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Singular value decomposition analysis of the secondary structure features contributing to the circular dichroism spectra of model proteins.

ABSTRACT: Amyloid fibril formation occurs in restricted environment, such as the interface between intercellular fluids and bio-membranes. Conformational interconversion from α-helix to β-structure does not progress in fluids; however, it can occur after sedimentary aggregation during amyloid fibril formation induced by heat treatment of hen egg white lysozyme (HEWL). Secondary structures of various proteins and denatured proteins titrated with 2,2,2-trifluoroethanol (TFE) were examined using their CD spectra. Gaussian peak/trough and singular value decompositions (SVD) showed that the spectral pattern of the α-helix comprised a sharp trough at wavelength 207 nm and a broad trough at 220 nm. Conversely, we distinguished two patterns for β-sheet-a spread barrel type, corresponding to ConA, and a tightly weaved type, corresponding to the soybean trypsin inhibitor. Herein, we confirmed that the spectral/conformational interconversion of the heat-treated HEWL was not observed in the dissolved fluid.

SUBMITTER: Shiratori T

PROVIDER: S-EPMC8528683 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature

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Singular value decomposition analysis of the secondary structure features contributing to the circular dichroism spectra of model proteins.

Shiratori Tomoki T Goto Satoru S Sakaguchi Tomoyo T Kasai Takahiro T Otsuka Yuta Y Higashi Kyohei K Makino Kosho K Takahashi Hideyo H Komatsu Kazushi K

Biochemistry and biophysics reports 20211018

Amyloid fibril formation occurs in restricted environment, such as the interface between intercellular fluids and bio-membranes. Conformational interconversion from α-helix to β-structure does not progress in fluids; however, it can occur after sedimentary aggregation during amyloid fibril formation induced by heat treatment of hen egg white lysozyme (HEWL). Secondary structures of various proteins and denatured proteins titrated with 2,2,2-trifluoroethanol (TFE) were examined using their CD spe ...[more]

PMID: 34712848

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Project description:BackgroundBoth microarrays and quantitative real-time PCR are convenient tools for studying the transcriptional levels of genes. The former is preferable for large scale studies while the latter is a more targeted technique. Because of platform-dependent systematic effects, simple comparisons or merging of datasets obtained by these technologies are difficult, even though they may often be desirable. These difficulties are exacerbated if there is only partial overlap between the experimental conditions and genes probed in the two datasets.ResultsWe show here that the generalized singular value decomposition provides a practical tool for merging a small, targeted dataset obtained by quantitative real-time PCR of specific genes with a much larger microarray dataset. The technique permits, for the first time, the identification of genes present in only one dataset co-expressed with a target gene present exclusively in the other dataset, even when experimental conditions for the two datasets are not identical. With the rapidly increasing number of publically available large scale microarray datasets the latter is frequently the case. The method enables us to discover putative candidate genes involved in the biosynthesis of the (1,3;1,4)-beta-D-glucan polysaccharide found in plant cell walls.ConclusionWe show that the generalized singular value decomposition provides a viable tool for a combined analysis of two gene expression datasets with only partial overlap of both gene sets and experimental conditions. We illustrate how the decomposition can be optimized self-consistently by using a judicious choice of genes to define it. The ability of the technique to seamlessly define a concept of "co-expression" across both datasets provides an avenue for meaningful data integration. We believe that it will prove to be particularly useful for exploiting large, publicly available, microarray datasets for species with unsequenced genomes by complementing them with more limited in-house expression measurements.

Dataset Information

Singular value decomposition analysis of the secondary structure features contributing to the circular dichroism spectra of model proteins.

Publications

Singular value decomposition analysis of the secondary structure features contributing to the circular dichroism spectra of model proteins.

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