Publications by authors named "Aswathy Muttathukattil"

Polymer-grafted nanoparticles are versatile building blocks that self-assemble into a diverse range of mesostructures. Coarse-grained molecular simulations have commonly accompanied experiments by resolving structure formation pathways and predicting phase behavior. Past simulations represented nanoparticles as spheres and the ligands as flexible chains of beads, isotropically tethered to the nanoparticles.

View Article and Find Full Text PDF

Nanoparticle self-assembly is an efficient bottom-up strategy for the creation of nanostructures. In a typical approach, ligands are grafted onto the surfaces of nanoparticles to improve the dispersion stability and control interparticle interactions. Ligands then remain secondary and usually are not expected to order significantly during superstructure formation.

View Article and Find Full Text PDF

Understanding the mechanism of ligands binding to their protein targets and the influence of various factors governing the binding thermodynamics is essential for rational drug design. The solution pH is one of the critical factors that can influence ligand binding to a protein cavity, especially in enzymes whose function is sensitive to the pH. Using computer simulations, we studied the pH effect on the binding of a guanidinium ion (Gdm) to the active site of hen egg-white lysozyme (HEWL).

View Article and Find Full Text PDF

Cells are equipped with cosolvents that modulate protein folding and aggregation to withstand water stress. The effect of cosolvents on the aggregation rates depends on whether the polypeptide sequence is an intrinsically disordered protein (IDP) or can fold into a specific native structure. Cosolvents, which act as denaturants generally slow down aggregation in IDPs, while expediting it in globular proteins.

View Article and Find Full Text PDF

Guanidinium cation (Gdm) interacts strongly with amino acids of different polarities modulating protein structure and function. Using density functional theory calculations and molecular dynamics simulations, we studied the interaction of Gdm with carboxylate ions mimicking its interaction with acidic amino acids and explored its effect in enzymatic folding and activity. We show that, in low concentrations, Gdm stabilizes carboxylate ion dimers by acting as a bridge between them, thereby reducing the electrostatic repulsion.

View Article and Find Full Text PDF

Cosolvents play an important role in regulating the stability and function of proteins present in the cell. We studied the role of cosolvents, urea and guanidinium chloride (GdmCl), which act as protein denaturants, in the catalytic activity and structural stability of the protein lysozyme using activity measurements, spectroscopy, and molecular dynamics simulations. We find that the activity of lysozyme increases on the addition of urea, whereas it decreases sharply on the addition of GdmCl.

View Article and Find Full Text PDF

Disulfide bonds in proteins can strongly influence the folding pathways by constraining the conformational space. Lysozyme has four disulfide bonds and is widely studied for its antibacterial properties. Experiments on lysozyme infer that the protein folds through a fast and a slow pathway.

View Article and Find Full Text PDF

Salts differ in their ability to stabilize protein conformations, thereby affecting the thermodynamics and kinetics of protein folding. We developed a coarse-grained protein model that can predict salt-induced changes in protein properties by using the transfer free-energy data of various chemical groups from water to salt solutions. Using this model and molecular dynamics simulations, we probed the effect of seven different salts on the folding thermodynamics of the DNA binding domain of lac repressor protein ( lac-DBD) and N-terminal domain of ribosomal protein (NTL9).

View Article and Find Full Text PDF

Understanding the role of naturally occurring protective osmolytes, such as trimethylamine N-oxide (TMAO), in the growth of amyloid fibrils implicated in neurodegenerative diseases is important to prevent fibril growth. The effect of TMAO on the growth of amyloid fibrils formed by the Sup35 prion peptide NNQQNY is studied using molecular dynamics simulations. The free-energy surface for the growth of the protofibril shows three major basins, corresponding to the free state where the peptide is in solution, the docked state where the peptide in solution interacts with the surface of the protofibril, and the locked state where the peptide is tightly bound to the protofibril, becoming a part of the fibril.

View Article and Find Full Text PDF