Rapid self-association of highly amyloidogenic H-fragments of insulin: Experiment and molecular dynamics simulations

Multiscale Modeling of Amyloid Fibrils Formed by Aggregating Peptides Derived from the Amyloidogenic Fragment of the A-Chain of Insulin

Computational prediction of molecular structures of amyloid fibrils remains an exceedingly challenging task. In this work, we propose a multi-scale modeling procedure for the structure prediction of amyloid fibrils formed by the association of ACC_1-13 aggregation-prone peptides derived from the N-terminal region of insulin’s A-chain. First, a large number of protofilament models composed of five copies of interacting ACC_1-13 peptides were predicted by application of CABS-dock coarse-grained (CG) docking simulations. Next, the models were reconstructed to all-atom (AA) representations and refined during molecular dynamics (MD) simulations in explicit solvent. The top-scored protofilament models, selected using symmetry criteria, were used for the assembly of long fibril structures. Finally, the amyloid fibril models resulting from the AA MD simulations were compared with atomic force microscopy (AFM) imaging experimental data. The obtained results indicate that the proposed multi-scale modeling procedure is capable of predicting protofilaments with high accuracy and may be applied for structure prediction and analysis of other amyloid fibrils.

A tale of two tails: Self-assembling properties of A- and B-chain parts of insulin's highly amyloidogenic H-fragment

Due to the spontaneous transition of native insulin into therapeutically inactive amyloid, prolonged storage decreases effectiveness of the hormone in treatment of diabetes. Various regions of the amino acid sequence have been implicated in insulin aggregation. Here, we focus on smaller fragments of the highly amyloidogenic H-peptide comprising disulfide-bonded N-terminal sections of insulin's A-chain (13 residues) and B-chain (11 residues). Aggregation patterns of N-terminal fragments of A-chain (ACC_1-13, ACC_1-11, ACC_6-13, ACC_6-11, all retaining Cys6A-Cys11A disulfide bond) and B-chain (B_1-11(7A)) are examined at acidic and neutral pH. ACC_1-11 is the smallest fragment found to be amyloidogenic at either pH; removal of the N-terminal GIVEQ section renders this fragment entirely non-amyloidogenic. The self-assembling properties of ACC_1-11 contrast with aggregation-resistant behavior of B_1-11(7A) and its disulfide-linked homodimer, (B_1-11)₂ aggregating only at neutral pH. Fibrillar ACC_1-11 is similar to insulin amyloid in terms of morphology and infrared features. Secondary nucleation is likely to account for the detected shortening of insulin aggregation lag phase at neutral pH upon cross-seeding with pre-formed fibrils of ACC_1-11 or (B_1-11)₂. An aggregation-enhancing effect of monomeric ACC_1-11 on co-dissolved native insulin is also observed. Our findings are discussed in the context of mechanisms of insulin aggregation.

Folding and self-assembly of short intrinsically disordered peptides and protein regions

Proteins and peptide fragments are highly relevant building blocks in self-assembly for nanostructures with plenty of applications. Intrinsically disordered proteins (IDPs) and protein regions (IDRs) are defined by the absence of a well-defined secondary structure, yet IDPs/IDRs show a significant biological activity. Experimental techniques and computational modelling procedures for the characterization of IDPs/IDRs are discussed. Directed self-assembly of IDPs/IDRs allows reaching a large variety of nanostructures. Hybrid materials based on the derivatives of IDPs/IDRs show a promising performance as alternative biocides and nanodrugs. Cell mimicking, in vivo compartmentalization, and bone regeneration are demonstrated for IDPs/IDRs in biotechnological applications. The exciting possibilities of IDPs/IDRs in nanotechnology with relevant biological applications are shown.

Reduction of a disulfide-constrained oligo-glutamate peptide triggers self-assembly of β2-type amyloid fibrils with the chiroptical properties determined by supramolecular chirality

Disulfide bonds prevent aggregation of globular proteins by stabilizing the native state. However, a disulfide bond within a disordered state may accelerate amyloidogenic nucleation by navigating fluctuating polypeptide chains towards an orderly assembly of β-sheets. Here, the self-assembly behavior of Glu-Cys-(Glu)₄-Cys-Glu peptide (E₆C₂), in which an intrachain disulfide bond is engineered into an amyloidogenic homopolypeptide motif, is investigated. To this end, the Thioflavin T (ThT) fluorescence kinetic assay is combined with infrared spectroscopy, circular dichroism (CD), atomic force microscopy (AFM) and Raman scattering measurements. Regardless of whether the disulfide bond is intact or reduced, E₆C₂ monomers remain disordered within a broad range of pH. On the other hand, only reduced E₆C₂ self-assembles into amyloid fibrils with the unique infrared traits indicative of three-center hydrogen bonds involving main-chain carbonyl as a bifurcating acceptor and main-chain NH and side-chain -COOH groups as hydrogen donors: the bonding pattern observed in so-called β₂-fibrils. AFM analysis of β₂-E₆C₂ reveals tightly packed rectangular superstructures whose presence coincides with strong chiroptical properties. Our findings suggest that formation of chiral amyloid superstructures may be a generic process accessible to various substrates, and that the fully extended conformation of a poly-Glu chain is a condition sine qua non for self-assembly of β₂-fibrils.

Extremely Amyloidogenic Single-Chain Analogues of Insulin's H-Fragment: Structural Adaptability of an Amyloid Stretch

Relatively short amino acid sequences often play a pivotal role in triggering protein aggregation leading to the formation of amyloid fibrils. In the case of insulin, various regions of A- and B-chains have been implicated as the most relevant to the protein's amyloidogenicity. Here, we focus on the highly amyloidogenic H-fragment of insulin comprising the disulfide-bonded N-terminal parts of both chains. Analysis of the aggregation behavior of single-chain peptide derivatives of the H-fragment suggests that the A-chain's part initiates the aggregation process while the disulfide-tethered B-chain reluctantly adapts to amyloid structure. Merging of both A- and B-parts into single-chain continuous peptides (A-B and B-A) results in extreme amyloidogenicity exceeding that of the double-chain H-fragment as reflected by almost instantaneous de novo fibrillization. Amyloid fibrils of A-B and B-A present distinct morphological and infrared traits and do not cross-seed insulin. Our study suggests that the N-terminal part of insulin's A-chain containing the intact Cys6-Cys11 intrachain disulfide bond may constitute insulin's major amyloid stretch which, through its bent conformation, enforces a parallel in-register alignment of β-strands. Comparison of the self-association behavior of H, A-B, and B-A peptides suggests that A-chain's N-terminal amyloid stretch is very versatile and adaptive to various structural contexts.