The Agrawal laboratory is engaged in studies of the protein-synthesizing machine, the ribosome, which interacts with messenger RNA (mRNA), transfer RNAs, and a number of protein factors, to facilitate translation of the genetic information encoded by the mRNA into the amino-acid sequence of a protein. In particular, his research explores (i) the structure and function of organellar ribosomes, and (ii) the structural dynamics of ligands that interact with the ribosome during protein synthesis.
Biochemical and molecular biology techniques, combined with cryo-electron microscopy (cryo-EM) and advanced computer image processing methods, are used to determine high-resolution three-dimensional (3D) structures of the macromolecular complexes. Molecular and mechanistic interpretations are made by atomic modeling of individual component molecules into the cryo-EM map. Organellar ribosomes synthesize specific sets of proteins required by the eukaryotic cell. Mitochondrial ribosomes synthesize components of protein complexes crucial in ATP synthesis, while chloroplast ribosomes synthesize proteins that participate in photosynthesis. Both of these organellar ribosomes possess a number of component proteins that are not present in the cytoplasmic ribosomes from the same cells. Furthermore, several of their homologous proteins possess unique N- or/and C-terminal extensions. Certain unique features of the translation process on organellar ribosomes suggest functional roles that could plausibly be filled by such novel components. For example, most mammalian mitochondrial mRNAs are leaderless, i.e., they do not possess either the Shine-Dalgarno sequence or the 5’ cap that guide the recruitment of mRNAs to cytoplasmic ribosomes. In addition, most of the ribosome-binding mitochondrial translational factors possess unique amino-acid segments.
The goal of studies in the Agrawal lab include the elucidation of mechanisms by which (i) leaderless mRNAs are recruited to the mitochondrial ribosome, and (ii) unique component ribosomal proteins and translational factors participate in the process of mitochondrial protein synthesis. His studies allow him to track conformational transitions undergone by the ribosome and its ligands during protein synthesis. Knowledge of specific conformational transitions is key to understanding the molecular mechanisms of protein synthesis itself, as well as the actions of antibiotics that target the bacterial ribosome or ribosomal ligands to inhibit such transitions. Comparison of results obtained for the bacterial ribosome complexes with those for the host cytosolic and mitochondrial ribosome complexes provides useful information that can lead to identification of new drug targets.