The protein frustratometer is an energy landscape theory-inspired algorithm that aims at localizing and quantifying the energetic frustration present in protein molecules. Frustration is a useful concept for analyzing proteins’ biological behavior. It compares the energy distributions of the native state with respect to structural decoys. The network of minimally frustrated interactions encompasses the folding core of the molecule. Sites of high local frustration often correlate with functional regions such as binding sites and regions involved in allosteric transitions. We present here an upgraded version of a webserver that measures local frustration. The new implementation that allows the inclusion of electrostatic energy terms, important to the interactions with nucleic acids, is significantly faster than the previous version enabling the analysis of large macromolecular complexes within a user-friendly interface. The webserver is freely available at URL: http://frustratometer.qb.fcen.uba.ar.

A predictive coarse-grained protein force field [associative memory, water-mediated, structure, and energy model for molecular dynamics (AWSEM)-MD] is used to study the energy landscapes and relative stabilities of amyloid-β protein in the monomer and all of its oligomeric forms up to an octamer. We find that an isolated monomer is mainly disordered with a short α-helix formed at the central hydrophobic core region (L17-D23). A less stable hairpin structure, however, becomes increasingly more stable in oligomers, where hydrogen bonds can form between neighboring monomers. We explore the structure and stability of both prefibrillar oligomers that consist of mainly antiparallel β-sheets and fibrillar oligomers with only parallel β-sheets. Prefibrillar oligomers are polymorphic but typically take on a cylindrin-like shape composed of mostly antiparallel β-strands. At the concentration of the simulation, the aggregation free energy landscape is nearly downhill. We use umbrella sampling along a structural progress coordinate for interconversion between prefibrillar and fibrillar forms to identify a conversion pathway between these forms. The fibrillar oligomer only becomes favored over its prefibrillar counterpart in the pentamer where an interconversion bottleneck appears. The structural characterization of the pathway along with statistical mechanical perturbation theory allow us to evaluate the effects of concentration on the free energy landscape of aggregation as well as the effects of the Dutch and Arctic mutations associated with early onset of Alzheimer's disease.misfolding | amyloid funnel | nucleation A lzheimer's disease is associated with the deposition of amyloid-β (Aβ) protein aggregates in the brain (1). Soluble Aβ oligomers, intermediates formed early in the aggregation process, can cause synaptic dysfunction, whereas the later-formed insoluble fibrils may function as reservoirs of the toxic oligomers (2). Owing to their stoichiometric complexity and transience, the early oligomeric forms are difficult to study in the laboratory. Nevertheless, distinct forms of oligomers, described as prefibrillar and fibrillar, have been found to bind differently to conformation-dependent antibodies (3): the fibrillar oligomers and mature fibrils both display a common epitope that is absent from the prefibrillar oligomers. The study of the secondary structure of Aβ species using Fourier transform infrared spectroscopy suggests that fibrillar forms of Aβ are organized in a parallel β-sheet conformation, much like in the complete fibril structure constructed from solid-state NMR data by Petkova et al. (4), whereas the prefibrillar oligomers contain mainly antiparallel β-sheets (5). Numerous computer simulation studies of both the monomer and higher aggregates using models ranging in complexity from fully atomistic simulations in solvent to lattice models have been undertaken to fill the knowledge gap (6-8). It remains, however, unclear what the exact tertiary arrangements of the β-sheets in the Aβ prefibrillar oligome...

Using a predictive coarse-grained protein force field, we compute and compare the free energy landscapes and relative stabilities of amyloid-β protein (1-42) and amyloid-β protein (1-40) in their monomeric and oligomeric forms up to the octamer. At the same concentration, the aggregation free energy profile of Aβ42 is more downhill, with a computed solubility that is about ten times smaller than that of Aβ40. At a concentration of 40 μM, the clear free energy barrier between the prefibrillar tetramer form and the fibrillar pentamer in the Aβ40 aggregation landscape disappears for Aβ42, suggesting that the Aβ42 tetramer has a more diverse structural range. To further compare the landcapes, we develop a cluster analysis based on the structural similarity between configurations and use it to construct an oligomerization map that captures the paths of easy interconversion between different but structurally similar states of oligomers for both species. A taxonomy of the oligomer species based on β-sheet stacking topologies is proposed. The comparison of the two oligomerization maps highlights several key differences in the landscapes that can be attributed to the two additional C-terminal residues that Aβ40 lacks. In general, the two terminal residues strongly stabilize the oligomeric structures for Aβ42 relative to Aβ40, and greatly facilitate the conversion from prefibrillar trimers to fibrillar tetramers.