Dynamics-guided directed evolution of protein function.
Directed evolution has proved to be a powerful technique to alter the protein functions for their industrial and therapeutic applications via genetic diversity and selections thereafter.
So far, this technique has been employed based on the read-outs from equilibrium properties of proteins such as fluorescence, pH-stability, thermostability, etc. By employing machine-learning models and the spectroscopic read-outs from protein conformational fluctuations, my laboratory will develop a dynamics-guided directed evolution platform. This platform will help us to develop efficient enzymes, novel antenna complexes, and bio-markers.
Biosensors for single-molecule and super-resolution microscopies.
Fluorescent proteins (FPs)-based biomarkers have remained the state-of-the-art in biological assays as they can be expressed on proteins of interest at stoichiometric levels. Small organic fluorophores although bright and photostable often cannot be incorporated or attach to multiple species, preventing clear conclusions. In the last decade, directed evolution has achieved remarkable feat in enhancing the brightness of these FPs. However, the low photostability and high blinking make these probes unsuitable in single molecule applications where high illumination intensities are used. On the other hand, localization-based super-resolution techniques like PALM or STED rely on the on/off switching of the fluorophores.
Our laboratory aims to develop bright photoswitching FPs for advanced nanoscopy applications like MINFLUX by controlling their dark state conversion (DSC) and ground state recovery (GSR) processes which ultimately relates to their blinking properties and photostability.
Enzymes for fast and efficient plastic degradation.
Due to their recalcitrant nature, majority of the plastic waste remains untreated and consequently accumulates in Nature. A study indicates by 2060 we will accumulate around 1000 million tons of plastic waste endangering marine life and ecosystems.
The chemical and mechanical recycling of the waste is of little help as it involves the release of large amounts of greenhouse gas.
Polyethylene terephthalate (PET), a semi-aromatic polyester, is one of the highly-consumed plastics with high resistance to biodegradation. However, recently discovered PET-degrading enzymes such as PETase or leaf-branch cutinase (LCC) offer promise to depolymerize PET in an environmental friendly manner. First, our laboratory will investigate the mechanistic aspect of such plastic-degrading enzymes using various bulk and single-molecule techniques. Later, insight gained from such studies will be employed to generate enzymes capable of degrading other kinds of plastic such as polyethylene via directed evolution approaches.
Far-red absorbing light-harvesting complexes.
With the world population approaching 8 billion soon, the disappearance of cultivable lands due to rapid urbanization, and the advent of anthropogenic climate change a food crisis is imminent. Several studies show that we need to double our food production by 2050 to avoid such a crisis. To meet this challenge, alternative avenues need to be discovered to increase agricultural output.
A promising avenue to enhance photosynthetic efficiency in plants is to extend the photosynthetically active radiations (PAR) to the infrared. Green plants use only the blue and red light for oxygenic photosynthesis leaving the green and infrared parts mostly unused. It can be shown that a modest extension in the PAR to 750 nm could lead to a 20% increase in photosynthetic efficiency. By employing a cohort of biochemical, biophysical, and bioinformatics tools, our laboratory aims to optimize the pigment-protein interactions beneficial for further far-red absorbing plant species.