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Characterizing protein conformational flexibility by means of enhanced-sampling MD simulations

Mardi 24 novembre 2015 11:00 - Duree : 1 heure
Lieu : ILL 4, Seminar Room, 71 avenue des Martyrs - Grenoble

Orateur : Alessandro BARDUCCI (Multiscale Biomolecular Modeling, Centre de Biochimie Structurale CNRS, MONTPELLIER, France)

Proteins are by no means static entities and they often undergo large-amplitude transitions that are intrinsically coupled to their cellular functions. In the last years, the crucial role of structural flexibility in protein function was further confirmed by the realization that many proteins are actually devoid of a well-defined, three-dimensional structure in native conditions. While several experimental techniques can provide information about protein conformational dynamics, they often suffer from limited spatial and temporal resolution and mostly report ensemble-averaged quantities that cannot be straightforwardly translated into single-molecule, atomistic information. Molecular Dynamics (MD) simulations are a valuable tool for complementing experimental techniques since they can provide a detailed description of biomolecular structure and dynamics. Unfortunately, this approach has been historically hindered by the huge computational effort required to properly sample the complex biomolecular free-energy landscapes. Indeed, the timescales accessible to brute-force MD simulations on standard computational clusters (10-6 seconds) are still extremely limited with respect to those characteristic of relevant biomolecular phenomena. This limitation can be circumvented by adopting enhanced sampling schemes which can significantly accelerate the exploration of the conformational space, while allowing the reconstruction the correct equilibrium properties. Here I will provide a general introduction to the popular metadynamics algorithm and its more recent variants and I will show how this approach can be applied to investigate conformational flexibility in several systems such as disordered peptides, multi-domain proteins and small protein complexes.

Contact : gerelli@ill.fr

Discipline évènement : (Physique)
Entité organisatrice : (ILL)
Nature évènement : (Séminaire)
Evènement répétitif : (Joint Theory Group / PSCM seminar)
Site de l'évènement : Polygone scientifique

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