Biology and Life Sciences | Annual Report 2008

Biology and Life Sciences


Action mechanisms in flavoenzymes: a MD study Leader: Milagros Medina Leader institution: Unversidad de Zaragoza Abstract The goal is to increase the knowledge of the parameters that maintain reactions involving flavoproteins, in particular those participating in electron transfer processes. Mechanism of interaction and electron transfer... Activation of glycoside hydrolases by specific carbohydrate-protein interactions Leader: Carme Rovira Leader institution: Parc Científic de Barcelona Abstract Understanding the mechanisms of substrate preactivation in glycoside hydrolases (GHs) is key for the design of new substrates and inhibitors. During the last decade there has been increasing evidence that several... Adaptation of a computer package for multi-scale simulations and its application to molecular and biomolecular actuators Leader: Carlos Alemán Llansó Leader institution: Universitat Politècnica de Catalunya Abstract In this project the group aims to prepare and demonstrate the methodology with all the necessary software components to simulate a micro-actuator made of a dye able to induce... Aligned profiles with multiples environments and methods: Selection of the best parameters Leader: Dr. Baldo Oliva Miguel Leader institution: Universitat Pompeu Fabra Abstract The comparison of multiple sequences might provide clues about the structure and function of a protein family. Sequence-profile or profile-profile alignment is important not only for protein annotation but also for... An efficient conformational sampling method for Homology Modelling Leader: Antonio Morreale Leader institution: centro de biologia molecular severo ochoa Abstract The structural refinement of protein models is a very challenging problem in protein structure prediction. Most attempts to refine comparative models lead to degradation rather than improvement in model... Analysis of large three-dimensional electron microscopy data sets by computationally intensive algorithms Leader: Sjors H.W. Scheres Leader institution: Centro Nacional de Biotecnologia - CSIC Abstract This activity is a joint collaboration between five experimentally oriented electron microscopy groups. These groups study a range of large macromolecular complexes that play distinct vital functions in... Assessment of Supercomputing Facilities for genomic data Leader: Sarah Hunter Leader institution: European Bioinformatics Institute Abstract Provide pilot technical and budgetary information on feasibility of utilising European Supercomputing Facilities to address tasks such as the InterProScan indexing task. Results obtained This was a feasibility study... Caracterización del metaboloma peroxisomal y origen evolutivo (continuación) Leader: Aurora Pujol Leader institution: IRO Abstract The peroxisome is a dynamic cell component that plays a key role in several metabolic routes, notably the oxidation of fatty acids and oxidative stress. These routes begin or end somewhere else in the cell, notably in mitochondria and ER... Characterization of the conformational free-energy landscape of the SH2 tandem from ZAP-70 Leader: José D. Faraldo-Gómez Leader institution: Max Planck Institute for Biophysics Abstract A wide range of cellular processes – including immunity, transcription and apoptosis – rely on the propagation of chemical signals from the cell surface into the interior. Multi-... Coarse grained molecular simulations of Triose Phospate Isomerase enzyme using NAMD Leader: Jordi Villa i Freixa Leader institution: University Pompeu Fabra Abstract The activity included the use of coarse grain techniques for the simulation of biochemical systems. This includes the study of the loop dynamics in nitrotirosinated triosephosphate isomerase and the study of the... Combining Protein Docking Methods with Experimental Small-Angle X-ray Scattering Data Leader: Pau Bernadó Leader institution: Institut de Recerca Biomèdica Abstract The association of two proteins leading to discrete complexes is essential in multitude of biological processes. The network of all protein-protein interactions occurring in a living being defines a new... Computational Modelling of Matrix Metalloproteinases: The full-length MMP-2 enzyme Leader: Natalia Díaz Fernández Leader institution: Universidad de Oviedo Abstract This activity is framed into a long-term research project devoted to the study of both the matrix metalloproteinase enzymes (MMPs) and their most relevant substrates, the collagen molecules. Although... Computational Study Of The Molecular Basis Of Allosteric Mechanisms And Its Conservation Amongst Species Leader: Francisco Javier de la Cruz Montserrat Leader institution: Institut de Recerca Biomèdica (IRB) Abstract Allosterism is a regulatory mechanism by which the structure of a protein's functional site is modified following the binding of a molecule to, or mutation of a residue in, a... De-novo protein folding and structure prediction with free-energy forcefields Leader: Wolfgang Wenzel Leader institution: Research Center Karlsruhe Abstract Protein structure prediction and the elucidation of the protein folding process remain important grand computational challenges with many application in the life-sciences. In recent years the group developed models and... Detecting evolutionary novelties generated by frameshift translation in several genomes Leader: Arcadi Navarro i Cuartiellas Leader institution: ICREA and Departament de Ciències Experimentals i de la Salut. Universitat Pompeu Fabra Abstract The project aims at exploring genetic novelties creation via frame-shift translation, in other words, detecting the apparition of a new... Determination of native ensembles for proteins using ensemble restrained simulations Leader: Xavier Salvatella Leader institution: Institut de Recerca Biomedica Abstract A description of the relationship between the structure and the function of proteins is not complete without a thorough understanding of protein dynamics. Methods are available for the characterization of the... Effect of selective mutations in Pre-A region on the NO detoxification activity of truncated hemoglobin HbN Leader: F J Luque Leader institution: Univ. Barcelona Abstract Nitric oxide is a signalling and defence molecule of major importance, but the basis of resistance to NO and reactive nitrogen species is poorly understood in many microbes. In the case of M. tuberculosis, it appears to be associated... Evolutionary algorithms and de novo peptide design Leader: Ernest Giralt Leader institution: Institut de Recerca Biomèdica Abstract The research group designed a software application that is able to design peptides that bind to user-specified protein targets. The software, known as ENPDA (Evolutionary de Novo Peptide Design Algorithm), uses... Exploring enzyme promiscuity of IPL: bi-dimensional QM/MM free energy surfaces Leader: Vicent Moliner Leader institution: Universitat Jaume I Abstract Isochorismate Pyruvate Lyase (IPL) catalyzes isochorismate transformation into pyruvate and salicylate but it also presents secondary activity catalyzing the transformation of chorismate into prephenate. This feature is called... Exploring the specificity of the relationship between cortical network function and biological simulation parameters with a particle swarm optimization algorithm Leader: Albert Compte Braquets Leader institution: Institut d Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) Abstract Traditionally, computational neuroscience approaches to generating computer implementations of neural circuits that perform specific brain functions, such as vision... Exploring the topology space for gene regulatory networks Leader: James Sharpe Leader institution: Center for Genomic Regulation Abstract Systems biology approaches have helped us to understand a number of specific biological processes. Due to the advent of more powerful computers, we now believe systems biology can go much further. By mapping out the... Genomic Distribution of Ancestral Natural Selection in Human Introns Leader: Arcadi Navarro i Cuartiellas Leader institution: ICREA and Departament de Ciències Experimentals i de la Salut. Universitat Pompeu Fabra. C/ Dr. Aiguader, 80. 08003, Barcelona Abstract Increasing evidence about the action of natural selection at the genomic scale has highlighted the... Ligand migration in truncated hemoglobin O from M. tuberculosis Leader: F J Luque Leader institution: Univ. Barcelona Abstract Nitric oxide is a signalling and defence molecule of major importance, but the basis of resistance to NO and reactive nitrogen species is poorly understood in many microbes. In the case of M. tuberculosis, it appears to be associated... Maximum-likelihood refinement of electron microscopy data Leader: Jose Maria Carazo Leader institution: Centro Nacional de Biotecnologia - CSIC Abstract This proposal is a continuation of ongoing work on maximum-likelihood classification of structurally heterogeneous cryo-electron microscopy data sets. The co-existence of macromolecular complexes in... Modelling the Thermal Stability of a Triple Helical Peptide Leader: Natalia Díaz Fernández Leader institution: Universidad de Oviedo Abstract Collagen is probably the most abundant protein in vertebrates. Its molecular hallmarks are the multiple repetitions of Gly-X-Y sequences and the unique triple helical structure. As a first step towards... Molecular Dynamics Simulation of Self-assembling Cyclopeptide Nanotubes Leader: Juan R. Granja Guillán Leader institution: Universidad de Santiago de Compostela Abstract Self-assembling peptide nanotubes (SPNs) made from ALPHA,GAMMA cyclic peptide nanotubes, consisting of alternating (1R,3S)-3-aminocyclohexane-or cyclopentane- carboxylic acid (GAMMA-Ach/Acp-OH)... Molecular Dynamics Simulation of the Folding/Unfolding Mechanism of Apoflavodoxin Leader: Francisco Javier de la Cruz Montserrat Leader institution: Molecular Modeling & Bioinformatics Unit (Parc Científic de Barcelona) Abstract This project aims to investigate the folding/unfolding mechanism of the 169 residue apoflavodoxin, an excellent model for proteins displaying... Molecular modeling of enzyme-substrate interactions and reaction mechanisms in carbohydrate-bound enzymes and aldo-keto reductases Leader: Carme Rovira Leader institution: Parc Científic de Barcelona Abstract The project aims to decipher the mechanisms of substrate specificity in aldo-keto reductases (AKRs), glycoside hydrolases (GHs), and glycosyl transferases (GTs) by means of ab initio QM/MM simulations. Aldo-keto... NO scavenging properties of truncated hemoglobin N from M. smegmatis Leader: F J Luque Leader institution: Univ. Barcelona Abstract Nitric oxide is a signalling and defence molecule of major importance, but the basis of resistance to NO and reactive nitrogen species is poorly understood in many microbes. In the case of M. tuberculosis, it appears to be associated... Optimization and Applications of MDmix, a druggability index based on first principles. Leader: Xavier Barril Alonso Leader institution: ICREA & Universitat de Barcelona Abstract Advances in molecular biology, genomics, proteomics and systems biology offer the possibility to expand the number and quality of potential therapeutic targets. Unfortunately, many targets with a sound... Parameter estimation and optimal design in computational systems biology Leader: Jordi Villa i Freixa Leader institution: University Pompeu Fabra Abstract The development of the tool ByoDyn (http://cbbl.imim.es/Byodyn), devoted to parameter estimation and optimal experimental design in metabolomics and functional genomics, led to the participation of the Group in two... Prediction of conformational diseases from simulation Leader: Prof. Javier Sancho Sanz Leader institution: Department of Biochemistry and Molecular and Cellular Biology, Sciences Faculty, University of Zaragoza Abstract Familial hypercholesterolemia is a conformational disease linked to mutations in the gene encoding the low-density lipoprotein... RAS superfamily and the interactions with their effectors: functional specificity Leader: Gloria Fuentes Leader institution: CNIO Abstract Ras genes code for small GTPases that act as GDP/GTP-regulated molecular switches involved in many biological pathways. Conformational changes allow them to interact with regulators and effectors. Structural techniques have partly unraveled... Rigid chiral dendronized systems based on proline with a thermally stable right-handed helical conformation Leader: Carlos Alemán Llansó Leader institution: Universitat Politècnica de Catalunya Abstract A tridimensional molecular model for a polydendronized system based on proline will be developed using atomistic molecular dynamics simulations. The suitability of the model will be... Rigid Polyelectrolytes Formed by Chiral Dendronized Polymers Based on Proline Leader: Carlos Enrique Alemán Llansó Leader institution: Universitat Politècnica de Catalunya Abstract A tridimensional molecular model for a positively charged polydendronized system based on substituted prolines will be developed using atomistic molecular dynamics... Simulation of peptide folding induced by inorganic materials (II) Leader: Piero Ugliengo Leader institution: University of Torino Abstract The interaction of biological systems with inorganic materials is a fascinating field with implications, for instance, in bionanotechnology, biomaterials, biodevices and proteomics. Recently, de novo peptide design-based works... Study of domain-induced membrane curvature by means of MD Leader: Manuel Palacín Prieto Leader institution: Universidad de Barcelona y Institute of Research in Biomedicine (Parc Científic de Barcelona) Abstract Heteromeric Amino acid Transporters (HATs) are composed of two subunits: a polytopic membrane protein, (the light subunit) and a... Synthetic residues in tumor treatment experiments Leader: Carlos Enrique Alemán Llansó Leader institution: Universitat Politècnica de Catalunya Abstract Non-proteogenic amino acids will be used to develop synthetic analogues of tumor-homing peptides containing 10 or more residues. Specifically, the aim is to increase the... The 3D code of DNA: understanding apparition of curvature from atomic detail to gene scale Leader: Agnes Noy Freixa Leader institution: IRB-BSC/University of Sheffield Abstract Recent experimental studies have suggested flexibility is crucial in gene regulation, thus, the idea that DNA genetic information might also be encoded through its 3D shape has appeared. Because DNA is a very long... Unraveling the reaction and drug activation mechanisms in catalase-peroxidases by means of QM/MM Car-Parrinello simulations Leader: Carme Rovira Leader institution: Parc Científic de Barcelona Abstract Catalase-peroxidases (KatGs) are bifunctional enzymes that are responsible for the activation of isoniazid as an anti-tubercular drug in Mycobacterium tuberculosis. Both the catalytic mechanism of the enzyme and... Use of TBLASTX to find regions of homology among multiple large-size full genomes Leader: Roderic Guigó Leader institution: Centro de Regulación Genética Abstract At the Genome Informatics laboratory (genome.crg.es), part of the "Centro de Regulació Genómica" (CRG) in Barcelona, the MareNostrum (MN) is used to run the... VSDMIP: Virtual Screening Data Management on an Integrated Platform Leader: Antonio Morreale Leader institution: Centro de Biologia Molecular Severo Ochoa Abstract The use of computer-based techniques to aid in the discovery of new drug candidates is a commonly employed strategy today. In this context, virtual screening is an emerging technology that tries to find...

Action mechanisms in flavoenzymes: a MD study

Leader: Milagros Medina Leader institution: Unversidad de Zaragoza Abstract The goal is to increase the knowledge of the parameters that maintain reactions involving flavoproteins, in particular those participating in electron transfer processes. Mechanism of interaction and electron transfer...

Activation of glycoside hydrolases by specific carbohydrate-protein interactions

Leader: Carme Rovira Leader institution: Parc Científic de Barcelona Abstract Understanding the mechanisms of substrate preactivation in glycoside hydrolases (GHs) is key for the design of new substrates and inhibitors. During the last decade there has been increasing evidence that several...

Adaptation of a computer package for multi-scale simulations and its application to molecular and biomolecular actuators

Leader: Carlos Alemán Llansó Leader institution: Universitat Politècnica de Catalunya Abstract In this project the group aims to prepare and demonstrate the methodology with all the necessary software components to simulate a micro-actuator made of a dye able to induce...

Aligned profiles with multiples environments and methods: Selection of the best parameters

Leader: Dr. Baldo Oliva Miguel Leader institution: Universitat Pompeu Fabra Abstract The comparison of multiple sequences might provide clues about the structure and function of a protein family. Sequence-profile or profile-profile alignment is important not only for protein annotation but also for...

An efficient conformational sampling method for Homology Modelling

Leader: Antonio Morreale Leader institution: centro de biologia molecular severo ochoa Abstract The structural refinement of protein models is a very challenging problem in protein structure prediction. Most attempts to refine comparative models lead to degradation rather than improvement in model...

Analysis of large three-dimensional electron microscopy data sets by computationally intensive algorithms

Leader: Sjors H.W. Scheres Leader institution: Centro Nacional de Biotecnologia - CSIC Abstract This activity is a joint collaboration between five experimentally oriented electron microscopy groups. These groups study a range of large macromolecular complexes that play distinct vital functions in...

Assessment of Supercomputing Facilities for genomic data

Leader: Sarah Hunter Leader institution: European Bioinformatics Institute Abstract Provide pilot technical and budgetary information on feasibility of utilising European Supercomputing Facilities to address tasks such as the InterProScan indexing task. Results obtained This was a feasibility study...

Caracterización del metaboloma peroxisomal y origen evolutivo (continuación)

Leader: Aurora Pujol Leader institution: IRO Abstract The peroxisome is a dynamic cell component that plays a key role in several metabolic routes, notably the oxidation of fatty acids and oxidative stress. These routes begin or end somewhere else in the cell, notably in mitochondria and ER...

Characterization of the conformational free-energy landscape of the SH2 tandem from ZAP-70

Leader: José D. Faraldo-Gómez Leader institution: Max Planck Institute for Biophysics Abstract A wide range of cellular processes – including immunity, transcription and apoptosis – rely on the propagation of chemical signals from the cell surface into the interior. Multi-...

Coarse grained molecular simulations of Triose Phospate Isomerase enzyme using NAMD

Leader: Jordi Villa i Freixa Leader institution: University Pompeu Fabra Abstract The activity included the use of coarse grain techniques for the simulation of biochemical systems. This includes the study of the loop dynamics in nitrotirosinated triosephosphate isomerase and the study of the...

Combining Protein Docking Methods with Experimental Small-Angle X-ray Scattering Data

Leader: Pau Bernadó Leader institution: Institut de Recerca Biomèdica Abstract The association of two proteins leading to discrete complexes is essential in multitude of biological processes. The network of all protein-protein interactions occurring in a living being defines a new...

Computational Modelling of Matrix Metalloproteinases: The full-length MMP-2 enzyme

Leader: Natalia Díaz Fernández Leader institution: Universidad de Oviedo Abstract This activity is framed into a long-term research project devoted to the study of both the matrix metalloproteinase enzymes (MMPs) and their most relevant substrates, the collagen molecules. Although...

Computational Study Of The Molecular Basis Of Allosteric Mechanisms And Its Conservation Amongst Species

Leader: Francisco Javier de la Cruz Montserrat Leader institution: Institut de Recerca Biomèdica (IRB) Abstract Allosterism is a regulatory mechanism by which the structure of a protein's functional site is modified following the binding of a molecule to, or mutation of a residue in, a...

De-novo protein folding and structure prediction with free-energy forcefields

Leader: Wolfgang Wenzel Leader institution: Research Center Karlsruhe Abstract Protein structure prediction and the elucidation of the protein folding process remain important grand computational challenges with many application in the life-sciences. In recent years the group developed models and...

Detecting evolutionary novelties generated by frameshift translation in several genomes

Leader: Arcadi Navarro i Cuartiellas Leader institution: ICREA and Departament de Ciències Experimentals i de la Salut. Universitat Pompeu Fabra Abstract The project aims at exploring genetic novelties creation via frame-shift translation, in other words, detecting the apparition of a new...

Determination of native ensembles for proteins using ensemble restrained simulations

Leader: Xavier Salvatella Leader institution: Institut de Recerca Biomedica Abstract A description of the relationship between the structure and the function of proteins is not complete without a thorough understanding of protein dynamics. Methods are available for the characterization of the...

Effect of selective mutations in Pre-A region on the NO detoxification activity of truncated hemoglobin HbN

Leader: F J Luque Leader institution: Univ. Barcelona Abstract Nitric oxide is a signalling and defence molecule of major importance, but the basis of resistance to NO and reactive nitrogen species is poorly understood in many microbes. In the case of M. tuberculosis, it appears to be associated...

Evolutionary algorithms and de novo peptide design

Leader: Ernest Giralt Leader institution: Institut de Recerca Biomèdica Abstract The research group designed a software application that is able to design peptides that bind to user-specified protein targets. The software, known as ENPDA (Evolutionary de Novo Peptide Design Algorithm), uses...

Exploring enzyme promiscuity of IPL: bi-dimensional QM/MM free energy surfaces

Leader: Vicent Moliner Leader institution: Universitat Jaume I Abstract Isochorismate Pyruvate Lyase (IPL) catalyzes isochorismate transformation into pyruvate and salicylate but it also presents secondary activity catalyzing the transformation of chorismate into prephenate. This feature is called...

Exploring the specificity of the relationship between cortical network function and biological simulation parameters with a particle swarm optimization algorithm

Leader: Albert Compte Braquets Leader institution: Institut d Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) Abstract Traditionally, computational neuroscience approaches to generating computer implementations of neural circuits that perform specific brain functions, such as vision...

Exploring the topology space for gene regulatory networks

Leader: James Sharpe Leader institution: Center for Genomic Regulation Abstract Systems biology approaches have helped us to understand a number of specific biological processes. Due to the advent of more powerful computers, we now believe systems biology can go much further. By mapping out the...

Genomic Distribution of Ancestral Natural Selection in Human Introns

Leader: Arcadi Navarro i Cuartiellas Leader institution: ICREA and Departament de Ciències Experimentals i de la Salut. Universitat Pompeu Fabra. C/ Dr. Aiguader, 80. 08003, Barcelona Abstract Increasing evidence about the action of natural selection at the genomic scale has highlighted the...

Ligand migration in truncated hemoglobin O from M. tuberculosis

Maximum-likelihood refinement of electron microscopy data

Leader: Jose Maria Carazo Leader institution: Centro Nacional de Biotecnologia - CSIC Abstract This proposal is a continuation of ongoing work on maximum-likelihood classification of structurally heterogeneous cryo-electron microscopy data sets. The co-existence of macromolecular complexes in...

Modelling the Thermal Stability of a Triple Helical Peptide

Leader: Natalia Díaz Fernández Leader institution: Universidad de Oviedo Abstract Collagen is probably the most abundant protein in vertebrates. Its molecular hallmarks are the multiple repetitions of Gly-X-Y sequences and the unique triple helical structure. As a first step towards...

Molecular Dynamics Simulation of Self-assembling Cyclopeptide Nanotubes

Leader: Juan R. Granja Guillán Leader institution: Universidad de Santiago de Compostela Abstract Self-assembling peptide nanotubes (SPNs) made from ALPHA,GAMMA cyclic peptide nanotubes, consisting of alternating (1R,3S)-3-aminocyclohexane-or cyclopentane- carboxylic acid (GAMMA-Ach/Acp-OH)...

Molecular Dynamics Simulation of the Folding/Unfolding Mechanism of Apoflavodoxin

Leader: Francisco Javier de la Cruz Montserrat Leader institution: Molecular Modeling & Bioinformatics Unit (Parc Científic de Barcelona) Abstract This project aims to investigate the folding/unfolding mechanism of the 169 residue apoflavodoxin, an excellent model for proteins displaying...

Molecular modeling of enzyme-substrate interactions and reaction mechanisms in carbohydrate-bound enzymes and aldo-keto reductases

Leader: Carme Rovira Leader institution: Parc Científic de Barcelona Abstract The project aims to decipher the mechanisms of substrate specificity in aldo-keto reductases (AKRs), glycoside hydrolases (GHs), and glycosyl transferases (GTs) by means of ab initio QM/MM simulations. Aldo-keto...

NO scavenging properties of truncated hemoglobin N from M. smegmatis

Optimization and Applications of MDmix, a druggability index based on first principles.

Leader: Xavier Barril Alonso Leader institution: ICREA & Universitat de Barcelona Abstract Advances in molecular biology, genomics, proteomics and systems biology offer the possibility to expand the number and quality of potential therapeutic targets. Unfortunately, many targets with a sound...

Parameter estimation and optimal design in computational systems biology

Leader: Jordi Villa i Freixa Leader institution: University Pompeu Fabra Abstract The development of the tool ByoDyn (http://cbbl.imim.es/Byodyn), devoted to parameter estimation and optimal experimental design in metabolomics and functional genomics, led to the participation of the Group in two...

Prediction of conformational diseases from simulation

Leader: Prof. Javier Sancho Sanz Leader institution: Department of Biochemistry and Molecular and Cellular Biology, Sciences Faculty, University of Zaragoza Abstract Familial hypercholesterolemia is a conformational disease linked to mutations in the gene encoding the low-density lipoprotein...

RAS superfamily and the interactions with their effectors: functional specificity

Leader: Gloria Fuentes Leader institution: CNIO Abstract Ras genes code for small GTPases that act as GDP/GTP-regulated molecular switches involved in many biological pathways. Conformational changes allow them to interact with regulators and effectors. Structural techniques have partly unraveled...

Rigid chiral dendronized systems based on proline with a thermally stable right-handed helical conformation

Leader: Carlos Alemán Llansó Leader institution: Universitat Politècnica de Catalunya Abstract A tridimensional molecular model for a polydendronized system based on proline will be developed using atomistic molecular dynamics simulations. The suitability of the model will be...

Rigid Polyelectrolytes Formed by Chiral Dendronized Polymers Based on Proline

Leader: Carlos Enrique Alemán Llansó Leader institution: Universitat Politècnica de Catalunya Abstract A tridimensional molecular model for a positively charged polydendronized system based on substituted prolines will be developed using atomistic molecular dynamics...

Simulation of peptide folding induced by inorganic materials (II)

Leader: Piero Ugliengo Leader institution: University of Torino Abstract The interaction of biological systems with inorganic materials is a fascinating field with implications, for instance, in bionanotechnology, biomaterials, biodevices and proteomics. Recently, de novo peptide design-based works...

Study of domain-induced membrane curvature by means of MD

Leader: Manuel Palacín Prieto Leader institution: Universidad de Barcelona y Institute of Research in Biomedicine (Parc Científic de Barcelona) Abstract Heteromeric Amino acid Transporters (HATs) are composed of two subunits: a polytopic membrane protein, (the light subunit) and a...

Synthetic residues in tumor treatment experiments

Leader: Carlos Enrique Alemán Llansó Leader institution: Universitat Politècnica de Catalunya Abstract Non-proteogenic amino acids will be used to develop synthetic analogues of tumor-homing peptides containing 10 or more residues. Specifically, the aim is to increase the...

The 3D code of DNA: understanding apparition of curvature from atomic detail to gene scale

Leader: Agnes Noy Freixa Leader institution: IRB-BSC/University of Sheffield Abstract Recent experimental studies have suggested flexibility is crucial in gene regulation, thus, the idea that DNA genetic information might also be encoded through its 3D shape has appeared. Because DNA is a very long...

Unraveling the reaction and drug activation mechanisms in catalase-peroxidases by means of QM/MM Car-Parrinello simulations

Leader: Carme Rovira Leader institution: Parc Científic de Barcelona Abstract Catalase-peroxidases (KatGs) are bifunctional enzymes that are responsible for the activation of isoniazid as an anti-tubercular drug in Mycobacterium tuberculosis. Both the catalytic mechanism of the enzyme and...

Use of TBLASTX to find regions of homology among multiple large-size full genomes

Leader: Roderic Guigó Leader institution: Centro de Regulación Genética Abstract At the Genome Informatics laboratory (genome.crg.es), part of the "Centro de Regulació Genómica" (CRG) in Barcelona, the MareNostrum (MN) is used to run the...

VSDMIP: Virtual Screening Data Management on an Integrated Platform

Leader: Antonio Morreale Leader institution: Centro de Biologia Molecular Severo Ochoa Abstract The use of computer-based techniques to aid in the discovery of new drug candidates is a commonly employed strategy today. In this context, virtual screening is an emerging technology that tries to find...