Stable and metastable states of human amylin in solution.

Patients with type II diabetes exhibit fibrillar deposits of human amylin protein in the pancreas. It has been proposed that amylin oligomers arising along the aggregation or fibril-formation pathways are important in the genesis of the disease. In a step toward understanding these aggregation pathways, in this work we report the conformational preferences of human amylin monomer in solution using molecular simulations and infrared experiments. In particular, we identify a stable conformer that could play a key role in aggregation. We find that amylin adopts three stable conformations: one with an α-helical segment comprising residues 9-17 and a short antiparallel ß-sheet comprising residues 24-28 and 31-35; one with an extended antiparallel ß-hairpin with the turn region comprising residues 20-23; and one with no particular structure. Using detailed calculations, we determine the relative stability of these various conformations, finding that the ß-hairpin conformation is the most stable, followed by the α-helical conformation, and then the unstructured coil. To test our predicted structure, we calculate its infrared spectrum in the amide I stretch regime, which is sensitive to secondary structure through vibrational couplings and linewidths, and compare it to experiment. We find that theoretically predicted spectra are in good agreement with the experimental line shapes presented herein. The implications of the monomer secondary structures on its aggregation pathway and on its interaction with cell membranes are discussed.

Strategies for extracting structural information from 2D IR spectroscopy of amyloid: application to islet amyloid polypeptide.

The 37-residue human islet amyloid polypeptide (hIAPP or amylin) self-assembles into fibers, the assembly of which has been associated with the disease mechanism of type II diabetes. Infrared spectroscopy in conjunction with isotope labeling is proving to be a powerful tool for studying the aggregation process of hIAPP and other amyloid forming proteins with residue specific structure and kinetic information, but the relationship between the spectroscopic observables and the structure is not fully established. We report a detailed analysis of the linear and 2D IR spectra of hIAPP fibers isotope labeled at seven different residue positions. The features of the 2D IR spectra, including the frequencies, linewidths, intensities, and polarization dependence of the diagonal and cross-peaks, rely heavily on the position of the isotope labeled residue. In order to understand how these measured parameters depend on fiber secondary and tertiary structure, we have simulated 1D and 2D IR spectra utilizing idealized structural models in addition to a recently published solid-state NMR based model of the amyloid fibril. The analysis provides a more rigorous foundation for interpreting the infrared spectra of amyloids. In addition, we demonstrate that 2D IR spectra can be employed to distinguish between residues in beta-sheets versus those in turn regions, and that transitional residues between secondary structures can be identified by the suppression of their cross-peaks in 2D IR spectra. This latter approach is not limited to amyloid fibrils and will be generally useful in identifying regions of secondary structure in proteins using 2D IR spectroscopy and isotope labeling.

Two-dimensional IR spectroscopy and isotope labeling defines the pathway of amyloid formation with residue-specific resolution.

There is considerable interest in uncovering the pathway of amyloid formation because the toxic properties of amyloid likely stems from prefibril intermediates and not the fully formed fibrils. Using a recently invented method of collecting 2-dimensional infrared spectra and site-specific isotope labeling, we have measured the development of secondary structures for 6 residues during the aggregation process of the 37-residue polypeptide associated with type 2 diabetes, the human islet amyloid polypeptide (hIAPP). By monitoring the kinetics at 6 different labeled sites, we find that the peptides initially develop well-ordered structure in the region of the chain that is close to the ordered loop of the fibrils, followed by formation of the 2 parallel beta-sheets with the N-terminal beta-sheet likely forming before the C-terminal sheet. This experimental approach provides a detailed view of the aggregation pathway of hIAPP fibril formation as well as a general methodology for studying other amyloid forming proteins without the use of structure-perturbing labels.

Two-dimensional infrared spectroscopy provides evidence of an intermediate in the membrane-catalyzed assembly of diabetic amyloid.

Islet amyloid polypeptide (IAPP, also known as amylin) is responsible for pancreatic amyloid deposits in type 2 diabetes. The deposits, as well as intermediates in their assembly, are cytotoxic to pancreatic beta-cells and contribute to the loss of beta-cell mass associated with type 2 diabetes. The factors that trigger islet amyloid deposition in vivo are not well understood, but peptide membrane interactions have been postulated to play an important role in islet amyloid formation. To better understand the role of membrane interactions in amyloid formation, two-dimensional infrared (2D IR) spectroscopy was used to compare the kinetics of amyloid formation for human IAPP both in the presence and in the absence of negatively charged lipid vesicles. Comparison of spectral features and kinetic traces from the two sets of experiments provides evidence for the formation of an ordered intermediate during the membrane-mediated assembly of IAPP amyloid. A characteristic transient spectral feature is detected during amyloid formation in the presence of vesicles that is not observed in the absence of vesicles. The spectral feature associated with the intermediate raises in intensity during the self-assembly process and subsequently decays in intensity in the classic manner of a kinetic intermediate. Studies with rat IAPP, a variant that is known to interact with membranes but does not form amyloid, confirm the presence of an intermediate. The analysis of 2D IR spectra in terms of specific structural features is discussed. The unique combination of time and secondary structure resolution of 2D IR spectroscopy has enabled the time-evolution of a hIAPP intermediate to be directly monitored for the first time. The data presented here demonstrates the utility of 2D IR spectroscopy for studying membrane-catalyzed amyloid formation.

Tracking fiber formation in human islet amyloid polypeptide with automated 2D-IR spectroscopy.

Amyloid forming proteins have been implicated in many human diseases. The kinetics of amyloid fiber formation are of particular interest because evidence points to intermediate folding structures as potential cytotoxic species. The standard methods for monitoring the kinetics are to use fluorescence or circular dichroism spectroscopy, which do not uniquely resolve secondary structures. In this work, we use a new technology for rapidly scanning 2D-IR spectra that allows us to follow the fiber formation kinetics of the human islet amyloid polypeptide (hIAPP) that is involved in type II diabetes. Spectroscopic markers are identified that uniquely monitor random coil versus beta-sheet secondary structures as well as probe beta-sheet elongation and stacking. Our measurements provide more rigorous kinetics for the secondary structure evolution of amyloid formation than is available with other techniques.

Automated 2D IR spectroscopy using a mid-IR pulse shaper and application of this technology to the human islet amyloid polypeptide.

The capability of 2D IR spectroscopy to elucidate time-evolving structures is enhanced by a programmable mid-IR pulse shaper that greatly improves the ease, speed, and accuracy of data collection. Traditional ways of collecting 2D IR spectra are difficult to implement, cause distorted peak shapes, and result in poor time resolution and/or phase problems. We report on several methods for collecting 2D IR spectra by using a computer-controlled germanium acoustooptic modulator that overcomes the above problems. The accuracy and resolution of each method is evaluated by using model metal carbonyl compounds that have well defined lineshapes. Furthermore, phase cycling can now be employed to largely alleviate background scatter from heterogeneous samples. With these methods in hand, we apply 2D IR spectroscopy to study the structural diversity in amyloid fibers of aggregated human islet amyloid polypeptide (hIAPP), which is involved with type 2 diabetes. The 2D IR spectra reveal that the beta-sheet fibers have a large structural distribution, as evidenced by an inhomogeneously broadened beta-sheet peak and strong coupling to random coil conformations. Structural diversity is an important characteristic of hIAPP because it may be that partly folded peptides cause the disease. This experiment on hIAPP is an example of how computer generation of 2D IR pulse sequences is a key step toward automating 2D IR spectroscopy, so that new pulse sequences can be implemented quickly and a diverse range of systems can be studied more easily.