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Sluchanko NN, Maksimov EG, Slonimskiy YB, Varfolomeeva LA, Bukhanko AY, Egorkin NA, Tsoraev GV, Khrenova MG, Ge B, Qin S, Boyko KM, Popov VO. Structural framework for the understanding spectroscopic and functional signatures of the cyanobacterial Orange Carotenoid Protein families. Int J Biol Macromol 2024; 254:127874. [PMID: 37939760 DOI: 10.1016/j.ijbiomac.2023.127874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/23/2023] [Accepted: 11/01/2023] [Indexed: 11/10/2023]
Abstract
The Orange Carotenoid Protein (OCP) is a unique photoreceptor crucial for cyanobacterial photoprotection. Best studied Synechocystis sp. PCC 6803 OCP belongs to the large OCP1 family. Downregulated by the Fluorescence Recovery Protein (FRP) in low-light, high-light-activated OCP1 binds to the phycobilisomes and performs non-photochemical quenching. Recently discovered families OCP2 and OCP3 remain structurally and functionally underexplored, and no systematic comparative studies have ever been conducted. Here we present two first crystal structures of OCP2 from morphoecophysiologically different cyanobacteria and provide their comprehensive structural, spectroscopic and functional comparison with OCP1, the recently described OCP3 and all-OCP ancestor. Structures enable correlation of spectroscopic signatures with the effective number of hydrogen and discovered here chalcogen bonds anchoring the ketocarotenoid in OCP, as well as with the rotation of the echinenone's β-ionone ring in the CTD. Structural data also helped rationalize the observed differences in OCP/FRP and OCP/phycobilisome functional interactions. These data are expected to foster OCP research and applications in optogenetics, targeted carotenoid delivery and cyanobacterial biomass engineering.
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Affiliation(s)
- Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.
| | - Eugene G Maksimov
- M.V. Lomonosov Moscow State University, Faculty of Biology, Moscow 119991, Russia
| | - Yury B Slonimskiy
- A.N. Bach Institute of Biochemistry, Federal Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Larisa A Varfolomeeva
- A.N. Bach Institute of Biochemistry, Federal Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Antonina Y Bukhanko
- M.V. Lomonosov Moscow State University, Faculty of Biology, Moscow 119991, Russia
| | - Nikita A Egorkin
- A.N. Bach Institute of Biochemistry, Federal Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; M.V. Lomonosov Moscow State University, Faculty of Biology, Moscow 119991, Russia
| | - Georgy V Tsoraev
- A.N. Bach Institute of Biochemistry, Federal Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Maria G Khrenova
- A.N. Bach Institute of Biochemistry, Federal Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; Lomonosov Moscow State University, Chemistry Department, Moscow 119991, Russia
| | - Baosheng Ge
- China University of Petroleum (Huadong), College of Chemistry and Chemical Engineering, Qingdao 266580, People's Republic of China
| | - Song Qin
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, People's Republic of China.
| | - Konstantin M Boyko
- A.N. Bach Institute of Biochemistry, Federal Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Vladimir O Popov
- A.N. Bach Institute of Biochemistry, Federal Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; M.V. Lomonosov Moscow State University, Faculty of Biology, Moscow 119991, Russia
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Adhav V, Saikrishnan K. The Realm of Unconventional Noncovalent Interactions in Proteins: Their Significance in Structure and Function. ACS OMEGA 2023; 8:22268-22284. [PMID: 37396257 PMCID: PMC10308531 DOI: 10.1021/acsomega.3c00205] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/22/2023] [Indexed: 07/04/2023]
Abstract
Proteins and their assemblies are fundamental for living cells to function. Their complex three-dimensional architecture and its stability are attributed to the combined effect of various noncovalent interactions. It is critical to scrutinize these noncovalent interactions to understand their role in the energy landscape in folding, catalysis, and molecular recognition. This Review presents a comprehensive summary of unconventional noncovalent interactions, beyond conventional hydrogen bonds and hydrophobic interactions, which have gained prominence over the past decade. The noncovalent interactions discussed include low-barrier hydrogen bonds, C5 hydrogen bonds, C-H···π interactions, sulfur-mediated hydrogen bonds, n → π* interactions, London dispersion interactions, halogen bonds, chalcogen bonds, and tetrel bonds. This Review focuses on their chemical nature, interaction strength, and geometrical parameters obtained from X-ray crystallography, spectroscopy, bioinformatics, and computational chemistry. Also highlighted are their occurrence in proteins or their complexes and recent advances made toward understanding their role in biomolecular structure and function. Probing the chemical diversity of these interactions, we determined that the variable frequency of occurrence in proteins and the ability to synergize with one another are important not only for ab initio structure prediction but also to design proteins with new functionalities. A better understanding of these interactions will promote their utilization in designing and engineering ligands with potential therapeutic value.
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