Tryptophan as a molecular microswitch: Integrating BioLiP statistical insights with MD simulations of 5-HT₂ receptors

Karina Pakosz, Paweł Śliwa — Mon, 17 Aug 2026 00:00:00 +0200

Tryptophan residues play a critical role in protein-ligand recognition owing to their unique aromatic character, high polarizability, and ability to participate in diverse noncovalent interactions, including π-π stacking, cation-π interactions, hydrogen bonding, and hydrophobic contacts. In this study, a two-stage approach was employed to elucidate the functional significance of tryptophan residues within ligand-binding sites across diverse protein systems. First, a large-scale statistical analysis was performed using a curated dataset of protein-ligand complexes extracted from the BioLiP database. The dataset was analysed with respect to enzymatic classification and Gene Ontology enrichment, revealing a pronounced enrichment of tryptophan residues in the binding sites of hydrolases, oxidoreductases, and transferases, as well as strong associations with metal-ion binding, redox-related functions, and membrane or cytoplasmic localization. Within the G protein-coupled receptor (GPCR) superfamily, rhodopsin-like class A receptors were identified as the most prominently represented group featuring tryptophan-mediated ligand interactions. In the second stage, molecular dynamics simulations were conducted for selected serotonin 5-HT₂ receptor subtypes (5-HT₂_A, 5-HT₂_B, and 5-HT₂_C) to provide atomistic insights into the role of the conserved W6.48 residue. The simulations reveal a stable spatial relationship between the ligand and W6.48, characterized by distances consistent with aromatic anchoring, supporting its role in maintaining ligand orientation and binding pocket organization. Collectively, these results highlight tryptophan as a key determinant of ligand recognition and stabilization across both enzymatic and receptor-mediated systems.

A preliminary study on the spatial distribution of heavy metals in different potato (Solanum tuberosum L.) varieties: implications for food safety and risk assessment

Michał Marek, Dominik Zdzieszyński, Piotr Simajchel, Krzysztof Kleszcz — Tue, 18 Aug 2026 00:00:00 +0200

Food safety regarding heavy metal contamination is a critical global challenge due to the toxic nature of these elements and their ability to bioaccumulate in the food chain. This pilot study investigates the spatial distribution of toxic elements such as lead (Pb), cadmium (Cd), arsenic (As) and also other metals – copper (Cu), and aluminum (Al) at different depths of potato tubers (Solanum tuberosum L.), to evaluate the efficacy of culinary processing in reducing toxic metal exposure. Three popular cultivars in southern Poland – ‘Soraya’, ‘Vineta’, and ‘Jelly’ were analyzed. Following the wet digestion step, the quantitative determination of selected metals was performed using Graphite–Furnace Atomic Absorption Spectrometry. The accuracy of the analyses was validated using certified reference materials. The most interesting findings indicate that while mechanical peeling of tubers effectively minimizes exposure to Pb, it does not significantly reduce Cd levels. Analysis of non-highly toxic metal, such as Al, revealed a distribution pattern similar to that observed for Pb, providing interesting insights into bioaccumulation.

Science, Technology and Innovation

Tryptophan as a molecular microswitch: Integrating BioLiP statistical insights with MD simulations of 5-HT₂ receptors

A preliminary study on the spatial distribution of heavy metals in different potato (Solanum tuberosum L.) varieties: implications for food safety and risk assessment