Dr Ranjit Vijayan

Computational modelling of ion channel biophysics

I am interested in studying ligand gated ion channels, specifically nicotinic acetylcholine receptors (nAChRs) and ionotropic glutamate receptors (iGluRs). I use homology modelling, docking, molecular dynamics and free energy calculations (thermodynamic integration (TI), free energy perturbation (FEP), steered MD (SMD) and potential of mean force (PMF) derived from umbrella sampling) to study these proteins.

My research is funded by the Wellcome Trust.

I completed my 4-year DPhil programme at the Life Sciences Interface (LSI) Doctoral Training Centre (DTC) and the Department of Biochemistry funded by a Clarendon Bursary and the Overseas Research Students (ORS) Awards Scheme.

Personal homepage: http://sbcb.bioch.ox.ac.uk/users/ranjit/

Publications

Vijayan R., Sahai M.A., Czajkowski T., and Biggin P.C. (2010) A comparative analysis of the role of water in the binding pockets of ionotropic glutamate receptors. Physical Chemistry Chemical Physics 12:14057-14066. PMID: 20856958. DOI: 10.1039/C004336B

Vijayan R., Iorga B., and Biggin P.C. (2010) Chapter: Computational approaches to ionotropic glutamate receptors in Molecular Simulations and Biomembranes: From Biophysics to Function RSC Publishing. ISBN: 978-0-85404-189-3. (Also cover image).

Vijayan R., and Biggin P.C. (2010) Conformational preferences of a 14-residue fibrillogenic peptide from acetylcholinesterase. Biochemistry 49:3678-3684. PMID: 20356043. DOI: 10.1021/bi1001807

Vijayan R., Plested A.J.R., Mayer M.L., and Biggin P.C. (2009) Selectivity and cooperativity of modulatory ions in a neurotransmitter receptor. Biophysical Journal. 96:1751-1760. PMID: 19254535. DOI: 10.1016/j.bpj.2008.11.039

Chew C., Vijayan R., Chang J., Zitzmann N., and Biggin P.C. (2009) Determination of pore-lining residues in the Hepatitis C virus p7 protein. Biophysical Journal 96:L10-L12. PMID: 19167280. DOI: 10.1016/j.bpj.2008.10.004

Vijayan R., and Biggin P.C. (2008) A steroid in a lipid bilayer: Localization, orientation and energetics. Biophysical Journal 95:L45-L47. PMID: 18689457. DOI: 10.1529/biophysj.108.140087

Plested A.J.R.*, Vijayan R.*, Biggin P.C., and Mayer M.L. (2008) Molecular basis of kainate receptor modulation by sodium. Neuron 58:720-735. PMID: 18549784. DOI: 10.1016/j.neuron.2008.04.001 (* - Joint first author)

Moroni M., Vijayan R., Carbone A., Zwart R., Biggin P.C., and Bermudez I. (2008) Non-agonist binding subunit interfaces confer distinct functional signatures to the alternate stoichiometries of the α4β2 nicotinic receptor: an α4-α4 interface is required for Zn²⁺ potentiation. Journal of Neuroscience 28:6884-6894. PMID: 18596163. DOI: 10.1523/jneurosci.1228-08.2008

Amiri S., Shimomura M., Vijayan R., Nishiwaki H., Akamatsu M., Matsuda K., Jones A.K., Sansom M.S.P., Biggin P.C., and Sattelle D.B. (2008) A role for Leu118 of loop E in agonist binding to the α7 nicotinic acetylcholine receptor. Molecular Pharmacology 73:1659-1667. PMID: 18339894. DOI:10.1124/mol.107.041590