Propensity to form amyloid fibrils is encoded as excitations in the free energy landscape of monomeric proteins

Protein aggregation, linked to many of diseases, is initiated when monomers access rogue conformations that are poised to form amyloid fibrils. We show, using simulations of src SH3 domain, that mechanical force enhances the population of the aggregation prone ($N^*$) states, which are rarely populated under force free native conditions, but are encoded in the spectrum of native fluctuations. The folding phase diagrams of SH3 as a function of denaturant concentration ($[C]$), mechanical force ($f$), and temperature exhibit an apparent two-state behavior, without revealing the presence of the elusive $N^*$ states. Interestingly, the phase boundaries separating the folded and unfolded states at all [C] and $f$ fall on a master curve, which can can be quantitatively described using an analogy to superconductors in a magnetic field. The free energy profiles as a function of the molecular extension ($R$), which are accessible in pulling experiments, ($R$), reveal the presence of a native-like $N^*$ with a disordered solvent-exposed amino terminal $\beta$-strand. The structure of the $N^*$ state is identical to that found in Fyn SH3 by NMR dispersion experiments. We show that the time scale for fibril formation can be estimated from the population of the $N^*$ state, determined by the free energy gap separating the native structure and the $N^*$ state, a finding that can be used to assess fibril forming tendencies of proteins. The structures of the $N^*$ state are used to show that oligomer formation and likely route to fibrils occur by a domain-swap mechanism in SH3 domain.Comment: 12 pages, 8 figures, 9 supplementary figures (on 5 more pages), 2 supplementary movies (on youtube

Probing the Origins of Increased Activity of the E22Q “Dutch” Mutant Alzheimer's β-Amyloid Peptide

AbstractThe amyloid peptide congener Aβ(10–35)-NH2 is simulated in an aqueous environment in both the wild type (WT) and E22Q “Dutch” mutant forms. The origin of the noted increase in deposition activity resulting from the Dutch mutation is investigated. Multiple nanosecond time scale molecular dynamics trajectories were performed and analyzed using a variety of measures of the peptide's average structure, hydration, conformational fluctuations, and dynamics. The results of the study support the conclusions that 1) the E22Q mutant and WT peptide are both stable in “collapsed coil” conformations consistent with the WT structure of Zhang et al. (2000, J. Struct. Biol. 130:130–141); 2) the E22Q peptide is more flexible in solution, supporting early claims that its equilibrium structural fluctuations are larger than those of the WT peptide; and 3) the local E22Q mutation leads to a change in the first solvation layer in the region of the peptide's “hydrophobic patch,” resulting in a more hydrophobic solvation of the mutant peptide. The simulation results support the view that the noted increase in activity due to the Dutch mutation results from an enhancement of the desolvation process that is an essential step in the aggregation of the peptide

Integration of In-Flight and Post-Flight Water Monitoring Resources in Addressing the U.S. Water Processor Assembly Total Organic Carbon (TOC) Anomaly

Beginning in June of 2010, the total organic carbon (TOC) concentration in the U.S. Water Processor Assembly (WPA) product water started to increase. A surprisingly consistent upward TOC trend was observed through weekly ISS total organic carbon analyzer (TOCA) monitoring. As TOC is a general organic compound indicator, return of water archive samples was needed to make better-informed crew health decisions on the specific compounds of concern and to aid in WPA troubleshooting. TOCA-measured TOC was more than halfway to the health-based screening limit of 3,000 g/L before archive samples were returned. Archive samples were returned on 22 Soyuz in September 2010 and on ULF5 in November of 2010. The samples were subjected to extensive analysis. Although TOC was confirmed to be elevated, somewhat surprisingly, none of the typical target compounds were detected at high levels. After some solid detective work, it was confirmed that the TOC was associated with a compound known as dimethylsilanediol (DMSD). DMSD is believed to be a breakdown product of siloxanes which are thought to be ubiquitous in the ISS atmosphere. A toxicological limit was set for DMSD and a forward plan was developed for conducting operations in the context of understanding the composition of the TOC measured in flight. This required careful consideration of existing ISS flight rules, coordination with ISS stakeholders, and development of a novel approach for the blending of inflight TOCA data with archive results to protect crew health. Among other challenges, team members had to determine how to utilize TOCA readings when making decisions about crew consumption of WPA water. This involved balancing very real concerns associated with the assumption that TOC would continue to be comprised of only DMSD. Demonstrated teamwork, multidisciplinary awareness, and innovative problem-solving were required to respond effectively to this anomaly