VIKAS NANDA

 

Laboratory of Computational Design and Molecular Evolution

Research  Publications  Current Members   Alumni  Funding  Contact

RESEARCH

We design proteins for applications in biomedical research, nanotechnology and use them as tools for understanding protein folding and evolution. Significant progress has been made using computer methods to engineer proteins with novel folds and functions. We maintain and develop software for protein design, structure prediction and docking of protein-ligand complexes. 

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PUBLICATIONS

1. Xu, F., Li, J., Jain, V., Tu, R., Huang, Q., Nanda, V. Compositional Control of Higher Order Assembly Using Synthetic Collagen Peptides.  J. Am. Chem. Soc. 2012; 134(1):47-50.



2. Hsieh, D., Davis, A., Nanda, V. A Knowledge Based Potential Highlights Unique Features of Membrane alpha-Helical and beta-Barrel Protein Insertion and Folding. Protein Science.  2012; 21(1):50-62.



3. Stapleton, J.A., Rodriguez-Granillo, A., Nanda, V. Artificial Enzymes. In: Nanobiotechnology Handbook (Y. Xie, ed.) (in press); Taylor-Francis.


4. Khan, I.J., Stapleton, J.A., Pike, D., Nanda, V. Electrostatics in Protein Engineering and Design. In: Electrostatics (in press)


5. Xu, F., Zahid, S., Silva, T., Nanda, V. Computational Design of a Collagen A:B:C-type Heterotrimer. J. Am. Chem. Soc. 2011; 133(39):15260-3.



6. Rodriguez-Granillo, A., Annavarapu, S., Zhang, L., Koder, R.L., Nanda, V. Computational Design of Thermostabilizing D-Amino Acid Substitutions. J. Am. Chem. Soc. 2011; 133(46): 18750-9.



7. Nanda, V., Zahid, S., Xu, F., Levine, D. Computational Design of Intermolecular Stability and Specificity in Protein Self-Assembly. In: Methods in Enzymology, Vol. 487 Computer Methods, Part C (M.L. Johnson and L. Brand eds.) 2011; Elsevier



8. Rodriguez-Granillo, A., Nanda, V. Designing new enzymes with molecular simulations. Biotech International. 2011; 23: 10-13.


9. Woronowicz, K., Sha, D. Frese, R.N., Sturgis, J.N., Nanda, V., Niederman, R.A. The effects of protein crowding in bacterial photosynthetic membranes on the flow of quinone redox species between the photochemical reaction center and the ubiquinol-cytochrome c(2) oxidoreductase. Metallomics. 2011; 3(8): 765-774.



10. Braun, P., Goldberg, E., Negron, C., von Jan, M., Xu, F., Nanda, V., Koder, R.L., Noy, D. Design Priniciples for Chlorophyll Binding Sites in Helical Proteins. Proteins: SFB. 2011; 79(2): 463-476



11. Grzyb, J., Xu, F., Weiner, L., Reijerse, E.J., Lubitz, W., Nanda, V., Noy, D. De Novo Design of a Non-Natural Fold for an Iron-Sulfur Cluster Binding Site in its Central Core. BBA BioEnergetics. 2010; 1797: 406-413.
    


12. Xu, F., Zhang, L., Koder, R.L., Nanda, V. De Novo Self-Assembling Collagen Heterotrimers Using Explicit Positive and Negative Design.  Biochemistry. 2010; 49: 2307-16.



13. Nanda, V., Koder, R.L. Designing Artificial Enzymes By Intuition and Computation. Nature Chemistry. 2010; 2: 15-24.



14. Annavarapu, S., Nanda, V. Mirrors in the PDB: left-handed alpha-turns guide design with D-amino acids. BMC Structural Biology. 2009; 9:61.



15. Kar, K., Ibrar, S., Nanda, V., Getz, T., Kunapuli, S., Brodsky, B.  Aromatic Interactions Promote Self-Association of Collagen Triple-Helical Peptides to Higher Order Structures. Biochemistry. 2009; 48: 7959-68.



16. Schmiedekamp, A.M., Nanda, V. Metal-Activated Histidine Carbon-Donor Hydrogen Bonds Contribute to Metalloprotein Folding and Function. J. Inorg. Biochem. 2009; 103: 1054-1060.



17. Nanda, V., Xu, F., Hsieh, D. Chapter 16: Modulation of Intrinsic Protein Properties by Computational Design. In: Protein Engineering and Design (J. Cochran and S. Park, eds.) 2009; CRC Press.


18. McAllister, K.A., Zou, H., Cochran, F.V., Bender, G.M., Senes, A., Fry, H.C., Nanda, V., Keenan, P.A., Lear, J.D., Saven, J.G., Therien, M.J., Blasie, J.K., DeGrado, W.F. Using a-helical Coiled-Coils to Design Nanostructured Metalloporphyrin Arrays. J. Am. Chem. Soc. 2008; 130: 11921-11927. 


19. Stouffer, A.L., Acharya, R., Salom, D., Levine, A.S., Di Costanzo, L., Soto, C., Tereshko, V., Nanda, V., Stayrook, S., DeGrado, W.F. Structural Basis for the Function and Inhibition of an Influenza Virus Protein Channel. Nature. 2008; 451: 596-599.


20. Nanda, V., Schmiedekamp, A.M. Are Aromatic Carbon Donor Hydrogen Bonds Linear in Proteins? Proteins: SFB. 2008; 70: 489-497.



21. Nanda, V. Do-it-yourself Enzymes. Nature Chemical Biology. 2008; 4:  273-275.


22. Nanda, V., Andrianarijaona, A., Narayanan, C. The Role of Protein Homochirality in Shaping the Energy Landscape of Folding. Prot. Sci. 2007; 16: 1667-1675.



23. Senes, A., Chadi, D.C., Law, P.B., Walters, R.F.S., Nanda, V., DeGrado, W.F. Ez, a Depth-dependent Potential for Assessing the Energies of Amino Acid Side-chains into Membranes: Derivation and Applications to Determining the Orientation of Transmembrane and Interfacial Helices. J. Mol. Biol. 2007; 366: 436-448


24. Nanda, V., DeGrado, W.F. Computational Design of Heterochiral Peptides Against a Helical Target. J. Am. Chem. Soc. 2006; 128: 809-16.


25. Tatko, C., Nanda, V., Lear, J.D., DeGrado, W.F. Polar Networks Control Membrane Protein Oligomerization. J. Am. Chem. Soc. 2006; 128: 4170-4171


26. Nanda, V., Rosenblatt, M.M., Osyczka, A., Kono, H., Getahun, Z., Dutton, P.L., Saven, J.G., DeGrado, W.F. De Novo Design of a Redox-Active Minimal Rubredoxin Mimic. J. Am. Chem. Soc. 2005; 127: 5804-5.


27. Adamian, L., Nanda, V., DeGrado, W.F., Liang, J. Empirical Lipid Propensities of Amino Acid Residues in Multispan Helical Membrane Proteins. Proteins: SFB. 2005; 59: 496-509.


28. Stouffer, A., Nanda, V., Lear, J.D., DeGrado, W.F. Sequence Determinants of a Membrane Proton Channel: An Inverse Relationship Between Stability and Function. J. Mol. Biol. 2005; 347: 169-79.


29. Duong-Ly, K., Nanda, V., DeGrado, W.F., Howard, K.P. M2TM Tetramer Conformation Depends on Lipid Bilayer Environment. Prot. Sci. 2005; 14: 856-61.


30. Cristian, L., Nanda, V., Lear, J.D., DeGrado, W.F. Synergistic Interactions between Aqueous and Membrane Domains of a Designed Protein Determine its Fold and Stability. J. Mol. Biol. 2005; 348: 1225-33.


31. Cochran, F.V., Wu, S., Wang, W., Nanda, V., Saven, J.G., Therien, M.J., DeGrado, W.F. Computational De Novo Design and Characterization of a Four-Helix Bundle Protein That Selectively Binds a Non-Biological Cofactor. J. Am. Chem. Soc. 2005; 127: 1346-7.


32. Howard, K., Liu, W., Crocker, E., Nanda, V., Lear, J., DeGrado, W.F., Smith, S.O. Rotational Orientation of Monomers Within a Designed Homo-Oligomer Transmembrane Helical Bundle. Prot. Sci. 2005; 14: 1019-24.


33. Li, W., Metcalf, D., Gorelik, R., Li, R., Mitra, N., Nanda, V., Law, P.B., Lear, J.D., DeGrado, W.F., Bennett, J.S. A Push-Pull Mechanism for Integrin Function. Proc. Natl. Acad. Sci. 2005; 102: 1424-29.


34. Nanda, V., DeGrado, W.F. Automated Use of Mutagenesis Data in Structure Prediction. Proteins: SFB. 2005; 59: 454-66.


35. Khajehpour, M., Troxler, T., Nanda, V., Vanderkooi, J.M. Mellitin as a Model System for Probing Interactions Between Proteins and Cyclodextrins. Proteins: SFB. 2004; 55: 275-87.


36. Tucker, M.J., Getahun, Z., Nanda, V., DeGrado, W.F., Gai, F. A New Method for Determining the Local Environment and Orientation of Individual Sidechains of Membrane-Binding Peptides. J. Am. Chem. Soc. 2004; 126: 5078-9.


37. Li, R., Gorelik, R., Nanda, V., Law, P.B., Lear, J.D., DeGrado, W.F., Bennett, J.S. Dimerization of the Transmembrane Domain of Integrin alpha-IIb Subunit in Cell Membranes. J. Biol. Chem. 2004; 279(25): 26666-73.


38. Lear, J.D., Stouffer, A.L., Gratkowski, H., Nanda, V., DeGrado, W.F. Association of a Model Transmembrane Peptide Containing Gly in a Heptad Sequence Motif. Biophys. J. 2004; 87: 3421-29.


39. Nanda, V., DeGrado, W.F. Simulated Evolution of Emergent Chiral Structures in Polyalanine. J. Am. Chem. Soc. 2004; 126: 14459-67.


40. Nanda, V., Brand, L. Aromatic Interactions in Homeodomains Contribute to the Low Quantum Yield of a Conserved, Buried Tryptophan. Proteins: SFG. 2000; 40: 112-25.


41. Nanda, V., Liang, S-M., Brand, L. Hydrophobic Clustering in Acid-Denatured IL-2 and Fluorescence of a Trp NH^…pi H-bond. Biochem. Biophys. Res. Comm. 2000; 279: 770-8.


42. Packard, B.Z., Komoriya, A., Nanda, V., Brand, L. Intramolecular Excitonic Dimers in Protease Substrates: Modifications of the Backbone Moiety to Probe the H-Dimer Structure. J. Phys. Chem. B. 1998; 102: 1820-7

Agustina Rodriguez-Granillo

Issac John Khan

Avanish Parmar

James Stapleton

Fei Xu

Daniel Hsieh

John Kim

Kenneth McGuinness

Agnes Yeboah

Joseph Izzo

Jose James

Douglas Pike

Sumana Giddu

Teresita Silva

Alex Davis

Mihir Joshi

Aisha Jasani

Pranali Shingala

Srinivas Annavarapu

Yolanda Hom

Orly Even-Dar

Daniel Levine

Sohail Zahid

Jonathan Wildman

Rashesh Shah

Rebekah Amarini

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