Michael Woodside, Principal Investigator
Professor, Department of Physics
Member, Li Ka Shing Institute of Virology
Member, Centre for Prions and Protein Folding Diseases[AT]


Krishna Neupane, Research Associate

I am interested in structure formation and dynamics of biomolecules. Some projects include: misfolding of the protein superoxide dismutase, associated with ALS disease; dynamics of eukaryotic ribosome during programmed frameshifting at stimulatory RNA structures (e.g. a pseudoknot), associated with many viral infections such as HIV; and dynamics of folding at the level of transition paths.


Chunhua Dong, Research Associate

My research interests include quantitative characterization with scanning probe microscopies for the study at nanoscale of nanomaterials and nanosystems: magnetic properties for bio-applications, as well as the study of oligomer formation and mechanism during the progression of Parkinson’s Disease.


Craig Garen, Technician

My research includes using molecular biology and protein biochemistry techniques to aid in the biophysical characterization of protein misfolding and aggregation in neurodegenerative disorders. This includes human superoxide dismutase (amyotrophic lateral sclerosis) and prion protein (spongiform encephalopathies).


Abhishek Narayan, Postdoctoral Fellow

We explore the misfolding of SOD1 (superoxide dismutase 1), a prominent cause for fatal neurological disease familial ALS (amyotrophic lateral sclerosis), in terms of general questions related to protein misfolding and aggregation and its medical relevance. Specifically, we are interested in answering questions like how SOD1 misfolds and spreads, why specific mutations lead to disease, and how different mutations change patient survival times, hampering searches for cures. Moreover, it has been observed that misfolded SOD1 propagates within a single cell and from one cell to other resulting in misfolding of properly folded protein molecules, a feature similar to propagation of prion-disease. Hence, we also aim to decipher the structural features of SOD1 and its mutants responsible for the propagation of misfolding.


Simanta Paul, Postdoctoral Fellow

I am studying the early stages of aggregation of proteins involved in neurodegenerative diseases like α-synuclein (Parkinson’s), PrP (prion diseases), aβ and tau (Alzheimer’s) by using single molecule techniques.


Sneha Munshi, Postdoctoral Fellow

The oligomers formed due to misfolding in α-synuclein are a leading cause of neurodegenerative Parkinson’s disease. My project aims to screen the potent inhibitors of oligomers using solution and in-cell (neuroblastoma cell lines) FCCS.


Anita Devi, Postdoctoral Fellow

My research focuses on evolution shapes protein folding by measuring transition paths in single molecule spectroscopy.


Shubhadeep Patra, Graduate Student

My research focus is on the study of interactions between Prion protein and anti-prion compounds for understanding the mechanisms of action such as changes in energy landscape, barrier height and location, rates, number and properties of intermediates.


Aaron Lyons, Graduate Student

My research focuses on the statistical characterization and analysis of single-molecule force spectroscopy data.


Rohith Vedhthaanth Sekar, Graduate Student

Glycosylation is a post translational modification to the prion protein. I am interested in investigating the effects of glycosylation in the prion folding/misfolding using both computational (molecular dynamics) and experimental techniques.


Daniiar Zhaguparov, Graduate Student

The class of viral RNAs that are extremely resistant to digestion by host cell’s ribonucleases due to their unique 3D topology is called exoribonuclease-resistant RNAs or xrRNAs. It was reported in our lab that xrRNA’s resistance to enzymatic degradation is strongly tied to the extreme mechanical rigidity of its structure. I study the necessary contacts in xrRNAs’ structures that provide such mechanical stability and kinetics of enzyme-xrRNA interaction. The understanding of the mechanisms during enzymatic digestion in xrRNAs will uncover new potential ways for antiviral therapeutics.



Bahar Hamzeh, Graduate Student

My research is based on studying proper structures that decrease or even stop the process of misfolding SOD enzymes which is the most important cause of a progressive nervous system disease named ALS (Amyotrophic Lateral Sclerosis).


Sandaru Ileperuma, Research Assistant

The Programmed Ribosomal Frameshifting sequence is a relatively conserved element in SARS-Cov2 which is required for the virus to function properly and thus drugs targeting the frameshifting element could hinder viral propagation. My work aims to identify these potential drug candidates experimentally through the use of luciferase assays with compounds which have been tested computationally against the SARS-Cov2 frameshifting element . These drugs are also tested on a wide range of bat coronavirus pseudo-knots in hopes of discovering a pan-coronaviral therapeutic approach to dealing with future and current coronavirus pandemics.



Ishrat Jahan Meghla, Research Assistant


Viral exoribonuclease-resistant RNAs (xrRNAs) are a special class of viral RNAs possessing unusual knot-like 3D topology that provides them with resistance against host ribonuclease digestion. The extreme resistance is due to the mechanical inflexibility of xrRNAs, leading to enhanced infection and pathogenicity. I perform and study the kinetics and mechanisms of the enzymic digestions on these xrRNAs. Understanding the mechanisms of these pseudoknots’ formations and their roles in resistance to digestion would help broaden the field of antiviral therapeutics.