The Prediction of NMR spin relaxation by Molecular dynamics: Dynamics is essential to proteins to perform interactions with biological partners. Among the vast landscape of biophysical methods, NMR possesses this exquisite potential to sample motions at different frequency through the measurement of various relaxation parameters. The interpretation of relaxation data is commonly subjected to the choice of a suitable model, like the model free approach for instance. We are seeking to develop an approach based on molecular dynamics to predict all the available NMR spin relaxation. See references related to the use of quaternion to predict the rotational diffusion tensor, the prediction of R1, R2 and NOEs and the use of polarisable force fields.
Elucidating the bacterial silver resistance mechanism: Silver antimicrobial properties have been used for thousands of years, from the Chaldeans as early as 4000 B.C.E. Despite this long-standing history and its demonstrated activity against Gram-negative bacteria, the complete bactericidal mode of action of silver remains unclear. To counteract the toxic effect of silver, Gram-negative bacteria have developed different resistance mechanisms, including the efficient transport of the metal out of the cell promoted by an efflux pump.
SilE is an interesting target to understand the silver resistance since this protein is only produced during bacterial growth in the presence of silver ions. Our research proposes to understand how SilE may transfer silver out of the cell by potentially interacting with possible protein partners like SilB, SilS or SilF. To reach our goal, we combine biophysical methods, namely Nuclear Magnetic Resonance (NMR) and Small Angle X-ray Scattering (SAXS) with hybrid molecular dynamics and in-vivo assays. See references related to the structural characterisation of SilE mimicking peptides, their interaction with silver and the interplay between SilB and SilE.
Host-parasite interactions – understanding immune evasion of parasitic worms: Parasitic trematodes of the genus Schistosoma are digenean with a complex life cycle, involving 2 free living stages and 2 hosts, a mollusk as intermediate and a mammal definitive one. Each life stage is adapted to its environment and modulates it in turn. We are interested in the macromolecules excreted and secreted by the stages infecting humans to understand their role in immune system modulation. In particular we focus on two families of highly variable proteins: Micro-exons genes (MEGs) and Venom antigen-like proteins (VALs). Both families have no enzymatic activities, are differently expressed during the lifetime and are particularly rich in Cys. On top of being transcribed by several genes, alternative splicing increases the variability and the number of isoforms per each gene product. We are producing in heterologous systems candidates of both families and characterising their structure by means of macromolecular crystallography (MX), SAXS, NMR and also their interactions with circulating host partners and receptors by means of molecular-scale biophysics (DLS, SPR, fluorescence spectroscopy). Moreover, given their abundance in blood circulation, VALs have been validated as biomarkers and are going to be exploited in a point-of-care (POC) diagnostic test, following the WHO NTD-Roadmap 2030.