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 ß-aggregation process of uperin 3.5 as well as two of its mutants, in which the positively charged residues Arg7 and Lys8 have been replaced by alanine. All three peptides rapidly underwent spontaneous aggregation and conformational transition from random coils to beta-rich structures. The simulations reveal that the initial and essential step of the aggregation process involves peptide dimerization and the formation of small beta-sheets. A decrease in positive charge and an increase in the number of hydrophobic residues in the mutant peptides lead to an increase in the rate of their aggregation.

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. Two stable configurations of peptides were found. In the bound state, the peptides in helical form were located right under the head group region in parallel orientation with respect to the bilayer surface. Stable transmembrane configuration was observed for wild-type uperin and its alanine mutant in both alpha-helical and extended unstructured forms. The potential of mean force characterized the process of peptide binding from water to the lipid bilayer and its insertion into the membrane, and revealed that the transition of uperins from the bound state to the transmembrane position was accompanied by the rotation of peptides and passes through the energy barrier of 4-5 kcal/mol. Uperins have a weak effect on membrane properties.

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. One of the main tools for obtaining amplitudes and correlation times of molecular motions in the µs time scale is measuring relaxation rate R(1)(ρ). Yet, there have been a couple of unresolved problems in the quantitative analysis of the relaxation rates. First, when the resonance offset of the spin-lock pulse is used, the spin-lock field can be oriented under an arbitrary angle in respect to B(0). Second, the spin-lock frequency can be comparable or even less than the magic angle spinning rate. Up to now, there have been no equations for R(1)(ρ) that would be applicable for any values of the spin-lock frequency, magic angle spinning rate and resonance offset of the spin-lock pulse. In this work such equations were derived for two most important relaxation mechanisms: heteronuclear dipolar coupling and chemical shift anisotropy. The validity of the equations was checked by numerical simulation of the R(1)(ρ) experiment using SPINEVOLUTION program. In addition to that, the applicability of the well-known model-free approach to the solid state NMR relaxation data analysis was considered. For the wobbling in a cone at 30° and 90° cone angles and two-site jump models, it has been demonstrated that the auto-correlation functions G(0)(t), G(1)(t), G(2)(t), corresponding to different spherical harmonics, for isotropic samples (powders, polycrystals, etc.) are practically the same regardless of the correlation time of motion. This means that the model-free approach which is widely used in liquids can be equally applied, at least assuming these two motional models, to the analysis of the solid state NMR relaxation data.

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. Here, conventional and targeted molecular dynamics simulations were used to study the conformational dynamics of GK in the stable configurations and in the transition from active to inactive state. Three phases of the structural reorganization of GK were detected. The first step is a transformation of GK from the active state to the intermediate structure, where the cleft between the domains is open, but alpha helix 13 is still inside the small domain. From this point, there are two alternative paths. One path leads to the inactive state through the release of helix 13 from the inside of small domain to the outside. Other path goes back to the active state. Simulation results reveal the critical role of helix 13 in the transformation of GK from the open state to inactive one and the influence of the loop 2 on the protein transformation between the open and the closed active states. Principal component analysis and covariance matrix analysis were carried out to analyze the dynamics of protein. Importance of hydrogen bonds in the stability of the closed conformation is shown. Overall, our simulations provide new information about the dynamics of GK and its structural transformation.Communicated by Ramaswamy H. Sarma.

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. While there are plenty of generative models, it is unclear how to compare and rank them. In this work, we introduce a benchmarking platform called Molecular Sets (MOSES) to standardize training and comparison of molecular generative models. MOSES provides training and testing datasets, and a set of metrics to evaluate the quality and diversity of generated structures. We have implemented and compared several molecular generation models and suggest to use our results as reference points for further advancements in generative chemistry research. The platform and source code are available at https://github.com/molecularsets/moses.

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 ß-structural peptides with multicomponent lipid bilayers consisting of two types of anionic (POPS, POPI) and two types of zwitterionic (POPE, POPC) lipids. The formation of semitoroidal pores was analyzed from a standpoint of self-organization of lipids and peptides. Our results showed that semitoroidal pores were mainly formed by POPI molecules with a strong negative charge. We found that peptide aggregation is a necessary step of pore formation; single peptide is unable to stabilize the semitoroidal pore. To characterize the influence of semitoroidal pores on membrane properties, we evaluated the bilayer thickness, the two-dimensional density maps of lipids, the deuterium order parameters, and the lateral diffusion coefficients of lipids. The pore formation induced perturbation of the phospholipid organization in membrane and facilitated the organization of zones with different electrostatic potential.

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 analysis of the flexibility of all residues confirmed the coupling between loops L1 (185-188) and L2 (221-224) and the residues in the active center. The significance of S1 pocket residues for the signal transduction from the active center to the substrate-binding site was confirmed by the dynamical network and covariance matrix analyses. Gaussian network model and principal component analysis demonstrated that the active center residues had zero amplitude in the slowest fluctuations acting as hinges or anchors. Overall, our results provide a new insight into protein-ligand interactions and show how the allosteric signaling may occur.

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. In most cases the latter process becomes superior for the commonly applied low and moderate spin-lock fields and practically does not provide information about the molecular dynamics. To suppress this undesired process and to expand the dynamic range of T1rho experiments, we present two approaches. The first one uses a resonance offset of the frequency of the spin-lock irradiation, which leads to a significant enhancement of the effective spin-lock frequency without the application of destructive high transmitter powers. We derive the theory and demonstrate the applicability of the method on various model compounds. The second approach utilizes heteronuclear 1H decoupling during the 13C/15N spin-lock irradiation which disrupts the contact between the 13C/15N Zeeman and 1H dipolar reservoirs. We demonstrate the method and discuss the results qualitatively.