Simulation of two-dimensional infrared spectroscopy of amyloid fibrils

Self Cite

Elucidating the structural features of the Aβ monomer, the peptide constituent of amyloid fibrils found in Alzheimer's disease, can enable a direct characterization of aggregation pathways. Recent studies support the view that the ensemble of Aβ42 monomers is a mixture of diverse ordered and disordered conformational species, which can be classified according to the formation of a characteristic β-hairpin conformation in a certain region. Despite the disparity in the structural features of these species, commonly used spectroscopic techniques such as NMR may not directly trace the conformational dynamics in the ensemble due to the limited time resolution and the lack of well-resolved spectral features for different comformers. Here we use molecular dynamics simulations combined with simulations of two-dimensional IR (2DIR) spectra to investigate the structure of these species, their interchange kinetics, and their spectral features. We show that while the discrimination efficiency of the ordinary, nonchiral 2DIR signal is limited due to its intrinsic dependence on common order parameters that are dominated by the generally unstructured part of the sequence, signals with carefully designed chirality-sensitive pulse configurations have the high resolution required for differentiating the various monomer structures. Our combined simulation studies indicate the power of the chirality-induced (CI) 2DIR technique in investigating early events in Aβ42 aggregation and open the possibility for their use as a novel experimental tool.amyloid | REMD | nonlinear spectroscopy

supporting

confidence: 80%

mentioning

confidence: 99%

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

Zhuang

Sgourakis

et al. 2010

Self Cite

“…Intensity below 1;610 cm −1 is largely due to side chain absorbances and the presence of 13 C at its natural abundance of 1.1% (18). More detailed descriptions of the structural origins of the spectra could be obtained by calculating 2D IR spectra from molecular dynamics simulations of the Protein Data Bank structure (11)(12)(13)(14)(15), but because the folds of the Greek keys are so similar, one domain cannot be distinguished from the other.…”

Section: Resultsmentioning

confidence: 99%

“…Mechanistic information is obtained from rapid-scan methods that track the kinetics of aggregate formation (6). Spectra can be calculated from molecular dynamics simulations allowing structural models to be tested (11)(12)(13)(14)(15). Isotope-edited 2D IR spectroscopy using 13 C ¼ 18 O labeled backbone amides has been used to study the fibril structure and mechanism of fibril formation for amyloid beta (Aβ) (8) and the human islet amyloid polypeptide (hIAPP) (6,7), as well as many membrane-bound (13,16) and soluble polypeptides (9,10).…”

mentioning

confidence: 99%

Two-dimensional IR spectroscopy and segmental ¹³ C labeling reveals the domain structure of human γD-crystallin amyloid fibrils

Moran

Woys

Buchanan

et al. 2012

128

307

The structural eye lens protein γD-crystallin is a major component of cataracts, but its conformation when aggregated is unknown. Using expressed protein ligation, we uniformly 13 C labeled one of the two Greek key domains so that they are individually resolved in two-dimensional (2D) IR spectra for structural and kinetic analysis. Upon acid-induced amyloid fibril formation, the 2D IR spectra reveal that the C-terminal domain forms amyloid β-sheets, whereas the N-terminal domain becomes extremely disordered but lies in close proximity to the β-sheets. Two-dimensional IR kinetics experiments show that fibril nucleation and extension occur exclusively in the C-terminal domain. These results are unexpected because the N-terminal domain is less stable in the monomer form. Isotope dilution experiments reveal that each C-terminal domain contributes two or fewer adjacent β-strands to each β-sheet. From these observations, we propose an initial structural model for γD-crystallin amyloid fibrils. Because only 1 μg of protein is required for a 2D IR spectrum, even poorly expressing proteins can be studied under many conditions using this approach. Thus, we believe that 2D IR and protein ligation will be useful for structural and kinetic studies of many protein systems for which IR spectroscopy can be straightforwardly applied, such as membrane and amyloidogenic proteins. C ataracts are a protein misfolding disease caused by the aggregation of lens crystallin proteins into insoluble deposits that blur vision (1, 2). Because these proteins are not regenerated, damage from UV radiation, oxidative stress, and other chemical modifications accumulates with time (1, 2). As a result, over 50% of the population over 55 develops age-related cataracts (2). Additionally, numerous mutations that destabilize crystallin protein folds are linked to inherited and juvenile-onset cataracts (1). Although the causative factors associated with this disease are known, the structures of the aggregates and the mechanisms by which they form are unknown.Like other protein aggregation diseases such as type II diabetes mellitus and Alzheimer's disease, the molecular structures of proteins in cataracts are difficult to determine. Atomic-level structures have been obtained for some amyloid aggregates of peptides using NMR spectroscopy (3, 4) and X-ray crystallography (5). However, the most widely used techniques for studying aggregate structures and aggregation mechanisms are circular dichroism spectroscopy, fluorescence spectroscopy, and transmission electron microscopy, which provide little detailed structural information. Two-dimensional (2D) IR spectroscopy is emerging as an important tool for studying protein aggregates such as amyloid fibrils (6-8) because it provides bond-by-bond structural resolution on kinetically evolving samples (6, 8-10). Two-dimensional IR spectroscopy probes secondary structure through cross peak couplings and solvent exposure through 2D lineshapes. Its bond-specific structural resolution comes from isotope labeling. Mech...

“…There has been a considerable amount of experimental work relating the 2D IR spectra of small peptide aggregates to their structure (13)(14)(15)(16)(17), and the recent experimental and theoretical applications of 2D IR have involved macromolecular systems such as folding proteins (18) and fibrils (19,20).…”

Section: A Myloid Fibrils Are Found In the Brain Tissue Of Persons Withmentioning

confidence: 99%

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

Kim

Liu

Axelsen

et al. 2008

131

224

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...