Sampling Performance of Multiple Independent Molecular Dynamics Simulations of an RNA Aptamer

Using multiple independent simulations instead of one long simulation has been shown to improve the sampling performance attained with the molecular dynamics (MD) simulation method. However, it is generally not known how long each independent simulation should be, how many independent simulations should be used, or to what extent either of these factors affects the overall sampling performance achieved for a given system. The goal of the present study was to assess the sampling performance of multiple independent MD simulations, where each independent simulation begins from a different initial molecular conformation. For this purpose, we used an RNA aptamer that is 25 nucleotides long as a case study. The initial conformations of the aptamer are derived from six de novo predicted 3D structures. Each of the six de novo predicted structures is energy minimized in solution and equilibrated with MD simulations at high temperature. Ten conformations from these six high-temperature equilibration runs are selected as initial conformations for further simulations at ambient temperature. In total, we conducted 60 independent MD simulations, each with a duration of 100 ns, to study the conformation and dynamics of the aptamer. For each group of 10 independent simulations that originated from a particular de novo predicted structure, we evaluated the potential energy distribution of the RNA and used recurrence quantification analysis to examine the sampling of RNA conformational transitions. To assess the impact of starting from different de novo predicted structures, we computed the density of structure projection on principal components to compare the regions sampled by the different groups of ten independent simulations. The recurrence rate and dependence of initial conformation among the groups were also compared. We stress the necessity of using different initial configurations as simulation starting points by showing long simulations from different initial structures suffer from being trapped in different states. Finally, we summarized the sampling efficiency for the complete set of 60 independent simulations and determined regions of under-sampling on the potential energy landscape. The results suggest that conducting multiple independent simulations using a diverse set of de novo predicted structures is a promising approach to achieve sufficient sampling. This approach avoids undesirable outcomes, such as the problem of the RNA aptamer being trapped in a local minimum. For others wishing to conduct multiple independent simulations, the analysis protocol presented in this study is a guide for examining overall sampling and determining if more simulations are necessary for sufficient sampling

Ligands with poly-fluorophenyl moieties promote a local structural rearrangement in the Spinach2 and Broccoli aptamers that increases ligand affinities

The interaction of nucleic acids with their molecular targets often involves structural reorganization that may traverse a complex folding landscape. With the more recent recognition that many RNAs, both coding and noncoding, may regulate cellular activities by interacting with target molecules, it becomes increasingly important to understand the means by which nucleic acids interact with their targets and how drugs might be developed that can influence critical folding transitions. We have extensively investigated the interaction of the Spinach2 and Broccoli aptamers with a library of small molecule ligands modified by various extensions from the imido nitrogen of DFHBI (3,5-difluoro-4-hydroxybenzylidene imidazolinone) that reach out from the Spinach2 ligand binding pocket. Studies of the interaction of these compounds with the aptamers revealed that poly-fluorophenyl-modified ligands initiate a slow change in aptamer affinity that takes an extended time (half-life of ~40 min) to achieve. The change in affinity appears to involve an initial disruption of the entrance to the ligand binding pocket followed by a gradual lockdown for which the most likely driving force is an interaction of the gateway adenine with a nearby 2’OH group. These results suggest that poly-fluorophenyl modifications might increase the ability of small molecule drugs to disrupt local structure and promote RNA remodeling.This is a pre-print of the article Anisuzzaman, Sharif, Ivan M. Geraskin, Muslum Ilgu, Lee Bendickson, George A. Kraus, and Marit Nilsen-Hamilton. "Ligands with poly-fluorophenyl moieties promote a local structural rearrangement in the Spinach2 and Broccoli aptamers that increases ligand affinities." RNA (2022): rna-079005. DOI: 10.1261/rna.079005.121. Copyright 2022 The Authors. Posted with permission

Inverted Classroom in der Informatik – ein Ansatz zum Erwerb überfachlicher Kompetenzen

Der Beitrag beschreibt die Entwicklung eines Inverted Classroom Konzeptes für ein Informatik-Grundlagenfach an einer Hochschule. Basierend auf Vorlesungsaufzeichnungen und Vorlesungsskript wurde hierbei besonderes Augenmerk auf die Gestaltung der gemeinsamen Präsenzzeit zwischen Studierenden und Lehrenden gelegt. Durch zahlreiche aktivierende Elemente sind die Studierenden hierbei gefordert, ihren Lernprozess selbst zu gestalten, um somit über die fachlichen Kompetenzen des Faches hinaus auch überfachliche Kompetenzen, wie beispielsweise Kommunikations- und Kooperationskompetenz, Selbstlernkompetenz und Eigenverantwortung zu trainieren