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Items: 1 to 50 of 151

1.

Protein model discrimination attempts using mutational sensitivity, predicted secondary structure, and model quality information.

Khare S, Bhasin M, Sahoo A, Varadarajan R.

Proteins. 2019 Jan 7. doi: 10.1002/prot.25654. [Epub ahead of print]

PMID:
30615225
2.

Bridging centrioles and PCM in proper space and time.

Varadarajan R, Rusan NM.

Essays Biochem. 2018 Dec 7;62(6):793-801. doi: 10.1042/EBC20180036. Print 2018 Dec 7. Review.

3.
4.

Design, display and immunogenicity of HIV1 gp120 fragment immunogens on virus-like particles.

Purwar M, Pokorski JK, Singh P, Bhattacharyya S, Arendt H, DeStefano J, La Branche CC, Montefiori DC, Finn MG, Varadarajan R.

Vaccine. 2018 Oct 8;36(42):6345-6353. doi: 10.1016/j.vaccine.2018.07.032. Epub 2018 Sep 14.

PMID:
30220462
5.

Rv0474 is a copper-responsive transcriptional regulator that negatively regulates expression of RNA polymerase β subunit in Mycobacterium tuberculosis.

Raghunandanan S, Ramachandran R, Gomez RL, Devanarayanan S, Bommakanti A, Kondapi AK, Varadarajan R, Kumar RA.

FEBS J. 2018 Oct;285(20):3849-3869. doi: 10.1111/febs.14637. Epub 2018 Sep 5.

PMID:
30120904
6.

Bacterially expressed HIV-1 gp120 outer-domain fragment immunogens with improved stability and affinity for CD4-binding site neutralizing antibodies.

Rathore U, Purwar M, Vignesh VS, Das R, Kumar AA, Bhattacharyya S, Arendt H, DeStefano J, Wilson A, Parks C, La Branche CC, Montefiori DC, Varadarajan R.

J Biol Chem. 2018 Sep 28;293(39):15002-15020. doi: 10.1074/jbc.RA118.005006. Epub 2018 Aug 9.

PMID:
30093409
7.

Open and Closed Form of Maltose Binding Protein in Its Native and Molten Globule State As Studied by Electron Paramagnetic Resonance Spectroscopy.

Selmke B, Borbat PP, Nickolaus C, Varadarajan R, Freed JH, Trommer WE.

Biochemistry. 2018 Sep 25;57(38):5507-5512. doi: 10.1021/acs.biochem.8b00322. Epub 2018 Sep 13.

PMID:
30004675
8.

Isolation of an in Vitro Affinity-Matured, Thermostable "Headless" HA Stem Fragment That Binds Broadly Neutralizing Antibodies with High Affinity.

Najar TA, Kar U, Flynn JA, Varadarajan R.

Biochemistry. 2018 Jul 3;57(26):3817-3829. doi: 10.1021/acs.biochem.8b00267. Epub 2018 Jun 13.

PMID:
29863853
9.

Rapid Mapping of Protein Binding Sites and Conformational Epitopes by Coupling Yeast Surface Display to Chemical Labeling and Deep Sequencing.

Najar TA, Khare S, Varadarajan R.

Methods Mol Biol. 2018;1785:77-88. doi: 10.1007/978-1-4939-7841-0_6.

PMID:
29714013
10.

Evolution of Neutralization Response in HIV-1 Subtype C-Infected Individuals Exhibiting Broad Cross-Clade Neutralization of HIV-1 Strains.

Cheedarla N, Hemalatha B, Anangi B, Muthuramalingam K, Selvachithiram M, Sathyamurthi P, Kailasam N, Varadarajan R, Swaminathan S, Tripathy SP, Vaniambadi SK, Vadakkupattu DR, Hanna LE.

Front Immunol. 2018 Mar 27;9:618. doi: 10.3389/fimmu.2018.00618. eCollection 2018.

11.

Insights into protein structure, stability and function from saturation mutagenesis.

Gupta K, Varadarajan R.

Curr Opin Struct Biol. 2018 Jun;50:117-125. doi: 10.1016/j.sbi.2018.02.006. Epub 2018 Mar 2. Review.

PMID:
29505936
12.

Protective efficacy of influenza group 2 hemagglutinin stem-fragment immunogen vaccines.

Sutton TC, Chakraborty S, Mallajosyula VVA, Lamirande EW, Ganti K, Bock KW, Moore IN, Varadarajan R, Subbarao K.

NPJ Vaccines. 2017 Dec 15;2:35. doi: 10.1038/s41541-017-0036-2. eCollection 2017.

13.

A centrosomal scaffold shows some self-control.

Varadarajan R, Hammer JA, Rusan NM.

J Biol Chem. 2017 Dec 15;292(50):20410-20411. doi: 10.1074/jbc.H117.806018. Review.

14.

A Trimeric HIV-1 Envelope gp120 Immunogen Induces Potent and Broad Anti-V1V2 Loop Antibodies against HIV-1 in Rabbits and Rhesus Macaques.

Jones AT, Chamcha V, Kesavardhana S, Shen X, Beaumont D, Das R, Wyatt LS, LaBranche CC, Stanfield-Oakley S, Ferrari G, Montefiori DC, Moss B, Tomaras GD, Varadarajan R, Amara RR.

J Virol. 2018 Feb 12;92(5). pii: e01796-17. doi: 10.1128/JVI.01796-17. Print 2018 Mar 1.

15.

Contribution of the Chromosomal ccdAB Operon to Bacterial Drug Tolerance.

Gupta K, Tripathi A, Sahu A, Varadarajan R.

J Bacteriol. 2017 Sep 5;199(19). pii: e00397-17. doi: 10.1128/JB.00397-17. Print 2017 Oct 1.

16.

Glycosylation of the core of the HIV-1 envelope subunit protein gp120 is not required for native trimer formation or viral infectivity.

Rathore U, Saha P, Kesavardhana S, Kumar AA, Datta R, Devanarayanan S, Das R, Mascola JR, Varadarajan R.

J Biol Chem. 2017 Jun 16;292(24):10197-10219. doi: 10.1074/jbc.M117.788919. Epub 2017 Apr 26.

17.

Cross-neutralizing anti-HIV-1 human single chain variable fragments(scFvs) against CD4 binding site and N332 glycan identified from a recombinant phage library.

Khan L, Kumar R, Thiruvengadam R, Parray HA, Makhdoomi MA, Kumar S, Aggarwal H, Mohata M, Hussain AW, Das R, Varadarajan R, Bhattacharya J, Vajpayee M, Murugavel KG, Solomon S, Sinha S, Luthra K.

Sci Rep. 2017 Mar 23;7:45163. doi: 10.1038/srep45163.

18.

Mapping Protein Binding Sites and Conformational Epitopes Using Cysteine Labeling and Yeast Surface Display.

Najar TA, Khare S, Pandey R, Gupta SK, Varadarajan R.

Structure. 2017 Mar 7;25(3):395-406. doi: 10.1016/j.str.2016.12.016. Epub 2017 Jan 26.

19.

Generation and characterisation of monoclonal antibodies specific to avian influenza H7N9 haemagglutinin protein.

Malik A, Mallajosyula V, Mishra NN, Arukha AP, Varadarajan R, Gupta SK.

Indian J Med Microbiol. 2016 Oct-Dec;34(4):489-494. doi: 10.4103/0255-0857.195366.

20.

Structure-based Design of Cyclically Permuted HIV-1 gp120 Trimers That Elicit Neutralizing Antibodies.

Kesavardhana S, Das R, Citron M, Datta R, Ecto L, Srilatha NS, DiStefano D, Swoyer R, Joyce JG, Dutta S, LaBranche CC, Montefiori DC, Flynn JA, Varadarajan R.

J Biol Chem. 2017 Jan 6;292(1):278-291. doi: 10.1074/jbc.M116.725614. Epub 2016 Nov 22.

21.

The Fission Yeast Pre-mRNA-processing Factor 18 (prp18+) Has Intron-specific Splicing Functions with Links to G1-S Cell Cycle Progression.

Vijaykrishna N, Melangath G, Kumar R, Khandelia P, Bawa P, Varadarajan R, Vijayraghavan U.

J Biol Chem. 2016 Dec 30;291(53):27387-27402. doi: 10.1074/jbc.M116.751289. Epub 2016 Nov 15.

22.

Homodimeric Escherichia coli Toxin CcdB (Controller of Cell Division or Death B Protein) Folds via Parallel Pathways.

Baliga C, Varadarajan R, Aghera N.

Biochemistry. 2016 Nov 1;55(43):6019-6031. Epub 2016 Oct 18.

PMID:
27696818
23.

Aid-in-dying practice in Europe and the United States: Legal and ethical perspectives for pharmacy.

Varadarajan R, Freeman RA, Parmar JR.

Res Social Adm Pharm. 2016 Nov - Dec;12(6):1016-1025. doi: 10.1016/j.sapharm.2015.11.008. Epub 2015 Nov 24.

PMID:
26711140
24.

Editorial overview: Engineering and design.

Tawfik DS, Varadarajan R.

Curr Opin Struct Biol. 2016 Aug;39:v-vi. doi: 10.1016/j.sbi.2016.08.004. Epub 2016 Aug 29. No abstract available.

PMID:
27595363
25.

Molecular Determinants of Mutant Phenotypes, Inferred from Saturation Mutagenesis Data.

Tripathi A, Gupta K, Khare S, Jain PC, Patel S, Kumar P, Pulianmackal AJ, Aghera N, Varadarajan R.

Mol Biol Evol. 2016 Nov;33(11):2960-2975. Epub 2016 Aug 25.

26.

Neutralization and Binding Profile of Monoclonal Antibodies Generated Against Influenza A H1N1 Viruses.

Shembekar N, Mallajosyula VV, Malik A, Saini A, Varadarajan R, Gupta SK.

Monoclon Antib Immunodiagn Immunother. 2016 Aug;35(4):191-8. doi: 10.1089/mab.2016.0015. Epub 2016 Jul 27.

PMID:
27463230
27.

A Randomized Trial of Factor VIII and Neutralizing Antibodies in Hemophilia A.

Peyvandi F, Mannucci PM, Garagiola I, El-Beshlawy A, Elalfy M, Ramanan V, Eshghi P, Hanagavadi S, Varadarajan R, Karimi M, Manglani MV, Ross C, Young G, Seth T, Apte S, Nayak DM, Santagostino E, Mancuso ME, Sandoval Gonzalez AC, Mahlangu JN, Bonanad Boix S, Cerqueira M, Ewing NP, Male C, Owaidah T, Soto Arellano V, Kobrinsky NL, Majumdar S, Perez Garrido R, Sachdeva A, Simpson M, Thomas M, Zanon E, Antmen B, Kavakli K, Manco-Johnson MJ, Martinez M, Marzouka E, Mazzucconi MG, Neme D, Palomo Bravo A, Paredes Aguilera R, Prezotti A, Schmitt K, Wicklund BM, Zulfikar B, Rosendaal FR.

N Engl J Med. 2016 May 26;374(21):2054-64. doi: 10.1056/NEJMoa1516437.

28.

Myt1 inhibition of Cyclin A/Cdk1 is essential for fusome integrity and premeiotic centriole engagement in Drosophila spermatocytes.

Varadarajan R, Ayeni J, Jin Z, Homola E, Campbell SD.

Mol Biol Cell. 2016 Jul 1;27(13):2051-63. doi: 10.1091/mbc.E16-02-0104. Epub 2016 May 11.

29.

Rational elicitation of cold-sensitive phenotypes.

Baliga C, Majhi S, Mondal K, Bhattacharjee A, VijayRaghavan K, Varadarajan R.

Proc Natl Acad Sci U S A. 2016 May 3;113(18):E2506-15. doi: 10.1073/pnas.1604190113. Epub 2016 Apr 18.

30.

Effect of Interbody Fusion on the Remaining Discs of the Lumbar Spine in Subjects with Disc Degeneration.

Ryu R, Techy F, Varadarajan R, Amirouche F.

Orthop Surg. 2016 Feb;8(1):27-33. doi: 10.1111/os.12219.

PMID:
27028378
31.

Stalking influenza by vaccination with pre-fusion headless HA mini-stem.

Valkenburg SA, Mallajosyula VV, Li OT, Chin AW, Carnell G, Temperton N, Varadarajan R, Poon LL.

Sci Rep. 2016 Mar 7;6:22666. doi: 10.1038/srep22666.

32.

Residue proximity information and protein model discrimination using saturation-suppressor mutagenesis.

Sahoo A, Khare S, Devanarayanan S, Jain PC, Varadarajan R.

Elife. 2015 Dec 30;4. pii: e09532. doi: 10.7554/eLife.09532.

33.

Generation and Characterization of Monoclonal Antibodies Specific to Avian Influenza H5N1 Hemagglutinin Protein.

Malik A, Mallajosyula VV, Mishra NN, Varadarajan R, Gupta SK.

Monoclon Antib Immunodiagn Immunother. 2015 Dec;34(6):436-41. doi: 10.1089/mab.2015.0047.

PMID:
26683184
34.

Hemagglutinin Sequence Conservation Guided Stem Immunogen Design from Influenza A H3 Subtype.

Mallajosyula VV, Citron M, Ferrara F, Temperton NJ, Liang X, Flynn JA, Varadarajan R.

Front Immunol. 2015 Jun 26;6:329. doi: 10.3389/fimmu.2015.00329. eCollection 2015.

35.

Humanized antibody neutralizing 2009 pandemic H1N1 virus.

Shembekar N, Mallajosyula VV, Chaudhary P, Upadhyay V, Varadarajan R, Gupta SK.

Biotechnol J. 2014 Dec;9(12):1594-603. doi: 10.1002/biot.201400083. Epub 2014 Aug 8.

PMID:
25044602
36.

Influenza hemagglutinin stem-fragment immunogen elicits broadly neutralizing antibodies and confers heterologous protection.

Mallajosyula VV, Citron M, Ferrara F, Lu X, Callahan C, Heidecker GJ, Sarma SP, Flynn JA, Temperton NJ, Liang X, Varadarajan R.

Proc Natl Acad Sci U S A. 2014 Jun 24;111(25):E2514-23. doi: 10.1073/pnas.1402766111. Epub 2014 Jun 9.

37.

Stabilizing the native trimer of HIV-1 Env by destabilizing the heterodimeric interface of the gp41 postfusion six-helix bundle.

Kesavardhana S, Varadarajan R.

J Virol. 2014 Sep 1;88(17):9590-604. doi: 10.1128/JVI.00494-14. Epub 2014 Jun 11.

38.

Immunogen design for HIV-1 and influenza.

Rathore U, Kesavardhana S, Mallajosyula VV, Varadarajan R.

Biochim Biophys Acta. 2014 Nov;1844(11):1891-1906. doi: 10.1016/j.bbapap.2014.05.010. Epub 2014 Jun 2. Review.

PMID:
24892211
39.

TSpred: a web server for the rational design of temperature-sensitive mutants.

Tan KP, Khare S, Varadarajan R, Madhusudhan MS.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W277-84. doi: 10.1093/nar/gku319. Epub 2014 Apr 29.

40.

Residue specific contributions to stability and activity inferred from saturation mutagenesis and deep sequencing.

Tripathi A, Varadarajan R.

Curr Opin Struct Biol. 2014 Feb;24:63-71. doi: 10.1016/j.sbi.2013.12.001. Epub 2014 Jan 7. Review.

PMID:
24721454
41.

MazF-induced growth inhibition and persister generation in Escherichia coli.

Tripathi A, Dewan PC, Siddique SA, Varadarajan R.

J Biol Chem. 2014 Feb 14;289(7):4191-205. doi: 10.1074/jbc.M113.510511. Epub 2013 Dec 27.

42.

A rapid, efficient, and economical inverse polymerase chain reaction-based method for generating a site saturation mutant library.

Jain PC, Varadarajan R.

Anal Biochem. 2014 Mar 15;449:90-8. doi: 10.1016/j.ab.2013.12.002. Epub 2013 Dec 9.

PMID:
24333246
43.

Dual phosphorylation of cdk1 coordinates cell proliferation with key developmental processes in Drosophila.

Ayeni JO, Varadarajan R, Mukherjee O, Stuart DT, Sprenger F, Srayko M, Campbell SD.

Genetics. 2014 Jan;196(1):197-210. doi: 10.1534/genetics.113.156281. Epub 2013 Nov 8.

44.

Experimental analysis to utilize the solid wastes in brick production.

Varadarajan R, Govindan V.

J Environ Sci Eng. 2013 Jul;55(3):343-50.

PMID:
25509952
45.

Depth: a web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pKa of ionizable residues in proteins.

Tan KP, Nguyen TB, Patel S, Varadarajan R, Madhusudhan MS.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W314-21. doi: 10.1093/nar/gkt503. Epub 2013 Jun 12.

46.

Effect of signal peptide on stability and folding of Escherichia coli thioredoxin.

Singh P, Sharma L, Kulothungan SR, Adkar BV, Prajapati RS, Ali PS, Krishnan B, Varadarajan R.

PLoS One. 2013 May 7;8(5):e63442. doi: 10.1371/journal.pone.0063442. Print 2013.

47.

In vitro and in vivo characterization of designed immunogens derived from the CD-helix of the stem of influenza hemagglutinin.

Mallajosyula VV, Citron M, Lu X, Meulen JT, Varadarajan R, Liang X.

Proteins. 2013 Oct;81(10):1759-75. doi: 10.1002/prot.24317. Epub 2013 Jul 23.

PMID:
23625724
48.

Design of an Escherichia coli expressed HIV-1 gp120 fragment immunogen that binds to b12 and induces broad and potent neutralizing antibodies.

Bhattacharyya S, Singh P, Rathore U, Purwar M, Wagner D, Arendt H, DeStefano J, LaBranche CC, Montefiori DC, Phogat S, Varadarajan R.

J Biol Chem. 2013 Apr 5;288(14):9815-25. doi: 10.1074/jbc.M112.425959. Epub 2013 Feb 21.

49.

Isolation of a high affinity neutralizing monoclonal antibody against 2009 pandemic H1N1 virus that binds at the 'Sa' antigenic site.

Shembekar N, Mallajosyula VV, Mishra A, Yeolekar L, Dhere R, Kapre S, Varadarajan R, Gupta SK.

PLoS One. 2013;8(1):e55516. doi: 10.1371/journal.pone.0055516. Epub 2013 Jan 31.

50.

Packing in molten globules and native states.

Bhattacharyya S, Varadarajan R.

Curr Opin Struct Biol. 2013 Feb;23(1):11-21. doi: 10.1016/j.sbi.2012.10.010. Epub 2012 Dec 25. Review.

PMID:
23270864

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