Professor, Department of Physics
Member, Li Ka Shing Institute of Virology
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.
Uttam Anand, Research Associate
I am working with Prion proteins using single molecule force spectroscopy (optical tweezers) to understand and correlate various factors that provide protection against misfolding and disease. This involves focusing on sequence effects, protective mutations and chemical chaperones that have anti-prion activity.
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).
Russell Kirchner, Technician
As a research technician, I assist Woodside group members with their projects and carry out a variety of tasks associated with the biophysical instrumentation.
Rafayel Petrosyan, Postdoctoral Fellow
In prion diseases, the protein PrP takes on an incorrect shape that is infectious and collects in clumps (aggregates). A number of potential drug molecules that bind to PrP have been found to give some form of protection against disease, however, the mechanisms of protection are poorly understood. My main projects aim is to find out how these molecules protect against disease that would help to develop new or roved drugs to treat prion diseases.
Meng Zhao, Postdoctoral Fellow
My research aims to understand the folding of exoribonuclease-resistant RNA (xrRNA) and the mechanism by which the exoribonuclease-resistance arises. I use the ultra-high resolution Optical Tweezers built in Woodside lab, which allows the direct observation of transient motions (μs- and nm-scale) of one molecule at a time under tension (pN scale), to understand how xrRNA folds and unfolds, and how it responds when encounters exoribonuclease and/or relevant biological molecules and entities.
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.
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
Sandaru Ileperuma, Research Assistant
I research the effect of various compounds on inhibiting programmed ribosomal frameshifting in viral RNA.
I study how specific mutations in the SARS-CoV-2 mRNA affect the structural dynamics of the mRNA pseudoknot, located within the translated region of the mRNA. Transitions between stable pseudoknot conformations have been shown to stimulate programmed ribosomal frameshifting (PRF), which is one way that SARS-CoV-2 can control the relative expression levels of the proteins it requires for replication. Understanding this sequence/structure/function relationship will aid in anti-PRF drug discovery efforts.
My research focuses on using single-molecule force spectroscopy to investigate superoxide dismutase 1 (SOD1) mutants associated with familial ALS.
My research focuses on the understanding the influence of folded exoribonuclease-resistant viral RNA on its resistant properties. The second project involves a study of ribosomal dynamics during -1 programmed translational frameshifting using single molecule force spectroscopy.
I use Surface Plasmon Resonance (SPR) and fluorescence techniques to study the effects of various ligands on programmed ribosomal frameshifting (PRF) in SARS-CoV-2 variants. These ligands bind to the pseudo knot found in the virus mRNA which is relatively conserved, suggesting high resistance to mutation.
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease that weakens muscles and causes the patient to lose control of their muscles. The number of people diagnosed with this disease is 5,760 to 6,400 per year, but unfortunately, there is currently no cure. We know that aggregation of TDP-43 proteins in the central nervous system is a characteristic of ALS. My research interest is investigating TDP-43 protein with optical tweezers on the level of individual molecules; determining the rates, energetics, and intermediates involved in misfolding vs. native folding. With this work, we hope to reach a better understanding of this process.