Nagarajan Vaidehi

Nagarajan Vaidehi, Ph.D.

  • Chair, Department of Computational and Quantitative Medicine

Nagarajan Vaidehi, Ph.D.

Research Focus :
  • Developing physics-based computational methods to study protein structure, dynamics and drug design
Nagarajan Vaidehi, Ph.D., is professor and chair of the Department Computational and Quantitative Medicine within Beckman Research Institute. Dr. Vaidehi also oversees the Computational Therapeutics Core.
 
Dr. Vaidehi received her Ph.D. in quantum chemistry from the Indian Institute of Technology in India, where she was honored with the Distinguished Alumni Award in 2016. Following her postdoctoral studies on protein dynamics simulation methods with Nobel Laureate Arieh Warshel, Ph.D., at University of Southern California, and William A Goddard III, Ph.D., at Caltech, she became the director of biomolecular simulations at the Materials and Process Simulation Center, Beckman Institute at Caltech. 
 
Dr. Vaidehi joined City of Hope in 2006 as a professor and has since advanced the use of computational methods to meet the challenges of designing therapeutics. She is an internationally recognized biophysicist for her contributions in developing constrained molecular dynamics simulation methods with emphasis on application to G-protein coupled receptors and drug design. 
  • 2018 - present, Professor and Chair of the Department Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA
  • 2018 - present, Professor, Department of Molecular Imaging & Therapy, Diabetes Metabolism Research Institute, City of Hope, Duarte, CA
  • 2005 - 2018, Professor, Department of Molecular Immunology, Beckman Research Institute of City of Hope, Duarte, CA
  • 1998 - 2005, Director of Biosimulations, Materials and Process Simulation Center, Caltech, Pasadena, CA
  • 1994 - 1998, Senior Scientist, Materials and Process Simulation Center, Caltech, Pasadena, CA
  • Computational and Quantitative Medicine
  • Molecular Imaging & Therapy
  • Computational Therapeutics Core

Degrees

  • 1986, Indian Institute of Technology, Ph.D., Theoretical Chemistry
  • 1981, Indian Institute of Technology, M.Sc., Chemistry (minor- Physics and Mathematics), Highest Honors

Fellowship

  • 1991 - 1994, Post-doctoral Fellow at Caltech
  • 1990 - 1991, Post-doctoral Fellow, University of Southern California, Prof. A. Warshel
  • 1989 - 1990, Post-doctoral fellow at University of Exeter, UK

Selected Publications

Please refer to Pubmed for a detailed listing.
 
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 Nov 12. doi: 10.1038/s41589-018-0152-y. [Epub ahead of print]

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 Nov 13;57(45):6387-6390. doi: 10.1021/acs.biochem.8b00729. Epub 2018 Oct 30.
 
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/j.tips.2015.09.005. 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.
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