How to Get Insight into Amyloid Structure and Formation from Infrared Spectroscopy

Moran, Sean D.; Zanni, Martin T.

doi:10.1021/jz500794d

Cited by 243 publications

(297 citation statements)

References 68 publications

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“…The comparison of the 1D-IR spectrum (in which the total oscillator strength is to a good approximation conserved) and the 2D-IR spectrum (in which the signal is nonlinearly dependent on the transition dipole of the IR modes4142) provides a measure of the excitonic delocalization of each structural component, making a combination of the techniques exceptionally useful to study amyloid systems, as has been shown by the work of the Zanni group43444546.…”

Section: D-ir On Amyloid Fibrilsmentioning

confidence: 99%

Evidence for Intramolecular Antiparallel Beta-Sheet Structure in Alpha-Synuclein Fibrils from a Combination of Two-Dimensional Infrared Spectroscopy and Atomic Force Microscopy

Roeters

Iyer

Pletikapić

et al. 2017

Sci Rep

122

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The aggregation of the intrinsically disordered protein alpha-synuclein (αS) into amyloid fibrils is thought to play a central role in the pathology of Parkinson’s disease. Using a combination of techniques (AFM, UV-CD, XRD, and amide-I 1D- and 2D-IR spectroscopy) we show that the structure of αS fibrils varies as a function of ionic strength: fibrils aggregated in low ionic-strength buffers ([NaCl] ≤ 25 mM) have a significantly different structure than fibrils grown in higher ionic-strength buffers. The observations for fibrils aggregated in low-salt buffers are consistent with an extended conformation of αS molecules, forming hydrogen-bonded intermolecular β-sheets that are loosely packed in a parallel fashion. For fibrils aggregated in high-salt buffers (including those prepared in buffers with a physiological salt concentration) the measurements are consistent with αS molecules in a more tightly-packed, antiparallel intramolecular conformation, and suggest a structure characterized by two twisting stacks of approximately five hydrogen-bonded intermolecular β-sheets each. We find evidence that the high-frequency peak in the amide-I spectrum of αS fibrils involves a normal mode that differs fundamentally from the canonical high-frequency antiparallel β-sheet mode. The high sensitivity of the fibril structure to the ionic strength might form the basis of differences in αS-related pathologies.

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Section: D-ir On Amyloid Fibrilsmentioning

confidence: 99%

Evidence for Intramolecular Antiparallel Beta-Sheet Structure in Alpha-Synuclein Fibrils from a Combination of Two-Dimensional Infrared Spectroscopy and Atomic Force Microscopy

Roeters

Iyer

Pletikapić

et al. 2017

Sci Rep

122

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“…1A) and long-range order along the protein backbone. 24 The couplings delocalize the vibrations, so that multiple amides along and across the β-strands vibrate in unison. Delocalization, in turn, changes the absorption frequencies, absorptivity coefficients, and anharmonicities, creating diagonal peaks and off-diagonal cross peaks (Fig.…”

Section: Introductionmentioning

confidence: 99%

Amyloid β-Sheet Secondary Structure Identified in UV-Induced Cataracts of Porcine Lenses using 2D IR Spectroscopy

Zhang

Alperstein

Zanni

2017

Journal of Molecular Biology

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Cataracts are formed by the aggregation of crystallin proteins in the eye lens. Many in vitro studies have established that crystallin proteins precipitate into aggregates that contain amyloid fibers when denatured, but there is little evidence that ex vivo cataracts contain amyloid. In this study, we collect two dimensional infrared (2D IR) spectra on tissue slices of porcine eye lenses. As shown in control experiments on in vitro αB- and γD-crystallin, 2D IR spectroscopy can identify amyloidogenic β-sheet secondary structure because this structure has exceptionally strong coupling and a high degree of ordering that creates characteristic diagonal and cross peaks. In ex vivo experiments of acid treated tissues, characteristic 2D IR features are observed and fibers >50 nm in length are resolved by TEM, consistent with amyloid fibers. In UV-irradiated lens tissues, fibers are not observed with TEM, but amyloidogenic β-sheet secondary structure is identified from the 2D IR spectra. The characteristic 2D IR features of amyloid β-sheet secondary structure are created by as few as 4 or 5 strands, and so identify amyloid secondary structure even if the aggregates themselves are too small to be resolved with TEM. We discuss these findings in the context of the chaperone system of the lens, which we hypothesize sequesters small aggregates, thereby preventing long fibers from forming. This study expands the scope of heterodyned 2D IR spectroscopy to tissues. The results provide a link between in vitro and ex vivo studies, and support the hypothesis that cataracts is an amyloid disease.

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“…Two-dimensional IR spectroscopy has often been used to measure femto-to picosecond dynamics of liquids, proteins, catalysts, and many other bulk systems at high concentrations or surface areas (11)(12)(13). When 2D IR was first invented 15 y ago, it was considered an achievement to measure spectra at millimolar protein concentrations, because that is the typical concentration used for protein NMR spectroscopy.…”

Section: Methods and Applications Of 2d Ir With Monolayer Sensitivitymentioning

confidence: 99%

Two-dimensional infrared spectroscopy measures the structural dynamics of a self-assembled film only one molecule thick

Zanni

2016

Proc. Natl. Acad. Sci. U.S.A.

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Since its first demonstration, many comparisons have been made between 2D infrared (2D IR) and NMR spectroscopy (1, 2). Both techniques use a series of pulses to manipulate and measure free induction decays that resolve couplings and dynamics through their characteristic multidimensional plots. The timescales are very different, with 2D IR spectroscopy using femtosecond pulses to measure the picosecond coherence times of vibrational modes, whereas NMR spectroscopy uses microsecond or millisecond pulses to measure nuclear spins that can last seconds. Thus, the two spectroscopies provide vastly different perspectives on structural dynamics. The article by Yan et al. (3), published in PNAS, uses the fast time resolution of 2D IR spectroscopy to study the structural dynamics of a functionalized self-assembled monolayer, providing insights into structural motions that are intimately related to chemistry. However, their experiments are also demonstrating an aspect of the technique that is only now being recognized as exceptional: the sensitivity of the technique to incredibly small amounts of material.NMR spectroscopy is often said to be insensitive (4). Although the level of sensitivity depends on many factors, such as the type of nuclei being measured and the magnetic field strength of the spectrometer, the statement itself refers to the differences in population between the nuclear spin states that create the free induction decays, given by the Boltzman distribution. At room temperature, the energy difference between nuclear spin states is much smaller than kT, resulting in nearly equal populations of states. The difference in population between two 1 H proton states in an 11.7-Tesla magnetic field is about 1 in 10 5 (4). In comparison, the energy difference between the υ = 0 and υ = 1 vibrational states is about eight-times larger than kT, resulting in an enormous difference in population between the states. In other words, vibrational states have almost the entire population in the ground state.Signal strength, and hence the sensitivity, are related to population differences because free induction decays are generated by unequal numbers of transitions between eigenstates (5). An ensemble of molecules with statistically equally populated eigenstates will produce no signal because there are as many absorption as emission transitions. (In fact, a commonly used trick in NMR is to purposely equilibrate eigenstates to eliminate unwanted signals.) Thus, the ultimate sensitivity of 2D IR spectroscopy is inherently much higher than NMR spectroscopy, because nearly all of the molecules in the ensemble are available for excitation. Dynamics of a Self-Assembled Film only One Molecule ThickIn their article, Yan et al. (3) demonstrate and use the sensitivity of 2D IR spectroscopy to measure a monolayer of molecules on a surface. The authors tethered a rhenium carbonyl vibrational probe to a monolayer of undecanethiol alkyl chains. Vibrational modes are sensitive to hydrogen bonding and electrostatics, and so the frequencies of...

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How to Get Insight into Amyloid Structure and Formation from Infrared Spectroscopy

Cited by 243 publications

References 68 publications

Evidence for Intramolecular Antiparallel Beta-Sheet Structure in Alpha-Synuclein Fibrils from a Combination of Two-Dimensional Infrared Spectroscopy and Atomic Force Microscopy

Evidence for Intramolecular Antiparallel Beta-Sheet Structure in Alpha-Synuclein Fibrils from a Combination of Two-Dimensional Infrared Spectroscopy and Atomic Force Microscopy

Amyloid β-Sheet Secondary Structure Identified in UV-Induced Cataracts of Porcine Lenses using 2D IR Spectroscopy

Two-dimensional infrared spectroscopy measures the structural dynamics of a self-assembled film only one molecule thick

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