Optimizing a coarse-grained model for the recognition of protein-protein binding

We are optimizing a force-field to be used with our coarsegrained protein model for the recognition of protein -protein binding. We have found that, apart from ranking correctly the ligand-receptor conformations generated in a protein-protein docking algorithm, our model is able to distinguish binding (experimental structure) from nonbinding (false positive) conformations for many complexes. This suggests us that the model could have a good performance in complete cross-docking, a method aimed to recognize the possible binding between any two proteins that are unknown to interact.Peer Reviewe

Optimizing a coarse-grained model for the recognition of protein-protein binding

We are optimizing a force-field to be used with our coarsegrained protein model for the recognition of protein -protein binding. We have found that, apart from ranking correctly the ligand-receptor conformations generated in a protein-protein docking algorithm, our model is able to distinguish binding (experimental structure) from nonbinding (false positive) conformations for many complexes. This suggests us that the model could have a good performance in complete cross-docking, a method aimed to recognize the possible binding between any two proteins that are unknown to interact.Peer Reviewe

The Impact of theoretical chemistry on biology

Els avenços en les bases dels mètodes teòrics i l'espectacular desenvolupament de la potència de càlcul han fet possible progressar enormement en el somni dels fundadors de la química, és a dir, ser capaços d'estudiar amb mètodes computacionals el conjunt de processos químics. Actualment, la química teòrica està completant el darrer avenç: intentar esdevenir l'eina més recent per a comprendre la naturalesa química dels éssers vius. Aquesta revisió pretén mostrar com els mètodes de la química teòrica, originalment desenvolupats per a examinar molècules petites en fase gas, han evolucionat per a assolir la complexa descripció de sistemes biològics.Recent advances in theoretical formalism together with the dramatic development of computer infrastructure have allowed enormous progress in achieving the dream of the founders of chemistry: to submit the majority of chemical phenomena to calculation. Currently, theoretical chemistry is working towards reaching the next step: to become the ultimate tool to understand the chemical nature of living organisms. This review summarizes how techniques originally developed to represent small molecules in the gas phase have evolved such that they are able to describe the complex behaviors of biological systems

Challenges of docking in large, flexible and promiscuous binding sites

After decades of work, the correct determination of the binding mode of a small molecule into a target protein is still a challenging problem, whose difficulty depends on: (i) the sizes of the binding site and the ligand; (ii) the flexibility of both interacting partners, and (iii) the differential solvation of bound and unbound partners. We have evaluated the performance of standard rigid(receptor)/flexible(ligand) docking approaches with respect to last-generation fully flexible docking methods to obtain reasonable poses in a very challenging case: soluble Epoxide Hydrolase (sEH), a flexible protein showing different binding sites. We found that full description of the flexibility of both protein and ligand and accurate description of solvation leads to significant improvement in the ability of docking to reproduce well known binding modes, and at the same time capture the intrinsic binding promiscuity of the protein.Peer ReviewedPostprint (author's final draft

Understanding the Connetion between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations

Cytosine methylation is one of the most important epigenetic marks that regulate the process of gene expression. Here, we have examined the effect of epigenetic DNA methylation on nucleosomal stability using molecular dynamics simulations and elastic deformation models. We found that methylation of CpG steps destabilizes nucleosomes, especially when these are placed in sites where the DNA minor groove faces the histone core. The larger stiffness of methylated CpG steps is a crucial factor behind the decrease in nucleosome stability. Methylation changes the positioning and phasing of the nucleosomal DNA, altering the accessibility of DNA to regulatory proteins, and accordingly gene functionality. Our theoretical calculations highlight a simple physical-based explanation on the foundations of epigenetic signaling

Protein disorder-to-order transition enhances the nucleosome-binding affinity of H1.

Intrinsically disordered proteins are crucial elements of chromatin heterogenous organization. While disorder in the histone tails enables a large variation of inter-nucleosome arrangements, disorder within the chromatin-binding proteins facilitates promiscuous binding to a wide range of different molecular targets, consistent with structural heterogeneity. Among the partially disordered chromatin-binding proteins, the H1 linker histone influences a myriad of chromatin characteristics including compaction, nucleosome spacing, transcription regulation, and the recruitment of other chromatin regulating proteins. Although it is now established that the long C-terminal domain (CTD) of H1 remains disordered upon nucleosome binding and that such disorder favours chromatin fluidity, the structural behaviour and thereby the role/function of the N-terminal domain (NTD) within chromatin is yet unresolved. On the basis of microsecond-long parallel-tempering metadynamics and temperature-replica exchange atomistic molecular dynamics simulations of different H1 NTD subtypes, we demonstrate that the NTD is completely unstructured in solution but undergoes an important disorder-to-order transition upon nucleosome binding: it forms a helix that enhances its DNA binding ability. Further, we show that the helical propensity of the H1 NTD is subtype-dependent and correlates with the experimentally observed binding affinity of H1 subtypes, suggesting an important functional implication of this disorder-to-order transition

An In-Depth Look at DNA Crystals through the Prism of Molecular Dynamics Simulations

X-ray crystallography is the primary tool for biomolecular structural determination. However, contacts formed through the crystal lattice are known to affect structures, especially for small and flexible molecules such as DNA oligomers, by introducing significant structural changes in comparison to solution. Furthermore, why molecules crystallize in certain symmetry groups, which role crystallization additives play, and whether they are just innocuous and unspecific crystallization catalysts remain unclear. By using one of the currently best-performing DNA force fields and applying significant computational effort, we described the nature of intermolecular forces that stabilize B-DNA crystals in various symmetry groups and solvent environments with an unprecedented level of detail. We showed a tight coupling between the lattice stability and the type of crystallization additives and that certain symmetry groups are stable only in the presence of a specific additive. Additives and crystal contacts induce small but non-negligible changes in the physical properties of DNA

Alternative Splicing of Transcription Factors' Genes: Beyond the Increase of Proteome Diversity

Functional modification of transcription regulators may lead to developmental changes and phenotypical differences between species. In this work, we study the influence of alternative splicing on transcription factors in human and mouse. Our results show that the impact of alternative splicing on transcription factors is similar in both species, meaning that the ways to increase variability should also be similar. However, when looking at the expression patterns of transcription factors, we observe that they tend to diverge regardless of the role of alternative splicing. Finally, we hypothesise that transcription regulation of alternatively spliced transcription factors could play an important role in the phenotypical differences between species, without discarding other phenomena or functional families

Correlated motions in DNA. Beyond base-pair step models of DNA flexibility.

Traditional mesoscopic models of DNA flexibility use a reductionist-local approach, which assumes that the flexibility of DNA can be expressed as local harmonic movements (at the base-pair step level) in the helical space, ignoring multimodality and correlations in DNA movements, which have in reality a large impact in modulating DNA movements. We present a new multimodal-harmonic correlated model, which takes both contributions into account, providing, with a small computational cost, results of an unprecedented local and global quality. The accuracy of this method and its computational efficiency make it an alternative to explore the dynamics of long segments of DNA, approaching the chromatin range