VIKAS NANDA

 

Laboratory of Computational Design and Molecular Evolution of Proteins

Research  Publications  Current Members Funding  Contact

Research

Our group is interested in constructing new proteins for applications in biomedical research, nanotechnology and as tools for understanding how proteins fold and evolve. Significant progress has been made in the last decade using sophisticated computer programs to design proteins with novel folds and functions. We maintain and develop software for protein design, structure prediction and docking of protein-ligand complexes. Several design projects our group pursues include the computational design of an extracellular matrix, thermostabilization of peptide therapeutics with D-amino acids and prediction of allergenicity of food proteins.

Design of a Synthetic Matrix - The extracellular matrix (ECM) is a complex network of collagens, laminins, fibronectins and proteoglycans that provides a surface upon which cells can adhere, differentiate and proliferate. Defects in the ECM are the underlying cause of a wide spectrum of diseases. The ECM mediates endothelial cell polarity and under normal conditions can suppress pre-oncogenic transitions to a neoplastic state. We are constructing artificial, de novo collagen-based matrices using a hierarchic computational approach. These matrices are physically characterized in the laboratory and used to probe the role of chemical and spatial organization in the ECM on the tumor forming potential of adhered cells.

Design of Peptide Therapeutics - Peptides are an emergent and important class of therapeutics with over forty compounds on the market and nearly 700 more in clinical or pre-clinical trials. During the development of peptide drugs, D-enantiomers of amino acids are frequently incorporated to improve pharmacokinetic and pharmacodynamic properties by lowering susceptibility to proteolysis. Typically, such modifications are introduced in lead compounds by trial-and-error or combinatorial approaches. Our laboratory is developing software to simulate the impact of non-natural amino acids on structure and stability. Using fundamental principles of protein design, we will pursue the computational, structure-based development of peptides with variable chirality, broadly extending our capacity to create safe and potent therapeutics.

Food Allergy - A crucial and unanswered question in the field of food allergy research is why certain proteins elicit an IgE mediated immune response, while others are tolerated. One compelling hypothesis is that non-allergens are more digestible, resulting in sufficient protein degradation in the stomach and intestine to render the remaining fragments immunologically inert. Despite efforts to contrast the proteolytic stability of allergens and non-allergens, a clear link between digestibility and allergenicity has yet to be established. Confounding variables such as interactions with other components in the food matrix, cross-reactivity with other allergens, or the pathway of sensitization (e.g. alimentary canal versus respiratory tract) complicate the interpretation of experimental outcomes. We are developing a highly defined system for exploring the relationship between digestibility and allergenicity. We hypothesize that the digestibility of a protein is dependent on its stability under acidic (pH less than 3.0) conditions. Using shrimp tropomyosin as a model system, we will computationally design acid sensitive variants that are rapidly proteolyzed in gastric fluid. These mutants will provide optimal reagents for comparative studies relating pH-stability to digestibility and eventually to allergenicity.

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Preprints

1. James, J.K., Nanda, V.  Phyla-specific correlated dynamics in tropomyosin.  bioRxiv

Publications

2019


1. Nanda, V.  Building bigger beta barrels.  eLife (in press)

2018


2. Loell, K., Nanda, V.  Marginal stability drives subcellular proteome isoelectric point.  PNAS (in press)


3. Kim, J.D., Pike, D.H., Tyryshkin, A.M., Swapna, G.V.T., Raanan, H., Montelione, G.T., Nanda, V., Falkowski, P.G.  Minimal hetereochiral de novo designed 4Fe-4S binding peptide capable of robust electron transfer.  JACS  2018. 140(36):11210-11213.


4. Candreva, J., Chau, E., Aoraha, E., Nanda, V., Kim, J.R.  Hetero-assembly of a dual beta-amyloid variant peptide system.  Chem. Commun. 2018 54(49):6380-6383.


5. Zheng, H., Lu, C., Lan, J., Fan, S., Nanda, V., Xu, F.  How electrostatic networks modulate specificity and stability of collagen.  PNAS 2018 115(24):6207-6212. 


6. James, J.K., Pike, D.H., Khan, I.J., Nanda, V.  Structural and dynamic properties of allergen and non-allergen forms of tropomyosin.  Structure 2018. 26(7):997-1006. 


7. Mushnoori, S., Schmidt, K., Nanda, V., Dutt, M.  Phenylalanine-based hybrid biological materials:  controlling morphology via molecular composition.  Org. Biomol. Chem. 2018, 16:2499-2507.


8. Ranaan, H., Pike, D.H., Moore, E.K., Falkowski, P.G., Nanda, V.  On the modular origins of biological electron transfer chains.  PNAS. 2018, 115(6):1280-1285.

Featured by NASA Astrobiology, the LA Times and NJTV



9. Grisham, D., Nanda, V.  Hydrodyanmic radius coincides with the slip plane position in the electrokinetic behavior of lysozyme.  PROTEINS:  Structure, Function and Bioinformatics 2018.  86(5):515-523
   



2017


10. Xu, F., Zheng, H-N., Clauvelin, N., Lu, X-J., Olson, W.K., Nanda, V.  Parallels between DNA and collagen - comparing elastic models of the double and triple helix.  Sci. Rep. 2017; 7:12802
    


11. Nanda, V., Belure, S., Shir, O.M.  Searching for the Pareto Frontier in Multi-Objective Protein Design.  Biophys. Rev. 2017; 9(4):339-344.
    


12. McGuinness, K., Nanda, V.  Collagen mimetic peptide discs promote assembly of a broad range of natural protein fibers through hydrophobic interactions. Org. Biomol. Chem. 2017; 15:5893-5898. 
    


13. Belure, S., Shir, O.M., Nanda, V. Protein Design by Multiobjective Optimization:  Evolutionary and Non-Evolutionary Approaches. Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2017), ACM Press: 1081-1088.
    


14. Li BI, Ababon MR, Matteson PG, Lin Y, Nanda V, Millonig JH. Congenital Cataract in Gpr161vl/vl Mice Is Modified by Proximal Chromosome 15. PLoS ONE 2017; 12(1): e0170724.



15. Cai, N., Bai, Z., Nanda, V., Runnels, L.W. Mass Spectrometric Analysis of TRPM6 and TRPM7 Phosphorylation Reveals Regulatory Mechanisms of the Channel-Kinases. Sci. Rep. 2017 7:42739


2016


16. Drzewiecki, K.E., Grisham, D.R., Parmar, A.V., Nanda, V., Shreiber, D.I. Circular Dichroism Spectroscopy of Collagen Fibrillogenesis:  A New Use for an Old Technique. Biophys. J. 2016; 111(11): 2377-2386.
    


17. Nanda, V.  Heterogeneous Epitaxy:  Peptides Scale Graphene's Surface.  Biophys. J. 2016; 110(11):  2291-2.
    



18. Maeda, Y., Ikezoe, Y., Pike, D.H., Nanda, V., Matsui, H.  Molecular self-assembly strategy for generating catalytic hybrid peptides.  PLoS ONE. 2016;  11(4): e0153700.
    


19. Parmar, A.S.*, James, J.K.*, Grisham, D.R., Pike, D.H., Nanda, V.  Dissecting electrostatic contributions to folding and self-assembly using designed multicomponent peptide systems. J. Amer. Chem. Soc. 2016; 138(13):  4362-67. *contributed equally 


20. Nanda, V., Senn, S., Pike, D.H., Rodriguez-Granillo, A., Hansen, W., Khare, S.D., Noy, D.  Structural principles for computational and de novo design of 4Fe-4S metalloproteins.  BBA Bioenergetics. 2016; 1857(5):  531-8.
    


21. Nanda, V.  Getting to the bottom of the TIM barrel.  Nature Chem Bio. 2016; 12(1): 2-3.
    


2015


22. Parmar, A.S., Xu, F., Pike, D.H., Belure, S., Hasan, N., Drzewiecki, K.E., Shreiber, D.I., Nanda, V.  Metal stabilization of collagen and de novo designed mimetic peptides. Biochemistry. 2015; 54(32): 4987–4997.
    
    
      


23. Stapleton, J.A., Whitehead, T.A., Nanda, V.  Computational redesign of the lipid-facing surface of the outer membrane protein OmpA.  Proc. Natl. Acad. Sci. 2015; 112(31):  9632-7.



24. Pike, D.H., Nanda, V.  Empirical evaluation of local dielectric constants:  toward atomistic design of collagen mimetic peptides.  Biopolymers - Peptide Science. 2015; 104(4): 360-70.  Special issue in honor of Bill DeGrado on the occasion of his 60th birthday.



25. Li, B.I., Matteson, P.G., Ababon, M.F., Nato, A.Q. Jr., Lin, Y., Nanda, V., Matise, T.C., Millonig, J.H.  The orphan GPCR, Gpr161, regulates the retinoic acid and canonical Wnt pathways during neurulation.  Dev. Bio. 2015; 402(1):  17-31.


2014


26. McGuinness, K., Khan, I.J., Nanda, V.  Morphological Diversity and Polymorphism of Self-Assembling Collagen Peptides Controlled by Length of Hydrophobic Domains.  ACS Nano. 2014; 8(12):12514-23.
    
    
    


27. Drzewiecki, K., Parmar, A.S., Gaudet, I., Branch, J., Pike, D., Nanda, V., Shreiber, D. Methacrylation Induces Rapid, Temperature Dependent, Reversible Self-Assembly of Type-I Collagen.  Langmuir.  2014; 30(37):11204-11.
    
    
    


28. Parmar, A.S., Pike, D., Nanda, V.  Computational Design of Metalloproteins.  Methods Mol. Biol. 2014; 1216:233-49.


29. Parmar, A.S., Zahid, S., Belure, S., Young, R., Hasan, N., Nanda, V.  Design of net-charged abc-type collagen heterotrimers.  J. Struct. Biol. 2014; 185(2): 163-167.
    


30. Senn, S., Nanda, V., Falkowski, P.G., Bromberg, Y.  Function Based Assessment of Structure Similarity Measurements Using Cofactor Orientation.  Proteins:  Struct. Func. Bioinf.  2014; 82(4): 648-656.
    


31. Huang L., Pike, D., Sleat, D.E., Nanda, V., Lobel, P.  Potential Pitfalls and Solutions for Use of Fluorescent Fusion Proteins to Study the Lysosome.  PLoS ONE. 2014; 9(2): e88893.


2013


32. Xu, F., Khan, I.J., McGuinness, K., Parmar, A.S., Silva, T., Murthy, S., Nanda, V.  Self-Assembly of Left and Right-Handed Molecular Screws.  J. Amer. Chem. Soc. 2013; 135(50):  18762-5.
    


33. Xu, F., Silva, T., Joshi, M., Zahid, S., Nanda, V.  Circular Permutation Directs Orthogonal Assembly in Complex Collagen Peptide Mixtures.  J. Biol. Chem. 2013; 288: 31616-23.


34. Khan, I.J., Di, R., Patel, P., Nanda, V.  Evaluating pH-induced Gastrointestinal Aggregation of Arachis Hypogea 1 Fragments as Potential Components of Peanut Allergy.  J. Agr. Food Chem. 2013; 61(35):  8430-35.
    


35. Nanda, V., Hsieh, D., Davis, A.  Prediction and Design of Outer Membrane Protein-Protein Interactions. Methods Mol. Biol. 2013; 1063: 183-96.


36. Kim, J.D., Yee, N., Nanda, V., Falkowski, P.G.  Anoxic Photochemical Oxidation of Siderite Generates Molecular Hydrogen and Iron Oxides.  Proc. Natl. Acad. Sci. 2013; 110(25): 10073-77.


37. Parmar, A.S., Joshi, M., Nosker, P.L., Hasan, N.F., Nanda, V.  Control of Collagen Stability and Heterotrimer Specificity Through Repulsive Electrostatic Interactions.  Biomolecules 2013; 3(4):  986-996.


38. Culik, R.M., Annavarapu, S., Nanda, V., Gai, F.  Using D-amino acids to delineate the mechanism of protein folding: application to Trp-cage.  Chemical Physics. 2013; 422: 131-4.


39. Nanda, V., Cristian, L., Toptygin, D., Brand, L., DeGrado, W.F.  Nanosecond dynamics of InfluenzaA/M2TM and an amantadine resistant mutant probed by time-dependent red shifts of a native tryptophan.  Chemical Physics 2013; 422:  73-79.
    


40. Giddu, S., Xu, F., Nanda, V.  Sequence Recombination Improves Target Specificity in a Redesigned Collagen Peptide abc-type Heterotrimer.  Proteins:  SFB.  2013; 81(3): 386-93.


2012


41. Hsieh, D., Nanda, V.  Dynamic surface charts for scattered 4D data in Excel spreadsheets.  Spreadsheets in Education. 2012; 6(1)


42. Kim, J.D., Rodriguez-Granillo, A., Case, D.A., Nanda, V., Falkowski, P.G.  Energetic Selection of Topology in Ferredoxins.  PLoS Computational Biology. 2012; 8(4)


43. Grzyb, J., Xu, F., Nanda, V., Luczkowska, R., Reijerse, E., Lubitz, W., Noy, D.  Empirical and computational design of iron-sulfur cluster proteins.  BBA - Bioenergetics.  2012; 1817:1256-62.


44. 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.
    


45. 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.


46. Stapleton, J.A., Rodriguez-Granillo, A., Nanda, V. Artificial Enzymes. In: Nanobiotechnology Handbook (Y. Xie, ed.) 2012; Taylor-Francis.


2011


47. 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. (*contributed equally)
    


48. 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. (*contributed equally)
    


49. 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


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


51. 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.


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


2010 and older


53. 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.


54. 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.
    


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


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


57. 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.


58. 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.


59. 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.


60. 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 alpha-helical Coiled-Coils to Design Nanostructured Metalloporphyrin Arrays. J. Am. Chem. Soc. 2008; 130: 11921-11927. 


61. 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.


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


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


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


65. 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


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


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


68. 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.
    


69. 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.


70. 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.


71. 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.


72. 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.


73. 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.


74. 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.


75. 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.


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


77. 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.


78. 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.


79. 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.


80. 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.


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


82. 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.


83. 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.


84. 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

Jose James

Daniel Grisham

Douglas Pike

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