Residue-Residue Mutual Work Analysis of Retinal-Opsin Interaction in Rhodopsin: Implications for Protein-Ligand Binding

Structural stability of Calmodulin-target peptide complex at different temperatures based on molecular dynamics simulation

Calmodulin (CaM) is a multifunctional protein commonly found in various eukaryotic cells that can bind Ca2+, making it highly valuable for research in agriculture, medicine, the environment, and other fields. Protein functionality is intricately linked to its structure. To understand how varying temperatures affect the structural integrity of CaM protein at the molecular level, the effect of temperature on the structural stability of CaM-peptide complex was investigated based on the molecular dynamics (MD) simulation. Some analyses including the root mean square deviation (RMSD) values, interaction energies, the decomposition of total energy of the system, the binding mechanism for Ca2+, and the secondary structure of CaM-peptide at different temperatures have been made in this work. The RMSD increased from 0.5277 nm (298 K) to 0.6949 nm (400 K), indicating a loss of structural stability. As temperature increases, the interaction energies between CaM-peptide and Ca2+ exhibit a decline, and the number of oxygen atoms in the 4 Å range around the CaM-peptide ion tends to decrease, with the average value of the number of oxygen atoms in the 4 Å range of CaM-peptide decreasing from 7.48039 (298 K) to 6.36614 (400 K) with Coulombic interactions playing a pivotal role in stabilizing Ca2+. This decline in hydrogen bonding is directly linked to a decrease in protein stability at higher temperatures, highlighting the thermal sensitivity of the protein's structural framework. The stable secondary structures, including the α-helix, are disrupted as temperatures increase, leading to the gradual unwinding of the α-helix and a loss of structural integrity. This work explores the molecular-level structural stability of CaM, enhancing our understanding of CaM protein and its potential applications.

In-vitro and in-silico analysis and antitumor studies of novel Cu(II) and V(V) complexes of N-p-Tolylbenzohydroxamic acid

Copper(L2Cu) and vanadium(L2VOCl) complexes of N-p-tolylbenzohydroxamic acid (LH) ligand have been investigated for DNA binding efficacy by multiple analytical, spectral, and computational techniques. The results revealed that complexes as groove binders as evidenced by UV absorption. Fluorescence studies including displacement assay using classical intercalator ethidium bromide as fluorescent probe also confirmed as groove binders. The viscometric analysis too supports the inferences as strong groove binders for both the complexes. Molecular docking too exposed DNA as a target to the complexes which precisely binds L2Cu, in the minor groove region while L2VOCl in major groove region. Molecular dynamic simulation performed on L2Cu complex revealing the interaction of complex with DNA within 20 ns time. The complex stacked into the nitrogen bases of oligonucleotides and the bonding features were intrinsically preserved for longer simulation times. In-vitro cytotoxicity study was undertaken employing MTT assay against the breast cancer cell line (MCF-7). Potential cytotoxic activities were observed for L2Cu and L2VOCl complexes with IC50 values of showing 71 % and 74 % of inhibition respectively.

Potential Energy Weighted Reactive Flux and Total Rate of Change of Potential Energy: Theory and Illustrative Applications

Reactive flux can be largely nonzero in a nonequilibrium ensemble of trajectories and provide insightful information for reactive transitions from the reactant state to the product state. Based on the reactive flux, a theoretical framework is proposed here for two quantities, the potential energy weighted reactive flux and the total rate of change of potential energy, which are useful for the identification of the mechanism from a nonequilibrium ensemble. From such quantities, two multidimensional free-energy analogues can be derived in the subspace of collective variables and they are equivalent in the regions where the reactive flux is divergence-free. These free-energy analogues are assumed to be closely related to the free energy in the subspace of collective variables, and they are reduced in the one-dimensional case to be the ensemble average of the potential energy weighted with reactive flux intensity, which was proposed recently [Li, W. J. Phys. Chem. A 2022, DOI: 10.1021/acs.jpca.2c04130] and could be decomposed into energy components at the per-coordinate level. In the subspace of collective variables, the decomposition of the multidimensional free-energy analogues at the per-coordinate level is theoretically possible and is numerically difficult to be calculated. Interestingly, the total rate of change of potential energy is able to identify the location of the transition state ensemble or the stochastic separatrix, in addition to the locations of the reactant and product states. The total rate of change of potential energy can be decomposed at the per-coordinate level, and its components can quantify the contribution of a coordinate to the reactive transition in the subspace of collective variables. We then illustrated the main insights and objects that can be provided by the approach in the applications to a two-dimensional system with various diffusion anisotropies and the alanine peptide in vacuum in various nonequilibrium ensembles of short trajectories, from which the results were found to be consistent.

Energy Decomposition along the Reaction Coordinate: Theory and Applications to Nonequilibrium Ensembles of Trajectories

A theoretical framework is proposed for an energy decomposition scheme along the reaction coordinate, in which the ensemble average of the potential energy weighted with reactive flux intensity is decomposed into energy components at the per-coordinate level. The decomposed energy quantity is demonstrated to be closely related to the free energy along the reaction coordinate, and its connection to the emergent potential energy is provided. In the application to alanine dipeptide under vacuum, illustrative calculations were performed in three nonequilibrium ensembles of trajectories: (1) transition path ensemble sampled with transition path sampling; (2) ensemble of short trajectories initiated from configurations around the transition-state region; and (3) ensemble of short trajectories shooting from configurations in several transition paths. The energy components on each coordinate were found to be consistent among the three ensembles of trajectories, indicating a broad applicability of the approach in biomolecular studies. In addition, the free energies along an optimized reaction coordinate obtained with these nonequilibrium ensembles were largely overlapped with a reference free energy calculated from a long equilibrium trajectory.