Exploring the Effect of Mutations on the Conformational Landscape of Amyloidogenic Antibody Fragments

Abstract

Antibodies are composed of heavy chains and light chains. In Light Chain Amyloidosis (AL), antibody-secreting cells export only the light chains. These light chains are prone to misfold, forming amyloid fibers, which get deposited in various organs, leading to organ disfunction and patient death. The transition from the native state to the amyloid fiber requires partial or total denaturation. The structures of monomeric precursors to the oligomeric nuclei, or of those assembled at the ends of the fibers, are unknown. There is an inverse correlation between the stability of the native state and the speed of fiber formation, suggesting that lower stability allows the population of “excited states” of the native ensemble, some of which could be amyloid fiber precursors. Starting from the crystal structure of a variable light chain domain belonging to class 6a (one of the most common in clinical cases of AL), we generated point mutants that eliminate charges (R24G and D52A) or a proline (P7S). These mutants destabilize the native state, and speed up fiber formation (for R24G and P7S). We carried out MD simulations at three temperatures (298, 398 and 498K), to explore the effect of these mutations on the conformational landscape. We found many metastable unfolding intermediates, which have eluded experimental detection because their fluorescence is indistinguishable from that of the native state. A common early unfolding intermediate exposes strand D, which has a high potential for fiber formation according to ZipperDB. Those variants with a higher speed of fiber formation expose this area with greater frequency.We are thankful for computer resources at: Centro Nacional de Supercomputo, IPICyT; Kan Balam, UNAM; Sputnik, IBT-UNAM; Orion, FC and CIQ-UAEM.Funding: CONACYT 102182 and 133294.