(626g) Modeling the Structure and Transition Kinetics of Small, Aggregation-Prone Proteins: Identifying Key Atomic Interactions Via Efficient Simulation Methods

In this work, several schemes were developed and used to increase the simulation efficiency of two proteins associated with human diseases, and give insights on their structure and the kinetics and mechanism of conformational transitions. Our studies focus on the recognition of particular structural markers that may lead to protein misfolding and aggregation. Two systems are studied, one where the main challenge is to characterize the varied structural motifs in a relatively floppy protein (amyloid β-42), and the other where distinct conformers exist and the main challenge is to elucidate the transition mechanism (insulin chain B).

Concerning structural identification, the conformational behavior of the wild-type amyloid β-42 (Aβ-42) monomer and two of its mutants was explored by a novel technique based on the replica exchange method, to identify structural features that may promote or deter early-stage oligomerization in water. The markers used for this purpose indicate that while the three peptides are relatively flexible they have distinct preferential structures and degree of rigidity. In particular, we found that one mutant that remains in the monomeric state in experiments displays a characteristic N-terminal structure that significantly enhances its rigidity. This finding is consistent with various studies that have detected a reduction in oligomerization frequency and Aβ-related toxicity upon sequence-specific antibody or ligand binding to the N-terminal tail of wild-type monomers, likely leading to the stabilization of this region. In general, our results highlight a potential role of the N-terminal segment on Aβ oligomerization and give insights into specific interactions that may be responsible for promoting the pronounced structural changes observed upon introducing point mutations on the wild-type Aβ-42 peptide. (Velez-Vega & Escobedo, J. Phys. Chem. B 2011, Early View)

Regarding kinetic and mechanistic characterization, an optimized Forward Flux Sampling Method is applied to the study of the unfolding transitions for insulin chain B monomer in explicit solvent at physiological conditions. Specifically, the simulations provide valuable insights on the biological relevance of key structural changes in the peptide’s N-terminal, for insulin’s dissociation and binding mechanisms.