ORCID Profile
0000-0002-9738-8472
Current Organisations
Vall d'Hebron Institute for Research (VHIR)
,
University of Limoges
,
CNRS
,
Instituciò Catalana de Recerca i Estudis Avancats
,
Universitat Internacional de Catalunya - Campus Sant Cugat
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Publications
Comparative study of radiation defect dynamics in 3C-SiC by X-ray diffraction, Raman scattering, and ion channeling
Publisher: Springer Science and Business Media LLC
Date: 15-12-2018
Linear response theory: An alternative to PB and GB methods for the analysis of molecular dynamics trajectories?
Publisher: Wiley
Date: 22-07-2004
DOI: 10.1002/PROT.20169
Abstract: We explore the use of classical Linear Response Theory (LRT) as an alternative strategy to the use of Molecular Mechanics/Poisson-Boltzmann strategies to compute the solvation free energy of macromolecules from molecular dynamics simulations using an explicit representation of solvent. The method reproduces well the free energy of solvation of standard amino acid side chains, small peptides, and proteins. The use of a fully discrete representation of solvent avoids the possible problems of continuum models to represent the solvation of systems containing tightly bound water molecules.
Cerebrospinal fluid-derived circulating tumour DNA better represents the genomic alterations of brain tumours than plasma
Publisher: Springer Science and Business Media LLC
Date: 10-11-2015
DOI: 10.1038/NCOMMS9839
Abstract: Cell-free circulating tumour DNA (ctDNA) in plasma has been shown to be informative of the genomic alterations present in tumours and has been used to monitor tumour progression and response to treatments. However, patients with brain tumours do not present with or present with low amounts of ctDNA in plasma precluding the genomic characterization of brain cancer through plasma ctDNA. Here we show that ctDNA derived from central nervous system tumours is more abundantly present in the cerebrospinal fluid (CSF) than in plasma. Massively parallel sequencing of CSF ctDNA more comprehensively characterizes the genomic alterations of brain tumours than plasma, allowing the identification of actionable brain tumour somatic mutations. We show that CSF ctDNA levels longitudinally fluctuate in time and follow the changes in brain tumour burden providing biomarkers to monitor brain malignancies. Moreover, CSF ctDNA is shown to facilitate and complement the diagnosis of leptomeningeal carcinomatosis.
A fast method for the determination of fractional contributions to solvation in proteins
Publisher: Wiley
Date: 11-2006
DOI: 10.1110/PS.062406706
An Atomistic View to the Gas Phase Proteome
Publisher: Elsevier BV
Date: 2009
DOI: 10.1016/J.STR.2008.11.006
Abstract: Extended all-atom molecular dynamics simulations on all protein metafolds have been performed to obtain a complete picture of the gas phase proteome. The structural atlas of the gas phase proteome obtained here shows an unexpected maintenance of the global and local structure and of the general deformability pattern upon transfer to the gas phase under electrospray conditions. Despite a general compression, the solution structure can be easily very well recognized from the gas phase one, and most structural details, such as secondary structure, are well preserved upon vaporization. Rehydration of the gas phase protein leads in most cases to a very fast transition from gas phase to solution structure. Overall, our massive analysis (over 4 micros in solution and over 12 micros in the gas phase) demonstrates that solution-like structures can be determined by using mass spectroscopy and related techniques to obtain fast approximations to the solution structure.
The amorphization of 3C-SiC irradiated at moderately elevated temperatures as revealed by X-ray diffraction
Publisher: Elsevier BV
Date: 11-2017
Characterization of the impact of alternative splicing on protein dynamics: The cases of glutathione S‐transferase and ectodysplasin‐A isoforms
Publisher: Wiley
Date: 18-06-2012
DOI: 10.1002/PROT.24112
Abstract: Recent studies have shown how alternative splicing (AS), the process by which eukaryotic genes express more than one product, affects protein sequence and structure. However, little information is available on the impact of AS on protein dynamics, a property fundamental for protein function. In this work, we have addressed this issue using molecular dynamics simulations of the isoforms of two model proteins: glutathione S-transferase and ectodysplasin-A. We have found that AS does not have a noticeable impact on global or local structure fluctuations. We have also found that, quite interestingly, AS has a significant effect on the coupling between key structural elements such as surface cavities. Our results provide the first atom-level view of the impact of AS on protein dynamics, as far as we know. They can contribute to refine our present view of the relationship between AS and protein disorder and, more importantly, they reveal how AS may modify structural dynamic couplings in proteins.
Histone H3.3 beyond cancer: Germline mutations in Histone 3 Family 3A and 3B cause a previously unidentified neurodegenerative disorder in 46 patients
Publisher: American Association for the Advancement of Science (AAAS)
Date: 04-12-2020
Abstract: Germ line mutations in H3F3A and H3F3B cause a previously unidentified neurodevelopmental syndrome.
Elucidating the molecular basis of MSH2‐deficient tumors by combined germline and somatic analysis
Publisher: Wiley
Date: 03-07-2017
DOI: 10.1002/IJC.30820
Abstract: In a proportion of patients presenting mismatch repair (MMR)-deficient tumors, no germline MMR mutations are identified, the so-called Lynch-like syndrome (LLS). Recently, MMR-deficient tumors have been associated with germline mutations in POLE and MUTYH or double somatic MMR events. Our aim was to elucidate the molecular basis of MSH2-deficient LS-suspected cases using a comprehensive analysis of colorectal cancer (CRC)-associated genes at germline and somatic level. Fifty-eight probands harboring MSH2-deficient tumors were included. Germline mutational analysis of MSH2 (including EPCAM deletions) and MSH6 was performed. Pathogenicity of MSH2 variants was assessed by RNA analysis and multifactorial likelihood calculations. MSH2 cDNA and methylation of MSH2 and MSH6 promoters were studied. Matched blood and tumor DNA were analyzed using a customized next generation sequencing panel. Thirty-five in iduals were carriers of pathogenic or probably pathogenic variants in MSH2 and EPCAM. Five patients harbored 4 different MSH2 variants of unknown significance (VUS) and one had 2 novel MSH6 promoter VUS. Pathogenicity assessment allowed the reclassification of the 4 MSH2 VUS and 6 probably pathogenic variants as pathogenic mutations, enabling a total of 40 LS diagnostics. Predicted pathogenic germline variants in BUB1, SETD2, FAN1 and MUTYH were identified in 5 cases. Three patients had double somatic hits in MSH2 or MSH6, and another 2 had somatic alterations in other MMR genes and/or proofreading polymerases. In conclusion, our comprehensive strategy combining germline and somatic mutational status of CRC-associated genes by means of a subexome panel allows the elucidation of up to 86% of MSH2-deficient suspected LS tumors.
Partition of protein solvation into group contributions from molecular dynamics simulations
Publisher: Wiley
Date: 29-10-2004
DOI: 10.1002/PROT.20292
Abstract: Linear response theory coupled to molecular dynamics simulations with an explicit solvent representation is used to derive fractional contributions of amino acid residues to the solvation of proteins. The new fractional methods developed here are compared with standard approaches based on empirical 1D and 3D statistical potentials, as well as with estimates obtained from the analysis of classical molecular interaction potentials. The new fractional methods, which have a clear physical basis and explicitly account for the effects due to protein structure and flexibility, provide an accurate picture of the contribution to solvation of different regions of the protein.
Molecular Dynamics Study of Naturally Existing Cavity Couplings in Proteins
Publisher: Public Library of Science (PLoS)
Date: 27-03-2015
Related Organisations
École Nationale Supérieure De Céramique Industrielle
Location: France
Universitat Internacional De Catalunya - Campus Sant Cugat
Location: Spain
Related Funding Activities
No related grants have been discovered for Fco. Xavier De la Cruz Montserrat.