Category Archives: CBBL News

Modeling of New Mutations in HFE2 and TFR2 Genes Causing Non HFE-Related Hereditary Hemochromatosis

Posted by 20 de December de 2021

Hereditary hemochromatosis (HH) is an iron metabolism disease clinically characterized by excessive iron deposition in parenchymal organs such as liver, heart, pancreas, and joints. It is caused by mutations in at least five different genes. HFE hemochromatosis is the most common type of hemochromatosis, while non-HFE related hemochromatosis are rare cases. Here, we describe six new patients of non-HFE related HH from five different families. Two families (Family 1 and 2) have novel nonsense mutations in the HFE2 gene have novel nonsense mutations (p.Arg63Ter and Asp36ThrfsTer96). In this new collaborative article led by Mayka Sánchez from the Department of Basic Sciences at UIC Barcelona, our lab gave the structural context for the effect of the identified mutations in TFR2 interactions.

Comparative modeling of the TFR2 dimer complexed with TF. (A) TFR2 chains are shown in cyan and pink, while TF chains are shown in green and orange. Dimeric interactions between TFR2 chains, close to Asp680 position (red circle at the α-15 helix, pink chain), are made between residues in the α-18 helix of one TFR2 chain (pink chain) and the loop located between the β-6 and β-7 strands of the other (cyan chain). (B) Sequence alignment of the TFR1 and TFR2 proteins near the TFR2 680 position (green arrow). Numbering is according to the TFR1 sequence, and the secondary structure depiction is based on the TFR1 structure (PDB ID 1CX8). The alignment coloring was produced by the ESPript 3.0 web server [40], where position with red background means absolute sequence conservation. (C–E) Structural context of positions TFR1-Asp648 (C, purple), TFR2-Asp680 (D, pink), and TFR2-Asp680Tyr (E, magenta). Residue names of TFR1/2 appear in white, while residues in TF are in black. Significant interactions are shown with dashed lines.

 

Hernández, G.; Ferrer-Cortès, X.; Venturi, V.; Musri, M.; Pilquil, M.F.; Torres, P.M.M.; Rodríguez, I.H.; Mínguez, M.À.R.; Kelleher, N.J.; Pelucchi, S.; Piperno, A.; Alberca, E.P.; Ricós, G.G.; Giró, E.C.; Pérez-Montero, S.; Tornador, C.; Villà-Freixa, J.; Sánchez, M. New Mutations in HFE2 and TFR2 Genes Causing Non HFE-Related Hereditary Hemochromatosis. Genes 2021, 12, 1980. https://doi.org/10.3390/genes12121980

A new period for the CBBL

Posted by 21 de December de 2014

The computational biochemistry and biophysics laboratory was created at the UPF in 2003 and remained there until May 2012, when I moved to the UVic-UCC. After a couple of years of strong managerial work that diverted the main research efforts of the lab, it is now rebuilding with evolved lines of research within the framework of the Bioinformatics and Medical Statistics Research Group. To make the story short, the CBBL devotes more and more to collaborative work with experimentalists, and a number of projects dealing with computational structural biology are being undertaken by the lab members. See the publications page for more details.

On the other hand, the interest of the lab to develop its own tools when needed is more than alive, and the combination between methodological development and applied research is the driving force of our members.

Doctorats industrials, la triple hèlix en acció (#DoctoratsIndustrials)

Posted by 8 de June de 2014

Diari ARA, 08/06/2014

La recerca bàsica, malgrat el sotrac de la crisi, ha experimentat al nostre país un avenç sense precedents en els darrers 15 anys, i ens ha situat com a pol d’atracció de talent reconegut internacionalment. En paral·lel, el teixit industrial català surt fortament tocat d’aquesta crisi, però per la seva capacitat de resistència i regeneració comença a donar signes de recuperació. Sortosament, són cada cop més els exemples de la integració de l’R+D+I al disseny i execució de processos productius, però encara som lluny d’exemples exitosos d’altres regions. Per obtenir les sinergies necessàries en aquest procés de reflotament, és imprescindible, doncs, un major diàleg entre els mons de la universitat i l’empresa.

És en aquest context que la Generalitat de Catalunya va llançar el 2012 una proposta engrescadora per incorporar talent a les empreses allà on han de reforçar el seu creixement. El Govern va identificar que la transferència de coneixement havia de donar pas a la concurrència d’interessos entre ambdós mons, i és en els recursos humans on aquesta col·laboració universitat-empresa s’accentua.

D’aquest esforç sorgeix el programa de doctorats industrials, en el qual la UVic-UCC té una participació molt activa. De la bona entesa en la triple hèlix empresa-administració-universitat n’estan sorgint propostes que impulsen nova riquesa basada en el coneixement i la seva aplicació que, sens dubte, ens ajudaran a superar aquests moments de depressió econòmica i anímica.

#CienciaSMW

Posted by 21 de February de 2014

Jordi Villà-Freixa, invited speaker at the event on “Internet i les eines de social media en la comunicació de la ciència”, during the 2014 Social Media Week at the Centre de Cultura Contemporània de Barcelona (CCCB).

In recent years the Internet and social networks have rapidly become part of many aspects of our daily lives. Facebook, Twitter, Google+, YouTube… make it easier to stay in touch with family and friends, join conversations of interest online and have access to more audiovisual material than there are hours in the day to watch’ l! Its ability to quickly spread and amplify content and to do so in an informal environment means that the Internet and social networks have become powerful tools to use in a professional context and also to attract and involve people in different causes.

The Web is today the great platform for researching scientific information, both specialized and dissemination. However, most scientists are yet to use these platforms to communicate their research. In this sense, science communicators can also make great use of it, beyond the online portals of the media where they work or the blogs where they publish their articles. It is in recent years that Facebook and Twitter have begun to be used as tools for the promotion and dissemination of their work or scientific information of general interest.

How to communicate science to society through the Internet and which ways to use to take advantage of the full potential of the Web remains a field that needs to be explored and exploited with more knowledge and tools.

This is why the Secretariat of Universities and Research of the Generalitat de Catalunya has organized a conference  as part of Social Media Week Barcelona (#SMWBCN). Coinciding with the commemoration of the three hundredth anniversary of the events of 1714, this day is included in the Tricentenary programme. The commemoration, launched by the Generalitat de Catalunya under the slogan “Érem.Som.Serem”, wants to transcend the historical perspective and is presented as an opportunity to share spaces for reflection and dialogue that allow us to jointly rethink a future project.

The conference brought together experts from companies such as Google, Yahoo and the BBC as well as working scientists, journalists specializing in science, university and research center communications managers to discuss the following issues:

  • How can you create attractive, potentially viral content on the Internet?
  • What are the formats with the most possibilities for disseminating science on the Web? it is everything invented on the internet or is there still room for innovation? What are the future trends?
  • What possibilities do Twitter, Facebook, YouTube… offer to communicate science? How can you get the most out of it to build a name on the Internet?
  • How can a platform like Facebook help create and position a brand a Internet? How can it benefit a research center to disseminate its work and obtain funding for future projects?

PROGRAM


SMWBCN2014.key

Participació en la conferència sobre ‘cloud’ i ciència, organitzada per Mind the Byte

Posted by 13 de June de 2013

Mind the Byte ha organitzat la primera Scientific Cloud Anual Conference (SciCloud) a Barcelona. La conferència SciCloud, que es farà anualment, reunirà experts de diferents àrees de serveis al núvol i la ciència per descobrir i intercanviar idees i avenços en aquest camp.

L’ús de tècniques computacionals és clau per optimitzar i accelerar els projectes d’R+D+I, especialment, el desenvolupament de fàrmacs. Sovint, però, suposa una forta inversió i manteniment que no són assumibles per a pimes i grups de recerca. El núvol com a infraestructura i el SaaS (Software as a Service) com a solució de programari de pagament per ús ajuden a racionalitzar aquestes tècniques computacionals a les necessitats de cada moment sense haver de comprar servidors ni infraestructura TI.

La sessió inaugural va anar a càrrec de la Dra. Montserrat Vendrell, directora general de Biocat, i el Dr. Jesús Purroy, director Científic del Parc Científic de Barcelona (PCB). També hi han participat com a ponents el Dr. Jordi Villà-Freixa, director de l’Escola Politècnica de la Universitat de Vic; Hakan Gurel, Solution architect d’Amazon Web Services; el Dr. Alfons Nonell-Canals, director general de Mind the Byte, i Oscar Huertas, director de Tecnologia de SOM Biotech.

Més informació a la web de Biocat.

New model for CFTR

Posted by 5 de July de 2012

The CBBL has completed part of the work of a three years long project on translational bioinformatics in cystic fibrosis (Activa). Our main role in the project was the determination of a model structure for CFTR, the chloride channel whose mutations are in the basis of the disease, as well as being a target for acute watery diarrhea drugs.

The new model, built in collaboration with Nir Ben-Tal’s lab at Tel Aviv University, proposes an open conformation of the channel, oposite to previous models, paving the way for the development of new drugs for both activation and blocking of the channel.

Janusz Bujnicki at the PRBB

Posted by 13 de March de 2012

Next Monday March 19 we will host the visit of Dr. Janusz Bujnicki , from the Laboratory of Bioinformatics and Protein Engineering at the International Institute of Molecular and Cell Biology, Warsaw, Poland.
The conference is included in the PRBB/CRG series of conferences and is open to everybody in the PRBB interested in the subject. It will be at 12:00 in the seminar room Marie Curie on the ground floor.

Seminar Title: “New methods for Structural Bioinformatics of RNA and RNPs”
Host: Jordi Villà i Freixa, Research Group on Biomedical Informatics ( GRIB) IMIM-UPF

X Barril – UB – Structure-based drug design: Towards accurate predictions of thermodynamic and kinetic parameters

Posted by 28 de February de 2012

Xavier Barril is visiting the PRBB this friday to give a seminar on the title topic.

Here it comes a short abstract of the talk:

The combination of increased availability of structural information, major boosts in computational power and methodological developments is
taking structure-based drug discovery to a higher level. I will present the main research lines of the group, focussing on the development of a new type of docking scoring functions and the elucidation of structure-kinetics relationships. Together with new experimental methods, these type of tools will enable the discovery of drugs with more diverse and effective mechanisms of action.