PLI: a web-based tool for the comparison of protein-ligand interactions observed on PDB structures.

Abstract Motivation: A large fraction of the entries contained in the Protein Data Bank describe proteins in complex with low molecular weight molecules such as physiological compounds or synthetic drugs. In many cases, the same molecule is found in distinct protein-ligand complexes. There is an increasing interest in Medicinal Chemistry in comparing protein binding sites to get insight on interactions that modulate the binding specificity, as this structural information can be correlated with other experimental data of biochemical or physiological nature and may help in rational drug design. Results: The web service protein-ligand interaction presented here provides a tool to analyse and compare the binding pockets of homologous proteins in complex with a selected ligand. The information is deduced from protein-ligand complexes present in the Protein Data Bank and stored in the underlying database. Availability: Freely accessible at http://bioinformatics.istge.it/pli/. Contact: [email protected]

H2020 ACCEPT project:D8.2 – ACCEPT exploitation plan & IPR management v1

The objective of this deliverable is to provide a comprehensive and detailed first version of the exploitation plan and the intellectual property rights (IPR) management for the ACCEPT project. As the development activities of the project are still underway, initial results are beginning to surface, providing valuable insights into the potential outcomes. The primary goal of this report is to clearly identify the Key Exploitable Results (KER) that have already emerged or are currently evolving. In addition, the report aims to outline the methodology and specific mechanisms that will be employed for the protection, exploitation, and sharing of these results, ensuring their maximum value and impact. For each of the KERs that have been discovered thus far, this report offers a concise yet comprehensive overview of their key characteristics and the areas that are currently being developed for the respective item, service, or method. Moreover, it emphasizes the uniqueness of each idea by comparing it to existing market offerings, products, services, and methods. By highlighting the distinctive features and advantages of each KER, the report provides a clear understanding of their value proposition and competitive edge. Additionally, any non-technical or legal barriers that may hinder their exploitation are thoroughly addressed, ensuring that the necessary measures are taken to overcome them effectively. Furthermore, the report meticulously outlines the strategy for future market positioning of the KERs. Taking into account crucial factors such as market timing and, when applicable, conducting a foreign patent scenario analysis, this strategy sets the groundwork for successful commercialization. Additionally, the report examines the warning signs associated with the available protection techniques, enabling the project team to proactively safeguard the intellectual property tied to the project's results. The deliverable also comprehends the patent analysis, a highly useful technique for investigating the environment surrounding a specific product, technology, etc. The method, which is thoroughly explained in the next chapters, will provide partners access to relevant information about who is working on a specific area, how much is invested in a given technology, and where and how high-potential markets are positioned. It is important to acknowledge that the current document is a dynamic work in progress. It will undergo continuous updates and refinements to ensure its final delivery in an official and comprehensive form. As the project progresses, partners are expected to provide detailed reports on the actual and anticipated utilization of their foreground IPR. This includes sharing their strategies and practical activities for effectively disseminating and exploiting the project's results. Looking ahead, the subsequent exploitation deliverable (D8.3) will encompass further information regarding the final IP protection strategy. This comprehensive strategy will outline the planned actions necessary to reach a Technology Readiness Level (TRL) of 9 for the project's KERs, signifying their advanced stage of development and readiness for commercialization. Moreover, partner expectations, including financial projections and goals, related to the commercialization of their products will be thoroughly addressed, ensuring a clear understanding of the pathway to success

The rhodanese/Cdc25 phosphatase superfamily: Sequence–structure–function relations

Rhodanese domains are ubiquitous structural modules occurring in the three major evolutionary phyla. They are found as tandem repeats, with the C-terminal domain hosting the properly structured active-site Cys residue, as single domain proteins or in combination with distinct protein domains. An increasing number of reports indicate that rhodanese modules are versatile sulfur carriers that have adapted their function to fulfill the need for reactive sulfane sulfur in distinct metabolic and regulatory pathways. Recent investigations have shown that rhodanese domains are also structurally related to the catalytic subunit of Cdc25 phosphatase enzymes and that the two enzyme families are likely to share a common evolutionary origin. In this review, the rhodanese/Cdc25 phosphatase superfamily is analyzed. Although the identification of their biological substrates has thus far proven elusive, the emerging picture points to a role for the amino-acid composition of the active-site loop in substrate recognition/specificity. Furthermore, the frequently observed association of catalytically inactive rhodanese modules with other protein domains suggests a distinct regulatory role for these inactive domains, possibly in connection with signaling

Mutational analysis of the ACVR1 gene in Italian patients affected with fibrodysplasia ossificans progressiva: confirmations and advancements

Fibrodysplasia ossificans progressiva (FOP, MIM 135100) is a rare genetic disorder characterized by congenital great toe malformations and progressive heterotopic ossification transforming skeletal muscles and connective tissues to bone following a well-defined anatomic pattern of progression. Recently, FOP has been associated with a specific mutation of ACVR1, the gene coding for a bone morphogenetic protein type I receptor. The identification of ACVR1 as the causative gene for FOP now allows the genetic screening of FOP patients to identify the frequency of the identified recurrent ACVR1 mutation and to investigate genetic variability that may be associated with this severely debilitating disease. We report the screening for mutations in the ACVR1 gene carried out in a cohort of 17 Italian patients. Fifteen of these displayed the previously described c.617G>A mutation, leading to the R206H substitution in the GS domain of the ACVR1 receptor. In two patients, we found a novel mutation c.774G>C, leading to the R258S substitution in the kinase domain of the ACVR1 receptor. In the three-dimensional model of protein structure, R258 maps in close proximity to the GS domain, a key regulator of ACVR1 activity, where R206 is located. The GS domain is known to bind the regulatory protein FKBP12 and to undergo multiple phosphorylation events that trigger a signaling cascade inside the cell. The novel amino-acid substitution is predicted to influence either the conformation/stability of the GS region or the binding affinity with FKBP12, resulting in a less stringent inhibitory control on the ACVR1 kinase activity

CD81 extracellular domain 3D structure: insight into the tetraspanin superfamily structural motifs

Human CD81, a known receptor for hepatitis C virus envelope E2 glycoprotein, is a transmembrane protein belonging to the tetraspanin family. The crystal structure of human CD81 large extracellular domain is reported here at 1.6 Å resolution. Each subunit within the homodimeric protein displays a mushroom-like structure, composed of five α-helices arranged in ‘stalk’ and ‘head’ subdomains. Residues known to be involved in virus binding can be mapped onto the head subdomain, providing a basis for the design of antiviral drugs and vaccines. Sequence analysis of 160 tetraspanins indicates that key structural features and the new protein fold observed in the CD81 large extracellular domain are conserved within the family. On these bases, it is proposed that tetraspanins may assemble at the cell surface into homo- and/or hetero-dimers through a conserved hydrophobic interface located in the stalk subdomain, while interacting with other liganding proteins, including hepatitis C virus E2, through the head subdomain. The topology of such interactions provides a rationale for the assembly of the so-called tetraspan-web

miRNA-Mediated KHSRP Silencing Rewires Distinct Post-transcriptional Programs during TGF-β-Induced Epithelial-to-Mesenchymal Transition

Epithelial-to-mesenchymal transition (EMT) confers several traits to cancer cells that are required for malignant progression. Here, we report that miR-27b-3p-mediated silencing of the single-strand RNA binding protein KHSRP is required for transforming growth factor β (TGF-β)-induced EMT in mammary gland cells. Sustained KHSRP expression limits TGF-β-dependent induction of EMT factors and cell migration, whereas its knockdown in untreated cells mimics TGF-β-induced EMT. Genome-wide sequencing analyses revealed that KHSRP controls (1) levels of mature miR-192-5p, a microRNA that targets a group of EMT factors, and (2) alternative splicing of a cohort of pre-mRNAs related to cell adhesion and motility including Cd44 and Fgfr2. KHSRP belongs to a ribonucleoprotein complex that includes hnRNPA1, and the two proteins cooperate in promoting epithelial-type exon usage of select pre-mRNAs. Thus, TGF-β-induced KHSRP silencing is central in a pathway leading to gene-expression changes that contribute to the cellular changes linked to EMT

The Three-dimensional Structure of the Nitrogen Regulatory Protein IIANtr from Escherichia coli

The bacterial rpoN operon codes for σ54, which is the key σ factor that, under nitrogen starvation conditions, activates the transcription of genes needed to assimilate ammonia and glutamate. The rpoN operon contains several other open reading frames that are cotranscribed with σ54. The product of one of these, the 17.9 kDa protein IIANtr, is homologous to IIA proteins of the phosphoenolpyruvate:sugar phosphotransferase (PTS) system. IIANtr influences the transcription of σ54-dependent genes through an unknown mechanism and may thereby provide a regulatory link between carbon and nitrogen metabolism. Here we describe the 2.35 Å X-ray structure of Escherichia coli IIANtr. It is the first structure of a IIA enzyme from the fructose-mannitol family of the PTS. The enzyme displays a novel fold characterized by a central mixed parallel/anti-parallel β-sheet surrounded by six α-helices. The active site His73 is situated in a shallow depression on the protein surface.