Water as a Structural Marker in Gelatin Hydrogels with Different Cross-Linking Nature.

We have studied the molecular properties of water in physically and chemically cross-linked gelatin hydrogels by FTIR-spectroscopy, NMR relaxation, and diffusivity and broadband dielectric spectroscopy, which are sensitive to dynamical properties of water, being a structural marker of polymer network. All experiments demonstrated definite reinforcement of the hydrogel net structure and an increase in the amount of hydrate water. FTIR experiments have shown that the chemical cross-linking of gelatin molecules initiates an increase in the collagen-like triple helices "strength", as a result of infused restriction on protein molecular mobility.

Thermal unfolding of alpha-lactalbumin at acidic pH: Insights from molecular dynamics simulations.

The transformation of globular proteins into fibrils passes through several stages, including the formation of partially expanded conformational states different from the native or fully unfolded forms. Here we used molecular dynamics simulations to characterize the thermal unfolding of alpha-lactalbumin on the microsecond timescale in the range of temperatures of 300-440 K. Comparative analysis of structural changes, mobility of different parts of protein, and pathways through the free energy landscape during the unfolding of alpha-lactalbumin at different temperatures reveals the existence of several intermediate states separated by small energy barriers.

Aggregation of Amyloidogenic Peptide Uperin-Molecular Dynamics Simulations.

Uperin 3.5 is a remarkable natural peptide obtained from the skin of toadlets comprised of 17 amino acids which exhibits both antimicrobial and amyloidogenic properties. Molecular dynamics simulations were performed to study the β-aggregation process of uperin 3.

Interaction of Uperin Peptides with Model Membranes: Molecular Dynamics Study.

The interaction of antimicrobial and amyloid peptides with cell membranes is a critical step in their activities. Peptides of the uperin family obtained from the skin secretion of Australian amphibians demonstrate antimicrobial and amyloidogenic properties. All-atomic molecular dynamics and an umbrella sampling approach were used to study the interaction of uperins with model bacterial membrane.

Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models.

Generative models are becoming a tool of choice for exploring the molecular space. These models learn on a large training dataset and produce novel molecular structures with similar properties. Generated structures can be utilized for virtual screening or training semi-supervized predictive models in the downstream tasks.

Molecular insight into conformational transformation of human glucokinase: conventional and targeted molecular dynamics.

Glucokinase (GK) plays a key role in the regulation of hepatic glucose metabolism. An unusual mechanism of positive cooperativity of monomeric GK containing only a single binding site for glucose is very interesting and still unclear. The activation process of GK is associated with a large-scale conformational change from the inactive to the active state.

Coarse-grained molecular dynamics of membrane semitoroidal pore formation in model lipid-peptide systems.

Transmembrane pores play an important role in various cell processes. However, the detailed structures of these pores and their influence on the membrane properties remain undetermined. We performed microsecond coarse-grained molecular dynamics simulations to study the interaction of cationic β-structural peptides with multicomponent lipid bilayers consisting of two types of anionic (POPS, POPI) and two types of zwitterionic (POPE, POPC) lipids.

Effect of ligand binding on the dynamics of trypsin. Comparison of different approaches.

The intramolecular signal transduction induced by the binding of ligands to trypsin was investigated by molecular dynamics simulations. Ligand binding changes the residue-residue interaction energies and suppresses the mobility of loops that are in direct contact with the ligand. The reduced mobility of these loops results in the altered flexibility of the nearby loops and thereby transmits the information from ligand binding site to the remote sites.

The nuclear magnetic resonance relaxation data analysis in solids: general R1/R1(ρ) equations and the model-free approach.

The advantage of the solid state NMR for studying molecular dynamics is the capability to study slow motions without limitations: in the liquid state, if orienting media are not used, all anisotropic magnetic interactions are averaged out by fast overall Brownian tumbling of a molecule and thus investigation of slow internal conformational motions (e.g., of proteins) in solution can be conducted using only isotropic interactions.

Expanding the frequency range of the solid-state T1rho experiment for heteronuclear dipolar relaxation.

Solid-state spin-lattice relaxation in the rotating frame permits the investigation of dynamic processes with correlation times in the range of microseconds. The relaxation process in organic solids is driven by the fluctuation of the local magnetic field due to the dipole-dipole interaction of the probe nuclei (13C,15N) with 1H in close proximity. However, its effect is often hidden by a competing relaxation process due to the contact between the rotating frame 13C/15N Zeeman and 1H dipolar reservoirs.