A novel regulatory unit in the N-terminal region of c-Src

[eng] c-Src is a central player in several cellular signaling pathways. It controls impor- tant cellular processes like cellular proliferation, survival or motility. Therefore, a number of tumoral diseases have been related to abnormal c-Src activity. Among them, colorectal cancer stands out, as c-Src deregulation correlates with tumor progression and clinical outcome. This tyrosine kinase is part of a larger group of functionally and structurally related proteins termed Src Family Kinases. These proteins share the same domain architecture: a cassette formed by a catalytic domain (SH1), two reg- ulatory domains, SH2 and SH3, and a variable intrinsically disordered region (the Unique domain) that ultimately anchors to the inner face of the cellular membrane via the N-terminal SH4 domain, also disordered. The sequence and structure of the cassette are highly conserved, and thus unsurprisingly Src Family Kinases perform closely related and often overlapping functions. However, the role of intrinsically disordered regions has remained unclear, although they are known to be functionally relevant. In this work, the structural and functional relationship between the intrinsically disordered SH4 and Unique domains with the neighboring folded SH3 domain in c-Src is explored. Interactions between disordered and ordered proteins are often characterized by the formation of complexes that are specific and functional but structurally heterogeneous. Moreover, conformational plasticity is a fundamental feature for function. These assemblies are known as fuzzy complexes. Here this theoretical framework, usually applied to isolated partners, is extended to the intramolecular interface between covalently bound domains instead of isolated pairs. The concept of fuzzy binding is also used in order to describe interactions based on sets of dynamic, transient, and promiscuous contacts between ill-defined sets of interactors. In order to characterize the system, an integrative strategy using short and long range Nuclear Magnetic Resonance techniques and Small Angle X-ray Scattering is applied to several constructs containing different combinations of bound or isolated domains. It is demonstrated that the folded SH3 domain acts as a scaffold for the disordered region, which interacts in a specific manner with its partner. Both disordered domains, SH4 and Unique, are involved in the process albeit they contribute differently. Additionally, it is shown that the Unique domain is not a random coil, but contains a significant degree of pre-arrangement that is independent of the scaffold. Sequence determinants are then searched by comparison of the sequences of different Src Family Kinases. Four conserved phenylalanine residues are found and their implication in Unique domain pre-organization and Unique:SH3 domain interaction tested. All these amino acids are found to favor compaction of the intrinsically disordered region, and at the same time to perturb close contact with the scaffold. In addition, mutations in the interacting zones of the SH3 domain are also studied to test reciprocity. In all, the fuzzy complex model is proven for the SH4:Unique:SH3 system. Then, the results are extrapolated to the full-length c-Src to test its biological relevance. A co evolutionary analysis suggests that the fuzzy model may be a general feature for the whole Src Family, so the closest member of the family, Yes, is also tested experimentally. The initial results on long-range contacts suggests a similar arrangement between the scaffold and the disordered region. In all, it is suggested that plastic, fuzzy interfaces between ordered and disordered domains may be a relevant mode for the transmission of functional information within multidomain proteins. Finally, a first approach for a structural study of the c-Src fuzzy complex in a native-like lipid environment, including natural co-translational modifications, is presented. A protocol for sample preparation is developed and Dynamic Nuclear Polarization solid state NMR is shown to be an adequate tool for further analysis.[spa] c-Src es una tirosina quinasa clave en múltiples rutas de señalización celulares. Su desregulación ha sido asociada a diversos procesos tumorales, entre los que destaca el cáncer de cólon. Una actividad anómala de c-Src se correlaciona con el desarrollo tumoral y pronóstico clínico desfavorable. c-Src forma parte de un grupo de proteínas relacionadas estructural y funcional- mente, la Familia de Quinasas Src. Todas ellas comparten la misma arquitectura modular, que incluye un dominio catalítico (SH1), dos dominios regulatorios, SH2 y SH3, y a continuación una región variable intrínsecamente desordenada que incluye los dominios Único y SH4. Mientras que el segmento ordenado está bien caracterizado, el papel de la región desordenada no está claro, aunque es funcionalmente relevante. En este trabajo se explora la relación estructural y funcional entre la región desordenada y el dominio ordenado adyacente SH3. Dado que este tipo de interacciones implican un grado significativo de heterogeneidad estructural, se ha aplicado el concepto de unión difusa para caracterizar este sistema. Este marco teórico permite modelar interacciones basadas en contactos dinámicos y transitorios entre múltiples interactores vagamente definidos, que sin embargo son específicos y funcionales. Para ello, se ha usado una estrategia que implica el uso combinado de técnicas de Resonancia Magnética Nuclear de largo y corto alcance, así como Dispersión de rayos X a Bajo Ángulo. Se demuestra así que el dominio plegado SH3 actúa como armazón para la región desordenada, que a su vez contiene un grado significativo de pre-organización estructural. Se han identificado cuatro fenilalaninas en el dominio Único responsables de esta pre-formación que también afectan a la interacción entre la región desordenada y el armazón. Los resultados demuestran que el conjunto de dominios SH4, Único y SH3 forman una unidad funcional que puede ser definida como un complejo difuso. Además, datos teóricos y experimentales de otros miembros de la familia sugieren que el modelo difuso es una característica común de todos ellos. Finalmente, se ha demostrado que la Resonancia Magnética de estado sólido con Polarización Dinámica Nuclear es una técnica adecuada para el estudio estructural de c-Src unida a una matriz lipídica similar a la natural

Intramolecular fuzzy interactions involving intrinsically disordered domains

Structural disorder is an essential ingredient for function in many proteins and protein complexes. Fuzzy complexes describe the many instances where disorder is maintained as a critical element of protein interactions. In this minireview we discuss how intramolecular fuzzy interactions function in signaling complexes. Focussing on the Src family of kinases, we argue that the intrinsically disordered domains that are unique for each of the family members and display a clear fingerprint of long range interactions in Src, might have critical roles as functional sensor or effectors and mediate allosteric communication via fuzzy interactions

Farseer-NMR: automatic treatment, analysis and plotting of large, multi-variable NMR data

We present Farseer-NMR (https ://git.io/vAueU), a software package to treat, evaluate and combine NMR spectroscopic data from sets of protein-derived peaklists covering a range of experimental conditions. The combined advances in NMR and molecular biology enable the study of complex biomolecular systems such as flexible proteins or large multibody complexes, which display a strong and functionally relevant response to their environmental conditions, e.g. the presence of ligands, site-directed mutations, post translational modifications, molecular crowders or the chemical composition of the solution. These advances have created a growing need to analyse those systems' responses to multiple variables. The combined analysis of NMR peaklists from large and multivariable datasets has become a new bottleneck in the NMR analysis pipeline, whereby information-rich NMR-derived parameters have to be manually generated, which can be tedious, repetitive and prone to human error, or even unfeasible for very large datasets. There is a persistent gap in the development and distribution of software focused on peaklist treatment, analysis and representation, and specifically able to handle large multivariable datasets, which are becoming more commonplace. In this regard, Farseer-NMR aims to close this longstanding gap in the automated NMR user pipeline and, altogether, reduce the time burden of analysis of large sets of peaklists from days/weeks to seconds/minutes. We have implemented some of the most common, as well as new, routines for calculation of NMR parameters and several publication-quality plotting templates to improve NMR data representation. Farseer-NMR has been written entirely in Python and its modular code base enables facile extension

A myristoyl binding site in the SH3 domain modulates c-Src membrane anchoring

The c-Src oncogene is anchored to the cytoplasmic membrane through its N-terminal myristoylated SH4 domain. This domain is part of an intramolecular fuzzy complex with the SH3 and Unique domains. Here we show that the N-terminal myristoyl group binds to the SH3 domain in the proximity of the RT loop, when Src is not anchored to a lipid membrane. Residues in the so-called Unique Lipid Binding Region modulate this interaction. In the presence of lipids, the myristoyl group is released from the SH3 domain and inserts into the lipid membrane. The fuzzy complex with the SH4 and Unique domains is retained in the membrane-bound form, placing the SH3 domain close to the membrane surface and restricting its orientation. The apparent affinity of myristoylated proteins containing the SH4, Unique, and SH3 domains is modulated by these intramolecular interactions, suggesting a mechanism linking c-Src activation and membrane anchoring

The SH3 domain acts as a scaffold for the N-terminal intrinsically disordered regions of c-Src

Regulation of c-Src activity by the intrinsically disordered Unique domain has been recently demonstrated. However, its connection with the classical regulatory mechanisms is still missing. Here we show that the Unique domain is part of a long loop closed by the interaction of the SH4 and SH3 domains. The conformational freedom of the Unique domain is further restricted through direct contacts with SH3 that are allosterically modulated by binding of a poly-proline ligand in the presence and in the absence of lipids. Our results highlight the scaffolding role of the SH3 domain for the c-Src N-terminal intrinsically disordered regions and suggest a connection between the regulatory mechanisms involving the SH3 and Unique domains

Evidence for conserved fuzzy complexes involving a preorganized Unique domain in the Src family of kinases

The N-terminal regulatory region of c-Src including the SH4, Unique and SH3 domains adopts a compact, yet highly dynamic, structure that can be described as an intramolecular fuzzy complex. Most of the long-range interactions within the Unique domain are also observed in constructs lacking the structured SH3, indicating a considerable degree of preorganization of the disordered Unique domain. Here we report that members of the Src family of kinases (SFK) share well-conserved sequence features involving aromatic residues in their Unique domains. This observation contrasts with the supposed lack of sequence homology implied by the name of these domains and suggests that the other members of SFK also have a regulatory region involving their Unique domains. We argue that the Unique domain of each SFK is sensitive to specific input signals, encoded by each specific sequence, but the entire family shares a common mechanism for connecting the disordered and structured domains

Pheno-genotyping of inherited thrombocytopenias: our experience in 50 families

Dada la heterogeneidad de las entidades comprendi- das en las trombocitopenias hereditarias y la escasez de marcadores distintivos, su diagnóstico constituye un verdadero desafío. El abordaje clásico se basa en la caracterización fenotípica seguida del estudio mo- lecular de genes candidatos, orientado según la sos- pecha clínica. La introducción de la secuenciación de nueva generación (NGS), que permite evaluar múltiples genes simultáneamente, constituye una al- ternativa diagnóstica de alto costo, siendo de acceso limitado en nuestro medio. Nos propusimos evaluar la utilidad del abordaje clásico en una cohorte conse- cutiva de 50 familias y describir la aplicación de NGS en un subgrupo de pacientes sin diagnóstico etioló- gico luego del enfoque clásico. Mediante el abordaje clásico se efectuó el diagnóstico en 27 (54%) familias. Posteriormente, 8 familias que quedaron sin diag- nóstico luego del algoritmo clásico, se evaluaron me- diante NGS, identificando el gen causal en 4 de ellas. Considerando ambos abordajes, el rédito diagnóstico fue 31/50 (62%) familias, con la siguiente distribu- ción: 38% desorden relacionado a MYH9, 8% síndro- me de Bernard-Soulier (4% clásico, 4% monoalélico), 4% síndrome de plaquetas grises, 4% desorden pla- quetario con predisposición a leucemia, 6% trom- bocitopenia relacionada a ANKRD26, 2% síndrome Wiskott-Aldrich. Los pacientes en los que no se pudo efectuar un diagnóstico etiológico presentaban trom- bocitopenia aislada leve, con aumento moderado del tamaño plaquetario y sangrado escaso.En conclusión, la aplicación de NGS permitió au- mentar el rédito diagnóstico, si bien sería necesa- rio ampliar la población estudiada para establecer el valor real de este abordaje en nuestro medio. Por lo tanto, el uso inicial del abordaje clásico, reserván- dose la aplicación posterior de NGS a los casos que permanecen sin diagnóstico luego de este enfoque, constituiría una alternativa útil en países con pocos recursos, apuntando a un diagnóstico adecuado que posibilite la pesquisa de complicaciones sindrómicas, oriente al tratamiento y consejo genético acertado.Diagnosis of inherited thrombocytopenias represents a true challenge owing to heterogeneity of these disorders and the absence of distinctive features in a substantial proportion of patients. Classical diagnostic approach is based on phenotypic characterization followed by molecular analysis of candidate genes guided by clinical suspicion. The introduction of next generation sequencing (NGS), that allows multiple genes analysis, is a high-cost alternative with limited access in our country. The aim of this work was to evaluate the utility of the classical approach in a consecutive cohort of 50 families and to describe the application of NGS in a subgroup of patients without an etiological diagnosis after the initial approach. Through the conventional approach, an etiologic diagnosis was made in 27 (54%) families. NGS was performed in 8 that remained without diagnosis after initial characterization, attaining a diagnosis in 4. Combining both approaches, the diagnostic yield was 31/50 (62%) families: 38% MYH9-related disorder, 8% Bernard-Soulier syndrome, 4% gray platelet syndrome, 4% familial platelet disorder with predisposition to leukemia, 6% ANKRD26-related thrombocytopenia, 2% Wiskott-Aldrich syndrome. Most patients without diagnosis had isolated macrothrombocytopenia and mild bleeding. NGS increased the diagnostic rate in this cohort, although it would be necessary to expand the population to establish its actual value in our setting. Therefore, the use of the classical approach and subsequent application of NGS in undiagnosed patients would represent a useful alternative in low-income countries, pointing out that a correct etiological diagnosis enables the detection of syndromic complications, appropriate treatment and adequate genetic counseling.Fil: Heller, Paula Graciela. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Médicas. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Médicas; ArgentinaFil: Goette, Nora Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Médicas. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Médicas; ArgentinaFil: Marin Oyarzún, Cecilia Paola. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Médicas. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Médicas; ArgentinaFil: Baroni Pietto, Maria Constanza. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Médicas. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Médicas; ArgentinaFil: Ayala, Daniela. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Médicas. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Médicas; ArgentinaFil: Altuna, Diana R.. Instituto Universidad Escuela de Medicina del Hospital Italiano; ArgentinaFil: Arrieta, Maria Elizabeth. Hospital Público Descentralizado Dr. Guillermo Rawson.; ArgentinaFil: Arbesú, Guillermo. Hospital Dr. Humberto Notti; ArgentinaFil: Basqueira, Ana L.. Hospital Privado Universitario de Cordoba.; ArgentinaFil: Bazack, Nora. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez"; ArgentinaFil: Bonacorso, Silvina. Universidad de Buenos Aires. Facultad de Medicina. Hospital de Clínicas General San Martín; ArgentinaFil: Brodsky, Andrés. Universidad de Buenos Aires. Facultad de Medicina. Hospital de Clínicas General San Martín; ArgentinaFil: Castro Rios, Miguel. No especifíca;Fil: Cosentini, María L.. Hospital Materno Infantil Doctor Hector Quintana ; Gobierno de la Provincia de Jujuy;Fil: Donato, Hugo Sebastian. Hospital Municipal del Niño de San Justo ; Municipalidad de la Matanza (buenos Aires);Fil: Korin, Jorge D.. No especifíca;Fil: Gomez, Silvina. No especifíca;Fil: Guglielmone, Hugo. Sanatorio Allende; ArgentinaFil: Lagrotta, Pablo. Hospital Nacional Profesor Alejandro Posadas.; ArgentinaFil: Marti, Alejandra. Provincia de Buenos Aires. Ministerio de Salud. Hospital Alta Complejidad en Red El Cruce Dr. Néstor Carlos Kirchner Samic; ArgentinaFil: Negro, Fernando Javier. Sanatorio Sagrado Corazon; ArgentinaFil: Rapetti, María C.. Hospital Municipal del Niño de San Justo ; Municipalidad de la Matanza (buenos Aires);Fil: Rosso, Diego. Universidad de Buenos Aires. Facultad de Medicina. Hospital de Clínicas General San Martín; Argentina. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños Pedro Elizalde (ex Casa Cuna); Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Ponzinibbio, Carlos. Hospital Italiano de La Plata; ArgentinaFil: Veber, Ernesto. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños Pedro Elizalde (ex Casa Cuna); ArgentinaFil: Zerga, Marta Elisa. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Oncología "Ángel H. Roffo"; ArgentinaFil: Molinas, Felisa Concepción. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Médicas. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Médicas; ArgentinaFil: Savoia, Anna. Instituto para la Salud Materna e Infancia; Italia. Università degli Studi di Trieste; ItaliaFil: Pecci, Alessandro. Universita Degli Studi Di Pavia; ItaliaFil: Marta, Rosana Fernanda. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Médicas. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Médicas; ArgentinaFil: Glembotsky, Ana Claudia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Médicas. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Médicas; Argentin

Integrating disorder in globular multidomain proteins: Fuzzy sensors and the role of SH3 domains

Intrinsically disordered proteins represent about one third of eukaryotic proteins. An additional third correspond to proteins containing folded domains as well as large intrinsically disordered regions (IDR). While IDRs may represent functionally autonomous domains, in some instances it has become clear that they provide a new layer of regulation for the activity displayed by the folded domains. The sensitivity of the conformational ensembles defining the properties of IDR to small changes in the cellular environment and the capacity to modulate this response through post-translational modifications makes IDR ideal sensors enabling continuous, integrative responses to complex cellular inputs. Folded domains (FD), on the other hand, are ideal effectors, e.g. by catalyzing enzymatic reactions or participating in binary on/off switches. In this perspective review we discuss the possible role of intramolecular fuzzy complexes to integrate the very different dynamic scales of IDR and FD, inspired on the recent observations of such dynamic complexes in Src family kinases, and we explore the possible general role of the SH3 domains connecting IDRs and FD

Integrating disorder in globular multidomain proteins: Fuzzy sensors and the role of SH3 domains

Intrinsically disordered proteins represent about one third of eukaryotic proteins. An additional third correspond to proteins containing folded domains as well as large intrinsically disordered regions (IDR). While IDRs may represent functionally autonomous domains, in some instances it has become clear that they provide a new layer of regulation for the activity displayed by the folded domains. The sensitivity of the conformational ensembles defining the properties of IDR to small changes in the cellular environment and the capacity to modulate this response through post-translational modifications makes IDR ideal sensors enabling continuous, integrative responses to complex cellular inputs. Folded domains (FD), on the other hand, are ideal effectors, e.g. by catalyzing enzymatic reactions or participating in binary on/off switches. In this perspective review we discuss the possible role of intramolecular fuzzy complexes to integrate the very different dynamic scales of IDR and FD, inspired on the recent observations of such dynamic complexes in Src family kinases, and we explore the possible general role of the SH3 domains connecting IDRs and FD

Intramolecular fuzzy interactions involving intrinsically disordered domains

Structural disorder is an essential ingredient for function in many proteins and protein complexes. Fuzzy complexes describe the many instances where disorder is maintained as a critical element of protein interactions. In this minireview we discuss how intramolecular fuzzy interactions function in signaling complexes. Focussing on the Src family of kinases, we argue that the intrinsically disordered domains that are unique for each of the family members and display a clear fingerprint of long range interactions in Src, might have critical roles as functional sensor or effectors and mediate allosteric communication via fuzzy interactions