Molecular pathology and therapeutic proteins

The aim is to understand at the molecular level the behavior of proteins and peptides involved in pathologies such as neurodegeneratives diseases (amyloid peptides, QR2 enzyme) or nosocomial diseases (rhomboid proteases, Escherichia coli porins).

Amyloid peptides

Collaborations: M. Waks(LIB), W. Urbach(LIB-ENS), S. Abel (CEA Saclay)

The elucidation of the mechanism by which proteins are converted into amyloid fibers, remains a major objective. The fact that many peptides and proteins, unrelated to known conditions, are capable of forming amyloid fibrils shows that the structural organization mode is an intrinsic property of the polypeptide chains. Various studies suggest that this process is reversible, thus opening the door to the process of disintegration. One example known is β-lactoglobulin (BLG), the major protein of the milk of mammals. One of the questions that the research does not address is the role of hydration in the formation and spread of amyloid aggregation, where the hydrophobic sequences of the proteins appear to play an important role. To elucidate this question, we examine the association of peptides that possess a part of the sequence of the BLG. These peptides are known to form fibers and amyloid aggregates. We examine molecular dynamics simulation aggregation of these peptides in water, and then we evaluate the changes induced by the presence of osmolytes such as sorbitol, trehalose and iboprufen.

Binding of QR2 enzyme to hydrophobic drugs

Involved people: M. Waks (LIB), W. Urbach (LIB-ENS), P. Fuchs (Institut Jacques Monod), Institut de Recherches Servier.

The enzyme quinone reductase II (QR2) seems to occupy a central role in some neurodegenerative diseases, and as such, represents a therapeutic target. We study the interaction of this enzyme with the active ingredients. We are particularly interested in the role of hydration in its constant association and related effects of this constant confinement. This study combines experimental measurements to molecular dynamics simulations.

Rhomboid proteases: a new therapeutic target for novel anti-microbial drugs

Involved people: H. Benabdelhak (LIB), W. Urbach (LIB-ENS).

Using a multidisciplinary and multi-scale approach, we study a new family of proteases called rhomboids at the molecular, cellular, and tissue intramembrane. Our motivation is based on the result showing that, in a mouse model, rhomboid protease of a pathogenic bacterium is involved in the virulence of the bacteria in vivo, probably by the intermediary of its involvement in the maturation of virulence factors. Our result opens a path hitherto unexplored, the study of the role of rhomboid proteases in the pathogenesis-related bacterial infections. Indeed these proteases catalyze the cleavage of integral membrane proteins, thus causing the transmission of a cellular signal. This reaction control various biological functions, including the regulation of epidermal growth factor (Drosophila melanogaster), the mitochondrial fusion (Saccharomyces cerevisiae), parasitic invasion (Plasmodium falciparum) and the generation of quorum-sensing * (Providencia stuartii opportunistic pathogenic bacterium). In prokaryotes, the role of this family of enzymes and their associated substrates are unknown, except AaRa, a rhomboid P. stuartii which activates a protein carrier (TATA) thereby releasing a signal molecule involved in the quorum. (*) The set of regulatory mechanisms that control the coordinated expression of some bacterial genes within the same population.

Ultrasonic stimulation of Escherichia coli

Involved people: H. Benabdelhak (LIB), W. Urbach (LIB-ENS)

The application of ultrasound increases the penetration of macromolecules across cellular membranes. It has thus been possible to increase the bactericidal activity of antibiotics on bacterial cultures planktonic or biofilm. The ultrasonic action the mechanism remains poorly understood. Notably, few studies have examined the effect of ultrasound on the solute transport through the modulation of the membrane channels. In this project we want to elucidate the mechanism of action of ultrasound on bacterial porins models, OmpF and OmpC, which in many Gram-negative bacteria, represent the main route of entry of common antibiotics such as β-lactams and some fluoroquinolones.