Home Department: Center for Biophysics and Computational Biology 

Email: rbgamini@ks.uiuc.edu

Telephone: 217-244-4361

Fax:
217-244-6078

Theoretical and Computational Biophysics Group
3157 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801


Education:

  • Ph.D. in Biophysics and Computational Biology, University of Illinois, Urbana-Champaign
  • M.Sc. in Biophysics, University of Madras, India
  • B.Sc. in Physics, University of Madras, India

Research Interests:

The Nuclear Pore Complex, an assembly of ~ 450 proteins is comprised of and rich in the Phe/Gly(non-polar) repeat proteins. Although one might immediately conclude the hydrophobic nature of the pore to have some basis for the gating function of the pore, brush-like structures with highly entropic behavior underlies a more precise mechanism for gating. I am interested in understanding the biophysical basis underlying the selective gating mechanism. I propose to use molecular simulation approaches which have possible advantage of studying dynamics of such events. More information about the assembly of these proteins can be found at our Nuclear pore complex website.

Mechanosensitive channels (MS) act as safety valves in bacteria. Osmoprotectants like Glutamate are known to be important for retaining cellular volume to protect the cell during osmotic shocks and these channels are known to be responsible for selective filtering of such osmolytes. The ionic properties and conformational states of these channels in their closed and open states have been studied using simulations in detail by Marcos Sotomayor from our lab (Presently, post-doc in Harvard). However, the selective filtering capacity of the cytoplasmic domain of MS channel, in particular those with small conductances, Mscs, remains to be elucidated. I am interested in understanding this function using molecular simulation approaches. More information about the functional role of the cytoplasmic domain of MscS can be found at our Mechanosensitive channel MscS website.


Publications:

    Assembly of Nsp1 nucleoporins provides insight into nuclear pore complex gating. PLOS Computational Biology DOI 10.1371/journal.pcbi.1003488

    Ramya Gamini, Wei Han, John E. Stone, Klaus Schulten

    Cytoplasmic domain filter function in the mechanosensitive channel of small conductance. Biophysical Journal 101: 80-89 (2011)

    Ramya Gamini, Marcos Sotomayor, Christophe Chipot, Klaus Schulten

  • Before Joining TCBG
    CADB: Conformation Angles DataBase of proteins. Nucleic Acids Research 31(1): 448-451 (2003)

    S. Sheik, P. Ananthalakshmi, G. Ramya Bhargavi, Krishna Sekar

    Side-chain conformation angles of amino acids: effect of temperature factor cut-off. Journal Of Structural Biology 143: 181-184 (2003)

    G Ramya Bhargavi, S S Sheik, D Velmurugan, K Sekar

    Correlations between nucleotide frequencies and amino acid composition in 115 bacterial species. Biochem. Biophys. Res. Commun. 315 (4):1097-103 (2004)

    D.Bhranidharan, G Ramya Bhargavi, Kavitha Uthanumallian, N Gautham

Teaching:

Computational Biophysics Workshop. UIUC, Champaign, IL, July 2009.
Computational Biophysics Workshop. UIUC, Urbana, IL, Nov. 2010.

Physics 550, Molecular Biophysics. Spring, 2011
A course on biophysics for graduate students in physics. I was a teaching assistant which i nvolved communicating with students, preparing solutions, and grading homeworks.

Computational Biophysics Workshop. Atlanta, Georgia, March. 2011.


Poster Presentations (conferences and workshops):

Cytoplasmic Domain Filter Function in the Mechanosensitive Channel of Small Conductance . Ramya Gamini, Marcos Sotomayor, Christophe Chipot, and Klaus Schulten. Biophysical Society Meeting, 2010. San Francisco, CA.

Coarse-grained molecular dynamics simulations of the nuclear pore complex . Ramya Gamini and Klaus Schulten. Nuclear Pore Complex: Biology, Physics, Nanotechnology Workshop II, 2010. Albuquerque, New Mexico.