Un nou mecanisme de regulació cel·lular al descobert

Les proteïnes són les encarregades de dur a terme les funcions cel·lulars. I per a fer-ho és molt important la seva forma: cada forma fa una funció. Però el coneixement actual del genoma ens diu que tota la varietat necessària de formes per a la gran quantitat de funcions de la cèl·lula no està codificada en els gens. El DNA proveeix proteïnes "menys específiques" que són "retocades", un cop ja formades. Aquestes modificacions poden consistir en afegir a la proteïna un sucre, un lípid, un grup fosfat o fins i tot una altra proteïna i qui les fa són els enzims. Investigadors de la UAB han publicat a The Journal of Biological Chemistry un nou mecanisme observat en l'enzim que afegeix la proteïna SUMO a un grup de proteïnes que participa en processos tan importants com la transcripció o la reparació del material genètic.Las proteínas son las encargadas de llevar a cabo las funciones celulares. Y para hacerlo es muy importante su forma: cada forma hace una función. Pero el conocimiento actual del genoma nos dice que toda la variedad necesaria de formas para la gran cantidad de funciones de la célula no está codificada en los genes. El ADN provee proteínas "menos específicas" que son "retocadas", una vez formadas. Estas modificaciones pueden consistir en añadir a la proteína un azúcar, un lípido, un grupo fosfato o incluso otra proteína y quien las hace son las enzimas. Investigadores de la UAB han publicado en The Journal of Biological Chemistry un nuevo mecanismo observado en la enzima que añade la proteína SUMO a un grupo de proteínas que participa en procesos tan importantes como la transcripción o la reparación del material genético

Descrit un nou sistema de regulació de proteïnes

Una recerca internacional amb participació de l'IBB i la UAB ha caracteritzat un nou i potent inhibidor proteic d'un mol·lusc tropical marí anomenat Nerita versicolor. La recerca ha estat publicada al Journal of Biological Chemistry i s'ha centrat en les carboxipeptidasesUna investigación internacional con participación del IBB y la UAB ha caracterizado un nuevo y potente inhibidor proteico de un molusco tropical marino llamado Nerita versicolor. La investigación, que ha sido publicada en el Journal of Biological Chemistry, se ha centrado en las carboxipeptidasas, unas proteínas cuya actividad es clave para numerosos procesos biológicos.An international research with the participation of IBB and UAB characterised a new and strong protein inhibitor of the tropical marine mollusc Nerita versicolor. The research was published in the Journal of Biological Chemistry and is focused on carboxypeptidases, proteins playing a key role in numerous biological processes

Structural basis for the SUMO protease activity of the atypical ubiquitin-specific protease USPL1

Post-translational protein modifications by ubiquitin and ubiquitin-like modifiers regulate many major pathways in the cell. These modifications can be reversed by de-ubiquitinating enzymes such as ubiquitin-specific proteases (USPs). Proteolytic activity towards ubiquitin-modified substrates is common to all USP family members except for USPL1, which shows a unique preference for the ubiquitin-like modifier SUMO. Here, we present the crystal structure of USPL1 bound to SUMO2, defining the key structural elements for the unusual deSUMOylase activity of USPL1. We identify specific contacts between SUMO2 and the USPL1 subdomains, including a unique hydrogen bond network of the SUMO2 C-terminal tail. In addition, we find that USPL1 lacks major structural elements present in all canonical USPs members such as the so-called blocking loops, which facilitates SUMO binding. Our data give insight into how a structural protein scaffold designed to bind ubiquitin has evolved to bind SUMO, providing an example of divergent evolution in the USP family

Effect of the substituents on the nature and strength of lone pair-carbonyl interactions in acyl halides

We have performed a combined structural and theoretical analysis of lone-pair-carbonyl interactions in several families of acyl halides (R-CO-X). CSD searches have allowed us to establish the geometrical preferences for such short contacts. The study of the molecular electrostatic potential (MEP) of several molecules along with an energy decomposition analysis (EDA) disclosed the nature of the interaction and the factors that affect its strength. To further understand lone-pair-carbonyl contacts, we have systematically analyzed, by means of DFT calculations, the effect of the lone pair as well as of the halogen atom (X) and the substituent attached to the carbonyl group (R). Interaction energies up to 3 kcal/mol suggest that these interactions can be exploited in crystal design and supramolecular chemistry

Structural insights into SUMO E1-E2 interactions in Arabidopsis uncovers a distinctive platform for securing SUMO conjugation specificity across evolution

SUMOylation of proteins involves the concerted action of the E1-activating enzyme, E2-conjugating enzyme and E3-ligases. An essential discrimination step in the SUMOylation pathway corresponds to the initial interaction between E1 ubiquitin-fold domain (UFD) and E2 enzymes. Although E2 orthologs possess high sequence identity, the E2 binding region of the UFD domains has diverged across evolution. Moreover, in reciprocal in vitro conjugation reactions Arabidopsis E1 and E2 SCE1 fail to interact efficiently with cognate human E2 Ubc9 and E1 partners, respectively. To gain more insights into the properties of this interface in evolutionary distant organisms, we solved the crystal structure of SUMO E2 SCE1 and its complex with E1 UFD in Arabidopsis. In addition to a few common structural determinants, the interface between the E1 UFD and E2 in Arabidopsis is distinct compared with human and yeast, in particular by the presence of a longer α-helix in the Arabidopsis UFD domain. Despite the variability of E1 UFD domains in these surfaces, they establish specific interactions with highly conserved surfaces of their cognate E2 enzymes. Functional analysis of the different E2 interface residues between human and Arabidopsis revealed Val37 (Met36 in human), as a determinant that provides specificity in the E1-E2 recognition in plants

Nou mecanisme molecular en la reparació de DNA

Un estudi liderat per un equip de recerca de l'IBB i del Departament de Bioquímica i Biologia Molecular de la UAB, ha revelat el funcionament d'un complex enzimàtic format per un conjunt de proteïnes: -una E3 lligasa unida a una E2 i a dos SUMO, i ha identificat els punts clau per al funcionament correcte d'aquesta E3 lligasa, que participa en la reparació de dany a l'ADN a través de modificacions post-traduccionals per SUMO.Un estudio liderado por un equipo de investigación del IBB y del Departamento de Bioquímica y Biología Molecular de la UAB ha revelado el funcionamiento de un complejo enzimático formado por un conjunto de proteínas: una E3 ligasa, unida a una E2 y a dos SUMO, y ha identificado los puntos clave para el correcto funcionamiento de esta E3 ligasa, que participa en la reparación de daño en el ADN a través de modificaciones post-traduccionales por SUMO.A study led by a researcher teams from the IBB and the Department of Biochemistry and Molecular Biology of the UAB has revealed the functioning of an enzyme complex formed by a set of proetines -an E3 ligase, linked to an E2 and two SUMOs, identifying the key points for the correct function of this E3 ligase that participates in the repair of DNA damage through post-translational modifications by SUMO

Signal Transduction and Pathogenic Modifications at the Melanocortin-4 Receptor: A Structural Perspective

The melanocortin-4 receptor (MC4R) can be endogenously activated by binding of melanocyte-stimulating hormones (MSH), which mediates anorexigenic effects. In contrast, the agouti-related peptide (AgRP) acts as an endogenous inverse agonist and suppresses ligand-independent basal signaling activity (orexigenic effects). Binding of ligands to MC4R leads to the activation of different G-protein subtypes or arrestin and concomitant signaling pathways. This receptor is a key protein in the hypothalamic regulation of food intake and energy expenditure and naturally-occurring inactivating MC4R variants are the most frequent cause of monogenic obesity. In general, obesity is a growing problem on a global scale and is of social, medical, and economic relevance. A significant goal is to develop optimized pharmacological tools targeting MC4R without adverse effects. To date, this has not been achieved because of inter alia non-selective ligands across the five functionally different MCR subtypes (MC1-5R). This motivates further investigation of (i) the three-dimensional MC4R structure, (ii) binding mechanisms of various ligands, and (iii) the molecular transfer process of signal transduction, with the aim of understanding how structural features are linked with functional-physiological aspects. Unfortunately, experimentally elucidated structural information is not yet available for theMC receptors, a group of class A G-protein coupled receptors (GPCRs). We, therefore, generated MC4R homology models and complexes with interacting partners to describe approximate structural properties associated with signaling mechanisms. In addition, molecular insights from pathogenic mutations were incorporated to discriminate more precisely their individual malfunction of the signal transfer mechanism

A quaternary tetramer assembly inhibits the deubiquitinating activity of USP25

USP25 deubiquitinating enzyme is a key member of the ubiquitin system, which acts as a positive regulator of the Wnt/β-catenin signaling by promoting the deubiquitination and stabilization of tankyrases. USP25 is characterized by the presence of a long insertion in the middle of the conserved catalytic domain. The crystal structure of USP25 displays an unexpected homotetrameric quaternary assembly that is directly involved in the inhibition of its enzymatic activity. The tetramer is assembled by the association of two dimers and includes contacts between the coiled-coil insertion domain and the ubiquitin-binding pocket at the catalytic domain, revealing a distinctive autoinhibitory mechanism. Biochemical and kinetic assays with dimer, tetramer and truncation constructs of USP25 support this mechanism, displaying higher catalytic activity in the dimer assembly. Moreover, the high stabilization of tankyrases in cultured cells by ectopic expression of a constitutive dimer of USP25 supports a biological relevance of this tetramerization/inhibition mechanism

Structural Characterization of the Enzymes Composing the Arginine Deiminase Pathway in Mycoplasma penetrans

The metabolism of arginine towards ATP synthesis has been considered a major source of energy for microorganisms such as Mycoplasma penetrans in anaerobic conditions. Additionally, this pathway has also been implicated in pathogenic and virulence mechanism of certain microorganisms, i.e. protection from acidic stress during infection. In this work we present the crystal structures of the three enzymes composing the gene cluster of the arginine deiminase pathway from M. penetrans: arginine deiminase (ADI), ornithine carbamoyltransferase (OTC) and carbamate kinase (CK). The arginine deiminase (ADI) structure has been refined to 2.3 Å resolution in its apo-form, displaying an "open" conformation of the active site of the enzyme in comparison to previous complex structures with substrate intermediates. The active site pocket of ADI is empty, with some of the catalytic and binding residues far from their active positions, suggesting major conformational changes upon substrate binding. Ornithine carbamoyltransferase (OTC) has been refined in two crystal forms at 2.5 Å and 2.6 Å resolution, respectively, both displaying an identical dodecameric structure with a 23-point symmetry. The dodecameric structure of OTC represents the highest level of organization in this protein family and in M.penetrans it is constituted by a novel interface between the four catalytic homotrimers. Carbamate kinase (CK) has been refined to 2.5 Å resolution and its structure is characterized by the presence of two ion sulfates in the active site, one in the carbamoyl phosphate binding site and the other in the β-phosphate ADP binding pocket of the enzyme. The CK structure also shows variations in some of the elements that regulate the catalytic activity of the enzyme. The relatively low number of metabolic pathways and the relevance in human pathogenesis of Mycoplasma penetrans places the arginine deiminase pathway enzymes as potential targets to design specific inhibitors against this human parasite