Can We Ever Develop an Ideal RNA Force Field? Lessons Learned from Simulations of the UUCG RNA Tetraloop and Other Systems.

Molecular dynamics (MD) simulations are an important and well-established tool for investigating RNA structural dynamics, but their accuracy relies heavily on the quality of the employed force field (). In this work, we present a comprehensive evaluation of widely used pair-additive and polarizable RNA s using the challenging UUCG tetraloop (TL) benchmark system. Extensive standard MD simulations, initiated from the NMR structure of the 14-mer UUCG TL, revealed that most s did not maintain the native state, instead favoring alternative loop conformations.

Computer Folding of Parallel DNA G-Quadruplex: Hitchhiker's Guide to the Conformational Space.

Guanine quadruplexes (GQs) play crucial roles in various biological processes, and understanding their folding pathways provides insight into their stability, dynamics, and functions. This knowledge aids in designing therapeutic strategies, as GQs are potential targets for anticancer drugs and other therapeutics. Although experimental and theoretical techniques have provided valuable insights into different stages of the GQ folding, the structural complexity of GQs poses significant challenges, and our understanding remains incomplete.

Effects of proline substitution/inclusion on the nanostructure of a self-assembling β-sheet-forming peptide.

Self-assembling peptides remain persistently interesting objects for building nanostructures and further assemble into macroscopic structures, hydrogels, at sufficiently high concentrations. The modulation of self-assembling β-sheet-forming peptide sequences, with a selection from the full library of amino acids, offers unique possibility for rational tuning of the resulting nanostructured morphology and topology of the formed hydrogel networks. In the present work, we explored how a known β-sheet-disassembling amino acid, proline (P), affects the self-assembly and gelation properties of amphipathic peptides.

2D Nitrogen-Doped Graphene Materials for Noble Gas Separation.

Noble gases, notably xenon, play a pivotal role in diverse high-tech applications. However, manufacturing xenon is an inherently challenging task, due to its unique properties and trace abundance in the Earth's atmosphere. Consequently, there is a pressing need for the development of efficient methods for the separation of noble gases.