Interdisciplinary blog

Interaction of the HHC-36 Peptide with Model Membranes

August 4, 2015
by Alister Boags

Part of the EPSRC Vacation Bursaries scheme 2015

Student name: Alister Boags

Student degree course: Chemistry (MChem in House)

Year of study: 3rd

Supervisor: Dr. Syma Khalid

Vacation Bursary Research project title: Interaction of the HHC-36 Peptide with Model Membranes

Tell us a bit about you and your chosen research field: 

Hi, I’m an undergraduate chemistry student, having just completed third year, I’ve decided to take up a ten week research project in computational chemistry, specifically in the area of Molecular Dynamics (MD), which consists of simulations of physical movements of atoms and molecules within a given volume allowing the trajectories of the atoms and molecules to be observed, specifically in my case utilising the MARTINI force field for coarse grained models. Running simulations in this fashion is advantageous due to the fact that one can see the whole trajectory of their subject of study, as an example the interaction of a cell membrane with a protein, whilst reducing the resources required in doing so as groups of similar atoms are represented as ‘pseudo-atoms’ vastly reducing the number of particles in the system. Uses of this field are to examine the interaction between molecules and bacterial or animal model membranes, as an example the various phases that a model animal membrane may adopt depending upon the water content of the surrounding environment.

Tell us about your specific research project: 

My research is particularly focused on the interaction of the antimicrobial peptide (AMP) HHC-36 with model bacterial membranes, where the interactions of various concentrations of the peptide on the lipopolysaccharide membrane have been observed and promising simulations have been extended on a larger timescale. In addition the interaction between these peptides and animal model membranes have been simulated. The driving force behind this is that AMPs are ideal candidates as novel medicinal agents, where they kill bacteria in short times upon contact, have a wide range of activity and in this case are considered to be non-harmful to the body’s own cells, especially considering that similar peptides already exist as part of the host immune system in many organisms. Unfortunately the mode of action of these peptides upon bacterial is currently not fully understood, which is the aim of my project, to attempt to understand the mechanism behind the destruction of bacterial cells in the presence of these peptides. I have also been simulating animal membranes in order to draw a comparison with bacterial membranes and to confirm that there is no degradation these membranes.

Describe any future plans regarding on-going study/postgraduate research connected to your Vacation Bursary project:

In September I will be starting my fourth and final year at the University of Southampton, I intend to continue in computational systems, hopefully remaining in the field of molecular dynamics in order to complete my research project, I will have to start a new project at that time, however the past seven weeks have been very intriguing and informative.

Categories: Blog. Tags: alister boags, Blog, epsrc, interdisciplinary, interdisciplinary research, syma khalid, University of Southampton, USRG, vacation bursaries, and vacation bursary.

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