In computational physics, chemistry, and biology, the implementation of new techniques in shared and open-source software lowers barriers to entry and promotes rapid scientific progress. However, effectively training new software users presents several challenges. Common methods like direct knowledge transfer and in-person workshops are limited in reach and comprehensiveness. Furthermore, while the COVID-19 pandemic highlighted the benefits of online training, traditional online tutorials can quickly become outdated and may not cover all the software’s functionalities. To address these issues, here we introduce “PLUMED Tutorials,” a collaborative model for developing, sharing, and updating online tutorials. This initiative utilizes repository management and continuous integration to ensure compatibility with software updates. Moreover, the tutorials are interconnected to form a structured learning path and are enriched with automatic annotations to provide broader context. This paper illustrates the development, features, and advantages of PLUMED Tutorials, aiming to foster an open community for creating and sharing educational resources.

Presentation of pathogen-derived epitopes by major histocompatibility complex I (MHC-I) can lead to the activation and expansion of specific CD8⁺ T cell clones, eventually resulting in the destruction of infected target cells. Altered peptide ligands (APLs), designed to elicit immunogenicity toward a wild-type peptide, may affect the overall stability of MHC-I/peptide (pMHC) complexes and modulate the recognition by T cell receptors (TCR). Previous works have demonstrated that proline substitution at position 3 (p3P) of different MHC-restricted epitopes, including the immunodominant LCMV-derived epitope gp33 and escape variants, may be an effective design strategy to increase epitope immunogenicity. These studies hypothesized that the p3P substitution increases peptide rigidity, facilitating TCR binding. Here, molecular dynamics simulations indicate that the p3P modification rigidifies the APLs in solution predisposing them for the MHC-I loading as well as once bound to H-2D^b, predisposing them for TCR binding. Our results also indicate that peptide position 6, key for interaction of H-2D^b/gp33 with the TCR P14, takes a suboptimal conformation before as well as after binding to the TCR. Analyses of H-2D^b in complex with APLs, in which position 6 was subjected to an l- to d-amino acid modification, revealed small conformational changes and comparable pMHC thermal stability. However, the l- to d-modification reduced significantly the binding to P14 even in the presence of the p3P modification. Our combined data highlight the sensitivity of the TCR for the conformational dynamics of pMHC and provide further tools to dissect and modulate TCR binding and immunogenicity via APLs.

Histone methyltransferase NSD2 (MMSET) overexpression in multiple myeloma (MM) patients plays an important role in the development of this disease subtype. Through the expansion of transcriptional activating H3K36me2 and the suppression of repressive H3K27me3 marks, NSD2 activates an aberrant set of genes that contribute to myeloma growth, adhesive and invasive activities. NSD2 transcriptional activity also depends on its non-catalytic domains, which facilitate its recruitment to chromatin through histone binding. In this study, using NMR, ITC and molecular dynamics simulations, we show that the tandem PHD domain of NSD2 (PHDVC5HCHNSD2) is a combinatorial reader of unmodified histone H3K4 and tri-methylated H3K27 (H3K27me3). This is the first PHD tandem cassette known to decode the methylation status of H3K27. Importantly, in a NSD2-dependent MM cellular model, we show that expression of NSD2 mutants, engineered to disrupt the interaction between H3K27me3 and PHDVC5HCH, display in comparison to wild-type NSD2: incomplete loss of H3K27 methylation throughout the genome, decreased activation of adhesive properties and cell adhesion genes, and a decrease of the corresponding H3K27ac signal at promoters. Collectively, these data suggest that the PHDVC5HCH domain of NSD2 plays an important role in modulating gene expression and chromatin modification, providing new opportunities for pharmacological intervention.

Background: One of the main challenges in cancer treatment is addressing the metabolic reprogramming of tumor cells, which require more energy and biomolecules than healthy cells. Cancer cells alter their metabolism by switching between glycolysis and oxidative phosphorylation (OXPHOS). These processes depend on transmembrane proteins that respond to the extracellular environment. Our research identified the transmembrane form of Chloride Intracellular Channel 1 (tmCLIC1) as a marker of malignancy and a potential therapeutic target. tmCLIC1 levels are increased in several solid tumors, supporting cancer growth and progression, whereas they are mostly absent in healthy cells. We confirmed that tmCLIC1 is the specific target of the antidiabetic drug metformin, an OXPHOS inhibitor in cancer cells. Methods: tmCLIC1 is the primary target of metformin in glioblastoma-initiating cells, as shown by single-channel patch-clamp recordings and NMR experiments. Various patient-derived glioblastoma cells with different genetic backgrounds were used to demonstrate that CLIC1 CRISPR-Cas9 knockout and/or its point mutation at arginine 29 removes metformin’s antitumor effects. Functional assays were used to assess the effects on proliferation, mitochondrial metabolism, and tumor growth in vitro and in vivo, using zebrafish and murine xenograft models. Results: Metformin inhibits the function of tmCLIC1 through direct and specific binding involving arginine 29 in the tmCLIC1 sequence. Additionally, during hypoglycemia, metformin promotes glioblastoma cell apoptosis by inhibiting the Cancerous Inhibitor of Protein Phosphatase 2 A (CIP2A) and activating the PP2A B56δ subunit. This leads to the dephosphorylation of Glycogen Synthase Kinase 3 Beta (GSK3β), resulting in the breakdown of the pro-survival protein MCL-1 and subsequent cell death. Inhibition of tmCLIC1 is crucial for this metformin-driven antineoplastic effect, mainly through regulating the PP2A-GSK3β-MCL-1 pathway under hypoglycemic conditions. The chronic presence of metformin within the tumors impairs in vivo growth at nanomolar concentrations. Conclusions: The therapeutic role of metformin to treat brain tumors remains debated. Our findings show that drug delivery is essential, as in vivo, tumor growth decreases at concentrations below 10 nanomolar. We propose that sustained CNS metformin levels may improve tmCLIC1 inhibition, providing a basis for optimizing interactions with metformin or related compounds to enhance therapeutic efficacy.