Revealing Topological Barriers against Knot Untying in Thermal and Mechanical Protein Unfolding by Molecular Dynamics Simulations

Salt-bridge mediated conformational dynamics in the figure-of-eight knotted ketol acid reductoisomerase (KARI)

The utility of knotted proteins in biological activities has been ambiguous since their discovery. From their evolutionary significance to their functionality in stabilizing the native protein structure, a unilateral conclusion hasn't been achieved yet. While most studies have been performed to understand the stabilizing effect of the knotted fold on the protein chain, more ideas are yet to emerge regarding the interactions in stabilizing the knot. Using classical molecular dynamics (MD) simulations, we have explored the dynamics of the figure-of-eight knotted domain present in ketol acid reductoisomerase (KARI). Our main focus was on the presence of a salt bridge network evident within the knotted region and its role in shaping the conformational dynamics of the knotted chain. Through the potential of mean forces (PMFs) calculation, we have also marked the specific salt bridges that are pivotal in stabilizing the knotted structure. The correlated motions have been further monitored with the help of principal component analysis (PCA) and dynamic cross-correlation maps (DCCM). Furthermore, mutation of the specific salt bridges led to a change in their conformational stability, vindicating their importance.

Nanoparticles traversing the extracellular matrix induce biophysical perturbation of fibronectin depicted by surface chemistry

While the filtering and accumulation effects of the extracellular matrix (ECM) on nanoparticles (NPs) have been experimentally observed, the detailed interactions between NPs and specific biomolecules within the ECM remain poorly understood and pose challenges for in vivo molecular-level investigations. Herein, we adopt molecular dynamics simulations to elucidate the impacts of methyl-, hydroxy-, amine-, and carboxyl-modified gold NPs on the cell-binding domains of fibronectin (Fn), an indispensable component of the ECM for cell attachment and signaling. Simulation results show that NPs can specifically bind to distinct Fn domains, and the strength of these interactions depends on the physicochemical properties of NPs. NP-NH3+ exhibits the highest affinity to domains rich in acidic residues, leading to strong electrostatic interactions that induce severe deformation, potentially disrupting the normal functioning of Fn. NP-CH3 and NP-COO- selectively occupy the RGD/PHSRN motifs, which may hinder their recognition by integrins on the cell surface. Additionally, NPs can disrupt the dimerization of Fn through competing for residues at the dimer interface or by diminishing the shape complementarity between dimerized proteins. The mechanical stretching of Fn, crucial for ECM fibrillogenesis, is suppressed by NPs due to their local rigidifying effect. These results provide valuable molecular-level insights into the impacts of various NPs on the ECM, holding significant implications for advancing nanomedicine and nanosafety evaluation.

Effect of Topology on the Statics and Dynamics of a Polymer Chain at the Fluid-Fluid Interface: A Molecular Dynamics Simulation Study

The effect of chain topology on the statics and dynamics of a chain at the interface of two immiscible fluids is studied by means of molecular dynamic simulations. For three topologically different chains, namely, linear, ring, and trefoil-knot, of the same molecular weight, the effect of varying both polymer-fluid and fluid-fluid interaction nature on the width of the fluid interface, chain conformation, shape, and chain dynamics is investigated. For a sharp-interface binary-fluid system, the interface width is insensitive to both topology and polymer-fluid interaction nature, while a weak nonmonotonic variation is seen for a broad-interface system. Chain extension normal to the interface plane is significantly affected by the topology with a trefoil-knot chain, due to the additional constraint, which has the largest value compared to both linear and ring polymers. Instantaneous shapes are also quantified through shape parameters. Furthermore, it is observed that the qualitative behavior of the center-of-mass mean-square displacement (MSD) is independent of topology, i.e., all the chain types show the same diffusion exponent α ( ∼ 1). However, the self-diffusion constant depends on the topology and it is the largest for the trefoil-knot chain. An interesting observation pertaining to the early time behavior of monomeric MSD is that, within the subdiffusive regime, the values of α for different parameters (independent of topology) are grouped into two distinct ranges (0.52 - 0.59 and 0.62 - 0.67), which are related to the different chain conformation for the polymer-fluid interaction range below and above a threshold value equal to that of the self-interaction of the pure fluid phase.