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Items: 1 to 50 of 107

1.

Machine Learning for Prioritization of Thermostabilizing Mutations for G-Protein Coupled Receptors.

Muk S, Ghosh S, Achuthan S, Chen X, Yao X, Sandhu M, Griffor MC, Fennell KF, Che Y, Shanmugasundaram V, Qiu X, Tate CG, Vaidehi N.

Biophys J. 2019 Dec 3;117(11):2228-2239. doi: 10.1016/j.bpj.2019.10.023. Epub 2019 Oct 24.

PMID:
31703801
2.

Generation of dual specific bivalent BiTEs (dbBIspecific T-cell engaging antibodies) for cellular immunotherapy.

Kujawski M, Li L, Bhattacharya S, Wong P, Lee WH, Williams L, Li H, Chea J, Poku K, Bowles N, Vaidehi N, Yazaki P, Shively JE.

BMC Cancer. 2019 Sep 5;19(1):882. doi: 10.1186/s12885-019-6056-8.

3.

EPHA2 mutations with oncogenic characteristics in squamous cell lung cancer and malignant pleural mesothelioma.

Tan YC, Srivastava S, Won BM, Kanteti R, Arif Q, Husain AN, Li H, Vigneswaran WT, Pang KM, Kulkarni P, Sattler M, Vaidehi N, Mambetsariev I, Kindler HL, Wheeler DL, Salgia R.

Oncogenesis. 2019 Sep 4;8(9):49. doi: 10.1038/s41389-019-0159-6.

4.

Prediction of Conformation Specific Thermostabilizing Mutations for Class A G Protein-Coupled Receptors.

Jana S, Ghosh S, Muk S, Levy B, Vaidehi N.

J Chem Inf Model. 2019 Sep 23;59(9):3744-3754. doi: 10.1021/acs.jcim.9b00175. Epub 2019 Aug 27.

PMID:
31408606
5.

Variable G protein determinants of GPCR coupling selectivity.

Okashah N, Wan Q, Ghosh S, Sandhu M, Inoue A, Vaidehi N, Lambert NA.

Proc Natl Acad Sci U S A. 2019 Jun 11;116(24):12054-12059. doi: 10.1073/pnas.1905993116. Epub 2019 May 29.

6.

Conformational plasticity of the intracellular cavity of GPCR-G-protein complexes leads to G-protein promiscuity and selectivity.

Sandhu M, Touma AM, Dysthe M, Sadler F, Sivaramakrishnan S, Vaidehi N.

Proc Natl Acad Sci U S A. 2019 Jun 11;116(24):11956-11965. doi: 10.1073/pnas.1820944116. Epub 2019 May 28.

7.

Leflunomide regulates c-Myc expression in myeloma cells through PIM targeting.

Buettner R, Morales C, Caserta E, Troadec E, Gunes EG, Viola D, Khalife J, Li H, Keats JJ, Christofferson A, Wu X, Synold TW, Palmer J, Sanchez JF, Pozhitkov A, Vaidehi N, Marcucci G, Krishnan A, Rosenzweig MA, Pichiorri F, Rosen ST.

Blood Adv. 2019 Apr 9;3(7):1027-1032. doi: 10.1182/bloodadvances.2018027227. No abstract available.

8.

Efficient and Selective Electrochemically Driven Enzyme-Catalyzed Reduction of Carbon Dioxide to Formate using Formate Dehydrogenase and an Artificial Cofactor.

Jayathilake BS, Bhattacharya S, Vaidehi N, Narayanan SR.

Acc Chem Res. 2019 Mar 19;52(3):676-685. doi: 10.1021/acs.accounts.8b00551. Epub 2019 Feb 11.

PMID:
30741524
9.

Dynamic Role of the G Protein in Stabilizing the Active State of the Adenosine A2A Receptor.

Lee S, Nivedha AK, Tate CG, Vaidehi N.

Structure. 2019 Apr 2;27(4):703-712.e3. doi: 10.1016/j.str.2018.12.007. Epub 2019 Jan 31.

10.

NMR analysis of free and lipid nanodisc anchored CEACAM1 membrane proximal peptides with Ca2+/CaM.

Ghazarian H, Hu W, Mao A, Nguyen T, Vaidehi N, Sligar S, Shively JE.

Biochim Biophys Acta Biomembr. 2019 Apr 1;1861(4):787-797. doi: 10.1016/j.bbamem.2019.01.004. Epub 2019 Jan 10.

PMID:
30639287
11.

Structural insights into the subtype-selective antagonist binding to the M2 muscarinic receptor.

Suno R, Lee S, Maeda S, Yasuda S, Yamashita K, Hirata K, Horita S, Tawaramoto MS, Tsujimoto H, Murata T, Kinoshita M, Yamamoto M, Kobilka BK, Vaidehi N, Iwata S, Kobayashi T.

Nat Chem Biol. 2018 Dec;14(12):1150-1158. doi: 10.1038/s41589-018-0152-y. Epub 2018 Nov 12.

12.

Engineering Salt Bridge Networks between Transmembrane Helices Confers Thermostability in G-Protein-Coupled Receptors.

Ghosh S, Bierig T, Lee S, Jana S, Löhle A, Schnapp G, Tautermann CS, Vaidehi N.

J Chem Theory Comput. 2018 Dec 11;14(12):6574-6585. doi: 10.1021/acs.jctc.8b00602. Epub 2018 Nov 6.

13.

Bitopic Inhibition of ATP and Substrate Binding in Ser/Thr Kinases through a Conserved Allosteric Mechanism.

Ma N, Lippert LG, Devamani T, Levy B, Lee S, Sandhu M, Vaidehi N, Sivaramakrishnan S.

Biochemistry. 2018 Nov 13;57(45):6387-6390. doi: 10.1021/acs.biochem.8b00729. Epub 2018 Oct 30.

14.

Allosteric Activation of Striatal-Enriched Protein Tyrosine Phosphatase (STEP, PTPN5) by a Fragment-like Molecule.

Tautermann CS, Binder F, Büttner FH, Eickmeier C, Fiegen D, Gross U, Grundl MA, Heilker R, Hobson S, Hoerer S, Luippold A, Mack V, Montel F, Peters S, Bhattacharya S, Vaidehi N, Schnapp G, Thamm S, Zeeb M.

J Med Chem. 2019 Jan 10;62(1):306-316. doi: 10.1021/acs.jmedchem.8b00857. Epub 2018 Sep 12.

PMID:
30207464
15.

C-NHEJ without indels is robust and requires synergistic function of distinct XLF domains.

Bhargava R, Sandhu M, Muk S, Lee G, Vaidehi N, Stark JM.

Nat Commun. 2018 Jun 27;9(1):2484. doi: 10.1038/s41467-018-04867-5.

16.

Identifying Functional Hotspot Residues for Biased Ligand Design in G-Protein-Coupled Receptors.

Nivedha AK, Tautermann CS, Bhattacharya S, Lee S, Casarosa P, Kollak I, Kiechle T, Vaidehi N.

Mol Pharmacol. 2018 Apr;93(4):288-296. doi: 10.1124/mol.117.110395. Epub 2018 Jan 24.

17.

How Does the Proliferating Cell Nuclear Antigen Modulate Binding Specificity to Multiple Partner Proteins?

Li H, Sandhu M, Malkas LH, Hickey RJ, Vaidehi N.

J Chem Inf Model. 2017 Dec 26;57(12):3011-3021. doi: 10.1021/acs.jcim.7b00171. Epub 2017 Nov 17.

PMID:
29095607
18.

Distinct structural mechanisms determine substrate affinity and kinase activity of protein kinase Cα.

Lee S, Devamani T, Song HD, Sandhu M, Larsen A, Sommese R, Jain A, Vaidehi N, Sivaramakrishnan S.

J Biol Chem. 2017 Sep 29;292(39):16300-16309. doi: 10.1074/jbc.M117.804781. Epub 2017 Aug 15.

19.

Cooperation of neurotrophin receptor TrkB and Her2 in breast cancer cells facilitates brain metastases.

Choy C, Ansari KI, Neman J, Hsu S, Duenas MJ, Li H, Vaidehi N, Jandial R.

Breast Cancer Res. 2017 Apr 26;19(1):51. doi: 10.1186/s13058-017-0844-3.

20.

Structure and dynamics of a constitutively active neurotensin receptor.

Krumm BE, Lee S, Bhattacharya S, Botos I, White CF, Du H, Vaidehi N, Grisshammer R.

Sci Rep. 2016 Dec 7;6:38564. doi: 10.1038/srep38564.

21.

How Do Short Chain Nonionic Detergents Destabilize G-Protein-Coupled Receptors?

Lee S, Mao A, Bhattacharya S, Robertson N, Grisshammer R, Tate CG, Vaidehi N.

J Am Chem Soc. 2016 Nov 30;138(47):15425-15433. Epub 2016 Nov 15.

22.

Allosteric communication pipelines in G-protein-coupled receptors.

Vaidehi N, Bhattacharya S.

Curr Opin Pharmacol. 2016 Oct;30:76-83. doi: 10.1016/j.coph.2016.07.010. Epub 2016 Aug 4. Review.

23.

Conserved Mechanism of Conformational Stability and Dynamics in G-Protein-Coupled Receptors.

Bhattacharya S, Salomon-Ferrer R, Lee S, Vaidehi N.

J Chem Theory Comput. 2016 Nov 8;12(11):5575-5584. Epub 2016 Oct 17.

24.

Structural Elements in the Gαs and Gαq C Termini That Mediate Selective G Protein-coupled Receptor (GPCR) Signaling.

Semack A, Sandhu M, Malik RU, Vaidehi N, Sivaramakrishnan S.

J Biol Chem. 2016 Aug 19;291(34):17929-40. doi: 10.1074/jbc.M116.735720. Epub 2016 Jun 21.

25.

Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations.

Kandel S, Salomon-Ferrer R, Larsen AB, Jain A, Vaidehi N.

J Chem Phys. 2016 Jan 28;144(4):044112. doi: 10.1063/1.4939532.

26.

How Can Mutations Thermostabilize G-Protein-Coupled Receptors?

Vaidehi N, Grisshammer R, Tate CG.

Trends Pharmacol Sci. 2016 Jan;37(1):37-46. doi: 10.1016/j.tips.2015.09.005. Epub 2015 Nov 5. Review.

27.

N-linked glycosylation of protease-activated receptor-1 at extracellular loop 2 regulates G-protein signaling bias.

Soto AG, Smith TH, Chen B, Bhattacharya S, Cordova IC, Kenakin T, Vaidehi N, Trejo J.

Proc Natl Acad Sci U S A. 2015 Jul 7;112(27):E3600-8. doi: 10.1073/pnas.1508838112. Epub 2015 Jun 22.

28.

CCR9-mediated signaling through β-catenin and identification of a novel CCR9 antagonist.

Lee S, Heinrich EL, Li L, Lu J, Choi AH, Levy RA, Wagner JE, Yip ML, Vaidehi N, Kim J.

Mol Oncol. 2015 Oct;9(8):1599-611. doi: 10.1016/j.molonc.2015.04.012. Epub 2015 May 12.

29.

Structural dynamics and thermostabilization of neurotensin receptor 1.

Lee S, Bhattacharya S, Tate CG, Grisshammer R, Vaidehi N.

J Phys Chem B. 2015 Apr 16;119(15):4917-28. doi: 10.1021/jp510735f. Epub 2015 Apr 7.

30.

Stereoselective synthesis, biological evaluation, and modeling of novel bile acid-derived G-protein coupled bile acid receptor 1 (GP-BAR1, TGR5) agonists.

Yu DD, Sousa KM, Mattern DL, Wagner J, Fu X, Vaidehi N, Forman BM, Huang W.

Bioorg Med Chem. 2015 Apr 1;23(7):1613-28. doi: 10.1016/j.bmc.2015.01.048. Epub 2015 Feb 11.

PMID:
25735208
31.

Internal coordinate molecular dynamics: a foundation for multiscale dynamics.

Vaidehi N, Jain A.

J Phys Chem B. 2015 Jan 29;119(4):1233-42. doi: 10.1021/jp509136y. Epub 2015 Jan 6.

32.

CXCR3 antagonist VUF10085 binds to an intrahelical site distinct from that of the broad spectrum antagonist TAK-779.

Nedjai B, Viney JM, Li H, Hull C, Anderson CA, Horie T, Horuk R, Vaidehi N, Pease JE.

Br J Pharmacol. 2015 Apr;172(7):1822-33. doi: 10.1111/bph.13027. Epub 2015 Feb 10.

33.

Rapid Computational Prediction of Thermostabilizing Mutations for G Protein-Coupled Receptors.

Bhattacharya S, Lee S, Grisshammer R, Tate CG, Vaidehi N.

J Chem Theory Comput. 2014 Nov 11;10(11):5149-5160. Epub 2014 Oct 14.

34.

Loss of signalling via Gα13 in germinal centre B-cell-derived lymphoma.

Muppidi JR, Schmitz R, Green JA, Xiao W, Larsen AB, Braun SE, An J, Xu Y, Rosenwald A, Ott G, Gascoyne RD, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Vaidehi N, Staudt LM, Cyster JG.

Nature. 2014 Dec 11;516(7530):254-8. doi: 10.1038/nature13765. Epub 2014 Sep 28.

35.

GneimoSim: a modular internal coordinates molecular dynamics simulation package.

Larsen AB, Wagner JR, Kandel S, Salomon-Ferrer R, Vaidehi N, Jain A.

J Comput Chem. 2014 Dec 5;35(31):2245-55. doi: 10.1002/jcc.23743. Epub 2014 Sep 27.

36.

Differences in allosteric communication pipelines in the inactive and active states of a GPCR.

Bhattacharya S, Vaidehi N.

Biophys J. 2014 Jul 15;107(2):422-434. doi: 10.1016/j.bpj.2014.06.015.

37.

Computational method to identify druggable binding sites that target protein-protein interactions.

Li H, Kasam V, Tautermann CS, Seeliger D, Vaidehi N.

J Chem Inf Model. 2014 May 27;54(5):1391-400. doi: 10.1021/ci400750x. Epub 2014 May 7.

PMID:
24762202
38.

Dynamic behavior of the active and inactive states of the adenosine A(2A) receptor.

Lee S, Bhattacharya S, Grisshammer R, Tate C, Vaidehi N.

J Phys Chem B. 2014 Mar 27;118(12):3355-65. doi: 10.1021/jp411618h. Epub 2014 Mar 17.

39.

Protein structure refinement of CASP target proteins using GNEIMO torsional dynamics method.

Larsen AB, Wagner JR, Jain A, Vaidehi N.

J Chem Inf Model. 2014 Feb 24;54(2):508-17. doi: 10.1021/ci400484c. Epub 2014 Jan 16.

40.

Human breast cancer metastases to the brain display GABAergic properties in the neural niche.

Neman J, Termini J, Wilczynski S, Vaidehi N, Choy C, Kowolik CM, Li H, Hambrecht AC, Roberts E, Jandial R.

Proc Natl Acad Sci U S A. 2014 Jan 21;111(3):984-9. doi: 10.1073/pnas.1322098111. Epub 2014 Jan 6.

41.

Fixman compensating potential for general branched molecules.

Jain A, Kandel S, Wagner J, Larsen A, Vaidehi N.

J Chem Phys. 2013 Dec 28;139(24):244103. doi: 10.1063/1.4851315.

42.

Structure and dynamics of G-protein coupled receptors.

Vaidehi N, Bhattacharya S, Larsen AB.

Adv Exp Med Biol. 2014;796:37-54. doi: 10.1007/978-94-007-7423-0_3. Review.

PMID:
24158800
43.

Thermostabilization of the β1-adrenergic receptor correlates with increased entropy of the inactive state.

Niesen MJ, Bhattacharya S, Grisshammer R, Tate CG, Vaidehi N.

J Phys Chem B. 2013 Jun 20;117(24):7283-91. doi: 10.1021/jp403207c. Epub 2013 Jun 5.

44.

Mapping conformational dynamics of proteins using torsional dynamics simulations.

Gangupomu VK, Wagner JR, Park IH, Jain A, Vaidehi N.

Biophys J. 2013 May 7;104(9):1999-2008. doi: 10.1016/j.bpj.2013.01.050.

45.

Advanced techniques for constrained internal coordinate molecular dynamics.

Wagner JR, Balaraman GS, Niesen MJ, Larsen AB, Jain A, Vaidehi N.

J Comput Chem. 2013 Apr 30;34(11):904-14. doi: 10.1002/jcc.23200. Epub 2013 Jan 23.

46.

Equipartition Principle for Internal Coordinate Molecular Dynamics.

Jain A, Park IH, Vaidehi N.

J Chem Theory Comput. 2012 Aug 14;8(8):2581-2587. Epub 2012 Jul 5.

47.

Critical analysis of the successes and failures of homology models of G protein-coupled receptors.

Bhattacharya S, Lam AR, Li H, Balaraman G, Niesen MJ, Vaidehi N.

Proteins. 2013 May;81(5):729-39. doi: 10.1002/prot.24195. Epub 2013 Feb 14.

48.

Role of specific cations and water entropy on the stability of branched DNA motif structures.

Pascal TA, Goddard WA 3rd, Maiti PK, Vaidehi N.

J Phys Chem B. 2012 Oct 11;116(40):12159-67. doi: 10.1021/jp306473u. Epub 2012 Oct 2.

PMID:
22998030
49.
50.

Receptor conformations involved in dopamine D(2L) receptor functional selectivity induced by selected transmembrane-5 serine mutations.

Fowler JC, Bhattacharya S, Urban JD, Vaidehi N, Mailman RB.

Mol Pharmacol. 2012 Jun;81(6):820-31. doi: 10.1124/mol.111.075457. Epub 2012 Mar 13.

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