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Items: 1 to 50 of 96


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 Nov 6. doi: 10.1021/acs.jctc.8b00602. [Epub ahead of print]


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 Oct 30. doi: 10.1021/acs.biochem.8b00729. [Epub ahead of print]


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. 2018 Sep 12. doi: 10.1021/acs.jmedchem.8b00857. [Epub ahead of print]


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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/ Epub 2015 Nov 5. Review.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


Identification of anti-malarial compounds as novel antagonists to chemokine receptor CXCR4 in pancreatic cancer cells.

Kim J, Yip ML, Shen X, Li H, Hsin LY, Labarge S, Heinrich EL, Lee W, Lu J, Vaidehi N.

PLoS One. 2012;7(2):e31004. doi: 10.1371/journal.pone.0031004. Epub 2012 Feb 3.


Structure refinement of protein low resolution models using the GNEIMO constrained dynamics method.

Park IH, Gangupomu V, Wagner J, Jain A, Vaidehi N.

J Phys Chem B. 2012 Mar 1;116(8):2365-75. doi: 10.1021/jp209657n. Epub 2012 Feb 16.


Multiscale computational methods for mapping conformational ensembles of G-protein-coupled receptors.

Vaidehi N, Bhattacharya S.

Adv Protein Chem Struct Biol. 2011;85:253-80. doi: 10.1016/B978-0-12-386485-7.00007-7. Review.


Small molecule chemokine mimetics suggest a molecular basis for the observation that CXCL10 and CXCL11 are allosteric ligands of CXCR3.

Nedjai B, Li H, Stroke IL, Wise EL, Webb ML, Merritt JR, Henderson I, Klon AE, Cole AG, Horuk R, Vaidehi N, Pease JE.

Br J Pharmacol. 2012 Jun;166(3):912-23. doi: 10.1111/j.1476-5381.2011.01660.x.


The role of conformational ensembles in ligand recognition in G-protein coupled receptors.

Niesen MJ, Bhattacharya S, Vaidehi N.

J Am Chem Soc. 2011 Aug 24;133(33):13197-204. doi: 10.1021/ja205313h. Epub 2011 Jul 29.


Interaction of actin with carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1) receptor in liposomes is Ca2+- and phospholipid-dependent.

Lu R, Niesen MJ, Hu W, Vaidehi N, Shively JE.

J Biol Chem. 2011 Aug 5;286(31):27528-36. doi: 10.1074/jbc.M111.235762. Epub 2011 Jun 13.


Folding of small proteins using constrained molecular dynamics.

Balaraman GS, Park IH, Jain A, Vaidehi N.

J Phys Chem B. 2011 Jun 16;115(23):7588-96. doi: 10.1021/jp200414z. Epub 2011 May 18.


Alkylation of cysteine 468 in Stat3 defines a novel site for therapeutic development.

Buettner R, Corzano R, Rashid R, Lin J, Senthil M, Hedvat M, Schroeder A, Mao A, Herrmann A, Yim J, Li H, Yuan YC, Yakushijin K, Yakushijin F, Vaidehi N, Moore R, Gugiu G, Lee TD, Yip R, Chen Y, Jove R, Horne D, Williams JC.

ACS Chem Biol. 2011 May 20;6(5):432-43. doi: 10.1021/cb100253e. Epub 2011 Feb 16.


Importance of receptor flexibility in binding of cyclam compounds to the chemokine receptor CXCR4.

Lam AR, Bhattacharya S, Patel K, Hall SE, Mao A, Vaidehi N.

J Chem Inf Model. 2011 Jan 24;51(1):139-47. doi: 10.1021/ci1003027. Epub 2010 Dec 15.


The role of conformational ensembles of seven transmembrane receptors in functional selectivity.

Vaidehi N, Kenakin T.

Curr Opin Pharmacol. 2010 Dec;10(6):775-81. doi: 10.1016/j.coph.2010.09.004. Review.


Dynamics and flexibility of G-protein-coupled receptor conformations and their relevance to drug design.

Vaidehi N.

Drug Discov Today. 2010 Nov;15(21-22):951-7. doi: 10.1016/j.drudis.2010.08.018. Epub 2010 Sep 8. Review.


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