(3bz) The Tail Wagging the Dog: Insights Into Catalysis In R67 Dihydrofolate

Enzymes are phenomenal catalysts. Different enzyme folds catalyzing same chemical reaction could provide vital insights into the enzyme mechanism. Hydride transfer reaction catalyzed by E. coli dihydrofolate reductase (EcDHFR) has been previously investigated. Plasmid encoded R67 DHFR, sharing no structure or sequence homology with EcDHFR, also catalyzes hydride transfer reaction between dihydrofolate (DHF) and its cofactor nicotinamide adenine dinucleotide phosphate (NADPH). R67 DHFR is a homotetramer and shows numerous characteristics of a primitive enzyme including promiscuity in binding of substrate/cofactor, formation of non-productive complexes, and the absence of a conserved acid in its active-site. Furthermore, R67's active-site is a pore, which is mostly accessible by bulk solvent. This present study uses a computational approach to characterize the mechanism of hydride transfer. Not surprisingly, NADPH remains fixed in one half of the active site pore using numerous interactions with R67. Also stacking between the nicotinamide ring of cofactor and the pteridine ring of substrate, DHF, at the hourglass center of the pore, holds the reactants in place. However, large movements of the para-aminobenzoylglutamate tail of DHF occur in the other half of the pore due to ion-pair switching between symmetry related K32 residues from two subunits. The tail movement at the edge of the active-site, coupled with the fixed position of the pteridine ring in the center of the pore, leads to puckering of the pteridine ring and promotes transition state formation. Flexibility coupled to R67 function is unusual as it contrasts with the paradigm that enzymes use increased rigidity to facilitate attainment of their transition states. A comparison with chromosomal DHFR indicates a number of similarities, including puckering of the nicotinamide ring and changes in the DHF tail angle, accomplished by different elements of the dissimilar protein folds.

 

Future research areas:

[A] High throughput screening and development of ionic liquids as a highly efficient catalysis medium for bio-ethanol production

Cellulosic ethanol from abundant biomass has attracted significant attention as a possible low-cost renewable energy source to reduce the nation’s dependence on foreign oil. This goal is hindered by the lack of technology enabling the release of fermentation sugars from biomass and a need to improve the catalytic efficiency of naturally occurring cellulases.  Normally, the catalytic efficiency of an enzyme can be altered through mutations or the use of different substrates.  A third option is the alteration of the dynamics of the enzyme based on solvent coupling. While water is considered the biological solvent, non aqueous enzyme dynamics remains unexplored and limited to volatile organics. Ionic liquids are novel materials which are environmentally friendly and have low vapor pressure and exits as liquids at room temperature.  These ionic liquids have been proposed as a medium for overcoming the recalcitrance of biomass by improving the dissolution of cellulose and improving the activity of cellulases. Ionic liquids with different functional groups can provide control over the local chemical micro-environment. We propose a systematic study based on computational methods to investigate neat and mixtures of solvents for developing highly efficient medium for catalysis and improved dissolution rates of biomass. The computational methods would involve both classical and first principles calculations to determine the thermodynamic and transport properties of neat ionic liquids and their interactions with cellulose and cellulase enzyme to quantify the solvent effect on dynamics of the ternary complex. The refinement of non-polarizable models and also development of explicit anharmonic and harmonic contributions to models/polarizable models will be considered based on the performance of the existing models. The objective function used to screen the existing ionic liquids would be the maximization of the catalytic efficiency and stability of the cellulase enzyme in these ionic liquids while macroscopic properties of the ionic liquids would be used as additional constraints. The fundamental chemical insights obtained will guide the synthesis of novel ionic liquids by variation of functional groups to match the requirements.

[B] Evaluation and ranking of free energy of adsorption as a rational design of ionic liquids for direct exfoliation of nanoscale graphene from graphite.

Research on graphenes—monolayers of carbon atoms arranged in a honeycomb lattice—is proceeding at a relentless pace as scientists of both experimental and theoretical bents seek to explore and exploit its superlative attributes including giant intrinsic charge mobility, and record-setting  thermal conductivity, stiffness, and strength. Of course, fully exploiting the remarkable properties of graphene requires reliable, large-scale production methods which are non-oxidative and introduce few defects, criteria not fully satisfied by any known approach. A major advance in this direction was the recent discovery by our group that ionic liquid (IL)-assisted exfoliation of graphite leads to isolation of few- and single-layer graphene sheets with yields two orders of magnitude higher than with earlier approaches using “surface energy-matched” solvents like N-methyl-pyrrolidone. The overarching goal of this research is to develop a molecular-level view of the IL/graphene interface to elucidate and better control key chemical interactions responsible for efficient exfoliation. Our approach takes full advantage of the modularity of IL solvents which offer an unprecedented opportunity to control the chemistry presented at the interface. A vital component of this research will involve computational calculations based on model nanographenes, with in silicofeedback informing experimental results. If successful, our findings will afford valuable insight, laying the foundation for the first rational route to preparing practical quantities of isolated, processable graphene sheets based upon properly designed ILs, facilitating the fabrication of graphene-based devices and catalyzing graphene expansion into other areas including batteries, supercapacitors, separation technologies, photovoltaics, membranes, catalysis, and environmental remediation.

Research Interests

Non-aqueous enzymology using novel media such as ionic liquids

The use of non-aqueous enzymology for the enhancement of catalytic activity of cellulase enzyme, overcome recalcitrance problem in biomass and increase the production and quality of the intermediates required for bioethanol production.

Protein dynamics and folding

Development of accurate non polarizable computational models and methods to understand the physics and mechanism of biomacromolecules structure and function, energetic materials and nanomaterials.

Drug Docking and Discovery

The understanding of protein motions, folding and catalytic activity in the presence of bound ligands/substrates through classical and semi-empirical computational models and neutron /x-ray scattering would help design novel drugs to combat diseases and also provide invitro methods to engineer novel materials to provide cost efficient energy.

The use of high throughput screening using theoretical methods and computation for materials ranging from special liquids to peptides and complementing the results with suitable experimentation forms the basis of this research.

Development of metal oxides for chemical warfare agents detection.

The use of computational methods to understand behaviors of hazardous chemicals and mechanisms for adsorption thereby enabling us to develop novel surfaces for chemical warfare agent’s detection.

 

I have a diverse professional and academic background in chemical engineering and bioscience. My experience at Wayne State University where I finished my PhD was in molecular modeling and determination of thermodynamic and transport properties of organic and energetic materials under Dr. Jeff. Potoff. This modeling capability was further advanced to biomacromolecules, when I did post doctoral studies at University of Maryland.  At Oak Ridge National Laboratory, these theoretical models were used to understand catalytic behavior and dynamics in variety of Rossman fold and cellulase enzymes.

The focus of my research is use of theoretical methods to evaluate and rank materials ranging from ionic liquids to graphene and peptides and being a contributor towards energy problems and combating diseases. Ionic liquids as media for biomass are considered to increase the solubility of biomass thereby overcoming the recalcitrance problem. Moreover the enhancement of catalytic activity of cellulase enzyme acting on the cellulose/biomass in the presence of aqueous/novel media is sought.  I consider this research to be in focus and very appropriate with your Department’s mission and also in line with the country’s mission of developing a sustainable renewable source of energy