Research Activities

CURRENT RESEARCH ACTIVITIES

Shawna Frazier
Biochemistry B.S./M.S. 5 year program

My project involves determining the contribution of hydrogen bonds to the anion selectivity filter of a synthetic channel-forming peptide derived from the second transmembrane segment of the glycine receptor alpha-1 subunit. A series of specific residue substitutions have been designed within these peptides to correlate hydrogen bonding strength with selectivity and permeation rates of the channel for chloride ions. Lab techniques employed for this study include:
    -solid phase peptide synthesis using Fmoc chemistries
    -peptide purification by reverse phase HPLC
    -peptide characterization by MALDI-TOF mass spectrometry
    -determination of peptide secondary structure by circular dichroism
    -electrophysiological studies on Ussing chambers to examine channel activity of peptide on epithelial monolayers

Alvaro I. Herrera
B.S. Chemical Engineering,
Universidad Nacional de Colombia 2002

One of the projects I am currently working on is a part of the series of structural studies for the development of a compound suitable for use in the clinic as a channel replacement therapeutic for treating channelopathies. We set to find a structure of minimal length that would retain desired characteristics, and decrease the possibility of inducing an immune or inflammatory response. I have recently solved the solution structure of the minimum length sequence (20 residues) in both an aqueous (50% TFE-d3) and membrane-like environment (SDS micells).

I collaborated with the Animal Science Department in Oklahoma State University, Stillwater in the solution structure determination of a Cationic antimicrobial peptide. Cationic antimicrobial peptides are natural occurring antibiotics that are actively being explored as a new class of anti-infective agents. The lab at Oklahoma State recently identified three linear cathelicidin antimicrobial peptides from the chicken. Among them is Fowlicidin-2 a 31 amino-acid peptide with potent, broad-spectrum bactericidal activities. I solved the solution structure of Fowlicidin-2 by NMR spectroscopy using 1D proton and 2D proton-proton NMR experiments.

Lab Activities:

-Peptide purification and characterization by HPLC and Mass Spectrometry.
-NMR peptide sample preparation and experiment setup.
-Structural studies of peptides by NMR spectroscopy, (DQF-COSY, NOESY, TOCSY, etc…)
-NMR 1D and 2D data processing and analysis using VNMR, Sparky, NMRPipe software.
-Structure calculation and refinement using DYANA, CNS software.
-Dynamics simulation and energy minimization of peptide structures using Sybyl 7.1 .
-CD spectroscopy of peptide samples.
-Transepithelial ion transport measurements using MDCK cells in an Ussing chamber.

Sushanth Gudlur
B.Sc. Biochemistry (University of Madras, India)
M.Sc. Biotechnology (University of Pune, India)

Liposomes and peptides (channel forming) with a few bicelles thrown in…that’s what I do in Dr.Tomich’s lab. To design stable and suitable liposomes that help the channel forming peptides synthesized in our lab to fold correctly and function optimally, while still mimicking the natural membrane, is my quest. Currently I am trying to stabilize the liposomes prepared in defined compositions of POPC,POPS, POPE & cholesterol and study the secondary structure of a 22 amino acid peptide(channel forming), when inserted into these liposomes. The techniques I come across in my study include Lipid Extrusion, Fluorescence and CD spectroscopy, Mass spec (MALDI-TOF) and HPLC.

And when I’m not thinking about liposomes, I spend my time playing badminton or play the role of a webmaster for the site (www.punebiotechs.com), I designed for my classmates at Pune (India). Of course! I plan to finish visiting all the 50 states in the U.S.A before I complete my Ph.D!!!