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Vikas Nanda, Ph.D. - Publications

Affiliations: 
Johns Hopkins University, Baltimore, MD 
 Biochemistry and Molecular Biology Rutgers University, New Brunswick, New Brunswick, NJ, United States 
Area:
dynamic structure and function of proteins, nucleic acids, glyco-conjugates, and membranes
Website:
https://cabm.rutgers.edu/faculty_and_research/nanda.php
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81 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Batra R, Loeffler TD, Chan H, Srinivasan S, Cui H, Korendovych IV, Nanda V, Palmer LC, Solomon LA, Fry HC, Sankaranarayanan SKRS. Machine learning overcomes human bias in the discovery of self-assembling peptides. Nature Chemistry. PMID 36316409 DOI: 10.1038/s41557-022-01055-3  0.627
2020 Mancini JA, Pike DH, Tyryshkin AM, Haramaty L, Wang M, Poudel S, Hecht M, Nanda V. Design of a Fe S Cluster into the Core of a De Novo 4-Helix Bundle. Biotechnology and Applied Biochemistry. PMID 32770861 DOI: 10.1002/Bab.2003  0.339
2020 Atkinson JT, Jones AM, Nanda V, Silberg JJ. Protein tolerance to random circular permutation correlates with thermostability and local energetics of residue-residue contacts. Protein Engineering, Design & Selection : Peds. PMID 32626892 DOI: 10.1093/Protein/Gzaa012  0.378
2020 Raanan H, Poudel S, Pike DH, Nanda V, Falkowski PG. Small protein folds at the root of an ancient metabolic network. Proceedings of the National Academy of Sciences of the United States of America. PMID 32188785 DOI: 10.1073/Pnas.1914982117  0.304
2020 Collier AM, Nemtsova Y, Kuber N, Banach-Petrosky W, Modak A, Sleat DE, Nanda V, Lobel P. Lysosomal protein thermal stability does not correlate with cellular half-life: Global observations and a case study of tripeptidyl-peptidase 1. The Biochemical Journal. PMID 31957806 DOI: 10.1042/Bcj20190874  0.325
2019 James JK, Nanda V. Cromparative Dynamics of Tropomyosin in Vertebrates and Invertebrates. Proteins. PMID 31390486 DOI: 10.1002/Prot.25797  0.354
2019 Mutter AC, Tyryshkin AM, Campbell IJ, Poudel S, Bennett GN, Silberg JJ, Nanda V, Falkowski PG. De novo design of symmetric ferredoxins that shuttle electrons in vivo. Proceedings of the National Academy of Sciences of the United States of America. PMID 31262814 DOI: 10.1073/Pnas.1905643116  0.314
2018 Loell K, Nanda V. Marginal protein stability drives subcellular proteome isoelectric point. Proceedings of the National Academy of Sciences of the United States of America. PMID 30385634 DOI: 10.1073/Pnas.1809098115  0.344
2018 Kim JD, Pike DH, Tyryshkin AM, Swapna GVT, Raanan H, Montelione GT, Nanda V, Falkowski PG. Minimal heterochiral de novo designed 4Fe-4S binding peptide capable of robust electron transfer. Journal of the American Chemical Society. PMID 30141918 DOI: 10.1021/Jacs.8B07553  0.372
2018 James JK, Pike DH, Khan IJ, Nanda V. Structural and Dynamic Properties of Allergen and Non-Allergen Forms of Tropomyosin. Structure (London, England : 1993). PMID 29887498 DOI: 10.1016/J.Str.2018.05.002  0.301
2018 Candreva J, Chau E, Aoraha E, Nanda V, Kim JR. Hetero-assembly of a dual β-amyloid variant peptide system. Chemical Communications (Cambridge, England). PMID 29872774 DOI: 10.1039/C8Cc02724B  0.335
2018 Zheng H, Lu C, Lan J, Fan S, Nanda V, Xu F. How electrostatic networks modulate specificity and stability of collagen. Proceedings of the National Academy of Sciences of the United States of America. PMID 29844169 DOI: 10.1073/Pnas.1802171115  0.343
2018 Mushnoori S, Schmidt K, Nanda V, Dutt M. Designing phenylalanine-based hybrid biological materials: controlling morphology via molecular composition. Organic & Biomolecular Chemistry. PMID 29565077 DOI: 10.1039/C8Ob00130H  0.387
2018 Grisham DR, Nanda V. Hydrodynamic radius coincides with the slip plane position in the electrokinetic behavior of lysozyme. Proteins. PMID 29383755 DOI: 10.1002/Prot.25469  0.317
2018 Raanan H, Pike DH, Moore EK, Falkowski PG, Nanda V. Modular origins of biological electron transfer chains. Proceedings of the National Academy of Sciences of the United States of America. PMID 29358375 DOI: 10.1073/Pnas.1714225115  0.303
2017 Nanda V, Belure SV, Shir OM. Searching for the Pareto frontier in multi-objective protein design. Biophysical Reviews. PMID 28799089 DOI: 10.1007/S12551-017-0288-0  0.302
2017 McGuinness K, Nanda V. Collagen mimetic peptide discs promote assembly of a broad range of natural protein fibers through hydrophobic interactions. Organic & Biomolecular Chemistry. PMID 28678287 DOI: 10.1039/C7Ob01073G  0.39
2016 Drzewiecki KE, Grisham DR, Parmar AS, Nanda V, Shreiber DI. Circular Dichroism Spectroscopy of Collagen Fibrillogenesis: A New Use for an Old Technique. Biophysical Journal. 111: 2377-2386. PMID 27926839 DOI: 10.1016/J.Bpj.2016.10.023  0.319
2016 Maeda Y, Fang J, Ikezoe Y, Pike DH, Nanda V, Matsui H. Molecular Self-Assembly Strategy for Generating Catalytic Hybrid Polypeptides. Plos One. 11: e0153700. PMID 27116246 DOI: 10.1371/Journal.Pone.0153700  0.402
2016 Parmar AS, James JK, Grisham DR, Pike DH, Nanda V. Dissecting electrostatic contributions to folding and self-assembly using designed multicomponent peptide systems. Journal of the American Chemical Society. PMID 26966815 DOI: 10.1021/Jacs.5B10304  0.412
2015 Nanda V. Protein Design: Getting to the bottom of the TIM barrel. Nature Chemical Biology. 12: 2-3. PMID 26678608 DOI: 10.1038/Nchembio.1987  0.302
2015 Parmar AS, Xu F, Pike DH, Belure SV, Hasan NF, Drzewiecki KE, Shreiber DI, Nanda V. Metal Stabilization of Collagen and de Novo Designed Mimetic Peptides. Biochemistry. 54: 4987-97. PMID 26225466 DOI: 10.1021/Acs.Biochem.5B00502  0.358
2015 Stapleton JA, Whitehead TA, Nanda V. Computational redesign of the lipid-facing surface of the outer membrane protein OmpA. Proceedings of the National Academy of Sciences of the United States of America. 112: 9632-7. PMID 26199411 DOI: 10.1073/Pnas.1501836112  0.372
2015 Pike DH, Nanda V. Empirical estimation of local dielectric constants: Toward atomistic design of collagen mimetic peptides. Biopolymers. 104: 360-70. PMID 25784456 DOI: 10.1002/Bip.22644  0.382
2015 McGuinness KN, Drzewiecki KE, Kopka MJ, Patel AA, Niederman RA, Shreiber DI, Nanda V. The Co-Assembly of Collagen-Mimetic Peptides and Natural Proteins Biophysical Journal. 108: 605a. DOI: 10.1016/J.Bpj.2014.11.3293  0.428
2014 McGuinness K, Khan IJ, Nanda V. Morphological diversity and polymorphism of self-assembling collagen peptides controlled by length of hydrophobic domains. Acs Nano. 8: 12514-23. PMID 25390880 DOI: 10.1021/Nn505369D  0.426
2014 Parmar AS, Pike D, Nanda V. Computational design of metalloproteins. Methods in Molecular Biology (Clifton, N.J.). 1216: 233-49. PMID 25213419 DOI: 10.1007/978-1-4939-1486-9_12  0.314
2014 Huang L, Pike D, Sleat DE, Nanda V, Lobel P. Potential pitfalls and solutions for use of fluorescent fusion proteins to study the lysosome. Plos One. 9: e88893. PMID 24586430 DOI: 10.1371/Journal.Pone.0088893  0.338
2014 Senn S, Nanda V, Falkowski P, Bromberg Y. Function-based assessment of structural similarity measurements using metal co-factor orientation. Proteins. 82: 648-56. PMID 24127252 DOI: 10.1002/Prot.24442  0.323
2014 Parmar AS, Zahid S, Belure SV, Young R, Hasan N, Nanda V. Design of net-charged abc-type collagen heterotrimers. Journal of Structural Biology. 185: 163-7. PMID 23603270 DOI: 10.1016/J.Jsb.2013.04.006  0.331
2014 Parmar AS, Pike D, Nosker P, Grisham D, Hasan NF, Yin D, Chen Y, Njoku F, Lockard J, Nanda V. PH Reversible Conjugates of Graphene Oxide with Peptides and Proteins Biophysical Journal. 106: 57a. DOI: 10.1016/J.Bpj.2013.11.395  0.391
2014 Hasan NF, Parmar AS, Joshi M, Nosker P, Nanda V. Charge Crowding Promotes Self-Assembly of Collagen Hetrotrimers Biophysical Journal. 106: 680a-681a. DOI: 10.1016/J.Bpj.2013.11.3768  0.395
2014 Nosker P, Pike D, Aramini JM, Ma L, Grasso E, Montelione GT, Nanda V. Computational and Biomolecular NMR Guided Design of Peptide Theraputics for Influenza A Biophysical Journal. 106: 188a. DOI: 10.1016/J.Bpj.2013.11.1124  0.434
2013 Culik RM, Annavarapu S, Nanda V, Gai F. Using D-Amino Acids to Delineate the Mechanism of Protein Folding: Application to Trp-cage. Chemical Physics. 422. PMID 24307748 DOI: 10.1016/J.Chemphys.2013.01.021  0.364
2013 Xu F, Khan IJ, McGuinness K, Parmar AS, Silva T, Murthy NS, Nanda V. Self-assembly of left- and right-handed molecular screws. Journal of the American Chemical Society. 135: 18762-5. PMID 24283407 DOI: 10.1021/Ja4106545  0.397
2013 Nanda V, Cristian L, Toptygin D, Brand L, Degrado WF. Nanosecond Dynamics of InfluenzaA/M2TM and an Amantadine Resistant Mutant Probed by Time-Dependent Red Shifts of a Native Tryptophan. Chemical Physics. 422. PMID 24273370 DOI: 10.1016/J.Chemphys.2012.12.018  0.623
2013 Xu F, Silva T, Joshi M, Zahid S, Nanda V. Circular permutation directs orthogonal assembly in complex collagen peptide mixtures. The Journal of Biological Chemistry. 288: 31616-23. PMID 24043622 DOI: 10.1074/Jbc.M113.501056  0.41
2013 Nanda V, Hsieh D, Davis A. Prediction and design of outer membrane protein-protein interactions. Methods in Molecular Biology (Clifton, N.J.). 1063: 183-96. PMID 23975778 DOI: 10.1007/978-1-62703-583-5_10  0.359
2013 Khan IJ, Di R, Patel P, Nanda V. Evaluating pH-induced gastrointestinal aggregation of Arachis hypogaea 1 fragments as potential components of peanut allergy. Journal of Agricultural and Food Chemistry. 61: 8430-5. PMID 23926999 DOI: 10.1021/Jf401701T  0.332
2013 Giddu S, Xu F, Nanda V. Sequence recombination improves target specificity in a redesigned collagen peptide abc-type heterotrimer. Proteins. 81: 386-93. PMID 23042255 DOI: 10.1002/Prot.24194  0.368
2013 McGuinness KN, Nanda V. 169 Polymorphic assembly of computationally designed hydrophobic-rich collagen peptides Journal of Biomolecular Structure and Dynamics. 31: 109-109. DOI: 10.1080/07391102.2013.786411  0.424
2013 Everson BH, French CA, Mutter AC, Nanda V, Koder RL. Hemoprotein Design using Minimal Sequence Information Biophysical Journal. 104: 661a. DOI: 10.1016/J.Bpj.2012.11.3649  0.369
2013 Parmar AS, Hasan NF, Nanda V. Structural Metal Mediated Self Assembly of Collagen Mimetic A:B:C Heterotrimer Peptides into Higher Oder Structures Biophysical Journal. 104: 48a. DOI: 10.1016/J.Bpj.2012.11.306  0.396
2013 Parmar AS, Xu F, pike D, Nanda V. Design of Structral Metal Sites in Heterospecific Collagen Peptides Biophysical Journal. 104: 400a. DOI: 10.1016/J.Bpj.2012.11.2230  0.365
2012 Kim JD, Rodriguez-Granillo A, Case DA, Nanda V, Falkowski PG. Energetic selection of topology in ferredoxins. Plos Computational Biology. 8: e1002463. PMID 22496635 DOI: 10.1371/Journal.Pcbi.1002463  0.404
2012 Grzyb J, Xu F, Nanda V, Luczkowska R, Reijerse E, Lubitz W, Noy D. Empirical and computational design of iron-sulfur cluster proteins. Biochimica Et Biophysica Acta. 1817: 1256-62. PMID 22342202 DOI: 10.1016/J.Bbabio.2012.02.001  0.327
2012 Xu F, Li J, Jain V, Tu RS, Huang Q, Nanda V. Compositional control of higher order assembly using synthetic collagen peptides. Journal of the American Chemical Society. 134: 47-50. PMID 22171825 DOI: 10.1021/Ja2077894  0.37
2012 Hsieh D, Davis A, Nanda V. A knowledge-based potential highlights unique features of membrane α-helical and β-barrel protein insertion and folding. Protein Science : a Publication of the Protein Society. 21: 50-62. PMID 22031179 DOI: 10.1002/Pro.758  0.357
2011 Rodriguez-Granillo A, Annavarapu S, Zhang L, Koder RL, Nanda V. Computational design of thermostabilizing D-amino acid substitutions. Journal of the American Chemical Society. 133: 18750-9. PMID 21978298 DOI: 10.1021/Ja205609C  0.362
2011 Xu F, Zahid S, Silva T, Nanda V. Computational design of a collagen A:B:C-type heterotrimer. Journal of the American Chemical Society. 133: 15260-3. PMID 21902217 DOI: 10.1021/Ja205597G  0.386
2011 Nanda V, Zahid S, Xu F, Levine D. Computational design of intermolecular stability and specificity in protein self-assembly. Methods in Enzymology. 487: 575-93. PMID 21187239 DOI: 10.1016/B978-0-12-381270-4.00020-2  0.355
2011 Braun P, Goldberg E, Negron C, von Jan M, Xu F, Nanda V, Koder RL, Noy D. Design principles for chlorophyll-binding sites in helical proteins. Proteins. 79: 463-76. PMID 21117078 DOI: 10.1002/Prot.22895  0.329
2010 Nanda V, Koder RL. Designing artificial enzymes by intuition and computation. Nature Chemistry. 2: 15-24. PMID 21124375 DOI: 10.1038/Nchem.473  0.321
2010 Xu F, Zhang L, Koder RL, Nanda V. De novo self-assembling collagen heterotrimers using explicit positive and negative design. Biochemistry. 49: 2307-16. PMID 20170197 DOI: 10.1021/Bi902077D  0.428
2010 Grzyb J, Xu F, Weiner L, Reijerse EJ, Lubitz W, Nanda V, Noy D. De novo design of a non-natural fold for an iron-sulfur protein: alpha-helical coiled-coil with a four-iron four-sulfur cluster binding site in its central core. Biochimica Et Biophysica Acta. 1797: 406-13. PMID 20035711 DOI: 10.1016/J.Bbabio.2009.12.012  0.315
2009 Annavarapu S, Nanda V. Mirrors in the PDB: left-handed alpha-turns guide design with D-amino acids. Bmc Structural Biology. 9: 61. PMID 19772623 DOI: 10.1186/1472-6807-9-61  0.354
2009 Kar K, Ibrar S, Nanda V, Getz TM, Kunapuli SP, Brodsky B. Aromatic interactions promote self-association of collagen triple-helical peptides to higher-order structures. Biochemistry. 48: 7959-68. PMID 19610672 DOI: 10.1021/Bi900496M  0.414
2008 McAllister KA, Zou H, Cochran FV, Bender GM, Senes A, Fry HC, Nanda V, Keenan PA, Lear JD, Saven JG, Therien MJ, Blasie JK, DeGrado WF. Using alpha-helical coiled-coils to design nanostructured metalloporphyrin arrays. Journal of the American Chemical Society. 130: 11921-7. PMID 18710226 DOI: 10.1021/Ja800697G  0.73
2008 Stouffer AL, Acharya R, Salom D, Levine AS, Di Costanzo L, Soto CS, Tereshko V, Nanda V, Stayrook S, DeGrado WF. Structural basis for the function and inhibition of an influenza virus proton channel. Nature. 451: 596-9. PMID 18235504 DOI: 10.1038/Nature06528  0.736
2007 Nanda V, Andrianarijaona A, Narayanan C. The role of protein homochirality in shaping the energy landscape of folding. Protein Science : a Publication of the Protein Society. 16: 1667-75. PMID 17600146 DOI: 10.1110/Ps.072867007  0.369
2007 Senes A, Chadi DC, Law PB, Walters RF, Nanda V, Degrado WF. 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. Journal of Molecular Biology. 366: 436-48. PMID 17174324 DOI: 10.1016/J.Jmb.2006.09.020  0.711
2006 Tatko CD, Nanda V, Lear JD, Degrado WF. Polar networks control oligomeric assembly in membranes. Journal of the American Chemical Society. 128: 4170-1. PMID 16568959 DOI: 10.1021/Ja055561A  0.527
2006 Nanda V, DeGrado WF. Computational design of heterochiral peptides against a helical target. Journal of the American Chemical Society. 128: 809-16. PMID 16417370 DOI: 10.1021/Ja054452T  0.562
2006 Cochran FV, Wu SP, Wang W, Nanda V, Saven JG, Therien aMJ, DeGrado WF. Computational De Novo Design and Characterization of a Four-Helix Bundle Protein that Selectively Binds a Nonbiological Cofactor [J. Am. Chem. Soc. 2005, 127, 1346−1347]. Journal of the American Chemical Society. 128: 663-663. DOI: 10.1021/Ja059923Q  0.481
2005 Cristian L, Nanda V, Lear JD, DeGrado WF. Synergistic interactions between aqueous and membrane domains of a designed protein determine its fold and stability. Journal of Molecular Biology. 348: 1225-33. PMID 15854657 DOI: 10.1016/J.Jmb.2005.03.053  0.601
2005 Nanda V, Rosenblatt MM, Osyczka A, Kono H, Getahun Z, Dutton PL, Saven JG, Degrado WF. De novo design of a redox-active minimal rubredoxin mimic. Journal of the American Chemical Society. 127: 5804-5. PMID 15839675 DOI: 10.1021/Ja050553F  0.494
2005 Adamian L, Nanda V, DeGrado WF, Liang J. Empirical lipid propensities of amino acid residues in multispan alpha helical membrane proteins. Proteins. 59: 496-509. PMID 15789404 DOI: 10.1002/Prot.20456  0.531
2005 Nanda V, DeGrado WF. Automated use of mutagenesis data in structure prediction. Proteins. 59: 454-66. PMID 15768404 DOI: 10.1002/Prot.20382  0.532
2005 Duong-Ly KC, Nanda V, Degrado WF, Howard KP. The conformation of the pore region of the M2 proton channel depends on lipid bilayer environment. Protein Science : a Publication of the Protein Society. 14: 856-61. PMID 15741338 DOI: 10.1110/Ps.041185805  0.567
2005 Howard KP, Liu W, Crocker E, Nanda V, Lear J, Degrado WF, Smith SO. Rotational orientation of monomers within a designed homo-oligomer transmembrane helical bundle. Protein Science : a Publication of the Protein Society. 14: 1019-24. PMID 15741331 DOI: 10.1110/Ps.041110605  0.57
2005 Stouffer AL, Nanda V, Lear JD, DeGrado WF. Sequence determinants of a transmembrane proton channel: an inverse relationship between stability and function. Journal of Molecular Biology. 347: 169-79. PMID 15733926 DOI: 10.1016/J.Jmb.2005.01.023  0.761
2005 Cochran FV, Wu SP, Wang W, Nanda V, Saven JG, Therien MJ, DeGrado WF. Computational de novo design and characterization of a four-helix bundle protein that selectively binds a nonbiological cofactor. Journal of the American Chemical Society. 127: 1346-7. PMID 15686346 DOI: 10.1021/Ja044129A  0.547
2005 Li W, Metcalf DG, Gorelik R, Li R, Mitra N, Nanda V, Law PB, Lear JD, Degrado WF, Bennett JS. A push-pull mechanism for regulating integrin function. Proceedings of the National Academy of Sciences of the United States of America. 102: 1424-9. PMID 15671157 DOI: 10.1073/Pnas.0409334102  0.752
2004 Nanda V, Degrado WF. Simulated evolution of emergent chiral structures in polyalanine. Journal of the American Chemical Society. 126: 14459-67. PMID 15521766 DOI: 10.1021/Ja0461825  0.52
2004 Lear JD, Stouffer AL, Gratkowski H, Nanda V, Degrado WF. Association of a model transmembrane peptide containing gly in a heptad sequence motif. Biophysical Journal. 87: 3421-9. PMID 15315956 DOI: 10.1529/Biophysj.103.032839  0.71
2004 Tucker MJ, Getahun Z, Nanda V, DeGrado WF, Gai F. A new method for determining the local environment and orientation of individual side chains of membrane-binding peptides. Journal of the American Chemical Society. 126: 5078-9. PMID 15099085 DOI: 10.1021/Ja032015D  0.551
2004 Li R, Gorelik R, Nanda V, Law PB, Lear JD, DeGrado WF, Bennett JS. Dimerization of the transmembrane domain of Integrin alphaIIb subunit in cell membranes. The Journal of Biological Chemistry. 279: 26666-73. PMID 15067009 DOI: 10.1074/Jbc.M314168200  0.641
2004 Khajehpour M, Troxler T, Nanda V, Vanderkooi JM. Melittin as model system for probing interactions between proteins and cyclodextrins. Proteins. 55: 275-87. PMID 15048821 DOI: 10.1002/Prot.20036  0.376
2004 Li W, Metcalf D, Gorelik R, Li R, Mitra N, Nanda V, Law PB, Lear JD, DeGrado WF, Bennett JS. Heteromeric and Homomeric Transmembrane Domain Associations Regulate αIIbβ3 Function. Blood. 104: 329-329. DOI: 10.1182/Blood.V104.11.329.329  0.759
2000 Nanda V, Liang SM, Brand L. Hydrophobic clustering in acid-denatured IL-2 and fluorescence of a Trp NH-pi H-bond. Biochemical and Biophysical Research Communications. 279: 770-8. PMID 11162427 DOI: 10.1006/Bbrc.2000.4033  0.531
2000 Nanda V, Brand L. Aromatic interactions in homeodomains contribute to the low quantum yield of a conserved, buried tryptophan. Proteins. 40: 112-25. PMID 10813836 DOI: 10.1002/(Sici)1097-0134(20000701)40:1<112::Aid-Prot130>3.0.Co;2-C  0.556
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