Sensitivity of circular dichroism to protein tertiary structure class

Manavalan, Parthasarathy; Johnson, W. Curtis

doi:10.1038/305831a0

Cited by 403 publications

(242 citation statements)

References 25 publications

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“…44,45 The agreement between calculation and experiment is worse than for other proteins in these cases, especially between 190 and 210 nm. In -II proteins, 44,45 the strands are rather short or not aligned in a parallel manner but often twisted and bent.…”

Section: Influence Of Secondary Structurementioning

confidence: 77%

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

et al. 2008

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Circular dichroism (CD) is widely used in the structural characterization and secondary structure determination of proteins. The vacuum UV region (below 190 nm), where charge-transfer transitions have an influence on the CD spectra, can be accessed using synchrotron radiation circular dichroism (SRCD) spectroscopy. Recently, charge-transfer transitions in a conformationally diverse set of dipeptides have been characterized ab initio using complete active space self-consistent field calculations, and the relevant charge distributions have been parametrized for use in the matrix method for calculations of protein CD. Here, we present calculations of the vacuum UV CD spectra of 71 proteins, for which experimental SRCD spectra and X-ray crystal structures are available. The theoretical spectra are calculated considering charge-transfer and side chain transitions. This significantly improves the agreement with experiment, raising the Spearman correlation coefficient between the calculated and the experimental intensity at 175 nm from 0.12 to 0.79. The influence of the conformation on charge-transfer transitions is analyzed in detail, showing that the n f π* charge-transfer transitions are most important in R-helical proteins, whereas in strand proteins the π f π* charge-transfer transition along the chain in the amino-to carboxy-end direction is most dominant.

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Section: Influence Of Secondary Structurementioning

confidence: 77%

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

et al. 2008

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“…Interestingly, similar CD spectra have also been shown for other proteins, including oxidized ribonuclease and a subclass of all-␤ proteins (termed ␤-II proteins) such as ␣-chymotrypsin, elastase, and soy bean trypsin inhibitor protein. X-ray diffraction data have shown that these ␤-sheet proteins are either highly distorted or made up of short irregular ␤ strands (30,31), and this could also hold true for IGFBP-5. The fluorescence spectra show that wt IGFBP-5, C-Term, and NTerm have very similar emission maxima, which indicates that the orientation of the Trp side chains is very similar in the three proteins.…”

Section: Discussionmentioning

confidence: 99%

Specific Amino Acid Substitutions Determine the Differential Contribution of the N- and C-terminal Domains of Insulin-like Growth Factor (IGF)-binding Protein-5 in Binding IGF-I

Shand

Beattie

Song

et al. 2003

Journal of Biological Chemistry

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“…2C and 2D), however, exhibits a different kind of CD spectrum, usually found for (␣ ϩ ␤)-proteins, which have two separate domains, one with mainly ␣-and one with mainly ␤-structure (16). The CD spectra of (␣ ϩ ␤) proteins usually have a larger intensity in the 210 nm band than in the 222 nm band; the reverse is true for (␣/␤) proteins and the minimum is always skewed towards the 222 nm band when there is a broad minimum (17).…”

Section: Influences On the Protein Fold As Measured By CD Spectroscopymentioning

confidence: 99%

Biophysical Characterization of Cyclic Nucleotide Phosphodiesterases

Hofmann

Tarasov

Grella

et al. 2002

Biochemical and Biophysical Research Communications

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We have compared selected biophysical properties of three phosphodiesterases, from Arabidopsis thaliana, Saccharomyces cerevisiae, and Escherichia coli. All of them belong to a recently identified family of cyclic nucleotide phosphodiesterases. Experiments elucidating folding stability, protein fluorescence, oligomerization behavior, and the effects of substrates were conducted, revealing differences between the plant and the yeast protein. According to CD spectroscopy, the latter protein exhibits an (␣ ؉ ␤) fold rather than an (␣/␤) fold as found with CPDase (A. thaliana). The redox-dependent structural reorganization recently found for the plant protein by X-ray crystallography could not be detected by CD spectroscopy due to its only marginal effect on the total percentage of helical content. However, in the present study a redoxdependent effect was also observed for the yeast CPDase. The enzymatic activity of wild type CPDase (A. thaliana) as well as of four mutants were characterized by isothermal titration calorimetry and the results prove the requirement of all four residues of the previously identified tandem signature motif for the catalytic function. Within the comparison of the three proteins in this study, the PDase Homolog/RNA ligase (E. coli) shares more similarities with the plant than with the yeast protein.

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Sensitivity of circular dichroism to protein tertiary structure class

Cited by 403 publications

References 25 publications

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

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

Specific Amino Acid Substitutions Determine the Differential Contribution of the N- and C-terminal Domains of Insulin-like Growth Factor (IGF)-binding Protein-5 in Binding IGF-I

Biophysical Characterization of Cyclic Nucleotide Phosphodiesterases

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