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]
  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-. doi: 10.3866/PKU.WHXB202407005
2. [2]
  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
3. [3]
  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
4. [4]
  Xiaochen Zhang , Fei Yu , Jie Ma . 多角度数理模拟在电容去离子中的前沿应用. Acta Physico-Chimica Sinica, 2024, 40(11): 2311026-. doi: 10.3866/PKU.WHXB202311026
5. [5]
  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
6. [6]
  Runze Xu , Rui Liu . U-Pb Dating in the Age of Dinosaurs. University Chemistry, 2024, 39(9): 243-247. doi: 10.12461/PKU.DXHX202404083
7. [7]
  Miaomiao He , Zhiqing Ge , Qiang Zhou , Jiaqing He , Hong Gong , Lingling Li , Pingping Zhu , Wei Shao . Exploring the Fascinating Realm of Quantum Dots. University Chemistry, 2024, 39(6): 231-237. doi: 10.3866/PKU.DXHX202310040
8. [8]
  Quanliang Chen , Zhaohui Zhou . Research on the Active Site of Nitrogenase over Fifty Years. University Chemistry, 2024, 39(7): 287-293. doi: 10.3866/PKU.DXHX202310133
9. [9]
  Ming Li , Zhaoyin Li , Mengzhu Liu , Shaoxiang Luo . Unveiling the Artistry of Mordant Dyeing: The Coordination Chemistry Beneath. University Chemistry, 2024, 39(5): 258-265. doi: 10.3866/PKU.DXHX202311085
10. [10]
  Gonglan Ye , Xia Yin , Feng Xu , Peng Yang , Yingpeng Wu , Huilong Fei . Innovations in “Four-in-One” Inorganic Chemistry Education. University Chemistry, 2024, 39(8): 136-141. doi: 10.3866/PKU.DXHX202401071
11. [11]
  Quanguo Zhai , Peng Zhang , Wenyu Yuan , Ying Wang , Shu'ni Li , Mancheng Hu , Shengli Gao . Reconstructing the “Fundamentals of Coordination Chemistry” in Inorganic Chemistry Course. University Chemistry, 2024, 39(11): 117-130. doi: 10.12461/PKU.DXHX202403065
12. [12]
  Lan Yang , Yu Li , Mou Jiang , Rui Zhou , Hengjiang Cong , Minghui Yang , Lei Zhang , Shenhui Li , Yunhuang Yang , Maili Liu , Xin Zhou , Zhong-Xing Jiang , Shizhen Chen . Fluorinated [2]rotaxanes as sensitive ¹⁹F MRI agents: Threading for higher sensitivity. Chinese Chemical Letters, 2024, 35(10): 109512-. doi: 10.1016/j.cclet.2024.109512
13. [13]
  Siyi ZHONG , Xiaowen LIN , Jiaxin LIU , Ruyi WANG , Tao LIANG , Zhengfeng DENG , Ao ZHONG , Cuiping HAN . Targeting imaging and detection of ovarian cancer cells based on fluorescent magnetic carbon dots. Chinese Journal of Inorganic Chemistry, 2024, 40(8): 1483-1490. doi: 10.11862/CJIC.20240093
14. [14]
  Weina Wang , Fengyi Liu , Wenliang Wang . “Extracting Commonality, Delving into Typicals, Deriving Individuality”: Constructing a Knowledge Graph of Crystal Structures. University Chemistry, 2024, 39(3): 36-42. doi: 10.3866/PKU.DXHX202308029
15. [15]
  Liangyu Gong , Jie Wang , Fengyu Du , Lubin Xu , Chuanli Ma , Shihai Yan , Zhuwei Song , Fuheng Liu , Xiuzhong Wang . Construction and Practice of “One-Point, Two-Lines and Three-Sides” Innovative Experimental Platform. University Chemistry, 2024, 39(4): 26-32. doi: 10.3866/PKU.DXHX202308023
16. [16]
  Jianjun Liu , Xue Yang , Chi Zhang , Xueyu Zhao , Zhiwei Zhang , Yongmei Chen , Qinghong Xu , Shao Jin . Preparation and Fluorescence Characterization of CdTe Semiconductor Quantum Dots. University Chemistry, 2024, 39(7): 307-315. doi: 10.3866/PKU.DXHX202311031
17. [17]
  Hongyan Feng , Weiwei Li . Reflections on the Safety of Chemical Science Popularization Activities. University Chemistry, 2024, 39(9): 379-384. doi: 10.12461/PKU.DXHX202404087
18. [18]
  Tao Jiang , Yuting Wang , Lüjin Gao , Yi Zou , Bowen Zhu , Li Chen , Xianzeng Li . Experimental Design for the Preparation of Composite Solid Electrolytes for Application in All-Solid-State Batteries: Exploration of Comprehensive Chemistry Laboratory Teaching. University Chemistry, 2024, 39(2): 371-378. doi: 10.3866/PKU.DXHX202308057
19. [19]
  Zunxiang Zeng , Yuling Hu , Yufei Hu , Hua Xiao . Analysis of Plant Essential Oils by Supercritical CO₂Extraction with Gas Chromatography-Mass Spectrometry: An Instrumental Analysis Comprehensive Experiment Teaching Reform. University Chemistry, 2024, 39(3): 274-282. doi: 10.3866/PKU.DXHX202309069
20. [20]
  Yanhui XUE , Shaofei CHAO , Man XU , Qiong WU , Fufa WU , Sufyan Javed Muhammad . Construction of high energy density hexagonal hole MXene aqueous supercapacitor by vacancy defect control strategy. Chinese Journal of Inorganic Chemistry, 2024, 40(9): 1640-1652. doi: 10.11862/CJIC.20240183

Get Citation

PDF

XML

Metrics

PDF Downloads(1424)
Abstract views(3562)
HTML views(91)

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