Computational studies of charge and energy transfer reactions in photosynthetic proteins

Research keywords

Electron and proton transfer reactions, Photosynthesis, Computational Chemistry, Density Functional Theory, Molecular Dynamics simulations, Multi Conformation Continuum Electrostatics, Photosynthetic proteins, Energy transfer, Membrane dynamics and function

Research interests        

All life forms rely on photosynthesis for the energy they require for survival. This process began billions of years ago and involved the conversion of earth’s abundant solar energy into the energy-rich compounds that drive biochemical processes such as carbon and nitrogen fixation and respiration. There is a great deal of interest in understanding the biophysics and evolution of photosynthesis because of the increasing importance of solar energy in meeting our energy needs.

Our research lab is focused on elucidating the structural and mechanistic details of photosynthetic proteins, mainly Photosystem I variants absorbing photons in the far-red light region, using advanced computational methods. The techniques include the use of the Monte Carlo (MC) based method Multi Conformation Continuum Electrostatics (MCCE), Molecular Dynamics (MD) along with quantum mechanics methods such as Density Functional Theory (DFT) and hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) methods. The advantage of using computational simulations is that these methods provide a fundamental understanding of the biological systems by comparing the results with the experimental observations.

Figure (A) shows the Molecular Dynamics (MD) simulation set up for Photosystem II (PSII) to study the nature of water channels in the protein (1). Red dots represent the water box, the cyan color represents lipids, and the protein is PSII. Figure (B) represents the MCCE method showing different conformations of amino acid residues threonine (Thr), serine (Ser), aspartic acid (Asp) and water (Wat), keeping the backbone of the protein fixed (2). Figure (C) shows the spin density distribution of the heliobacterial reaction center (Bacteriochlorophyll g’ dimer) using the DFT method (manuscript in preparation). All this computational work is being done in collaboration with experimental groups who carry out detailed spectroscopic and structural studies. These studies provide an underlying basis for designing artificial complexes with different spectral or redox characteristics for efficient solar energy conversion into biofuels.

References: 1. D. Kaur, et al., Proton exit pathways surrounding the oxygen evolving complex of photosystem II. Biochim Biophys Acta Bioenerg 1862, 148446 (2021).

2. Y. Song, J. Mao, M. R. Gunner, MCCE2: Improving protein pK_a calculations with extensive side chain rotamer sampling. J. Comput. Chem. 30, 2231–2247 (2009).

Students Opportunities

• Our research lab group is committed to recruiting team members from under-represented groups, racialized, women, and international, Indigenous peoples, persons with disabilities and LGBTQ+.
• We are actively recruiting graduate students through Brock University’s MSc. and PhD programs in Chemistry. 
• Prospective postdoctoral candidates should send their CVs and a description of their research interests. The postdoctoral candidates will be working with me on writing the research proposals for applying for various scholarships. 
• Please note that our research lab is actively seeking applicants with experience in EDI leadership or initiatives. 
• Due to time constraints, only the selected candidates will be contacted within 14 days of applying. The candidates are selected based on their overall GPA and research experience. Prior experience in programming is considered a plus but not a requirement. 
• Selected candidates will be offered partial stipends and/or part-time employment once accepted into the program.
• There are multiple research project opportunities available for Brock University undergraduates. 

        For further enquiries: Email Dr. Divya Kaur Matta (dmatta@brocku.ca)

B.Sc (Hons) Chemistry, University of Delhi, India (2007)

M.Sc (Chemistry), University of Delhi, India (2009)

M.Phil (Chemistry), The Graduate Center, The City University of New York (2017)

Ph.D (Chemistry), The Graduate Center, The City University of New York (2015-2021), supervisor: Marilyn R Gunner

Postdoctoral Fellow, Brock University (2021-2022), supervisor: Art van der Est

• CHEM 2P12- Introduction to Modern Physical Chemistry
• CHEM 3P53- Atomic and Molecular Structure and Spectroscopy
• CHEM 2P63- Introduction to Biophysical Chemistry
• BTEC 2P09- Introduction to Biotechnology