Exploration of the Conformational Landscape of an Amyloidogenic Ig Domain

Abstract

On their way from the denatured state to their native conformation, proteins can jump into aggregation funnels. This is the underlying cause of a large group of misfolding diseases, such as light chain amyloidosis. In this particular case, variable light chain immunoglobulin domains are expressed in excess, due to a B-cell dyscrasia, and form fibers that deposit primarily in the kidneys and heart. We explore the conformational dynamics of lambda 6 VL domains, both in native and in denaturing conditions, through extensive molecular dynamics simulations in explicit solvent. Denaturation pathways are characterized following the loss of native contacts for selected residues, and the increase in solvent accessibility for the most amyloid prone regions of the protein, as determined by ZipperDB. We have identified putative unfolding intermediates, which have lost many of the antiaggregation moieties of Ig domains, and could thus constitute seeds for fiber nuclei. Comparison of amyloidogenic versus non-amyloidogenic Ig domains reveals that the former have more regions with higher propensities for forming fibers, and these are located in more structurally labile zones of the folded protein. Furthermore, the structures generated in simulations at 398K of non-amyloidogenic proteins resemble those populated by amyloid prone variants, at room temperature. This is in line with the thermodynamic hypothesis, which states that unstable proteins are more likely to form amyloid fibers.Funded by CONACyT (102182). The simulations were carried out in Centro Nacional de Supercomputo (San Luis Potosi), Sputnik II (Instituto de Biotecnologia, UNAM), Orion (PROMEP-UAEM), and Entalpia (Facultad de Medicina, UNAM)