Unsupervised classification of PSII with and without water-oxidizing complex samples by PARAFAC resolution of excitation-emission fluorescence images

Somayyeh Akbarian, Mohsen Kompany-Zareh, Mohammad Mahdi Najafpour, Tatsuya Tomo, Suleyman Allakhverdiev

Research output: Contribution to journalArticle

Abstract

The potential of excitation-emission fluorescence spectroscopy combined with three-way analysis was investigated for discriminating the photosystem II (PSII)(with the water-oxidizing complex)and without the water-oxidizing complex (wPSII)using unsupervised classification methods. The water-oxidizing complex within PSII carry out the reaction of water splitting which is as a vital process on the earth. Therefore, discriminating the presence of the water-oxidizing complex in protein samples is crucial. Low cost and accurate spectroscopic determination of the amount of clusters inside PSII or any other protein containing species are important when investigating the inclusion and exclusion of such clusters into and from species. Fluorescence data of samples were similar, and we showed the potential usefulness of multivariate methods, such as parallel factor analysis (PARAFAC)and principal component analysis (PCA)for recognition of the two types of samples. Both techniques were applied to the excitation-emission fluorescence matrices (EEM)of solutions at two of different pH values (2.0 and 12.0). Three fluorescent components were found for all samples that are related to tyrosine (Tyr), tryptophan (Trp)and phenylalanine (Phe)amino acids. These three amino acids are representative of all datasets and indicate their similarities and differences. We then found the effectual wavelengths for separation of samples in a specific acidity, including the excitation wavelengths of 220 and 230 nm and the emission wavelengths of 300 and 305 nm. The acidity of the solutions has various influences on the conformation of proteins. In PSII and PSII the without water-oxidizing complex samples conformational changes can change their spectra which was applied for discrimination purpose. This separation was better in pH = 12.0. We also showed the effect of time on small conformational changes within datasets were higher in pH = 2.0. In the end, for indicating the high distribution of spectral data from proteins which is the result of conformational changes, we compared the distribution of measured spectral data with that from a simple organic molecule, fluorescein. Altogether, we could distinguish between the two groups of protein samples properly at pH = 12.0 using low-cost EEM spectral images and PARAFAC.

Original languageEnglish
Pages (from-to)58-66
Number of pages9
JournalJournal of Photochemistry and Photobiology B: Biology
Volume195
DOIs
Publication statusPublished - Jun 1 2019
Externally publishedYes

Fingerprint

factor analysis
Photosystem II Protein Complex
Statistical Factor Analysis
Fluorescence
fluorescence
Water
proteins
water
excitation
acidity
Proteins
amino acids
Amino Acids
Costs and Cost Analysis
wavelengths
Protein Conformation
Fluorescence Spectrometry
water splitting
phenylalanine
Principal Component Analysis

Keywords

  • Excitation-emission fluorescence
  • PARAFAC
  • pH
  • Photosystem II
  • Unsupervised classification
  • Water splitting complex

ASJC Scopus subject areas

  • Radiation
  • Radiological and Ultrasound Technology
  • Biophysics
  • Radiology Nuclear Medicine and imaging

Cite this

Unsupervised classification of PSII with and without water-oxidizing complex samples by PARAFAC resolution of excitation-emission fluorescence images. / Akbarian, Somayyeh; Kompany-Zareh, Mohsen; Najafpour, Mohammad Mahdi; Tomo, Tatsuya; Allakhverdiev, Suleyman.

In: Journal of Photochemistry and Photobiology B: Biology, Vol. 195, 01.06.2019, p. 58-66.

Research output: Contribution to journalArticle

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AU - Tomo, Tatsuya

AU - Allakhverdiev, Suleyman

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