Detail Analysis for Energy Transfer and Pigment Assembling in C-Phycocyanin through Time-Resolved Spectroscopy and AlphaFold2

被引：0

作者：

Xiao, Chao ^{[1
]}

Guo, Na ^{[1
]}

Liang, Zidong ^{[1
]}

Zhao, Fuli ^{[1
]}

Xie, Mingyuan ^{[1
]}

机构：

[1] Sun Yat sen Univ, Sch Phys, State Key Lab Optoelect Mat & Technol, Guangzhou 510275, Peoples R China

来源：

CRYSTALS | 2022年 / 12卷 / 11期

关键词：

C-phycocyanin; AlphaFold2; energy transfer; time-resolved; ANABAENA-VARIABILIS; TRANSFER PATHWAYS; STRUCTURAL BASIS; RATE CONSTANTS; PHYCOBILISOME; FLUORESCENCE; ANNIHILATION; SIMULATION; HEXAMER; DOCKING;

D O I：

10.3390/cryst12111595

中图分类号：

O7 [晶体学];

学科分类号：

0702 ; 070205 ; 0703 ; 080501 ;

摘要：

The time-resolved fluorescence spectroscopy of the C-phycocyanin (C-PC) complex from the cyanobacterium Spirulina platensis (S. platensis) hexamer with the sub-picosecond resolution was detected, and the energy transfer pathways and related transfer rates were identified through the multiexponential analysis based on Monte-Carlo method. With the purpose to construct the relationship between the functions and the structure in vivo, the three-dimension (3D) protein structure was predicted via AlphaFold2, and the arrangement of chromophores treated as the energy transfer nodes were obtained. The experiment results have been matched well with the structure prediction. This work suggests a new way to investigate structure prediction in vivo and the corresponding functions.

引用

页数：11

共 34 条

[1]

[Anonymous], 1991, CELL CULTURE SOMATIC

[2] Covalent docking using autodock: Two-point attractor and flexible side chain methods [J].

Bianco, Giulia ;

Forli, Stefano ;

Goodsell, David S. ;

Olson, Arthur J. .

PROTEIN SCIENCE, 2016, 25 (01) :295-301

[3]

Blankenship RE, 2014, Molecular Mechanisms of Photosynthesis, V2nd, DOI DOI 10.1002/9780470758472

[4] Structural organization of an intact phycobilisome and its association with photosystem II [J].

Chang, Leifu ;

Liu, Xianwei ;

Li, Yanbing ;

Liu, Cui-Cui ;

Yang, Fan ;

Zhao, Jindong ;

Sui, Sen-Fang .

CELL RESEARCH, 2015, 25 (06) :726-737

[5] COMPARISON OF CALCULATED AND EXPERIMENTALLY RESOLVED RATE CONSTANTS FOR EXCITATION-ENERGY TRANSFER IN C-PHYCOCYANIN .2. TRIMERS [J].

DEBRECZENY, MP ;

SAUER, K ;

ZHOU, JH ;

BRYANT, DA .

JOURNAL OF PHYSICAL CHEMISTRY, 1995, 99 (20) :8420-8431

[6] COMPARISON OF CALCULATED AND EXPERIMENTALLY RESOLVED RATE CONSTANTS FOR EXCITATION-ENERGY TRANSFER IN C-PHYCOCYANIN .1. MONOMERS [J].

DEBRECZENY, MP ;

SAUER, K ;

ZHOU, JH ;

BRYANT, DA .

JOURNAL OF PHYSICAL CHEMISTRY, 1995, 99 (20) :8412-8419

[7] Computational protein-ligand docking and virtual drug screening with the AutoDock suite [J].

Forli, Stefano ;

Huey, Ruth ;

Pique, Michael E. ;

Sanner, Michel F. ;

Goodsell, David S. ;

Olson, Arthur J. .

NATURE PROTOCOLS, 2016, 11 (05) :905-919

[8] Molecular insights into the terminal energy acceptor in cyanobacterial phycobilisome [J].

Gao, Xiang ;

Wei, Tian-Di ;

Zhang, Nan ;

Xie, Bin-Bin ;

Su, Hai-Nan ;

Zhang, Xi-Ying ;

Chen, Xiu-Lan ;

Zhou, Bai-Cheng ;

Wang, Zhi-Xin ;

Wu, Jia-Wei ;

Zhang, Yu-Zhong .

MOLECULAR MICROBIOLOGY, 2012, 85 (05) :907-915

[9]

GLAZER AN, 1985, ANNU REV BIOPHYS BIO, V14, P47, DOI 10.1146/annurev.biophys.14.1.47

[10] Highly accurate protein structure prediction with AlphaFold [J].

Jumper, John ;

Evans, Richard ;

Pritzel, Alexander ;

Green, Tim ;

Figurnov, Michael ;

Ronneberger, Olaf ;

Tunyasuvunakool, Kathryn ;

Bates, Russ ;

Zidek, Augustin ;

Potapenko, Anna ;

Bridgland, Alex ;

Meyer, Clemens ;

Kohl, Simon A. A. ;

Ballard, Andrew J. ;

Cowie, Andrew ;

Romera-Paredes, Bernardino ;

Nikolov, Stanislav ;

Jain, Rishub ;

Adler, Jonas ;

Back, Trevor ;

Petersen, Stig ;

Reiman, David ;

Clancy, Ellen ;

Zielinski, Michal ;

Steinegger, Martin ;

Pacholska, Michalina ;

Berghammer, Tamas ;

Bodenstein, Sebastian ;

Silver, David ;

Vinyals, Oriol ;

Senior, Andrew W. ;

Kavukcuoglu, Koray ;

Kohli, Pushmeet ;

Hassabis, Demis .

NATURE, 2021, 596 (7873) :583-+

← 1 2 3 4 →