Laboratoire de Biochimie Théorique
Présentation
The Laboratory of Theoretical Biochemistry (LBT) is one of five laboratories within Institut de Biologie Physico-Chimique (IBPC) in Paris.
LBT belongs to the French national research agency CNRS through its Institute of Chemistry, and is associated with Paris Diderot University. The laboratory was created at IBPC in 1958 as Laboratoire de Biochimie Théorique. Our field is theoretical and computational biochemistry, at the interface between biology, chemistry, physics, and computing.
Our strategic objectives are twofold: invent simulation algorithms to reproduce and predict physical properties of biomolecules either in vitro or in the cell, and understand the molecular or conformational factors responsible for the biological functions of living systems, and diseases. The equilibrium between these two aspects is the key point of the laboratory policy.
LBT is organized as a team of independent researchers with complementary interests and domains of expertise, both in method development and in biophysical, biochemical, and biomedical applications. Advances in each of these domains emerge from the association of different sets of researchers around individual projects.
Thèmes de recherche
Les axes de recherches du LBT se concentrent sur les développements méthodologiques et algorithmiques pour l’étude de la structure, la dynamique, la mécanique et les interactions des macromolécules biologiques.
Les objectifs sont donc d'utiliser les ordinateurs pour ouvrir des fenêtres vers le monde moléculaire, en aidant à comprendre les facteurs qui sous-tendent des faits expérimentaux, et en prédisant les propriétés et le comportement des molécules biologiques.
Equipes de recherche
Directeur : Marc Baaden
[hal-04750660] Ludopédagogie et débriefing
Date: 23 10 月 2024 - 18:51
Desc: Après avoir fait joué à un jeu de piste en ligne, l'objectif était d'apporter aux participants de cette conférence un regard réflexif sur la manière d'orchestrer une séance ludopédagogique et notamment la partie débriefing.
[hal-04245445] Accounting for loop flexibility during protein–protein docking
Date: 17 10 月 2023 - 10:58
Desc: Abstract Although reliable docking can now be achieved for systems that do not undergo important induced conformational change upon association, the presence of flexible surface loops, which must adapt to the steric and electrostatic properties of a partner, generally presents a major obstacle. We report here the first docking method that allows large loop movements during a systematic exploration of the possible arrangements of the two partners in terms of position and rotation. Our strategy consists in taking into account an ensemble of possible loop conformations by a multi‐copy representation within a reduced protein model. The docking process starts from regularly distributed positions and orientations of the ligand around the whole receptor. Each starting configuration is submitted to energy minimization during which the best‐fitting loop conformation is selected based on the mean‐field theory. Trials were carried out on proteins with significant differences in the main‐chain conformation of the binding loop between isolated form and complexed form, which were docked to their partner considered in their bound form. The method is able to predict complexes very close to the crystal complex both in terms of relative position of the two partners and of the geometry of the flexible loop. We also show that introducing loop flexibility on the isolated protein form during systematic docking largely improves the predictions of relative position of the partners in comparison with rigid‐body docking. Proteins 2006. © 2005 Wiley‐Liss, Inc.
[hal-01497986] Homologous Pairing between Long DNA Double Helices
Date: 29 Mar 2017 - 17:03
Desc: Molecular recognition between two double stranded (ds) DNA with homologous sequences may not seem compatible with the B-DNA structure because the sequence information is hidden when it is used for joining the two strands. Nevertheless, it has to be invoked to account for various biological data. Using quantum chemistry, molecular mechanics, and hints from recent genetics experiments, I show here that direct recognition between homologous dsDNA is possible through the formation of short quadruplexes due to direct complementary hydrogen bonding of major-groove surfaces in parallel alignment. The constraints imposed by the predicted structures of the recognition units determine the mechanism of complexation between long dsDNA. This mechanism and concomitant predictions agree with the available experimental data and shed light upon the sequence effects and the possible involvement of topoisomerase II in the recognition.
[hal-01498063] Moving through the gate in ATP-activated P2X receptors
Date: 29 Mar 2017 - 17:04
Desc: no abstract
[hal-02127512] Highlights from the Faraday Discussion on Artificial Water Channels, Glasgow, UK
Date: 7 2 月 2023 - 14:35
Desc: An abstract was not provided in the original work, so a preliminary abstract has been prepared as follows. The Faraday Discussion on Artificial Water Channels brought together experts from various fields related to water transport, including biological porins, artificial water channels, carbon nanotubes and graphene-based materials, and membranes for desalination and water treatment. During the discussion, the structure and function of natural proteins for water transport were discussed, as well as the formation of supramolecular tetrameric structures and structure-activity relationships in artificial water channels. The discussion also covered the modeling and enhancement of water hydrodynamics, and the application of artificial water channels to water transport systems, including reverse osmosis membranes integrated with aquaporins. The conference also featured poster presentations and social events for networking and discussion.
Autres contacts
Institut de Biologie Physico-Chimique (IBPC)
13, rue Pierre et Marie Curie
75252 PARIS CEDEX 05