Société Française de Bioinformatique

Our team, as part of a research network consortium, has identified the presence of NOSs in few algae genomes, andd a complete and integrative study of the role of these NOS, and of NO, in the physiology of these algae. These NOSs display some similarities with mammal NOSs, especially in the oxidase domain (OX), but also diverge in some structural and maybe functional features, in the reductase domain (RED) and the connecting domains. RED is an essential domain of the redox chain mechanism operated by NOSs. This project aims at characterizing the structure of this domain in algae NOSs, and to predict its impact on their catalytic activity.

Goals

The study will mainly focus on the canonical reductase domain Flavodoxin-FNR (RED), without taking into account the connecting domains in N- and C-terminal edges of the full-length protein

A – Structural bioinformatic approach

• Genomic databases investigation : distribution of RED domains in NOSs family.
• Structural analysis and classification of RED domains : diversity, variability, classification in sub-families (to be proposed)
• Extension of the study to a selection of RED domains found in cytochromes P450 family, identified as being full-length P450 integrating RED+OX domains, or specific reductase partners of cytochrome P450 (CPR or CYPOR) : structural comparison between NOS-RED and CYP-RED
• Molecular phylogenetic study : comparison of phylogenetic trees of NOS-RED domains with knownphylogenies of NOSs and CYP-REDs.
• Classification, structural analysis and functional predictions on RED domains of algae NOSs.

B – Molecular modeling

• 3D homology modeling of protein sub-domains Flavodoxin and FNR, with possible templates available in PDB, in the few released crystal structures of these protein modules.
• 3D homology modeling of the full RED domains of selected algae NOSs, based on crystal structures of NOS or CYP reductase domains.
• Structural analysis of sequence variations (inserts ; gaps, mutations)
• Molecular dynamics studies of the rebuilt model for optimization, stabilization, and study of the molecular assembly and quaternary structure of the full-length enzyme: inter sub-domains interactions, interface mapping, dimerization, co-factor binding site.
• Simulation of the dynamics of the flavodoxin domain between FNR and OX domains (open/closed conformations, regulatory elements...)
• Hypotheses on the redox mechanism of RED domains and holoenzymes functioning (electron transfer inter- and intra-domains)

Management

The internship is open in the Oxidative Stress and Detoxification Lab (LSOD) in CEA-Saclay and will be conducted under the joint supervision of Drs François ANDRE and Jérôme SANTOLINI. The LSOD laboratory developed an established expertise on functional characterization and molecular modeling of NO-Synthases, and Activity-Structure Relationship studies on other hemoproteins such as CYPs.

The candidate should have a PhD. in bioinformatics or computational biology. We are looking for a strong and independent person, with excellent skills in Structural Bioinformatics, numerical simulations and homology modeling approaches. The candidate must be fluent in English and comfortable with Linux environment. Due to the transdisciplinary nature of the project, the candidate must possess strong communication skills and be ready to work in close collaboration with experimentalist partners.

Knowledge required to perform the duties:

• Practical knowledge in Structural Biology (especially protein structures)
• Some knowledge of genome annotation and molecular phylogeny
• General knowledge in Enzymology and Redox biology is appreciated.
• Relational sense, rigor, creativity, scientific writing ability.

Technical skills specific to the functions:

• Linux environment, scripting language for job submission on clusters
• Molecular Dynamics simulations with multi-domain proteins, and/or partially disordered connecting domains.
• Cofactors parametrization.
• Protein-protein interactions (interaction Oxygenase-Reductase)

The position is available from June 1st, 2021 and for a duration of one year.
If you have any questions about the position, please email the following contacts:

Francois.andre@i2bc.paris-saclay.fr Jerome.santolini@cea.fr