28 research outputs found
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
Discrete Molecular Dynamics Approach to the Study of Disordered and Aggregating Proteins
Discrete Molecular Dynamics Approach to the Study of Disordered and Aggregating Proteins
We present a refinement of the Coarse Grained PACSAB force field for Discrete Molecular Dynamics (DMD) simulations of proteins in aqueous conditions. As the original version, the refined method provides good representation of the structure and dynamics of folded proteins but provides much better representations of a variety of unfolded proteins, including some very large, impossible to analyze by atomistic simulation methods. The PACSAB/DMD method also reproduces accurately aggregation properties, providing good pictures of the structural ensembles of proteins showing a folded core and an intrinsically disordered region. The combination of accuracy and speed makes the method presented here a good alternative for the exploration of unstructured protein systems
Multipole modes and spin features in the Raman spectrum of nanoscopic quantum rings
We present a systematic study of ground state and spectroscopic properties of many-electron nanoscopic quantum rings. Addition energies at zero magnetic field (B) and electrochemical potentials as a function of B are given for a ring hosting up to 24 electrons. We find discontinuities in the excitation energies of multipole spin and charge density modes, and a coupling between the charge and spin density responses that allow to identify the formation of ferromagnetic ground states in narrow magnetic field regions. These effects can be observed in Raman experiments, and are related to the fractional Aharonov-Bohm oscillations of the energy and of the persistent current in the rin
Residues coevolution guides the systematic identification of alternative functional conformations in proteins
We present here a new approach for the systematic identification of functionally relevant conformations in proteins. Our fully automated pipeline, based on discrete molecular dynamics enriched with coevolutionary information, is able to capture alternative conformational states in 76% of the proteins studied, providing key atomic details for understanding their function and mechanism of action. We also demonstrate that, given its sampling speed, our method is well suited to explore structural transitions in a high-throughput manner, and can be used to determine functional conformational transitions at the entire proteome level
Accurate Description of Protein–Protein Recognition and Protein Aggregation with the Implicit-Solvent-Based PACSAB Protein Model
We used the PACSAB protein model, based on the implicit solvation approach, to simulate protein–protein recognition and study the effect of helical structure on the association of aggregating peptides. After optimization, the PACSAB force field was able to reproduce correctly both the correct binding interface in ubiquitin dimerization and the conformational ensemble of the disordered protein activator for hormone and retinoid receptor (ACTR). The PACSAB model allowed us to predict the native binding of ACTR with its binding partner, reproducing the refolding upon binding mechanism of the disordered protein
Discrete Molecular Dynamics Approach to the Study of Disordered and Aggregating Proteins
We present a refinement of the Coarse Grained PACSAB force field for Discrete Molecular Dynamics (DMD) simulations of proteins in aqueous conditions. As the original version, the refined method provides good representation of the structure and dynamics of folded proteins but provides much better representations of a variety of unfolded proteins, including some very large, impossible to analyze by atomistic simulation methods. The PACSAB/DMD method also reproduces accurately aggregation properties, providing good pictures of the structural ensembles of proteins showing a folded core and an intrinsically disordered region. The combination of accuracy and speed makes the method presented here a good alternative for the exploration of unstructured protein systems
Vertically coupled quantum dots in the local spin-density functional theory
We have investigated the structure of double quantum dots vertically coupled at zero magnetic field within local-spin-density functional theory. The dots are identical and have a finite width, and the whole system is axially symmetric. We first discuss the effect of thickness on the addition spectrum of one single dot. Next we describe the structure of coupled dots as a function of the interdot distance for different electron numbers. Addition spectra, Hund's rule, and molecular-type configurations are discussed. It is shown that self-interaction corrections to the density-functional results do not play a very important role in the calculated addition spectr