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Zabelin AA, Kovalev VB, Shkuropatov AY. On the Mechanism of Selective Chemical Exchange of Bacteriopheophytins in the Reaction Centers of Rhodobacter sphaeroides R-26. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:1119-1129. [PMID: 36273880 DOI: 10.1134/s0006297922100054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/11/2022] [Accepted: 08/10/2022] [Indexed: 06/16/2023]
Abstract
To elucidate the mechanism of site-selective chemical replacement of chromophores in the reaction centers (RCs) of photosynthetic bacteria by external pigments, we investigated how the efficiency of incorporation of plant pheophytin a (Pheo) into the binding sites for bacteriopheophytin a molecules (BPheo) in the isolated Rhodobacter sphaeroides R-26 RCs depended on the incubation medium temperature, Pheo aggregation state, and the presence of organic solvent (acetone). When Pheo was in a form of monomers in free detergent micelles in a water-detergent incubation medium, the degree of selective replacement of photochemically inactive BPheo HB molecules upon incubation of the RC/Pheo mixture at 5°C was ~15%. The exchange efficiency increased to 40% upon incubation at 25°C and reached 100% at the same temperature when 10% acetone was added to the incubation medium. At both 5 and 25°C, the degree of pigment exchange increased approximately twice, when a mixture of Pheo monomers and dimers in the presence of 10% acetone was used as the incubation medium. The removal of acetone from this medium with the preservation of pigment forms led to a significant decrease in the efficiency of Pheo incorporation. The effect of acetone on the pigment exchange was also observed at an elevated incubation temperature (43.5°C), when functionally active BPheo HA molecules were partially replaced. The results are discussed in terms of the mechanism according to which (i) the temperature-dependent internal movements of the RC protein facilitate the release of the BPheo molecule from the binding site with simultaneous insertion of the Pheo molecule into the same site in a coupled process, (ii) the role of temperature largely depends on the steric accessibility of binding pockets in the RC protein, (iii) the incorporation of Pheo occurs from a pool of monomeric molecules included in the RC-detergent micelles, and (iv) the presence of acetone in the incubation medium facilitates the exchange of Pheo monomers between micelles in the solution and the detergent belt of the RC complex.
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Affiliation(s)
- Alexey A Zabelin
- Institute of Basic Biological Problems, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | - Vyacheslav B Kovalev
- Institute of Basic Biological Problems, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Anatoly Ya Shkuropatov
- Institute of Basic Biological Problems, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
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Tiwari SP, Fuglebakk E, Hollup SM, Skjærven L, Cragnolini T, Grindhaug SH, Tekle KM, Reuter N. WEBnm@ v2.0: Web server and services for comparing protein flexibility. BMC Bioinformatics 2014; 15:427. [PMID: 25547242 PMCID: PMC4339738 DOI: 10.1186/s12859-014-0427-6] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Accepted: 12/11/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Normal mode analysis (NMA) using elastic network models is a reliable and cost-effective computational method to characterise protein flexibility and by extension, their dynamics. Further insight into the dynamics-function relationship can be gained by comparing protein motions between protein homologs and functional classifications. This can be achieved by comparing normal modes obtained from sets of evolutionary related proteins. RESULTS We have developed an automated tool for comparative NMA of a set of pre-aligned protein structures. The user can submit a sequence alignment in the FASTA format and the corresponding coordinate files in the Protein Data Bank (PDB) format. The computed normalised squared atomic fluctuations and atomic deformation energies of the submitted structures can be easily compared on graphs provided by the web user interface. The web server provides pairwise comparison of the dynamics of all proteins included in the submitted set using two measures: the Root Mean Squared Inner Product and the Bhattacharyya Coefficient. The Comparative Analysis has been implemented on our web server for NMA, WEBnm@, which also provides recently upgraded functionality for NMA of single protein structures. This includes new visualisations of protein motion, visualisation of inter-residue correlations and the analysis of conformational change using the overlap analysis. In addition, programmatic access to WEBnm@ is now available through a SOAP-based web service. Webnm@ is available at http://apps.cbu.uib.no/webnma . CONCLUSION WEBnm@ v2.0 is an online tool offering unique capability for comparative NMA on multiple protein structures. Along with a convenient web interface, powerful computing resources, and several methods for mode analyses, WEBnm@ facilitates the assessment of protein flexibility within protein families and superfamilies. These analyses can give a good view of how the structures move and how the flexibility is conserved over the different structures.
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Affiliation(s)
- Sandhya P Tiwari
- Department of Molecular Biology, University of Bergen, Bergen, Norway.
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
| | - Edvin Fuglebakk
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
| | - Siv M Hollup
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
| | - Lars Skjærven
- Department of Biomedicine, University of Bergen, Bergen, Norway.
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
| | - Tristan Cragnolini
- Department of Molecular Biology, University of Bergen, Bergen, Norway.
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
- Present address: University Chemical Laboratories, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Svenn H Grindhaug
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
| | - Kidane M Tekle
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
| | - Nathalie Reuter
- Department of Molecular Biology, University of Bergen, Bergen, Norway.
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
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