Two-dimensional infrared spectra of isotopically diluted amyloid fibrils from Aβ40

Abstract

The 2D IR spectra of the amide-I vibrations of amyloid fibrils from A␤40 were obtained. The matured fibrils formed from strands having isotopic substitution by 13 CA 18 O at Gly-38, Gly-33, Gly-29, or Ala-21 show vibrational exciton spectra having reduced dimensionality. Indeed, linear chain excitons of amide units are seen, for which the interamide vibrational coupling is measured in fibrils grown from 50% and 5% mixtures of labeled and unlabeled strands. The data prove that the 1D excitons are formed from parallel in-register sheets. The coupling constants show that for each of the indicated residues the amide carbonyls in the chains are separated by 0.5 ؎ 0.05 nm. The isotope replacement of Gly-25 does not reveal linear excitons, consistent with the region of the strand having a different structure distribution. The vibrational frequencies of the amide-I modes, freed from effects of amide vibrational excitation exchange by 5% dilution experiments, point to there being a component of an electric field along the fibril axis that increases through the sequence Gly-38, Gly-33, Gly-29. The field is dominated by side chains of neighboring residues.␤-amyloid 40 ͉ exciton ͉ two-dimensional infrared spectroscopy A myloid fibrils are found in the brain tissue of persons with Alzheimer's disease, where they accumulate as plaques surrounded by regions of neuronal death. Although it remains unclear whether fibril formation is a cause of the neuronal loss in Alzheimer's disease, or a byproduct of another neurotoxic process, the formation and structure of amyloid fibrils is of intense interest.Fibrils are composed primarily of ␤-amyloid (A␤) proteins that range in length from 39 to 42 residues. They diffract x-rays with a characteristic ''cross-␤'' pattern (1-3), indicating that the polypeptide strands lie transverse to the fibril axis, with an interstrand spacing that is typical of a ␤-sheet. Solid-state NMR (4) and EPR (5) studies have shown that the ␤-sheet configuration is parallel and in register. Based on information from NMR, supplemented with information from atomic force microscopy, electron microscopy, and cross-linking studies, Tycko and coworkers (6, 7) have developed detailed models of the fibrils formed by 40-residue (A␤40) proteins. These models feature parallel in-register ␤-sheets involving residues 9-24 and 30-40 and a loop region, 23-29, that can vary with fibrillization conditions. A monofilament is formed by folding of each polypeptide chain such that the two sheets are apposed to each other, and two such monofilaments comprise the fibril (Fig. 1A). There is significant plasticity in the structural features of amyloid fibrils (8), and alternative models have been proposed (9).In the current work the structure and internal dynamics of amyloid fibrils are examined by 2D IR spectroscopy (10-12). There has been a considerable amount of experimental work relating the 2D IR spectra of small peptide aggregates to their structure (13-17), and the recent experimental and theoretical applications of 2D IR have in...

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

“…We found that upon isotope dilution, the frequencies of these 3 residues lie within 5 cm Ϫ1 of each other (1,589-1,594 cm Ϫ1 ), indicating that their local electrostatic environments are comparable. Moreover, the isotope frequencies are higher when diluted, indicating that the coupling between isotope labels causes a negative frequency shift, which is consistent with the negative coupling constants predicted for ␤-sheets in amyloid fibril (12). These results emphasize that the isotope-labeled features that are the focus of this study arise from delocalized vibrational modes that involve the cooperative motions of several labeled amide I groups (18).…”

“…Isotope labeling and IR spectroscopy have been used previously to study amyloids, which have provided insight into general aggregation mechanisms (11,12). Most studies rely on small peptide fragments, which do not necessarily translate into the context of the full protein.…”

Discriminating early stage Aβ42 monomer structures using chirality-induced 2DIR spectroscopy in a simulation study

“…(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19). Recent evidence supports the view that, at the monomeric level, the ensemble of Aβ is a mixture of multiple, nearly isoenergenic conformational species, in agreement with the energy landscape view of protein dynamics proposed by Frauenfelder and coworkers (22).…”

“…Optical 2D techniques have been successfully used toward the study of fast peptide folding kinetics (32,34), hydrogen bonding dynamics (35), ultrafast chemical exchange (30,31), and energy transport in photosynthetic antennae (36). Very recently, there has been considerable interest in the 2DIR field in studying the structure and formation kinetics of various kinds of amyloid aggregates (12)(13)(14)(15).…”

Vibrational dynamics of a non-degenerate ultrafast rotor: The (C12,C13)-oxalate ion

“…This labeling tactic has been successfully employed to investigate isolated amide units in different peptides and proteins. [16][17][18] Thus, the aim of this study was to explore the vibrational and conformational changes of the (C13,C12)-oxalate ion, from here on referred to as C13-oxalate. To this end, femtosecond IR transient absorption, ultrafast photon echo, and linear absorption IR spectroscopy were employed.…”