Vibrational circular dichroism of polypeptides. II. Solution amide II and deuteration results

Sen, Ashish; Keiderling, Timothy A.

doi:10.1002/bip.360230808

Cited by 65 publications

(51 citation statements)

References 30 publications

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“…FTIR are widely used to explore the secondary structure of polypeptides [21,22]. Absorption of stretching of the C@O (amide I) at ca.1655 cm À1 and the deformation and stretching of the NAH bond (amide II) at ca.1550 cm À1 indicate that an a-helix conformation is adopted by the polypeptide blocks [23].…”

Section: Conformation Of Polypeptide Blocks In Bulkmentioning

confidence: 99%

“…Here, the secondary structures under this condition were estimated in detail using an internet available CD reference database ''DICHRO-WEB'' via Continll program [26,27]. It was found that the peptides adopted a complex secondary structure upon heating, which consisted of 16.3% a-helix, 22.3% b-sheet, 26.4% turns, and 35% unordered coil at 70°C, whereas they showed a well-defined conformation of 94.7% a-helix and 5.3% b-sheet at 5°C. It is known that the a-helix originates from intramolecular hydrogen bond between peptide chains.…”

Section: Conformation Of Polypeptide Blocks In Solutionmentioning

confidence: 99%

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Synthesis, characterization, conformation and self-assembly behavior of polypeptide-based brush with oligo (ethylene glycol) side chains

Huang¹,

Luo

Ye³

2015

Journal of Molecular Structure

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Section: Conformation Of Polypeptide Blocks In Bulkmentioning

confidence: 99%

Section: Conformation Of Polypeptide Blocks In Solutionmentioning

confidence: 99%

Synthesis, characterization, conformation and self-assembly behavior of polypeptide-based brush with oligo (ethylene glycol) side chains

Huang¹,

Luo

Ye³

2015

Journal of Molecular Structure

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“…Deuteration has definite effects on the helix VCD, changing the amide I from a couplet to a three-feature band shape (Sen & Keiderling, 1984;Baumruk & Keiderling, 1993). It is reasonable to assume that some, perhaps smaller, changes will occur for the VCD of other secondary structure types on deuteration.…”

Section: Limitations Of the Methodsmentioning

confidence: 99%

Comparison of and limits of accuracy for statistical analyses of vibrational and electronic circular dichroism spectra in terms of correlations to and predictions of protein secondary structure

et al. 1995

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This work provides a systematic comparison of vibrational CD (VCD) and electronic CD (ECD) methods for spectral prediction of secondary structure. The VCD and ECD data are simplified to a small set of spectral parameters using the principal component method of factor analysis (PC/FA). Regression fits of these parameters are made to the X-ray-determined fractional components (FC) of secondary structure. Predictive capability is determined by computing structures for proteins sequentially left out of the regression. All possible combinations of PC/FA spectral parameters (coefficients) were used to form a full set of restricted multiple regressions with the FC values, both independently for each spectral data set as well as for the two VCD sets and all the data grouped together. The complete search over all possible combinations of spectral parameters for different types of spectral data is a new feature of this study, and the focus on prediction is the strength of this approach. The PC/FA method was found to be stable in detail to expansion of the training set. Coupling amide I1 to amide I' parameters reduced the standard deviations of the VCD regression relationships, and combining VCD and ECD data led to the best fits. Prediction results had a minimum error when dependent on relatively few spectral coefficients. Such a limited dependence on spectral variation is the key finding of this work, which has ramifications for previous studies as well as suggests future directions for spectral analysis of structure. The best ECD prediction for helix and sheet uses only one parameter, the coefficient of the first subspectrum. With VCD, the best predictions sample coefficients of both the amide I' and I1 bands, but error is optimized using only a few coefficients. In this respect, ECD is more accurate than VCD for a-helix, and the combined VCD (amide I'+II) predicts the P-sheet component better than does ECD. Combining VCD and ECD data sets yields exceptionally good predictions by utilizing the strengths of each. However, the residual error, its distribution, and, most importantly, the lack of dependence of the method on many of the significant components derived from the spectra leads to the conclusion that the heterogeneity of protein structure is a fundamental limitation to the use of such spectral analysis methods. The underutilization of these data for prediction of secondary structure suggests spectral data could predict a more detailed descriptor.

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“…In fact, VCD has been successfully used in the past to determine secondary structural information in peptides and proteins. 17 We have made use of VCD for deducing the structure of gramicidin in different environments. 18 The solution and crystalline structures need not be the same, because packing effects in the crystalline state can influence the structure.…”

Section: Introductionmentioning

confidence: 99%

A study of the conformations of valinomycin in solution phase

2004

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Vibrational absorption and vibrational circular dichroism (VCD) spectra of valinomycin are measured, in different solvents, in the ester and amide carbonyl stretching regions. The influence of cations, namely Li(+), Na(+), K(+), and Cs(+), in methanol-d(4) solvent is also investigated. Ab initio quantum mechanical calculations using density functional theory and 6-31G* basis set are used to predict the absorption and VCD spectra. A bracelet-type structure for valinomycin that reproduces the experimental absorption and VCD spectra in inert solvents is identified. For the structure of valinomycin in polar solvents, a propeller-type structure was optimized, but further investigations are required to confirm this structure. A symmetric octahedral environment for the ester carbonyl groups in the valinomycin-K(+) complex is supported by the experimental VCD spectra. The results obtained in the present study demonstrate that even for large macrocyclic peptides, such as valinomycin, VCD can be used as an independent structural tool for the study of conformations in solution.

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Vibrational circular dichroism of polypeptides. II. Solution amide II and deuteration results

Cited by 65 publications

References 30 publications

Synthesis, characterization, conformation and self-assembly behavior of polypeptide-based brush with oligo (ethylene glycol) side chains

Synthesis, characterization, conformation and self-assembly behavior of polypeptide-based brush with oligo (ethylene glycol) side chains

Comparison of and limits of accuracy for statistical analyses of vibrational and electronic circular dichroism spectra in terms of correlations to and predictions of protein secondary structure

A study of the conformations of valinomycin in solution phase

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