Vikas Nanda

Summary

Affiliation: Rutgers University
Country: USA

Publications

  1. pmc Designing artificial enzymes by intuition and computation
    Vikas Nanda
    Robert Wood Johnson Medical School UMDNJ Biochemistry, Center for Advanced Biotechnology and Medicine, 679 Hoes Lane West, Piscataway, New Jersey 08854, USA
    Nat Chem 2:15-24. 2010
  2. pmc The role of protein homochirality in shaping the energy landscape of folding
    Vikas Nanda
    Center for Advanced Biotechnology and Medicine, Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854, USA
    Protein Sci 16:1667-75. 2007
  3. ncbi request reprint Computational design of heterochiral peptides against a helical target
    Vikas Nanda
    Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854, USA
    J Am Chem Soc 128:809-16. 2006
  4. ncbi request reprint Are aromatic carbon donor hydrogen bonds linear in proteins?
    Vikas Nanda
    Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854, USA
    Proteins 70:489-97. 2008
  5. doi request reprint Computational design of intermolecular stability and specificity in protein self-assembly
    Vikas Nanda
    Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, Piscataway, New Jersey, USA
    Methods Enzymol 487:575-93. 2011
  6. pmc De novo self-assembling collagen heterotrimers using explicit positive and negative design
    Fei Xu
    Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, and Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854, USA
    Biochemistry 49:2307-16. 2010
  7. pmc Self-assembly of left- and right-handed molecular screws
    Fei Xu
    Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854, United States
    J Am Chem Soc 135:18762-5. 2013
  8. pmc Circular permutation directs orthogonal assembly in complex collagen peptide mixtures
    Fei Xu
    From the Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854
    J Biol Chem 288:31616-23. 2013
  9. pmc Computational design of thermostabilizing D-amino acid substitutions
    Agustina Rodriguez-Granillo
    Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey UMDNJ and Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854, USA
    J Am Chem Soc 133:18750-9. 2011
  10. doi request reprint Prediction and design of outer membrane protein-protein interactions
    Vikas Nanda
    Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School UMDNJ, Piscataway, NJ, USA
    Methods Mol Biol 1063:183-96. 2013

Collaborators

Detail Information

Publications36

  1. pmc Designing artificial enzymes by intuition and computation
    Vikas Nanda
    Robert Wood Johnson Medical School UMDNJ Biochemistry, Center for Advanced Biotechnology and Medicine, 679 Hoes Lane West, Piscataway, New Jersey 08854, USA
    Nat Chem 2:15-24. 2010
    ..Looking forward, we examine strategies employed by natural enzymes that could be used to improve the speed and selectivity of artificial catalysts...
  2. pmc The role of protein homochirality in shaping the energy landscape of folding
    Vikas Nanda
    Center for Advanced Biotechnology and Medicine, Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854, USA
    Protein Sci 16:1667-75. 2007
    ....
  3. ncbi request reprint Computational design of heterochiral peptides against a helical target
    Vikas Nanda
    Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854, USA
    J Am Chem Soc 128:809-16. 2006
    ..We explore the application of HCMC to simulating the preferential enantioselectivity of heterochiral complexes. Implications for biomimetic design in molecular recognition are discussed...
  4. ncbi request reprint Are aromatic carbon donor hydrogen bonds linear in proteins?
    Vikas Nanda
    Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854, USA
    Proteins 70:489-97. 2008
    ..The implications for protein modeling and design are discussed...
  5. doi request reprint Computational design of intermolecular stability and specificity in protein self-assembly
    Vikas Nanda
    Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, Piscataway, New Jersey, USA
    Methods Enzymol 487:575-93. 2011
    ..Here, we explore various computational methods for designing stable and specific oligomeric systems, with a focus on α-helix and collagen self-assembly...
  6. pmc De novo self-assembling collagen heterotrimers using explicit positive and negative design
    Fei Xu
    Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, and Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854, USA
    Biochemistry 49:2307-16. 2010
    ....
  7. pmc Self-assembly of left- and right-handed molecular screws
    Fei Xu
    Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854, United States
    J Am Chem Soc 135:18762-5. 2013
    ..X-ray scattering measurements of interhelical spacing in these sheets support a tight ridges-in-grooves packing of left- and right-handed triple helices. ..
  8. pmc Circular permutation directs orthogonal assembly in complex collagen peptide mixtures
    Fei Xu
    From the Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854
    J Biol Chem 288:31616-23. 2013
    ..Combining the synthetic collagen model and bioinformatic analysis provides insight on how fibrillar collagens might have arisen from the duplication of smaller domains. ..
  9. pmc Computational design of thermostabilizing D-amino acid substitutions
    Agustina Rodriguez-Granillo
    Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey UMDNJ and Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854, USA
    J Am Chem Soc 133:18750-9. 2011
    ..Stabilities of individual substitutions can be understood in terms of the balance of intramolecular forces both at the α-helix C-terminus and throughout the protein...
  10. doi request reprint Prediction and design of outer membrane protein-protein interactions
    Vikas Nanda
    Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School UMDNJ, Piscataway, NJ, USA
    Methods Mol Biol 1063:183-96. 2013
    ..Current computational strategies for detecting/predicting PPIs are introduced, and examples of computational and rational engineering strategies applied to OMPs are presented...
  11. pmc Sequence recombination improves target specificity in a redesigned collagen peptide abc-type heterotrimer
    Sumana Giddu
    Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854, USA
    Proteins 81:386-93. 2013
    ..Quantitative meta-analysis of these results and published stability measurements on closely related peptides was used to discriminate the contributions of backbone propensity and side-chain electrostatics to collagen stability...
  12. doi request reprint 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 c2 oxidoreductase
    Kamil Woronowicz
    Department of Molecular Biology and Biochemistry, Rutgers University, Busch Campus, 604 Allison Road, Piscataway, NJ 08854 8082, USA
    Metallomics 3:765-74. 2011
    ..This supports the proposal that in this type of ICM, a network of RC-LH1 core complexes observed in AFM provides a pathway for long-range quinone diffusion that is unaffected by differences in LH complex composition or organization...
  13. pmc A knowledge-based potential highlights unique features of membrane α-helical and β-barrel protein insertion and folding
    Daniel Hsieh
    BioMaPS Institute and the Graduate Program in Computational Biology and Molecular Biophysics, Rutgers University, Piscataway, NJ 08854, USA
    Protein Sci 21:50-62. 2012
    ..This potential can predict orientation within the membrane and identify functional residues involved in intermolecular interactions...
  14. pmc Computational design of a collagen A:B:C-type heterotrimer
    Fei Xu
    Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ and the Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854, United States
    J Am Chem Soc 133:15260-3. 2011
    ..This study highlights the power of automated computational design, providing model systems to probe the biophysics of collagen assembly and developing general methods for the design of fibrous proteins...
  15. pmc Mirrors in the PDB: left-handed alpha-turns guide design with D-amino acids
    Srinivas Annavarapu
    Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, NJ 08854, USA
    BMC Struct Biol 9:61. 2009
    ..Molecular mechanisms used in proteins to stabilize left-handed elements by L-amino acids are structurally enantiomeric to potential synthetic strategies for stabilizing right-handed elements with D-amino acids...
  16. pmc Design of net-charged abc-type collagen heterotrimers
    Avanish S Parmar
    Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, UMDNJ and Center for Advanced Biotechnology and Medicine, Piscataway, NJ 08854, United States
    J Struct Biol 185:163-7. 2014
    ..Structural characterization indicates the net-negative charge balance on the new designs enhances the specificity of the target state at the expense of its stability. ..
  17. pmc Evaluating pH-induced gastrointestinal aggregation of Arachis hypogaea 1 fragments as potential components of peanut allergy
    I John Khan
    Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, 679 Hoes Lane, Piscataway, New Jersey 08854, United States
    J Agric Food Chem 61:8430-5. 2013
    ..It is proposed that peptide fragments which survive gastric conditions form large aggregates in basic environments such as the small intestine, making epitopes available for triggering an allergic response. ..
  18. pmc Compositional control of higher order assembly using synthetic collagen peptides
    Fei Xu
    Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ and the Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854, USA
    J Am Chem Soc 134:47-50. 2012
    ..By varying stoichiometry and concentration, we are able to dissect the stages of higher order assembly. Insight gained from this study will improve the molecular design of biomimetic materials...
  19. pmc Aromatic interactions promote self-association of collagen triple-helical peptides to higher-order structures
    Karunakar Kar
    Department of Biochemistry, University of Medicine and Dentistry of New Jersey Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
    Biochemistry 48:7959-68. 2009
    ..pi interactions between aromatic residues in the telopeptides and Pro/Hyp residues within the triple helix...
  20. ncbi request reprint Automated use of mutagenesis data in structure prediction
    Vikas Nanda
    Department of Biochemistry and Molecular Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
    Proteins 59:454-66. 2005
    ..Furthermore, by separating misfolded conformations from the target score, the ensemble energy serves to speed up conformational search algorithms such as Monte Carlo-based methods...
  21. ncbi request reprint Simulated evolution of emergent chiral structures in polyalanine
    Vikas Nanda
    Department of Biochemistry and Molecular Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
    J Am Chem Soc 126:14459-67. 2004
    ..Our studies show that simulated evolution of chirality with backbone flexibility can be a powerful tool in the design of novel heteropolymers with tuned stereochemical properties...
  22. pmc Using alpha-helical coiled-coils to design nanostructured metalloporphyrin arrays
    Karen A McAllister
    Department of Biochemistry and Molecular Biophysics, Johnson Foundation, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    J Am Chem Soc 130:11921-7. 2008
    ..The successful extension of the two-porphyrin array demonstrates how this methodology serves as a foundation to create linear assemblies of organized electrically and optically responsive cofactors...
  23. doi request reprint Do-it-yourself enzymes
    Vikas Nanda
    Nat Chem Biol 4:273-5. 2008
  24. ncbi request reprint A new method for determining the local environment and orientation of individual side chains of membrane-binding peptides
    Matthew J Tucker
    Department of Chemistry, University of Pennsylvania, Philadelphia, 19104 USA
    J Am Chem Soc 126:5078-9. 2004
    ..We have also shown that polarized ATR-FTIR measurements can further be used to uncover information regarding the spatial orientation of individual side chains as well as their conformational preference within the lipid bilayer...
  25. pmc Association of a model transmembrane peptide containing gly in a heptad sequence motif
    James D Lear
    Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
    Biophys J 87:3421-9. 2004
    ..These results also suggest that a left-handed Gly heptad repeat motif can drive membrane helix association, but the affinity is likely to be less strong than the previously reported right-handed motif described for glycophorin A...
  26. pmc A push-pull mechanism for regulating integrin function
    Wei Li
    Department of Medicine, Hematology Oncology Division, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
    Proc Natl Acad Sci U S A 102:1424-9. 2005
    ....
  27. ncbi request reprint Computational de novo design and characterization of a four-helix bundle protein that selectively binds a nonbiological cofactor
    Frank V Cochran
    Department of Biochemistry and Molecular Biophysics, Johnson Foundation, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
    J Am Chem Soc 127:1346-7. 2005
    ..These findings open a path for the selective incorporation of more elaborate cofactors into designed scaffolds for constructing molecularly well-defined nanoscale materials...
  28. ncbi request reprint Sequence determinants of a transmembrane proton channel: an inverse relationship between stability and function
    Amanda L Stouffer
    Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia PA, 19104 6059, USA
    J Mol Biol 347:169-79. 2005
    ..A structural model of the amantadine bound state of M2TM was generated using a novel protocol that optimizes a structure for an ensemble of neutral and disruptive mutations. The model structure is consistent with the mutational data...
  29. pmc Rotational orientation of monomers within a designed homo-oligomer transmembrane helical bundle
    Kathleen P Howard
    Department of Chemistry, Swarthmore College, Swarthmore, PA 19081, USA
    Protein Sci 14:1019-24. 2005
    ..The (2)H NMR line shapes of the three different peptides are consistent with a trimer structure formed by the designed peptide that is stabilized by inter-helical hydrogen bonding of asparagines at positions 7 and 14...
  30. pmc The conformation of the pore region of the M2 proton channel depends on lipid bilayer environment
    Krisna C Duong-Ly
    Department of Chemistry, Swarthmore College, Swarthmore, PA 19081, USA
    Protein Sci 14:856-61. 2005
    ..The various structural models for M2TM proposed to date--each defined by a different set of criteria and in a different environment--might provide snapshots of the distinct conformational states sampled by the protein...
  31. ncbi request reprint Empirical lipid propensities of amino acid residues in multispan alpha helical membrane proteins
    Larisa Adamian
    Department of Bioengineering, University of Illinois at Chicago, Illinois 60612 7340, USA
    Proteins 59:496-509. 2005
    ..We also compare performance of TMLIP with another lipid propensity scale, kPROT, and with several hydrophobicity scales using hydrophobic moment analysis...
  32. ncbi request reprint De novo design of a redox-active minimal rubredoxin mimic
    Vikas Nanda
    Department of Biochemistry and Biophysics, Johnson Foundation, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, Japan
    J Am Chem Soc 127:5804-5. 2005
    ..The protein folds into a beta-structure in the presence and absence of metal ions and binds Fe(II/III) to form a redox-active site that is stable to repeated cycles of oxidation and reduction, even in an aerobic environment...
  33. ncbi request reprint Synergistic interactions between aqueous and membrane domains of a designed protein determine its fold and stability
    Lidia Cristian
    Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 6059, USA
    J Mol Biol 348:1225-33. 2005
    ....
  34. ncbi request reprint Polar networks control oligomeric assembly in membranes
    Chad D Tatko
    Department of Chemistry, School of Medicine, University of Pennsylvania, Philadelphia, 19104, USA
    J Am Chem Soc 128:4170-1. 2006
    ..Analytical ultracentrifugation and fluorescence resonance energy transfer studies indicate that a trimer assembly is established where each membrane-embedded hydrogen bond contributes 1 kcal mol-1...
  35. ncbi request reprint E(z), a depth-dependent potential for assessing the energies of insertion of amino acid side-chains into membranes: derivation and applications to determining the orientation of transmembrane and interfacial helices
    Alessandro Senes
    Deparment of Biochemistry and Molecular Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 6059, USA
    J Mol Biol 366:436-48. 2007
    ..In membrane protein design applications, the potential allows an environment-dependent selection of amino acid identities...
  36. ncbi request reprint Melittin as model system for probing interactions between proteins and cyclodextrins
    Mazdak Khajehpour
    Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Proteins 55:275-87. 2004
    ..HPBCD inhibits the aggregation of melittin. This inhibition and the spectroscopic results are consistent with the lone aromatic tryptophan of the peptide being intercalated within HPBCD...

Research Grants2

  1. Computational Design of a Synthetic Extracellular Matrix
    Vikas Nanda; Fiscal Year: 2009
    ..Artificial, nano-scale matrices will help us study the role of the matrix in disease, and provide safe biomaterials for tissue engineering. ..
  2. A Computational Approach to Developing Heterochiral Peptide Therapeutics
    Vikas Nanda; Fiscal Year: 2010
    ..Computer engineering of peptide drugs has a lot to contribute both to medicine and to our basic understanding of how proteins function. ..