CAPITO—a web server-based analysis and plotting tool for circular dichroism data

Wiedemann, Christoph; Bellstedt, Peter; Görlach, Matthias

doi:10.1093/bioinformatics/btt278

Cited by 224 publications

(202 citation statements)

References 44 publications

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“…Measurements were recorded at room temperature at 0.5-nm wavelength increments from 260 to 195 nm at 20 nm/min, by using a 0.1-cm path length cell, 1-nm band width, 1-s response time, and five accumulations. The CD spectra were analyzed using the web-based programs CAPITO [28] and SOMCD [29] and the software package CDPro [30].…”

Section: Circular Dichroismmentioning

confidence: 99%

Recombinant production of functional full-length and truncated human TRAM/TICAM-2 adaptor protein involved in Toll-like receptor and interferon signaling

Ullah

Valkov

et al. 2015

Protein Expression and Purification

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Section: Circular Dichroismmentioning

confidence: 99%

Recombinant production of functional full-length and truncated human TRAM/TICAM-2 adaptor protein involved in Toll-like receptor and interferon signaling

Ullah

Valkov

et al. 2015

Protein Expression and Purification

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“…Thermal denaturation was performed heating up protein solution from 20 to 90 °C and following the change in ellipticity at 222 nm. CAPITO (Wiedemann et al 2013) was used to evaluate the degree of protein folding according to the CD spectrum. The fraction of α-helices in each selected protein was calculated from mean residue ellipticity at 222 nm, according to the equation f H = [(θ) obs − (θ) c ]/[(θ)] H − (θ) c ], where (θ) obs is the protein ellipticity at 222 nm, (θ) c is the calculated ellipticity at 222 nm for 100 % random coil conformation and (θ) H is the calculated ellipticity at 222 nm for 100 % helical content (Rohl and Baldwin 1997).…”

Section: Circular Dichroism Spectroscopymentioning

confidence: 99%

“…CAPITO conformational classification of FvPRKRIP, FvSMP,, as compared to a set of reference proteins with different degrees of structure (indicated as empty circles and crosses), as previously described(Wiedemann et al 2013) Fig. 5 Circular dichroism spectrum of a FvPRKRIP, b FvFAM32A-like, c FvSMP and d FvPCD-4 at 20 °C (blue), 90 °C (red), 20 °C after denaturation (green).…”

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confidence: 99%

Unfoldome variation upon plant-pathogen interactions: strawberry infection by Colletotrichum acutatum

et al. 2015

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Intrinsically disordered proteins (IDPs) are proteins that lack secondary and/or tertiary structure under physiological conditions. These proteins are very abundant in eukaryotic proteomes and play crucial roles in all molecular mechanisms underlying the response to environmental challenges. In plants, different IDPs involved in stress response have been identified and characterized. Nevertheless, a comprehensive evaluation of protein disorder in plant proteomes under abiotic or biotic stresses is not available so far. In the present work the transcriptome dataset of strawberry (Fragaria X ananassa) fruits interacting with the fungal pathogen Colletotrichum acutatum was actualized onto the woodland strawberry (Fragaria vesca) genome. The obtained cDNA sequences were translated into protein sequences, which were subsequently subjected to disorder analysis. The results, providing the first estimation of disorder abundance associated to plant infection, showed that the proteome activated in the strawberry red fruit during the active fungal propagation is remarkably depleted in disorder. On the other hand, in the resistant white fruit, no significant disorder reduction is observed in the proteins expressed in response to fungal infection. Four representative proteins, FvSMP, FvPRKRIP, FvPCD-4 and FvFAM32A-like, predicted as mainly disordered and never experimentally characterized before, were isolated, and the absence of structure was validated at the secondary and tertiary level using circular dichroism and differential scanning fluorimetry. Their quaternary structure was also established using light scattering. The results are discussed considering the role of protein disorder in plant defense.

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“…The spectra were analysed using the CDtool software. The thermal transition was reversible by cooling of the solution.To calculate the structure content we used Dichroweb software (Whitmore and Wallace, 2004;, and CAPITO (CD Analysis and Plotting Tool) server that is specific for intrinsically disordered proteins (Uversky et al, 2002;Wiedemann et al, 2013).…”

Section: Circular Dichroismmentioning

confidence: 99%

Conformational Analysis of Rat Seminal Vesicle Secretory Protein 4, an Intrinsically Disordered Protein Having Interesting Pharmacological Properties

Costantini¹,

Gautam²,

Maria³

et al. 2015

IJC

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Rat seminal vesicle protein 4 (RSV4) is a member of the seminal vesicle protein family present in rats, 90 residues long. When secreted, it is involved in many functions related to the reproduction ranging from semen coagulation to sperm capacitation, but its fragments have also shown in vitro pharmacological properties such as anti-inflammatory and pro-coagulant activity, important in the cancer development. However, no three-dimensional model of this protein is yet available probably because of the presence of intrinsic disorder in the structure. In this article we report structural studies in solution of RSV4 by SEC (size exclusion chromatography) and CD (circular dichroism). In solution the monomer is highly flexible and poorly organized with the presence of highly fluctuating helical segments and, as also suggested by SEC, is classifiable as NU-PMG (natively unfolded pre-molten globule). The lack of a cooperative sigmoidal structural transition induced by thermal and GdmCl perturbation in monomer supports the poor structural organization expected for a NU-PMG conformational model. The structure of RSV4 monomer was modeled computationally and subjected to molecular dynamics simulations to study its conformational changes and energetic stability.

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CAPITO—a web server-based analysis and plotting tool for circular dichroism data

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 224 publications

References 44 publications

Recombinant production of functional full-length and truncated human TRAM/TICAM-2 adaptor protein involved in Toll-like receptor and interferon signaling

Recombinant production of functional full-length and truncated human TRAM/TICAM-2 adaptor protein involved in Toll-like receptor and interferon signaling

Unfoldome variation upon plant-pathogen interactions: strawberry infection by Colletotrichum acutatum

Conformational Analysis of Rat Seminal Vesicle Secretory Protein 4, an Intrinsically Disordered Protein Having Interesting Pharmacological Properties

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