Unexpected Importance of Aromatic-Aliphatic and Aliphatic Side Chain-Backbone Interactions in the Stability of Amyloids

Dual Activity BLEG-1 from Bacillus lehensis G1 Revealed Structural Resemblance to B3 Metallo-β-Lactamase and Glyoxalase II: An Insight into Its Enzyme Promiscuity and Evolutionary Divergence

Metallo-β-lactamases (MBLs) are class B β-lactamases from the metallo-hydrolase-like MBL-fold superfamily which act on a broad range of β-lactam antibiotics. A previous study on BLEG-1 (formerly called Bleg1_2437), a hypothetical protein from Bacillus lehensis G1, revealed sequence similarity and activity to B3 subclass MBLs, despite its evolutionary divergence from these enzymes. Its relatedness to glyoxalase II (GLXII) raises the possibility of its enzymatic promiscuity and unique structural features compared to other MBLs and GLXIIs. This present study highlights that BLEG-1 possessed both MBL and GLXII activities with similar catalytic efficiencies. Its crystal structure revealed highly similar active site configuration to YcbL and GloB GLXIIs from Salmonella enterica, and L1 B3 MBL from Stenotrophomonas maltophilia. However, different from GLXIIs, BLEG-1 has an insertion of an active-site loop, forming a binding cavity similar to B3 MBL at the N-terminal region. We propose that BLEG-1 could possibly have evolved from GLXII and adopted MBL activity through this insertion.

Genesis of Neurotoxic Hybrid Nanofibers from the Coassembly of Aromatic Amino Acids

Considering the relevance of accumulation and self-assembly of metabolites and aftermath of biological consequences, it is important to know whether they undergo coassembly and what properties the resultant hybrid higher-order structures would exhibit. This work reveals the inherent tendency of aromatic amino acids to undergo a spontaneous coassembly process under physiologically mimicked conditions, which yields neurotoxic hybrid nanofibers. Resultant hybrid nanostructures resembled the β-structured conformers stabilized by H-bonds and π-π stacking interactions, which were highly toxic to human neuroblastoma cells. The hybrid nanofibers also showed strong cross-seeding potential that triggered in vitro aggregation of diverse globular proteins and brain extract components, converting the native structures into cross-β-rich amyloid aggregates. The heterogenic nature of the hybrid nanofibers seems crucial for their higher toxicity and faster cross-seeding potential as compared to the homogeneous amino acid nanofibers. Our findings reveal the importance of aromaticity-driven optimized intermolecular arrangements for the coassembly of aromatic amino acids, and the results may provide important clues to the fundamental understanding of metabolite accumulation-related complications.

Nanostructures Formed by Custom-Made Peptides Based on Amyloid Peptide Sequences and Their Inhibition by 2-Hydroxynaphthoquinone

Extensive research on amyloid fibril formations shows that certain core sequences within Aβ peptide play an important role in their formation. It is impossible to track these events in vivo. Many proteins and peptides with such core sequences form amyloid fibrils and such Aβ sheet mimics have become excellent tools to study amyloid fibril formation and develop therapeutic strategies. A group of peptides based on amyloid peptide sequences obtained from PDB searches, where glycine residues are substituted with alanine and isoleucine, are tested for aggregation by SEM and ThT binding assay. SEM of different peptide sequences showed morphologically different structures such as nanorods, crystalline needles and nanofibrils. The peptides were co-incubated with HNQ (a quinone) to study its effect on the process of aggregation and/or fibrillation. In conclusion, this group of peptides seem to be Aβ sheet mimics and can be very useful in understanding the different morphologies of amyloid fibrils arising from different peptide sequences and the effective strategies to inhibit or anneal them.

Role of aromatic amino acids in amyloid self-assembly

Amyloids are proteins of a cross-β structure found as deposits in several diseases and also in normal tissues (nails, spider net, silk). Aromatic amino acids are frequently found in amyloid deposits. Although they are not indispensable, aromatic amino acids, phenylalanine, tyrosine and tryptophan, enhance significantly the kinetics of formation and thermodynamic stability, while tape or ribbon-like morphology is represented in systems with experimentally detected π-π interactions between aromatic rings. Analysis of geometries and energies of the amyloid PDB structures indicate the prevalence of aromatic-nonaromatic interactions and confirm that aromatic-aromatic interactions are not crucial for the amyloid formation.

Study of stacking interactions between two neutral tetrathiafulvalene molecules in Cambridge Structural Database crystal structures and by quantum chemical calculations

Tetrathiafulvalene (TTF) and its derivatives are very well known as electron donors with widespread use in the field of organic conductors and superconductors. Stacking interactions between two neutral TTF fragments were studied by analysing data from Cambridge Structural Database crystal structures and by quantum chemical calculations. Analysis of the contacts found in crystal structures shows high occurrence of parallel displaced orientations of TTF molecules. In the majority of the contacts, two TTF molecules are displaced along their longer C 2 axis. The most frequent geometry has the strongest TTF–TTF stacking interaction, with CCSD(T)/CBS energy of −9.96 kcal mol−1. All the other frequent geometries in crystal structures are similar to geometries of the minima on the calculated potential energy surface.