A scattering study of concentrated lens protein solutions and mixtures - Towards understanding the molecular origin of presbyopia

Healthy eye lenses are transparent and flexible, able to adapt shape in order to focus on far away and close-by objects. With age, however, this flexibility is lost, leading to a condition known as presbyopia. This vision disorder where close-by objects appear blurred commonly starts around the age of 40. The aim of this thesis is to elucidate the molecular origin of the gradual hardening of the core of the eye lens, made of fibre cells filled with concentrated mixtures of proteins, the so-called crystallins, which leads to the formation of presbyopia. To this end, various scattering techniques, static and dynamic light scattering (SLS & DLS), small-angle X-ray scattering (SAXS) and neutron spin echo (NSE), are used to study solutions of crystallins at concentrations up to those present in the lens. The first part of this work deals with solutions of the individual proteins. We show that different techniques allow us to access solution dynamics on different length scales. While DLS probes the collective dynamics, NSE accesses length scales corresponding to the average distance between nearest neighbors in the solution. We find that the dynamic behavior of protein solutions depends on the nature of the protein interactions, as well as on their patchiness. For the largest of the lens proteins, α-crystallin, well described by a model of polydisperse (20%) colloidal hard spheres, we find a slowing down of the local dynamics over a large range of volume fraction

Molecular architecture of the Jumonji C family histone demethylase KDM5B

Abstract The full length human histone 3 lysine 4 demethylase KDM5B (PLU-1/Jarid1B) has been studied using Hydrogen/Deuterium exchange mass spectrometry, homology modelling, sequence analysis, small angle X-ray scattering and electron microscopy. This first structure on an intact multi-domain Jumonji histone demethylase reveal that the so-called PLU region, in the central region of KDM5B, has a curved α-helical three-dimensional structure, that acts as a rigid linker between the catalytic core and a region comprising four α-helices, a loop comprising the PHD2 domain, two large intrinsically disordered loops and the PHD3 domain in close proximity. The dumbbell shaped and curved KDM5B architecture observed by electron microscopy is complementary to the nucleosome surface and has a striking overall similarity to that of the functionally related KDM1A/CoREST complex. This could suggest that there are similarities between the demethylation mechanisms employed by the two histone 3 lysine 4 demethylases at the molecular level

Evidence-based approach to thrombophilia testing

Thrombophilia can be identified in about half of all patients presenting with VTE. Testing has increased tremendously for various indications, but whether the results of such tests help in the clinical management of patients has not been settled. I use evidence from observational studies to conclude that testing for hereditary thrombophilia generally does not alter the clinical management of patients with VTE, with occasional exceptions for women at fertile age. Because testing for thrombophilia only serves limited purpose this should not be performed on a routine basis

Cluster-Driven dynamical arrest in concentrated lysozyme solutions

We present a detailed experimental and numerical study of the structural and dynamical properties of salt-free lysozyme solutions. In particular, by combining small-angle X-ray scattering (SAXS) data with neutron spin echo (NSE) and rheology experiments, we are able to identify that an arrest transition takes place at intermediate densities, driven by the slowing down of the cluster motion. Using an effective pair potential among proteins, based on the combination of short-range attraction and long-range repulsion, we account remarkably well for the peculiar volume fraction dependence of the effective structure factor measured by SAXS. We show that a transition from a monomer to a cluster-dominated fluid happens at volume fractions larger than ϕ ***Missing image substitution*** 0.05 where the close agreement between NSE measurements and Brownian dynamics simulations confirms the transient nature of the clusters. Clusters even stay transient above the geometric percolation found in simulation at ϕ > 0.15, though NSE reveals a cluster lifetime that becomes increasingly large and indicates a divergence of the diffusivity at ϕ ≃ 0.26. Macroscopic measurements of the viscosity confirm this transition where the long-lived-nature of the clusters is at the origin of the simultaneous dynamical arrest at all length scales

Unusual Dynamics of Concentration Fluctuations in Solutions of Weakly Attractive Globular Proteins

The globular protein γB-crystallin exhibits a complex phase behavior, where liquid–liquid phase separation characterized by a critical volume fraction ϕc = 0.154 and a critical temperature Tc = 291.8 K coexists with dynamical arrest on all length scales at volume fractions around ϕ ≈ 0.3–0.35, and an arrest line that extends well into the unstable region below the spinodal. However, although the static properties such as the osmotic compressibility and the static correlation length are in quantitative agreement with predictions for binary liquid mixtures, this is not the case for the dynamics of concentration fluctuations described by the dynamic structure factor S(q,t). Using a combination of dynamic light scattering and neutron spin echo measurements, we demonstrate that the competition between critical slowing down and dynamical arrest results in a much more complex wave vector dependence of S(q,t) than previously anticipated