Substrate recognition and catalysis by LytB, a pneumococcal peptidoglycan hydrolase involved in virulence

17 p.-7 fig.-2 tab. Rico-Lastres, Palma et al.Streptococcus pneumoniae is a major cause of life-threatening diseases worldwide. Here we provide an in-depth functional characterization of LytB, the peptidoglycan hydrolase responsible for physical separation of daughter cells. Identified herein as an N-acetylglucosaminidase, LytB is involved also in colonization and invasion of the nasopharynx, biofilm formation and evasion of host immunity as previously demonstrated. We have shown that LytB cleaves the GlcNAc-β-(1,4)-MurNAc glycosidic bond of peptidoglycan building units. The hydrolysis occurs at sites with fully acetylated GlcNAc moieties, with preference for uncross-linked muropeptides. The necessity of GlcN acetylation and the presence of a single acidic moiety (Glu585) essential for catalysis strongly suggest a substrate-assisted mechanism with anchimeric assistance of the acetamido group of GlcNAc moieties. Additionally, modelling of the catalytic region bound to a hexasaccharide tripentapeptide provided insights into substrate-binding subsites and peptidoglycan recognition. Besides, cell-wall digestion products and solubilisation rates might indicate a tight control of LytB activity to prevent unrestrained breakdown of the cell wall. Choline-independent localization at the poles of the cell, mediated by the choline-binding domain, peptidoglycan modification, and choline-mediated (lipo) teichoic-acid attachment contribute to the high selectivity of LytB. Moreover, so far unknown chitin hydrolase and glycosyltransferase activities were detected using GlcNAc oligomers as substrate.Research was funded by grants from the Ministerio de Ciencia e Innovación (MICINN) and the Ministerio de Economía y Competitividad (MINECO) to P. García (SAF2009-10824 and SAF2012-39444-C02-01) and M. Menéndez (BFU2009-10052 and BFU2012-36825), the Consejería de Educación de la Comunidad de Madrid (S2010/BMD/2457) to M. Menéndez. The work in the United Kingdom and the US was supported by grants from the BBSRC (BB/G015902/1) to W. Vollmer and from the National Institutes of Health (GM61629) to S. Mobashery. Additional funding was provided by the CIBER de Enfermedades Respiratorias (CIBERES), an initiative of the Instituto de Salud Carlos III (ISCIII). Palma Rico-Lastres and Roberto Díez-Martínez were the recipients of fellowships from the MICINN (FPI program).Peer reviewe

Binding site plasticity in viral PPxY Late domain recognition by the third WW domain of human NEDD4

The recognition of PPxY viral Late domains by the third WW domain of the HECT-E3 ubiquitin ligase NEDD4 (hNEDD4-WW3) is essential for the completion of the budding process of numerous enveloped viruses, including Ebola, Marburg, HTLV1 or Rabies. hNEDD4-WW3 has been validated as a promising target for the development of novel host-oriented broad spectrum antivirals. Nonetheless, finding inhibitors with good properties as therapeutic agents remains a challenge since the key determinants of binding affinity and specificity are still poorly understood. We present here a detailed structural and thermodynamic study of the interactions of hNEDD4-WW3 with viral Late domains combining isothermal titration calorimetry, NMR structural determination and molecular dynamics simulations. Structural and energetic differences in Late domain recognition reveal a highly plastic hNEDD4-WW3 binding site that can accommodate PPxY-containing ligands with varying orientations. These orientations are mostly determined by specific conformations adopted by residues I859 and T866. Our results suggest a conformational selection mechanism, extensive to other WW domains, and highlight the functional relevance of hNEDD4-WW3 domain conformational flexibility at the binding interface, which emerges as a key element to consider in the search for potent and selective inhibitors of therapeutic interest.This research has been financed by grants BIO2009-13261-C02, BIO2012-39922-CO2 and BIO2016-78746-C2-1-R from the Spanish Ministry of Education and Science (I.L.) including AEI/FEDER EU funds, by CTQ2017-83810-R grant (F.J.B) and by BFU2014-53787-P, the IRB Barcelona and the BBVA Foundation (M.J.M)

Phage display identification of nanomolar ligands for human NEDD4-WW3: Energetic and dynamic implications for the development of broad-spectrum antivirals

This research has been financed by grants BIO2016-78746-C2-1-R and PID2020-112895RB-100 from the Spanish Ministry of Education and Science (I.L.) including AEI/FEDER EU funds. R.N.H. was funded in part by National Institutes of Health grants AI138052 and AI138630. M. I.B. and J.M.C. were recipients of a research contract from the Spanish Ministry of Education and Science. F.C. was funded by a predoctoral fellowship from the Andalusian Government P10-CVI-5915. J.M.C. ac-knowledges a reincorporation research contract from the University of Granada. We thank Dr. Sachdev Sidhu for his invaluable assistance setting up the phage display techniques in our laboratory. We also thank the support of the C.I.C. of the University of Granada.The recognition of PPxY viral Late domains by the third WW domain of the human HECT-E3 ubiquitin ligase NEDD4 (NEDD4-WW3) is essential for the budding of many viruses. Blocking these interactions is a promising strategy to develop broad-spectrum antivirals. As all WW domains, NEDD4-WW3 is a challenging therapeutic target due to the low binding affinity of its natural interactions, its high conformational plasticity, and its complex thermodynamic behavior. In this work, we set out to investigate whether high affinity can be achieved for monovalent ligands binding to the isolated NEDD4-WW3 domain. We show that a competitive phage-display set-up allows for the identification of high-affinity peptides showing inhibitory activity of viral budding. A detailed biophysical study combining calorimetry, nuclear magnetic resonance, and molecular dynamic simulations reveals that the improvement in binding affinity does not arise from the establishment of new interactions with the domain, but is associated to conformational restrictions imposed by a novel C-terminal -LFP motif in the ligand, unprecedented in the PPxY interactome. These results, which highlight the complexity of WW domain interactions, provide valuable insight into the key elements for high binding affinity, of interest to guide virtual screening campaigns for the identification of novel therapeutics targeting NEDD4-WW3 interactions.Spanish Government BIO2016-78746-C2-1-R PID2020-112895RB-100 AEI/FEDER EU funds AI138052 AI138630United States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA P10-CVI-5915German Research Foundation (DFG)University of Granad

La importancia de los intereses académicos en la política científica y tecnológica catalana

Publicado en: 'Papers: Revista de Sociología', 70: 11-40, 2003Este artículo describe la emergencia y orientación de las políticas de I+D e innovación en Cataluña. Se analizan cuáles son los factores más influyentes en la orientación de estas políticas y, en definitiva, en las opciones políticas que se toman. La política de ciencia y tecnología desarrollada por el gobierno regional catalán desde principios de los años ochenta ha sido una política en la que, a pesar de las preferencias manifestadas en el discurso político, ha predominado un modelo de política académico sobre el de orientación empresarial. Asimismo, en términos organizativos e institucionales, en la Administración autonómica, la política científica ha estado separada y diferenciada de la política tecnológica a pesar del diseño inicial de instituciones interdepartamentales. La principal razón de que la política de I+D catalana no siguiera un modelo más industrial, ligado al mundo empresarial, fue la presión que ejercieron las universidades catalanas para que, tanto el diseño institucional como el contenido de la política se adaptara a sus necesidades. La trayectoria académica previa de los gestores también contribuyó a la reorientación de las preferencias políticas. A pesar de la importancia de las empresas catalanas en la I+D, éstas no se movilizaron ni presionaron a los gobiernos suficientemente. Analíticamente, este caso ilustra cómo la sola creación política de instituciones no garantiza la realización de las preferencias políticas. También pone de manifiesto cómo el horizonte temporal de la toma de decisiones gubernamental tiene un efecto en las expectativas de los actores, que desarrollan procesos de aprendizaje a partir de las experiencias en arenas políticas similares a otros niveles. Por último, destaca la importancia del poder en las instituciones de gestión en este tipo de política distributiva.Peer reviewe

La importancia de los intereses académicos en la política científica y tecnológica catalana

Publicado en: 'Papers: Revista de Sociología', 70: 11-40, 2003Este artículo describe la emergencia y orientación de las políticas de I+D e innovación en Cataluña. Se analizan cuáles son los factores más influyentes en la orientación de estas políticas y, en definitiva, en las opciones políticas que se toman. La política de ciencia y tecnología desarrollada por el gobierno regional catalán desde principios de los años ochenta ha sido una política en la que, a pesar de las preferencias manifestadas en el discurso político, ha predominado un modelo de política académico sobre el de orientación empresarial. Asimismo, en términos organizativos e institucionales, en la Administración autonómica, la política científica ha estado separada y diferenciada de la política tecnológica a pesar del diseño inicial de instituciones interdepartamentales. La principal razón de que la política de I+D catalana no siguiera un modelo más industrial, ligado al mundo empresarial, fue la presión que ejercieron las universidades catalanas para que, tanto el diseño institucional como el contenido de la política se adaptara a sus necesidades. La trayectoria académica previa de los gestores también contribuyó a la reorientación de las preferencias políticas. A pesar de la importancia de las empresas catalanas en la I+D, éstas no se movilizaron ni presionaron a los gobiernos suficientemente. Analíticamente, este caso ilustra cómo la sola creación política de instituciones no garantiza la realización de las preferencias políticas. También pone de manifiesto cómo el horizonte temporal de la toma de decisiones gubernamental tiene un efecto en las expectativas de los actores, que desarrollan procesos de aprendizaje a partir de las experiencias en arenas políticas similares a otros niveles. Por último, destaca la importancia del poder en las instituciones de gestión en este tipo de política distributiva.Este trabajo se ha realizado gracias a la financiación del Programa Marco de I+D, del PRICIT de la Comunidad de Madrid y del III Plan Nacional de I+D de la CICYT (SEC 1999-0829-C02-01).Peer reviewe

WW Domains of the Yes-Kinase-Associated-Protein (YAP) Transcriptional Regulator Behave as Independent Units with Different Binding Preferences for PPxY Motif-Containing Ligands

YAP is a WW domain-containing effector of the Hippo tumor suppressor pathway, and the object of heightened interest as a potent oncogene and stemness factor. YAP has two major isoforms that differ in the number of WW domains they harbor. Elucidating the degree of co-operation between these WW domains is important for a full understanding of the molecular function of YAP. We present here a detailed biophysical study of the structural stability and binding properties of the two YAP WW domains aimed at investigating the relationship between both domains in terms of structural stability and partner recognition. We have carried out a calorimetric study of the structural stability of the two YAP WW domains, both isolated and in a tandem configuration, and their interaction with a set of functionally relevant ligands derived from PTCH1 and LATS kinases. We find that the two YAP WW domains behave as independent units with different binding preferences, suggesting that the presence of the second WW domain might contribute to modulate target recognition between the two YAP isoforms. Analysis of structural models and phage-display studies indicate that electrostatic interactions play a critical role in binding specificity. Together, these results are relevant to understand of YAP function and open the door to the design of highly specific ligands of interest to delineate the functional role of each WW domain in YAP signaling.This work was supported by the Spanish Ministry of Education and Science [grant BIO2009-13261-CO2], the Spanish Ministry of Economy and Competitivity [grant BIO2012-39922-CO2] including FEDER (European Funds for Regional Development) funds and the Governement of Andalusia [grant CVI-5915]. Marius Sudol was supported by PA Breast Cancer Coalition Grants (#60707 and #920093) plus the Geisinger Clinic

Dominios ww: estudio del equilibrio conformacional y del reconocimiento de ligandos

Tesis Univ. Granada. Departamento de Química Física. Leída el 22 de junio de 201

Csl2, a novel chimeric bacteriophage lysin to fight infections caused by Streptococcus suis, an emerging zoonotic pathogen

Abstract Streptococcus suis is a Gram-positive bacterium that infects humans and various animals, causing human mortality rates ranging from 5 to 20%, as well as important losses for the swine industry. In addition, there is no effective vaccine for S. suis and isolates with increasing antibiotic multiresistance are emerging worldwide. Facing this situation, wild type or engineered bacteriophage lysins constitute a promising alternative to conventional antibiotics. In this study, we have constructed a new chimeric lysin, Csl2, by fusing the catalytic domain of Cpl-7 lysozyme to the CW_7 repeats of LySMP lysin from an S. suis phage. Csl2 efficiently kills different S. suis strains and shows noticeable activity against a few streptococci of the mitis group. Specifically, 15 µg/ml Csl2 killed 4.3 logs of S. suis serotype 2 S735 strain in 60 min, in a buffer containing 150 mM NaCl and 10 mM CaCl2, at pH 6.0. We have set up a protocol to form a good biofilm with the non-encapsulated S. suis mutant strain BD101, and the use of 30 µg/ml Csl2 was enough for dispersing such biofilms and reducing 1–2 logs the number of planktonic bacteria. In vitro results have been validated in an adult zebrafish model of infection

PL3 amidase, a tailor-made lysin constructed by domain shuffling with potent killing activity against Pneumococci and related species

13 p.-7 fig.-1 tab.The emergence and spread of antibiotic-resistant bacteria is pushing the need of alternative treatments. In this context, phage therapy is already a reality to successfully fight certain multiresistant bacteria. Among different phage gene products, murein hydrolases responsible of phage progeny liberation (also called lysins or endolysins) are weapons that target specific peptidoglycan bonds, leading to lysis and death of susceptible bacteria when added from the outside. In the pneumococcal system, all but one phage murein hydrolases reported to date share a choline-binding domain that recognizes cell walls containing choline residues in the (lipo)teichoic acids. Some purified pneumococcal or phage murein hydrolases, as well as several chimeric proteins combining natural catalytic and cell wall-binding domains (CBDs) have been used as effective antimicrobials. In this work we have constructed a novel chimeric N-acetylmuramoyl-L-alanine amidase (PL3) by fusing the catalytic domain of the Pal amidase (a phage-coded endolysin) to the CBD of the LytA amidase, the major pneumococcal autolysin. The physicochemical properties of PL3 and the bacteriolytic effect against several pneumococci (including 48 multiresistant representative strain) and related species, like Streptococcus pseudopneumoniae, Streptococcus mitis, and Streptococcus oralis, have been studied. Results have shown that low doses of PL3, in the range of 0.5–5 mg/ml, are enough to practically sterilize all choline-containing strains tested. Moreover, a single 20-mg dose of PL3 fully protected zebrafish embryos from infection by S. pneumoniae D39 strain. Importantly, PL3 keeps 95% enzymatic activity after 4 weeks at 37 C and can be lyophilized without losing activity, demonstrating a remarkable robustness. Such stability, together with a prominent efficacy against a narrow spectrum of human pathogens, confers to PL3 the characteristic to be an effective therapeutic. In addition, our results demonstrate that the structure/functionbased domain shuffling approach is a successful method to construct tailor-made endolysins with higher bactericidal activities than their parental enzymes.Research wasfunded by grants from the Ministerio de Economía y Competitividad (MINECO) to PG (SAF2012-39444- C02-01) and MM (BFU2012-36825 and BFU2015-70052-R), the Consejería de Educación de la Comunidad de Madrid (S2010/BMD/2457) to MM. Additional funding was provided by the CIBER de Enfermedades Respiratorias (CIBERES),an initiative of the Instituto de Salud Carlos III (ISCIII).Peer reviewe