Research Statement

Research statement

1. Intrinsically disordered proteins, aggregation and neurodegenerative diseases

Parkinson’s disease (PD) is the second most common late-onset neurodegenerative disorder that affects about seven million people globally. The pathology of PD is characterized by intracytoplasmic aggregation of α-synuclein (asyn) fibrils in Lewy bodies and Lewy neurites (1). Asyn is a 140-residue protein that accounts for up to 1% of all proteins in the neuronal cytosol (2). Asyn was shown to exist as an intrinsically disordered protein (IDP) in the cytoplasm, which adopts a helical conformation upon binding to membranes. Recent studies have suggested a role of the membrane-bound state in promoting aggregation into fibrils. While the role of the fibrillar state is a hallmark of the disease, the mechanism of transition from the monomeric to fibrillar states remains unclear. Unraveling this mechanism is essential for developing effective strategies to prevent the formation of fibrils and therefore the amelioration of the disease. While recent studies have led to tremendous advances in our understanding of the role of solution conditions, membrane composition, among others, in the formation of fibrils, insights into the early stages of the aggregation pathway remain elusive.

My doctoral research at Rutgers University on α-synuclein, an IDP whose aggregation into fibrils is implicated in the pathology of Parkinson’s disease, provided important insights into the conformational characteristics of the monomeric form of α-synuclein under physiological and altered pH conditions. The long-term goal of my research is to gain insights into the transition from the native disordered conformation of asyn to the toxic fibrillar states implicated in disease. The short-term goals to achieve this challenging task are 1) to characterize the early oligomeric and fibrillar states of asyn and its disease variants (A30P, A53T, E46K, H50Q, G51D) in solution, 2) probe the effect of pH and solvent conditions on the aggregation propensities of early-onset PD mutations, 3) identify small molecule targets to prevent the formation of toxic oligomeric and fibrillar aggregates.

2. Development of novel antimicrobial peptides

The World Health Organization reports that infectious diseases cause over seven million deaths worldwide every year. Emergence of antibiotic resistance has necessitated the development of novel antibacterial agents, in addition to the need for understanding the underlying mechanisms of bacterial resistance. Antimicrobial proteins and peptides (AMPs) have been shown to act against a broad range of microbes and have thus emerged as attractive candidates for targeting drug-resistant microbes. Members of the human pancreatic ribonuclease (RNase) superfamily are known to participate in host-defense functions, including antimicrobial activities. Five of the eight RNases identified in humans have been implicated in host-defense functions such as antibacterial, antiviral and antihelminthic activities. AMPs derived from some of these RNases were observed to be effective antibacterial agents. 

Future projects: 1) identify co-evolving amino acid networks that are conserved among all antibacterial RNases to design novel AMPs with greater stability and antimicrobial activities, 2) design short peptides based on amino acid residues identified above. Develop AMP candidates that display high antibacterial but low or no cytotoxic effects using the rational and semi-rational design approaches.

3. Enzyme engineering for Biomass degradation

Biomass is an extensively available resource for sustainable production of sugars used in manufacturing biofuels and other materials through fermentation and other degradation processes. Current biomass degradation approaches involve use of harsh chemical breakdown, in addition to enzymatic hydrolysis of biomass. Enzymatic breakdown of lignocellulosic biomass is a very promising, environmentally friendly technology. However, resistance of plant cell wall to enzymatic hydrolysis, recalcitrance, presents a major challenge in the large-scale implementation of this technology. Industrial processes use xylanases of the glycoside hydrolase enzyme family. Despite its industrial use, few advances have been made to improve the efficiency of these enzymes. Engineering these enzymes to improve catalytic efficiency will greatly benefit large-scale degradation of biomass. My research on xylanase B2 at INRS provided important insights into the role of conformational exchange on the millisecond timescale and consequently the function of glycoside hydrolase enzymes. 

Future projects: 1) Integrating computational approaches with docking and rational design and/or directed evolution approaches to identify structural and dynamical changes affecting ligand binding stability and catalytic efficiency of laccases, 2) Engineering laccase enzymes, such as the commercial bacterial laccase MetZyme, and other newly identified fungal laccases to generate variants with enhanced enzyme efficiency and tolerance to temperature and pH.