Dheeraj Prakaash

Profile

In 2014, I obtained my graduate degree from Bangalore University, India, with a background in experimental techniques in Biotechnology, Microbiology, and Chemistry. Soon after, I pursued MSc in Bioinformatics at Manipal Academy of Higher Education, India, and imbibed a computational skill-set in visualizing and analysing biological data. Parallel to my coursework during this time, I worked on structural homology studies of metalloproteinases, and a mini-thesis on the regulation of toll-like receptors in diabetic conditions using proteomics and microarray-based computational approach.

My master's thesis project was on the molecular dynamics and protein-lipid interactions of Aquaporin-Z in a membrane under the supervision of Prof Lin Qingsong at the Department of Biological Sciences, National University of Singapore. By the end of my master's degree in 2016, I had identified my interest in studying membrane protein structures and dynamics.

After obtaining my degree, I was affiliated with Robust Materials Technology Pvt. Ltd. till May 2017 where I worked on a self-designed project titled ‘Virtual Reality: A Railroad for Structural Bioinformatics towards Advanced Cancer Research’. This project focussed on designing a concept and researching practical tools to incorporate a 'sense of touch' to a virtual molecular world, and aimed to benefit education and scientific research. “Imagine shrinking yourself to be able to touch tumours, feel their mass, elasticity, surface tension, look into cell organelles, induce structural modifications to DNA/ proteins by hand and study them in real-time... or even just have a meeting with your molecular model levitating over the desk”.

In 2018, I interned at the Computational & Data Science department, Indian Insitute of Science, under the supervision of Prof Debnath Pal where I studied the architecture of the CGMM (coarse-grained molecular mechanics) forcefield and methods to incorporate it into Gromacs (MD simulation software).

Research interests

Membrane proteins constitute roughly 30% of all translated proteins in a living cell and only a minority have been researched to date. A huge number of them are strongly linked to disease-causing phenotypes and hold great potential in clinical therapeutics. Increasing computing power and trending in silico techniques are encouraging us to study the activity of membrane proteins and their lipid environments in unprecedented detail. My interests lie in researching protein-lipid, protein-protein interactions, conformational protein dynamics, and other structural biological phenomena that act as back-end keys to cellular functions. To conduct such studies, I employ computational approaches such as molecular modelling, atomistic and coarse-grained molecular dynamics simulations. I also tend to maintain a parallel interest in combining computational simulations with virtual/ augmented reality techniques.

My PhD research focusses on the structure and dynamics of

• the T-cell antigen receptor (TCR), and

• the Lymphocyte-specific protein-tyrosine kinase (LCK)

The TCR is a multi-subunit antigen receptor protein found in the plasma membrane of T cells. This forms the fundamental basis for most immune responses against foreign antigens in our bodies. LCK is the primary peripheral protein that associates with the TCR to initiate T-cell signalling. This signalling process is fundamental for our adaptive immune system and is yet to be understood in molecular detail. TCR signalling is associated with cancers, autoimmune disorders, etc., thus forming the basis for many immunotherapies. This work is supervised by Dr Antreas Kalli and Prof Graham Cook. My research is also in collaboration with Prof Oreste Acuto and his group at the University of Oxford.

Qualifications

• MSc Bioinformatics
• BSc Biotechnology, Microbiology, Chemistry