1,721,423 research outputs found
Structural determinants of ligands recognition by the human mitochondrial basic amino acids transporter SLC25A29. Insights from molecular dynamics simulations of the c-state
Full text linkIn mitochondria, metabolic processes require the trafficking of solutes and organic molecules, such as amino acids. This task is accomplished by the Mitochondrial Carrier Family members (also known as SLC25), among which the SLC25A29 is responsible for the translocation of basic amino acids. In this regard, nitric oxide levels originated by the arginine mitochondrial catabolism have been shown to strongly affect cancer cells’ metabolic status. Furthermore, the metabolic disease saccharopinuria has been linked to a mitochondrial dysregulation caused by a toxic intermediate of the lysine catabolism. In both cases, a reduction of the activity of SLC25A29 has been shown to ameliorate these pathological conditions. However, no detailed structural data are available on SLC25A29. In the present work, molecular modelling, docking and dynamics simulations have been employed to analyse the structural determinants of ligands recognition by SLC25A29 in the c-state. Results confirm and reinforce earlier predictions that Asn73, Arg160 and Glu161, and Arg257 represent the ligand contact points I, II, and III, respectively, and that Arg160, Trp204 and Arg257 form a stable interaction, likely critical for ligand binding and translocation. These results are discussed in view of the experimental data available for SLC25A29 and other homologous carriers of the same family
Modeling the different conformations of the human mitochondrial ADP/ATP carrier using AlphaFold and molecular dynamics simulations of the protein-ligand complexes
No full textThe ADP/ATP Carrier (AAC), a member of the mitochondrial Solute Carrier Family 25 (SLC25), facilitates the exchange of cytosolic ADP for mitochondrial ATP across the inner mitochondrial membrane (IMM). It serves as a master regulator of the cellular ADP/ATP ratio and is involved in various pathologies, including cancer. Its transport mechanism involves a conformational transition that alternates the accessibility of the binding site between the cytoplasmic (c-state) and mitochondrial (m-state) sides of the IMM. In this study, the human AAC was used as a case study to evaluate the performance of AlphaFold2 (AF2) and AlphaFold3 (AF3) for structural modeling of members of the SLC25 family. The study also compared the AF3 approach for predicting protein-ligand complexes with the standard methodology of modeling followed by molecular docking. Both AF2 and AF3 display a bias toward the c-state conformation. On the other hand, ColabFold implementation of AF2 successfully generated the first ab initio structural model of the human AAC in the m-state conformation. Modeling of the complexes coupled to molecular dynamics (MD) simulations allowed to obtain structural insight into AAC’s substrate binding and stabilization mechanisms, and the possible effects of pathogenic mutations on its conformational dynamics and functionality. These analyses provided a deeper understanding of AAC’s alternating access mechanism and highlighted the potential of AF3 in modeling protein-ligand interactions, though only in the c-state. This work demonstrates the reliability of AlphaFold models when aligned with experimental data and provides further confirmation of their utility for investigating solute carriers and membrane proteins
Inclusive education in Italy. A case study
Full text linkHistorically speaking, the origin of the inclusive education model in Italy could be traced back to the promulgation
of the Italian Constitution in 1948. Many years later, in 1977, the Parliament approved an important piece of legislation known
as integrazione scolastica: according to this policy, all students can be enrolled in public schools regardless of any physical or
mental impairment. As a result, the Italian policy context seems to create an ideal situation for the development of inclusive
education and of a human rights approach to education. Does such perception correspond to reality? Our paper will briefly
outline the historical evolution of the Italian model of inclusive education and present its current state of development. Clearly,
inclusion works in reality not only as a result of legislation and procedures, but also depending on the will, dedication and
investment of each school institution, on the context in which it operates, on the competence and motivation of its teachers and staff. In our paper we chose to present the case study of a vocational high school in Rome, considered a best practice at the local and national level for the success of its inclusion projects. After describing the environment and the challenges faced from the viewpoint of integrazione scolastica, we will try to emphasize its peculiarities and to highlight the factors and managerial choices that, in our view, contribute to the excellent results of this institution in the area of inclusion
Molecular evolution of the polyamine oxidase gene family in Metazoa
Full text linkBackground: Polyamine oxidase enzymes catalyze the oxidation of polyamines and acetylpolyamines. Since polyamines are basic regulators of cell growth and proliferation, their homeostasis is crucial for cell life. Members of the polyamine oxidase gene family have been identified in a wide variety of animals, including vertebrates, arthropodes, nematodes, placozoa, as well as in plants and fungi. Polyamine oxidases (PAOs) from yeast can oxidize spermine, N 1-acetylspermine, and N1-acetylspermidine, however, in vertebrates two different enzymes, namely spermine oxidase (SMO) and acetylpolyamine oxidase (APAO), specifically catalyze the oxidation of spermine, and N1-acetylspermine/N1-acetylspermidine, respectively. Little is known about the molecular evolutionary history of these enzymes. However, since the yeast PAO is able to catalyze the oxidation of both acetylated and non acetylated polyamines, and in vertebrates these functions are addressed by two specialized polyamine oxidase subfamilies (APAO and SMO), it can be hypothesized an ancestral reference for the former enzyme from which the latter would have been derived. Results: We analysed 36 SMO, 26 APAO, and 14 PAO homologue protein sequences from 54 taxa including various vertebrates and invertebrates. The analysis of the full-length sequences and the principal domains of vertebrate and invertebrate PAOs yielded consensus primary protein sequences for vertebrate SMOs and APAOs, and invertebrate PAOs. This analysis, coupled to molecular modeling techniques, also unveiled sequence regions that confer specific structural and functional properties, including substrate specificity, by the different PAO subfamilies. Molecular phylogenetic trees revealed a basal position of all the invertebrates PAO enzymes relative to vertebrate SMOs and APAOs. PAOs from insects constitute a monophyletic clade. Two PAO variants sampled in the amphioxus are basal to the dichotomy between two well supported monophyletic clades including, respectively, all the SMOs and APAOs from vertebrates. The two vertebrate monophyletic clades clustered strictly mirroring the organismal phylogeny of fishes, amphibians, reptiles, birds, and mammals. Evidences from comparative genomic analysis, structural evolution and functional divergence in a phylogenetic framework across Metazoa suggested an evolutionary scenario where the ancestor PAO coding sequence, present in invertebrates as an orthologous gene, has been duplicated in the vertebrate branch to originate the paralogous SMO and APAO genes. A further genome evolution event concerns the SMO gene of placental, but not marsupial and monotremate, mammals which increased its functional variation following an alternative splicing (AS) mechanism. Conclusions: In this study the explicit integration in a phylogenomic framework of phylogenetic tree construction, structure prediction, and biochemical function data/prediction, allowed inferring the molecular evolutionary history of the PAO gene family and to disambiguate paralogous genes related by duplication event (SMO and APAO) and orthologous genes related by speciation events (PAOs, SMOs/APAOs). Further, while in vertebrates experimental data corroborate SMO and APAO molecular function predictions, in invertebrates the finding of a supported phylogenetic clusters of insect PAOs and the co-occurrence of two PAO variants in the amphioxus urgently claim the need for future structure-function studies. © 2012 Polticelli et al.; licensee BioMed Central Ltd
Computational studies of the mitochondrial carrier family SLC25. Present status and future perspectives
Full text linkThe members of the mitochondrial carrier family, also known as solute carrier family 25 (SLC25), are transmembrane proteins involved in the translocation of a plethora of small molecules between the mitochondrial intermembrane space and the matrix. These transporters are characterized by three homologous domains structure and a transport mechanism that involves the transition between different conformations. Mutations in regions critical for these transporters' function often cause several diseases, given the crucial role of these proteins in the mitochondrial homeostasis. Experimental studies can be problematic in the case of membrane proteins, in particular concerning the characterization of the structure-function relationships. For this reason, computational methods are often applied in order to develop new hypotheses or to support/explain experimental evidence. Here the computational analyses carried out on the SLC25 members are reviewed, describing the main techniques used and the outcome in terms of improved knowledge of the transport mechanism. Potential future applications on this protein family of more recent and advanced in silico methods are also suggested
In silico analysis of huntingtin homologs in lower eukaryotes
Full text linkHuntington’s disease is a rare neurodegenerative and autosomal dominant disorder. HD is caused by a mutation in the gene coding for huntingtin (Htt). The result is the production of a mutant Htt with an abnormally long polyglutamine repeat that leads to pathological Htt aggregates. Although the structure of human Htt has been determined, albeit at low resolution, its functions and how they are performed are largely unknown. Moreover, there is little information on the structure and function of Htt in other organisms. The comparison of Htt homologs can help to under-stand if there is a functional conservation of domains in the evolution of Htt in eukaryotes. In this work, through a computational approach, Htt homologs from lower eukaryotes have been analysed, identifying ordered domains and modelling their structure. Based on the structural models, a putative function for most of the domains has been predicted. A putative C. elegans Htt-like protein has also been analysed following the same approach. The results obtained support the notion that this protein is a orthologue of human Htt
PROPOSTA PER LA DEFINIZIONE DI UN SAFETY MANAGEMENT SYSTEM PER IMPRESE A PART EASA 145
No full textCNIM-Comitato Nazionale Italiano per la Manutenzion
Low-temperature optical spectroscopy of cobalt in Cu,Co superoxide dismutase: A structural dynamics study of the solvent-unaccessible metal site RID F-2353-2010 RID F-2664-2011 RID A-4573-2009
No full textThe temperature dependence (300 to 10 K) of the electronic absorption spectra of the cobalt chromophore in bovine superoxide dismutase (SOD) having the native Zn(II) ion selectively replaced by Co(II) has been investigated in four different derivatives: Cu(II),Co(II) SOD, N-3(-)-Cu(II),Co(II) SOD, Cu(I),Co(II) SOD, and E,Co(II) SOD in which the copper ion has been selectively removed. In the Cu(II),Co(lI) SOD, the cobalt spectrum is characterized at room temperature by three bands centered at 18,472, 17,670, and 16,793 cm(-1); the low-frequency band is split, at low temperatures, into two components, indicating a lower symmetry contribution to a predominantly tetrahedral crystal field. Addition of N-3(-) to the Cu(II),Co(II) SOD introduces slight changes in all the Co(II) visible bands, indicating the occurrence of minor perturbations of the structural cobalt site upon anion binding to the catalytic copper site. Analysis of the spectra in the Cu(I),Co(II) and E,Co(II) enzymes indicates that the His61 imidazolate bridge is released from the copper upon reduction. This is also confirmed by the analysis of the zeroth, first, and second moments of the various bands in the different derivatives. The cobalt site is characterized by a harmonic dynamics, at variance with what observed in the solvent accessible copper site [Cupane, A., Leone, M., Militello, V., Stroppolo, M. E., Polticelli, F., & Desideri, A. (1994) Biochemistry 33, 15103-15109]. The degree of local microheterogeneity at the cobalt site is smaller than that observed for the copper site and increases in the order N-3(-)-Cu(II),Co(II)approximate to Cu(I),Co(II) < Cu(I),Co(II) < E,Co(II) indicating a different local packing and the presence of different constraints on the cobalt site in the four derivatives. The different dynamic behavior with respect to the catalytic, solvent-accessible, copper site is discussed
- …
