Publications by authors named "G Pierdominici-Sottile"
Article Synopsis
- Nonsense correlations can occur between random variables over time, especially in multidimensional random walks, which complicates data analysis.
- PCA aims to maximize correlations, but this can lead to misleading interpretations when analyzing trajectories influenced by these random correlations.
- To improve PCA results, concatenating trajectories from multiple simulations is recommended, helping to mitigate issues observed in protein models like human serum albumin and lysozyme.
Flavin-dependent monooxygenases (FMOs) constitute a diverse enzyme family that catalyzes crucial hydroxylation, epoxidation, and Baeyer-Villiger reactions across various metabolic pathways in all domains of life. Due to the intricate nature of this enzyme family's mechanisms, some aspects of their functioning remain unknown. Here, we present the results of molecular dynamics computations, supplemented by a bioinformatics analysis, that clarify the early stages of their catalytic cycle.
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- Molecular dynamics (MD) simulations are effective for studying protein functions at an atomic level and are increasingly being used for RNA research.
- Implementing MD simulations for RNA in solution presents specific challenges that practitioners need to understand for proper usage.
- The chapter covers the basics of MD simulations, details the unique aspects of RNA simulations, discusses the technique's pros and cons, and gives examples of how it helps in understanding small RNA behavior.
Principal Component Analysis (PCA) is a procedure widely used to examine data collected from molecular dynamics simulations of biological macromolecules. It allows for greatly reducing the dimensionality of their configurational space, facilitating further qualitative and quantitative analysis. Its simplicity and relatively low computational cost explain its extended use.
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- CsrA/RsmE is a regulatory protein in bacteria that inhibits target mRNA expression by binding to their untranslated regions, which can be countered by small RNAs like RsmZ.
- The study utilized umbrella sampling simulations to investigate how RsmE unbinds from the AGGAC motif in RsmZ, revealing key residues involved in this process and highlighting a hairpin-like conformation essential for binding.
- Molecular dynamics simulations indicated that the flexible single-stranded region of RsmZ significantly influences its ability to engage with RsmE, suggesting that structural dynamics play a critical role in RNA-protein interactions.