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Etude du repliement des protéines par RMN temps réel et autres méthodes biophysiques : l'exemple de la Beta-2-microglobuline

Abstract : Beta-2-microglobulin is a 12kDa protein, involved in a misfolding disease: dialysis related amyloidosis. It is therefore a model for amyloid fibril formation and protein folding studies. B2M is both a fruitful and difficult object of study. B2M production is complex, requiring optimization to obtain a well folded protein and reach yields suitable to NMR and SAXS studies. B2M folding is highly sensitive on buffer, temperature, concentration and often preparation conditions. Yet our studies, using several biophysical methods, revealed several essential facts of the folding mechanism and of the structure and dynamics of folding intermediates. A first outcome of our studies is that folding and oligomerization are co-existing processes. A major finding is the existence of a monomer-oligomer equilibrium between I1 and I2 folding intermediate states. Indirectly detected using real time NMR methods like SOFAST, I2 was directly detected and characterized using SAXS: I2 is likely to be a dimer. Folding intermediate states of B2M had been shown to favor fibril formation: this is easily explained by the existence of a dimeric folding intermediate state with an important population. A combination of biophysical methods allows the characterization of this monomer-oligomer equilibrium. Using SAXS, and later confirmed by NMR relaxation experiments, stoichiometry is shown to be a monomer-dimer equilibrium. Further work based on the methodology applied to the folding of the W60G-B2M mutant, including a further optimization of the sensitivity of the experiment, will give a sharper picture of the I1-I2 equilibrium for the WT protein, and may provide information on the timescale of the equilibrium. The thorough study of the folding of B2M pushes biophysical methods to their limits: sensitivity and acquisition time for NMR, polydispersity for SAXS. Yet in both cases a large oligomer (I3) that disappears within minutes was detected, and confirmed using UV-fluo. Characterization of I3 will demand further methodological developments, a new experimentation plan including a full dilution scale, or double jump experiments, for example. A question that arises is the comparison of this large oligomer and oligomeric intermediate states that are populated during the formation of fibrils. Other biophysical methods, such as ESI mass spectroscopy, may be an interesting input. Tackling the limits of biophysical methods leads to methodological developments. For example, to study the structure and dynamics of I1, the continuous data acquisition method allowed the assignment of this species that has a half-lifetime of tens of minutes. A conformational exchange was discovered for the I1 state of the W60G-B2M mutant, through the development of a spin relaxation measurement experiment: R2-BEST-TROSY. The methods developed for this study may be later used to study the folding and folding intermediate states of other proteins, such as alpha-lactalbumin , or in other contexts in which the short lifetime of the protein is an issue, as for in-cell NMR experiments. Our studies are of course far from an application or a concrete result in the fight against misfolding diseases such as dialysis related amyloidosis or Parkinson's. But the discovery of oligomeric folding intermediate states underlines that oligomerization (including fibril formation) and folding should not be studied separately, and are processes that are closely related. Methodological developments included in our work can be applied to other proteins as well as other contexts. Hopefully these questionings and developments will constitute a step forward a better understanding of this diseases.
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Thomas Cutuil. Etude du repliement des protéines par RMN temps réel et autres méthodes biophysiques : l'exemple de la Beta-2-microglobuline. Autre [cond-mat.other]. Université de Grenoble, 2012. Français. ⟨NNT : 2012GRENY097⟩. ⟨tel-00849137⟩

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