Environment Polarity in Proteins Mapped Noninvasively by FTIR Spectroscopy

Manor, Joshua; Feldblum, Esther S.; Zanni, Martin T.; Arkin, Isaiah T.

doi:10.1021/jz300150v

Cited by 25 publications

(24 citation statements)

References 59 publications

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“…1595 cm −1 is about 10 cm −1 lower frequency than before UV-B damage (compare solid to dashed lines). The only reasonable way that a lower frequency can be created is by larger negative coupling constants – dehydration would produce a higher frequency shift and hydration caused by unfolding would create a peak no lower than 1610 cm −1 (55) . This frequency range is most consistent with a β-sheet structure that is more strongly coupled than the β-sandwich domains in native γD-crystallin, but less ordered than fully formed amyloid fibers (See Table 1).…”

Section: Resultsmentioning

confidence: 99%

Amyloid Fiber Formation in Human γD-Crystallin Induced by UV–B Photodamage

et al. 2013

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γD-crystallin is an abundant structural protein of the lens that is found in native and modified forms in cataractous aggregates. We establish that UV-B irradiation of γD-crystallin leads to structurally specific modifications and precipitation via two mechanisms: amorphous aggregates and amyloid fibers. UV-B radiation causes cleavage of the backbone, in large measure near the interdomain interface, where side chain oxidations are also concentrated. 2D IR spectroscopy and expressed protein ligation localize fiber formation exclusively to the C-terminal domain of γD-crystallin. The native β-sandwich domains are not retained upon precipitation by either mechanism. The similarity between the amyloid forming pathway when induced by either UV-B radiation or low pH suggests that it is the propensity for the C-terminal β-sandwich domain to form amyloid β-sheets that determines the misfolding pathway independent of the mechanism of denaturation.

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Section: Resultsmentioning

confidence: 99%

Amyloid Fiber Formation in Human γD-Crystallin Induced by UV–B Photodamage

et al. 2013

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“…Hydrophobic membrane peptides can absorb as high as 1660 cm −1 as can dehydrated random coils and turns. 16,52,53 Interpretation of a standard SFG spectrum based on frequency alone has the same difficulties as the FTIR response. Chiral SFG responses, which are sensitive to secondary structure in a similar manner as CD spectroscopy, can lend insight into secondary structure, 25,26 but are difficult to measure for samples on gold due to suppression of s-polarized responses.…”

Section: Discussionmentioning

confidence: 99%

Two-Dimensional Sum-Frequency Generation Reveals Structure and Dynamics of a Surface-Bound Peptide

Laaser¹,

Skoff²,

Ho³

et al. 2014

J. Am. Chem. Soc.

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116

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Surface-bound polypeptides and proteins are increasingly used to functionalize inorganic interfaces such as electrodes, but their structural characterization is exceedingly difficult with standard technologies. In this paper, we report the first two-dimensional sum-frequency generation (2D SFG) spectra of a peptide monolayer, which is collected by adding a mid-IR pulse shaper to a standard femtosecond SFG spectrometer. On a gold surface, standard FTIR spectroscopy is inconclusive about the peptide structure because of solvation-induced frequency shifts, but the 2D lineshapes, anharmonic shifts, and lifetimes obtained from 2D SFG reveal that the peptide is largely α-helical and upright. Random coil residues are also observed, which do not themselves appear in SFG spectra due to their isotropic structural distribution, but which still absorb infrared light and so can be detected by cross-peaks in 2D SFG spectra. We discuss these results in the context of peptide design. Because of the similar way in which the spectra are collected, these 2D SFG spectra can be directly compared to 2D IR spectra, thereby enabling structural interpretations of surface-bound peptides and biomolecules based on the well-studied structure/2D IR spectra relationships established from soluble proteins.

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“…For instance, random coils absorb at about 1645 cm −1 , which overlaps with α-helices that absorb between 1635 cm −1 and 1655 cm −1 , depending on whether they are soluble or membrane bound. [3][4][5][6][7][8] In principle, one can fit the amide I absorption band, but it is difficult to be confident in fits because structural disorder causes symmetry forbidden transitions to appear and because the absorption bands themselves have complex lineshapes, among other problematic issues. [9][10][11][12][13][14][15][16] In this paper, we report a method for measuring transition dipole strengths from 1D and 2D IR spectroscopy and illustrate the utility of using transition dipole strengths to identify secondary structure.…”

Section: Introductionmentioning

confidence: 99%

Quantification of transition dipole strengths using 1D and 2D spectroscopy for the identification of molecular structures via exciton delocalization: Application to α-helices

Grechko

Zanni

2012

The Journal of Chemical Physics

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171

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Vibrational and electronic transition dipole strengths are often good probes of molecular structures, especially in excitonically coupled systems of chromophores. One cannot determine transition dipole strengths using linear spectroscopy unless the concentration is known, which in many cases it is not. In this paper, we report a simple method for measuring transition dipole moments from linear absorption and 2D IR spectra that does not require knowledge of concentrations. Our method is tested on several model compounds and applied to the amide I band of a polypeptide in its random coil and α-helical conformation as modulated by the solution temperature. It is often difficult to confidently assign polypeptide and protein secondary structures to random coil or α-helix by linear spectroscopy alone, because they absorb in the same frequency range. We find that the transition dipole strength of the random coil state is 0.12 ± 0.013 D 2 , which is similar to a single peptide unit, indicating that the vibrational mode of random coil is localized on a single peptide unit. In an α-helix, the lower bound of transition dipole strength is 0.26 ± 0.03 D 2 . When taking into account the angle of the amide I transition dipole vector with respect to the helix axis, our measurements indicate that the amide I vibrational mode is delocalized across a minimum of 3.5 residues in an α-helix. Thus, one can confidently assign secondary structure based on exciton delocalization through its effect on the transition dipole strength. Our method will be especially useful for kinetically evolving systems, systems with overlapping molecular conformations, and other situations in which concentrations are difficult to determine.

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Environment Polarity in Proteins Mapped Noninvasively by FTIR Spectroscopy

Cited by 25 publications

References 59 publications

Amyloid Fiber Formation in Human γD-Crystallin Induced by UV–B Photodamage

Amyloid Fiber Formation in Human γD-Crystallin Induced by UV–B Photodamage

Two-Dimensional Sum-Frequency Generation Reveals Structure and Dynamics of a Surface-Bound Peptide

Quantification of transition dipole strengths using 1D and 2D spectroscopy for the identification of molecular structures via exciton delocalization: Application to α-helices

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