Home

Citation: XU Si-Chuan, DENG Sheng-Rong, MA Li-Ying, SHI Qiang, GE Mao-Fa, ZHANG Xing-Kang. Active Sites for Retinal Binding to Bovine Rhodopsin[J]. Acta Physico-Chimica Sinica, ;2009, 25(07): 1290-1296. doi: 10.3866/PKU.WHXB20090701 shu

Active Sites for Retinal Binding to Bovine Rhodopsin

1.
Key Laboratory for Medicinal Chemistry of Natural Resource, Ministry of Education, Laboratory on the Origin of Life, College of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China

Received Date: 12 January 2009
Available Online: 14 April 2009

Rhodopsin is a membrane protein and its retinal (RET) active binding sites are related to the process of vision and the pathology of some ophthalmic ailments. Based on the bovine rhodopsin crystal structure (PDB code: 1U19), computations were performed using density functional theory to explore the interaction and binding energies between the RET-Lys296 residue and each of the 30 amino acid residues arranged in a sphere with 0.6 nm radius around a RET molecule. Results show that Glu113, Glu181 and Glu122 residues are the active binding sites for the protonated RET-Lys296 residue and that their binding energies are -333.38, -205.67 and -194.56 kJ·mol-1, respectively. They each have one negative charge to interact with the protonated RET-Lys296 residue through a strong electrostatic interaction. Other residues Ala292, Cys187, Phe293, Pro291 and Trp265 have smaller binding energies with the protonated RET-Lys296 residue at the 1U19 protein. When the RET-Lys296 residue is deprotonated, the interactions mentioned above disappear therefore to promote the dissociation of retinal from rhodopsin. Our results demonstrate that two crystal H2O molecules that form hydrogen bonds to Glu113 and Glu181 residues also play an important role in stabilizing the RET-Lys296 residue.
- Rhodopsin,
- Retinal,
- 1U19,
- Active site,
- Density functional theory
1. [1]
  Hao XU , Ruopeng LI , Peixia YANG , Anmin LIU , Jie BAI . Regulation mechanism of halogen axial coordination atoms on the oxygen reduction activity of Fe-N₄ site: A density functional theory study. Chinese Journal of Inorganic Chemistry, 2025, 41(4): 695-701. doi: 10.11862/CJIC.20240302
2. [2]
  Jianan Hong , Chenyu Xu , Yan Liu , Changqi Li , Menglin Wang , Yanwei Zhang . Decoding the interfacial competition between hydrogen evolution and CO₂ reduction via edge-active-site modulation in photothermal catalysis. Acta Physico-Chimica Sinica, 2025, 41(9): 100099-0. doi: 10.1016/j.actphy.2025.100099
3. [3]
  Xue Liu , Lipeng Wang , Luling Li , Kai Wang , Wenju Liu , Biao Hu , Daofan Cao , Fenghao Jiang , Junguo Li , Ke Liu . Research on Cu-Based and Pt-Based Catalysts for Hydrogen Production through Methanol Steam Reforming. Acta Physico-Chimica Sinica, 2025, 41(5): 100049-0. doi: 10.1016/j.actphy.2025.100049
4. [4]
  Xiaofeng Zhu , Bingbing Xiao , Jiaxin Su , Shuai Wang , Qingran Zhang , Jun Wang . Transition Metal Oxides/Chalcogenides for Electrochemical Oxygen Reduction into Hydrogen Peroxides. Acta Physico-Chimica Sinica, 2024, 40(12): 2407005-0. doi: 10.3866/PKU.WHXB202407005
5. [5]
  Meifeng Zhu , Jin Cheng , Kai Huang , Cheng Lian , Shouhong Xu , Honglai Liu . Classical Density Functional Theory for Understanding Electrochemical Interface. University Chemistry, 2025, 40(3): 148-152. doi: 10.12461/PKU.DXHX202405166
6. [6]
  Kaifu Zhang , Shan Gao , Bin Yang . Application of Theoretical Calculation with Fun Practice in Raman Spectroscopy Experimental Teaching. University Chemistry, 2025, 40(3): 62-67. doi: 10.12461/PKU.DXHX202404045
7. [7]
  Jie ZHAO , Sen LIU , Qikang YIN , Xiaoqing LU , Zhaojie WANG . Theoretical calculation of selective adsorption and separation of CO₂ by alkali metal modified naphthalene/naphthalenediyne. Chinese Journal of Inorganic Chemistry, 2024, 40(3): 515-522. doi: 10.11862/CJIC.20230385
8. [8]
  Jie ZHAO , Huili ZHANG , Xiaoqing LU , Zhaojie WANG . Theoretical calculations of CO₂ capture and separation by functional groups modified 2D covalent organic framework. Chinese Journal of Inorganic Chemistry, 2025, 41(2): 275-283. doi: 10.11862/CJIC.20240213
9. [9]
  Maitri Bhattacharjee , Rekha Boruah Smriti , R. N. Dutta Purkayastha , Waldemar Maniukiewicz , Shubhamoy Chowdhury , Debasish Maiti , Tamanna Akhtar . Synthesis, structural characterization, bio-activity, and density functional theory calculation on Cu(Ⅱ) complexes with hydrazone-based Schiff base ligands. Chinese Journal of Inorganic Chemistry, 2024, 40(7): 1409-1422. doi: 10.11862/CJIC.20240007
10. [10]
  Weina Wang , Lixia Feng , Fengyi Liu , Wenliang Wang . Computational Chemistry Experiments in Facilitating the Study of Organic Reaction Mechanism: A Case Study of Electrophilic Addition of HCl to Asymmetric Alkenes. University Chemistry, 2025, 40(3): 206-214. doi: 10.12461/PKU.DXHX202407022
11. [11]
  Zhengkun QIN , Zicong PAN , Hui TIAN , Wanyi ZHANG , Mingxing SONG . A series of iridium(Ⅲ) complexes with fluorophenyl isoquinoline ligand and low-efficiency roll-off properties: A density functional theory study. Chinese Journal of Inorganic Chemistry, 2025, 41(6): 1235-1244. doi: 10.11862/CJIC.20240429
12. [12]
  Tongqi Ye , Yanqing Wang , Qi Wang , Huaiping Cong , Xianghua Kong , Yuewen Ye . Reform of Classical Thermodynamics Curriculum from the Perspective of Computational Chemistry. University Chemistry, 2025, 40(7): 387-392. doi: 10.12461/PKU.DXHX202409128
13. [13]
  Wei Sun , Yongjing Wang , Kun Xiang , Saishuai Bai , Haitao Wang , Jing Zou , Arramel , Jizhou Jiang . CoP Decorated on Ti₃C₂T_x MXene Nanocomposites as Robust Electrocatalyst for Hydrogen Evolution Reaction. Acta Physico-Chimica Sinica, 2024, 40(8): 2308015-0. doi: 10.3866/PKU.WHXB202308015
14. [14]
  Xiaochen Zhang , Fei Yu , Jie Ma . Cutting-Edge Applications of Multi-Angle Numerical Simulations for Capacitive Deionization. Acta Physico-Chimica Sinica, 2024, 40(11): 2311026-0. doi: 10.3866/PKU.WHXB202311026
15. [15]
  Qiqi Li , Su Zhang , Yuting Jiang , Linna Zhu , Nannan Guo , Jing Zhang , Yutong Li , Tong Wei , Zhuangjun Fan . Preparation of High Density Activated Carbon by Mechanical Compression of Precursors for Compact Capacitive Energy Storage. Acta Physico-Chimica Sinica, 2025, 41(3): 2406009-0. doi: 10.3866/PKU.WHXB202406009
16. [16]
  .
  南开大学师唯/华北电力大学（保定）刘景维：二维配位聚合物中有序的亲锂冠醚位点用于无枝晶锂沉积
  . CCS Chemistry, 2025, 7(0): -.
17. [17]
  Hui Wang , Abdelkader Labidi , Menghan Ren , Feroz Shaik , Chuanyi Wang . Recent Progress of Microstructure-Regulated g-C₃N₄ in Photocatalytic NO Conversion: The Pivotal Roles of Adsorption/Activation Sites. Acta Physico-Chimica Sinica, 2025, 41(5): 100039-0. doi: 10.1016/j.actphy.2024.100039
18. [18]
  Zhigang Zeng , Changzhou Liao , Lei Yu . Molecules for COVID-19 treatment. Chinese Chemical Letters, 2024, 35(7): 109349-. doi: 10.1016/j.cclet.2023.109349
19. [19]
  Runze Xu , Rui Liu . U-Pb Dating in the Age of Dinosaurs. University Chemistry, 2024, 39(9): 243-247. doi: 10.12461/PKU.DXHX202404083
20. [20]
  Yihui Song , Shangshang Qin , Kai Wu , Chengyun Jin , Bin Yu . 生物化学在高水平创新型药学人才培养中的交叉融合应用——以去甲基化酶LSD1抑制剂的活性评价为例. University Chemistry, 2025, 40(6): 341-352. doi: 10.12461/PKU.DXHX202406018

Get Citation

PDF

XML

Metrics

PDF Downloads(1424)
Abstract views(3686)
HTML views(97)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142

Address：Zhongguancun North First Street 2,100190 Beijing, PR China Tel: +86-010-82449177-888

DownLoad: Full-Size Img PowerPoint

Return

Active Sites for Retinal Binding to Bovine Rhodopsin

南开大学师唯/华北电力大学（保定）刘景维：二维配位聚合物中有序的亲锂冠醚位点用于无枝晶锂沉积

Metrics

通讯作者: 陈斌, bchen63@163.com