBIR
May 02, 2013
Professor William Craelius has been awarded a $539K, 3 year grant from the New Jersey Commission on Brain Injury Research (NJCBIR) to study , "Continuous monitoring of hemodynamic autoregulatory...
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