Atomistic molecular dynamics study on the influence of high temperatures on the structure of peptide nanomembranes candidates for organic supercapacitor electrode

Effects of pressure on microstructure evolution of liquid Fe–S–Bi alloy during rapid solidification: A molecular dynamics study

To understand the effects of pressure on microstructural evolution, a molecular dynamics simulation study has been performed under pressures of 0-20 GPa for liquid Fe-S-Bi alloy during the solidification process. The variations in the radial distribution function, average atomic energy, and H-A bond index of the cooling system are analyzed. The rapid solidification process of liquid Fe-S-Bi alloy into crystalline and amorphous alloys is investigated from different perspective. The results show that the glass transition temperature T_g, the sizes of the MnS atomic groups, and major bond-types increase almost linearly with increasing pressure. In addition, the recovery rate of Bi increased first and then decreased with increasing pressure, reaching a peak of 68.97% under 5 GPa. The manganese sulfide compound is embedded in the alloy with a spindle-shape under 20 GPa, which is a better clusters structure.

Polar Zipper on a Peptide Nanomembrane: A Characterization by Potential of Mean Force

In this work, nanomembranes formed by the I₃XGK (X = Q, S, or N) polar peptides are studied to characterize the average force and energy required to separate two neighboring β-sheets laterally joined by polar zippers. The results presented are obtained using a methodology (state of the art) involving the pulling umbrella method to generate the samples (umbrella sampling) and the potential of mean force (PMF) to evaluate the energetic variation evolved in the process of separating the polar zipper. It was observed that the maximum force required to separate the regions linked by polar zippers is 1.48 kJ/mol nm for the I₃NGK nanomembrane and 1.22 kJ/mol nm [1.30 kJ/mol nm] for the I₃QGK [I₃SGK] nanomembranes, emphasizing that polar zippers play an important role in the interaction that interconnects β-sheets in broad and robust two-dimensional structures (tapes and membranes), offering an agile route to the construction of distinct nanomaterials from β-sheets. Also, negative values were obtained for energy as a function of the reaction coordinate for the regions where the formation of polar zippers occurs, showing that the lateral union of neighboring β-sheets is energetically favorable, with a value up to -3.0 kJ/mol, in the case of I₃NGK nanomembranes.

Exploring the multiple conformational states of RNA genome through interhelical dynamics and network analysis

The structural variation of RNA is often very transient and can be easily missed in experiments. Molecular dynamics simulation studies along with network analysis can be an effective tool to identify prominent conformations of such dynamic biomolecular systems. Here we describe a method to effectively sample different RNA conformations at six different temperatures based on the changes in the interhelical orientations. This method gives the information about prominent states of the RNA as well as the probability of the existence of different conformations and their interconnections during the process of evolution. In the case of the SARS-CoV-2 genome, the change of prominent structures was found to be faster at 333 K as compared to higher temperatures due to the formation of the non-native base pairs. ΔΔG calculated between 288 K and 363 K are found to be 10.31 kcal/mol (88 nt) considering the contribution from the multiple states of the RNA which agrees well with the experimentally reported denaturation energy for E. coli α mRNA pseudoknot (∼16 kcal/mol, 112 nt) determined by calorimetry/UV hyperchromicity and human telomerase RNA telomerase (4.5-6.6 kcal/mol, 54 nt) determined by FRET analysis.

Understanding the role of water on temperature-dependent structural modifications of SARS CoV-2 main protease binding sites

Thermally stable and labile proteases are found in microorganisms. Protease mediates the cleavage of polyproteins in the virus replication and transcription process. 6 µs MD simulations were performed for monomer/dimer SARS CoV-2 main protease system in both SPC/E and mTIP3P water model to analyse the temperature-dependent behaviour of the protein. It is found that maximum conformational changes are observed at 348 K which is near the melting temperature. Network distribution of evolved conformations shows an increase in the number of communities with the rise in the temperature. The global conformation of the protein was found to be intact whereas a local conformational space evolved due to thermal fluctuations. The global conformational change in the free energy ΔΔG value for the monomer and the dimer between 278 K and 383 K is found to be 2.51 and 2.10 kJ/mol respectively. A detailed analysis was carried out on the effect of water on the temperature-dependent structural modifications of four binding pockets of SARS CoV-2 main protease namely, catalytic dyad, substrate-binding site, dimerization site and allosteric site. It is found that the water structure around the binding sites is altered with temperature. The water around the dimer sites is more ordered than the monomer sites regardless of the rise in temperature due to structural rigidity. The energy expense of binding the small molecules at substrate binding is less compared to the allosteric site. The water-water hydrogen bond lifetime is found to be more near the cavity of His41. Also, it is observed that mTIP3P water molecules have a similar effect to that of SPC/E water molecules on the main protease.

Molecular dynamics analysis of the structural properties of the transglutaminases of Kutzneria albida and Streptomyces mobaraensis

The microbial transglutaminase (TGase) from Streptomyces mobaraensis (MTGase) is widely used for industrial applications. However, in the last decades, TGases from other bacteria have been described. We focused our attention on TGase, from Kutzneria albida (KalbTGase), recently characterized as more selective than MTGase and proposed for applications in drug delivery. By comparison of the crystallographic structures, the volume of the catalytic site results smaller in KalbTGase. We compared KalbTGase and MTGase structural flexibility by molecular dynamics (MD) simulations at different conditions. KalbTGase is more rigid than MTGase at 300 K, but the catalytic site has a preserved conformation in both structures. Preliminary studies at higher temperatures suggest that KalbTGase acquires enhanced conformational flexibility far from the active site region. The volume of the catalytic active site pocket of KalbTGase at room temperature is smaller than that of MTGase, and decreases at 335 K, remaining stable after further temperature increase. On the contrary, in MTGase the pocket volume continues to decrease as the temperature increases. Overall, the results of our study suggest that at room temperature the enhanced specificity of KalbTGase could be related to a more closed catalytic pocket and lower flexibility than MTGase. Moreover, by preliminary results at higher temperature, KalbTGase structural flexibility suggests an adaptability to different substrates not recognized at room temperature. Lower adaptability of MTGase at higher temperature with a reduction of the catalytic pocket, instead, suggests a reduction of its activity.