Charge-Transfer Transitions in the Vacuum-Ultraviolet of Protein Circular Dichroism Spectra

Bulheller, Benjamin M.; Miles, Andrew; Wallace, B.A.; Hirst, Jonathan D.

doi:10.1021/jp077462k

Cited by 52 publications

(65 citation statements)

References 51 publications

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“…There has been a great effort spent to establish the theoretical basis of the origin of protein CD spectra in the last decades. Generally, the appearance of the far-UV CD spectrum is attributed to the nπ*, ππ* electronic transitions of the peptide bonds reviewed by Sreerama and Woody (34) and charge transfer transitions between the neighboring peptide bonds (35,36). Theoretical calculations of the CD spectrum were carried out by ab initio and semiempirical calculations, thoroughly reviewed by Woody (37).…”

Section: Discussionmentioning

confidence: 99%

Accurate secondary structure prediction and fold recognition for circular dichroism spectroscopy

Micsonai

Wien

Kernya

et al. 2015

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

1,376

1,337

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Circular dichroism (CD) spectroscopy is a widely used technique for the study of protein structure. Numerous algorithms have been developed for the estimation of the secondary structure composition from the CD spectra. These methods often fail to provide acceptable results on α/β-mixed or β-structure-rich proteins. The problem arises from the spectral diversity of β-structures, which has hitherto been considered as an intrinsic limitation of the technique. The predictions are less reliable for proteins of unusual β-structures such as membrane proteins, protein aggregates, and amyloid fibrils. Here, we show that the parallel/antiparallel orientation and the twisting of the β-sheets account for the observed spectral diversity. We have developed a method called β-structure selection (BeStSel) for the secondary structure estimation that takes into account the twist of β-structures. This method can reliably distinguish parallel and antiparallel β-sheets and accurately estimates the secondary structure for a broad range of proteins. Moreover, the secondary structure components applied by the method are characteristic to the protein fold, and thus the fold can be predicted to the level of topology in the CATH classification from a single CD spectrum. By constructing a web server, we offer a general tool for a quick and reliable structure analysis using conventional CD or synchrotron radiation CD (SRCD) spectroscopy for the protein science research community. The method is especially useful when X-ray or NMR techniques fail. Using BeStSel on data collected by SRCD spectroscopy, we investigated the structure of amyloid fibrils of various disease-related proteins and peptides. circular dichroism | secondary structure determination | protein fold | protein aggregation | amyloid O ptically active macromolecules, such as proteins, exhibit differential absorption of circular polarized light. The far-UV circular dichroism (CD) spectroscopy of proteins and peptides (180-250 nm) is predominantly based on the excitation of electronic transitions in amide groups. The peptide backbone forms characteristic secondary structures such as α-helices, β-pleated sheets, turns, and disordered sections with specific Φ, Ψ dihedral angles and H-bond patterns affecting the CD spectrum (1). CD has been exploited for protein folding and stability assays, intermolecular interactions, and ligand binding studies, and has recently been applied in the investigations of protein disorder (2, 3). Synchrotron radiation CD (SRCD) spectroscopy is an emerging technique complementary to small-angle X-ray scattering or infrared spectroscopy, synergistic to biochemical and biophysical assays characterizing the protein folding state. SRCD extends the limits of conventional CD spectroscopy by broadening the spectral range, increasing the signal-to-noise ratio, and accelerating the data acquisition, in the presence of absorbing components (buffers, salts, etc.) (4). Additionally, SRCD has the capability of time-resolved and stopped-flow measurements as well as hig...

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Section: Discussionmentioning

confidence: 99%

Accurate secondary structure prediction and fold recognition for circular dichroism spectroscopy

Micsonai

Wien

Kernya

et al. 2015

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

1,376

1,337

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“…Spectral features in this area have previously been ascribed to np* or pp* charge transfer transitions for a-helical and b-sheet geometries, respectively. [25][26][27] Only limited band shifting can be observed, predominantly for the perpendicular exciton peak (190 nm) for which a slight red-shift occurs upon drying. There is no clear tendency in the intensity differences.…”

Section: Spectral Features Are Preserved For Dry Phase Spectramentioning

confidence: 99%

Characterization of dry globular proteins and protein fibrils by synchrotron radiation vacuum UV circular dichroism

et al. 2008

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Circular dichroism using synchrotron radiation (SRCD) can extend the spectral range down to approximately 130 nm for dry proteins, potentially providing new structural information. Using a selection of dried model proteins, including alpha-helical, beta-sheet, and mixed-structure proteins, we observe a low-wavelength band in the range 130-160 nm, whose intensity and peak position is sensitive to the secondary structure of the protein and may also reflect changes in super-secondary structure. This band has previously been observed for peptides but not for globular proteins, and is compatible with previously published theoretical calculations related to pi-orbital transitions. We also show that drying does not lead to large changes in the secondary structure and does not induce orientational artifacts. In combination with principal component analysis, our SRCD data allow us to distinguish between two different types of protein fibrils, highlighting that bona fide fibrils formed by lysozyme are structurally more similar to the nonclassical fibrillar aggregates formed by the SerADan peptide than with the amyloid formed by alpha-synuclein. Thus, despite the lack of direct structural conclusions, a comprehensive SRCD-based database of dried protein spectra may provide a useful method to differentiate between various types of supersecondary structure and aggregated protein species.

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“…These transitions are assigned to charge-transfer transitions in which an n-or pelectron in one amide is excited into the p*-orbital of a neighboring amide. [5][6][7] We know that there are higher energy transitions in peptides and proteins. In fact there are a huge number of such transitions, but we know very little about them.…”

Section: Introductionmentioning

confidence: 99%

A significant role for high‐energy transitions in the ultraviolet circular dichroism spectra of polypeptides and proteins

Woody

2010

Chirality

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The nπ* and ππ* transitions of polypeptides mix significantly with very high energy transitions in the poly(Pro)II conformation, as evidenced by the strongly nonconservative CD spectrum in the 170-250 nm region. Because of this, the exciton model, the standard quantum mechanical model for predicting absorption and CD spectra of polypeptides, gives poor results for the poly(Pro) II (P(II)) conformation, although it works well for the α-helix, β-sheet, and β-turns. The exciton theory has been extended to include the effects of mixing of discrete peptide transitions near 200 nm with the large number of uncharacterized transitions in the deep ultraviolet. These latter transitions dominate the polarizability, and their mixing with the discrete transitions can be described via bond and lone-pair polarizability tensors, derivable by ab initio methods. This extended exciton method gives a good description of the CD spectrum of (Ala)(n) oligomers in the P(II) conformation. For this conformation, the polarizability contributions lead to a strong negative band near 200 nm that dominates the calculated and observed CD spectrum. The model does not give a good description of the CD of (Pro)(n) oligomers, probably because of conformational heterogeneity or nonadditive contributions of the Pro side chains. The model improves the calculated CD spectra of α-helical (Ala)(n) oligomers. Although the high-energy transitions make only a small net contribution to the CD of the α-helix in the 200 nm region, they enhance the negative exciton band at ∼205 nm and largely cancel the negative exciton band near 175 nm, substantially improving agreement with experiment.

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Charge-Transfer Transitions in the Vacuum-Ultraviolet of Protein Circular Dichroism Spectra

Cited by 52 publications

References 51 publications

Accurate secondary structure prediction and fold recognition for circular dichroism spectroscopy

Accurate secondary structure prediction and fold recognition for circular dichroism spectroscopy

Characterization of dry globular proteins and protein fibrils by synchrotron radiation vacuum UV circular dichroism

A significant role for high‐energy transitions in the ultraviolet circular dichroism spectra of polypeptides and proteins

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