Research

Investigation of the non-native intermediate states of protein-protein binding at atomistic resolution is challenging. Free energy profiles are considered the “holy Grail” of computational biophysics as they provide information about energetics as well as structural changes involved with rare events. I computed the free energy landscape of atomistic protein-protein interactions for the insulin dimer for the first time (Proc. Natl. Acad. Sci. 117(5), 2302-2308(2020); J. Chem. Phys. 149, 114902 (2018); J. Chem. Phys. 150, 084902(2019)). I implemented a combination of metadynamics, and parallel tempering methods with the well-tempered ensemble approach to study insulin dimer dissociation. This is a robust method that not only reveals the non-native protein-protein interactions at atomistic resolution which is crucial to increase drug specificity, but also captures the impact of solvent-mediated interactions. 

There was a long-standing effort to understand the role of water in biomolecular processes, especially for protein-protein binding. I quantified the contribution of hydrophobic hydration and dewetting transition in protein-protein interactions, for the first time using this method (Proc. Natl. Acad. Sci. 117(5), 2302-2308(2020)).

Several previous studies have demonstrated that ethanol consumption could act as a risk factor for developing type II diabetes mellitus at heavy consumption, while it could be beneficial in case of moderate consumption. I have investigated dimer dissociation of insulin in the presence of co-solvent ethanol following the same simulation strategy (J. Chem. Phys. 150, 084902(2019)). The computed free energy surfaces in the presence of 5% and 10% water-ethanol binary mixtures suggest that the presence of ethanol reduces the energy barrier of dimer dissociation which agrees with the experimental findings.  The structural analysis of proteins and their solvation surface elucidates the molecular mechanism behind the enhanced rate of insulin dimer dissociation in the presence of ethanol.

One of the unresolved problems in chemistry and biophysics is the time-scale and length-scale gap between computational and experimental methods, for which a possible way is to use coarse-graining (CG), a technique that enables long-time simulations of large-scale systems to become computationally tractable by decreasing the number of degrees of freedom. The primary two challenges in CG modeling are 1. how to define the correspondence between all-atom and CG degrees of freedom, i.e., CG mapping, and 2. how to define the interactions between CG beads, i.e., CG energetics. I use "bottom-up" CG methodologies that aim to reproduce microscopic (mapped atomistic) statistics of protein-protein interactions. A unique combination of multiscale modeling methods captured the molecular-level dynamics of specific protein-protein interactions at the binding interface at the coarse-grained level and enabled the study of protein crystallization/nucleation dynamics on the membrane and can be used to study peptide/small molecule mediated protein crystallization process using realistic “non-rigid” CG models of proteins/peptides (Biophysical Journal, 123, 42-56 (2024)). 

Protein-mediated drug/substrate/lipid transport is relevant for therapeutic development, however, none of the existing methods can compute the free energy surface (FES) of complex membrane transport processes through the inner/outer groove of membrane proteins using more-reliable atomistic forcefield. For the first time, I have computed FES of lipid scrambling mediated by human SERINC protein which acts as a HIV-1 restriction factor. This method is able to identify different pathways of lipid/substrate/drug transport, identify intermediate states at atomistic resolution and energetics along those pathways. 

The HIV-1 assembly process packages all the necessary components like proteins, RNA, and cofactors in this newly formed immature virion. The maturation process makes this newly formed immature virion infectious.  Gag protein is the main structural protein of HIV-1. During the viral replication, Gag is synthesized and remains as a monomer/dimer in the cytoplasm. Prior to the plasma membrane binding it binds to viral RNA and then multimerize on the membrane and finally forms spherical-shaped virions. In this process, it packages two copies of unspliced, single-stranded, full-length RNA genome into the virion. During the maturation phase, Gag polyprotein is cleaved by the viral protease at five sites, resulting in a major change in the structure and morphology of the virus. My work primarily focuses on the following five major events:

1. Immature Gag polyprotein lattice assembly on the membrane.

2. Role of genomic RNA binding in the assembly phase; Synergy between protein-protein, protein-membrane and protein-RNA interactions during viral assembly.

3. Membrane binding mechanism of matrix domain (peripheral membrane protein) of Gag polyprotein during the initial phase of the assembly.

4. Mechanism of reorganization of matrix protein lattice on the surface of the viral membrane during maturation.

5. Mechanism of protease access to the immature Gag polyprotein lattice during the maturation phase.