Novel Matrix Descriptor for Secondary Structure Segments in Proteins: Demonstration of Predictability from Circular Dichroism Spectra

Pančoška, Petr; Janota, Vı́t; Keiderling, Timothy A.

doi:10.1006/abio.1998.2960

Cited by 38 publications

(21 citation statements)

References 28 publications

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“…Magg et al (62) observed a stretching of the second ␤-strand upon collapse, suggesting that the CD signal observed in our experiments could be due to strands of lengths approaching those in the native state. The question of segment length could possibly also be addressed with new methods for the analysis of CD spectra in terms of the number and size of structured segments in proteins (63,64), but the current quality of our CD spectra for collapsed unfolded CspTm does not yet warrant such detailed deconvolution. The further development of kinetic SRCD and its combination with single-molecule fluorescence will be an important complementation of NMR methods in clarifying these structural details and the question of whether the behavior of CspTm is an exception or possibly a more general characteristic of such small all-␤ proteins.…”

Section: Discussionmentioning

confidence: 99%

Mapping protein collapse with single-molecule fluorescence and kinetic synchrotron radiation circular dichroism spectroscopy

Hoffmann

Kane

Nettels

et al. 2007

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

215

338

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We have used the combination of single-molecule Fö rster resonance energy transfer and kinetic synchrotron radiation circular dichroism experiments to probe the conformational ensemble of the collapsed unfolded state of the small cold shock protein CspTm under near-native conditions. This regime is physiologically most relevant but difficult to access experimentally, because the equilibrium signal in ensemble experiments is dominated by folded molecules. Here, we avoid this problem in two ways. One is the use of single-molecule Fö rster resonance energy transfer, which allows the separation of folded and unfolded subpopulations at equilibrium and provides information on long-range intramolecular distance distributions. From experiments with donor and acceptor chromophores placed at different positions within the chain, we find that the distance distributions in unfolded CspTm agree surprisingly well with a Gaussian chain not only at high concentrations of denaturant, where the polypeptide chain is expanded, but also at low denaturant concentrations, where the chain is collapsed. The second, complementary approach is synchrotron radiation circular dichroism spectroscopy of collapsed unfolded molecules transiently populated with a microfluidic device that enables rapid mixing. The results indicate a ␤-structure content of the collapsed unfolded state of Ϸ20% compared with the folded protein. This suggests that collapse can induce secondary structure in an unfolded state without interfering with long-range distance distributions characteristic of a random coil, which were previously found only for highly expanded unfolded proteins.Gaussian chain ͉ microfluidic mixing ͉ protein folding ͉ random coil ͉ secondary structure W ith the discovery of small proteins that fold in the absence of populated intermediates (1), our quantitative understanding of the elementary properties of protein folding reactions has made significant advances, including the structural characterization of transition states for folding (2) and the prediction of folding rates from native structure (3-5). One of the most severe limitations for the further development of these approaches is our ignorance about the energetic or structural properties of unfolded † † states of proteins. Because of the structural heterogeneity and complexity of the ensembles of conformations populated by unfolded proteins, their experimental characterization has proven extremely difficult. Traditional methods, such as small-angle scattering techniques (6), provide only global physical properties, e.g., the radius of gyration. In some cases, more detailed structural information can be obtained from NMR (7-10), but these studies usually provide information about the denatured state only under nonnative conditions, typically in the presence of large concentrations of denaturant, or through severe destabilization of the native state induced by covalent modification or mutations. The most interesting and physiologically relevant situation, however, is that of an unfolded sta...

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Section: Discussionmentioning

confidence: 99%

Mapping protein collapse with single-molecule fluorescence and kinetic synchrotron radiation circular dichroism spectroscopy

Hoffmann

Kane

Nettels

et al. 2007

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

215

338

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“…10,11 Aromatic groups may contribute to the overall spectrum, as may the interactions between amino acids far off in the sequence (tertiary interactions). Moreover, the contribution of ␣-helix to the spectrum depends on chain length.…”

Section: ϫ7mentioning

confidence: 99%

“…11 Recently, Pancoska et al 10 have designed a matrix descriptor for secondary structure segments that estimates the connectivity and numbers of segments.…”

Section: ϫ7mentioning

confidence: 99%

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SOMCD: Method for evaluating protein secondary structure from UV circular dichroism spectra

et al. 2001

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This article presents SOMCD, an improved method for the evaluation of protein secondary structure from circular dichroism spectra, based on Kohonen's self-organizing maps (SOM). Protein circular dichroism (CD) spectra are used to train a SOM, which arranges the spectra on a twodimensional map. Location in the map reflects the secondary structure composition of a protein. With SOMCD, the prediction of ␤-turn has been included. The number of spectra in the training set has been increased, and it now includes 39 protein spectra and 6 reference spectra. Finally, SOM parameters have been chosen to minimize distortion and make the network produce clusters with known properties. Estimation results show improvements compared with the previous version, K2D, which, in addition, estimated only three secondary structure components; the accuracy of the method is more uniform over the different secondary structures.

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“…Most work has been done using a curve fitting approach which basically relies on band narrowing and decomposition of mostly the amide I band shape into its underlying components [5,[8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23]. More recently, pattern recognition based methods have been suggested [24][25][26][27][28][29][30][31][32][33][34][35]. Here, we introduce an alternative pattern recognition approach based on neural networks trained by a locally adaptive learning scheme, "resilient backpropagation" [36].…”

Section: Introductionmentioning

confidence: 99%

Automatic amide I frequency selection for rapid quantification of protein secondary structure from Fourier transform infrared spectra of proteins

2002

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Here we report the development of a new neural network based approach for rapid quantification of protein secondary structure from Fourier transform infrared (FTIR) spectra of proteins. A technique for efficiently reducing the amount of spectral data by almost 90% is suggested to facilitate faster neural network analysis. Additionally, an automatic procedure is introduced for selecting only those regions within the amide I band of protein FTIR spectra, which can be best related to secondary structure contents by subsequent neural network analysis. Based on a given reference set of FTIR spectra from proteins with known secondary structure, a subset of merely 29 out of 101 amide I absorbance values could be identified, which lead to an improved prediction accuracy. The average prediction accuracy achieved for helix, sheet, turn, bend, and other is 4.96% which is better than that achieved by alternative methods that have been previously reported indicating the significant potential of this approach. Our suggested automatic amide I frequency selection procedure may be easily extended to identify promising regions from spectral data recorded by other spectroscopic techniques, like for example circular dichroism spectroscopy.

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Novel Matrix Descriptor for Secondary Structure Segments in Proteins: Demonstration of Predictability from Circular Dichroism Spectra

Cited by 38 publications

References 28 publications

Mapping protein collapse with single-molecule fluorescence and kinetic synchrotron radiation circular dichroism spectroscopy

Mapping protein collapse with single-molecule fluorescence and kinetic synchrotron radiation circular dichroism spectroscopy

SOMCD: Method for evaluating protein secondary structure from UV circular dichroism spectra

Automatic amide I frequency selection for rapid quantification of protein secondary structure from Fourier transform infrared spectra of proteins

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