Citation: Qiang Wang, Jian Wu Wang, Zheng Ting Cai, Wei Ren Xu. A molecular dynamics simulation study of peptide deformylase from Leptospira interrogans complex: Exploring the closing mechanism of the substrate pocket[J]. Chinese Chemical Letters, ;2008, 19(4): 497-500. doi: 10.1016/j.cclet.2008.01.027 shu

A molecular dynamics simulation study of peptide deformylase from Leptospira interrogans complex: Exploring the closing mechanism of the substrate pocket

a Institute of Theoretical Chemistry, Shandong University, Jinan 250100, China;
b Institute of Organic Chemistry, Shandong University, Jinan 250100, China;
c Tianjin Institute of the Pharmaceutical Research, Tianjin 300193, China

Received Date: 5 November 2007

Fund Project: The authors acknowledge the supports of the National Key Basic Research Priorities Program (No. 2003CCA027) and the National Natural Science Foundation of China (No. 20573064).

To explore the closing mechanism of the substrate pocket, we perform a 16, 000 ps molecular dynamics simulation separately on the ligand-free and actinonin-bound peptide deformylase from Leptospira interrogans. Our results show that the CD-loop, hydrophilic inhibitor and hydrophobic cluster are necessary for the formation of semi-open conformation, and Tyr71 plays an important role in mediating the movements of CD-loop. The average MD structure of the actinonin-bound LiPDF complex approaches to the crystal structure. These are consistent with experiment very well.
- Peptide deformylase,
- Leptospira interrogan,
- Molecular dynamics simulation
1. [1]
  Jinqi Yang , Xiaoxiang Hu , Yuanyuan Zhang , Lingyu Zhao , Chunlin Yue , Yuan Cao , Yangyang Zhang , Zhenwen Zhao . Direct observation of natural products bound to protein based on UHPLC-ESI-MS combined with molecular dynamics simulation. Chinese Chemical Letters, 2025, 36(5): 110128-. doi: 10.1016/j.cclet.2024.110128
2. [2]
  Congying Lu , Fei Zhong , Zhenyu Yuan , Shuaibing Li , Jiayao Li , Jiewen Liu , Xianyang Hu , Liqun Sun , Rui Li , Meijuan Hu . Experimental Improvement of Surfactant Interface Chemistry: An Integrated Design for the Fusion of Experiment and Simulation. University Chemistry, 2024, 39(3): 283-293. doi: 10.3866/PKU.DXHX202308097
3. [3]
  Zhenming Xu , Yibo Wang , Zhenhui Liu , Duo Chen , Mingbo Zheng , Laifa Shen . Experimental Design of Computational Materials Science and Computational Chemistry Courses Based on the Bohrium Scientific Computing Cloud Platform. University Chemistry, 2025, 40(3): 36-41. doi: 10.12461/PKU.DXHX202403096
4. [4]
  Zhi Zhou , Yu-E Lian , Yuqing Li , Hui Gao , Wei Yi . New Insights into the Molecular Mechanism Behind Clinical Tragedies of “Cephalosporin with Alcohol”. University Chemistry, 2025, 40(3): 42-51. doi: 10.12461/PKU.DXHX202403104
5. [5]
  Shiyu Hou , Maolin Sun , Liming Cao , Chaoming Liang , Jiaxin Yang , Xinggui Zhou , Jinxing Ye , Ruihua Cheng . Computational fluid dynamics simulation and experimental study on mixing performance of a three-dimensional circular cyclone-type microreactor. Chinese Chemical Letters, 2024, 35(4): 108761-. doi: 10.1016/j.cclet.2023.108761
6. [6]
  Weiyu Chen , Zenghui Li , Chenguang Zhao , Lisha Zha , Junfeng Shi , Dan Yuan . Enzyme-modulate conformational changes in amphiphile peptide for selectively cell delivery. Chinese Chemical Letters, 2024, 35(12): 109628-. doi: 10.1016/j.cclet.2024.109628
7. [7]
  Xiaofang Luo , Ye Wu , Xiaokun Zhang , Min Tang , Feiye Ju , Zuodong Qin , Gregory J Duns , Wei-Dong Zhang , Jiang-Jiang Qin , Xin Luan . Peptide-based strategies for overcoming multidrug-resistance in cancer therapy. Chinese Chemical Letters, 2025, 36(1): 109724-. doi: 10.1016/j.cclet.2024.109724
8. [8]
  Rui Wang , He Qi , Haijiao Zheng , Qiong Jia . Light/pH dual-responsive magnetic metal-organic frameworks composites for phosphorylated peptide enrichment. Chinese Chemical Letters, 2024, 35(7): 109215-. doi: 10.1016/j.cclet.2023.109215
9. [9]
  Cheng-Yan Wu , Yi-Nan Gao , Zi-Han Zhang , Rui Liu , Quan Tang , Zhong-Lin Lu . Enhancing self-assembly efficiency of macrocyclic compound into nanotubes by introducing double peptide linkages. Chinese Chemical Letters, 2024, 35(11): 109649-. doi: 10.1016/j.cclet.2024.109649
10. [10]
  Shaofeng Gong , Zi-Wei Deng , Chao Wu , Wei-Min He . Stabilized carbon radical-mediated three-component functionalization of amino acid/peptide derivatives. Chinese Chemical Letters, 2025, 36(5): 110936-. doi: 10.1016/j.cclet.2025.110936
11. [11]
  Huimin Gao , Zhuochen Yu , Xuze Zhang , Xiangkun Yu , Jiyuan Xing , Youliang Zhu , Hu-Jun Qian , Zhong-Yuan Lu . A mini review of the recent progress in coarse-grained simulation of polymer systems. Chinese Journal of Structural Chemistry, 2024, 43(5): 100266-100266. doi: 10.1016/j.cjsc.2024.100266
12. [12]
  Jianhui Yin , Wenjing Huang , Changyong Guo , Chao Liu , Fei Gao , Honggang Hu . Tryptophan-specific peptide modification through metal-free photoinduced N-H alkylation employing N-aryl glycines. Chinese Chemical Letters, 2024, 35(6): 109244-. doi: 10.1016/j.cclet.2023.109244
13. [13]
  Chuanfeng Fan , Jian Gao , Yingkai Gao , Xintong Yang , Gaoning Li , Xiaochun Wang , Fei Li , Jin Zhou , Haifeng Yu , Yi Huang , Jin Chen , Yingying Shan , Li Chen . A non-peptide-based chymotrypsin-targeted long-wavelength emission fluorescent probe with large Stokes shift and its application in bioimaging. Chinese Chemical Letters, 2024, 35(10): 109838-. doi: 10.1016/j.cclet.2024.109838
14. [14]
  Chenghao Ge , Peng Wang , Pei Yuan , Tai Wu , Rongjun Zhao , Rong Huang , Lin Xie , Yong Hua . Tuning hot carrier transfer dynamics by perovskite surface modification. Chinese Chemical Letters, 2024, 35(10): 109352-. doi: 10.1016/j.cclet.2023.109352
15. [15]
  Fang-Yuan Chen , Wen-Chao Geng , Kang Cai , Dong-Sheng Guo . Molecular recognition of cyclophanes in water. Chinese Chemical Letters, 2024, 35(5): 109161-. doi: 10.1016/j.cclet.2023.109161
16. [16]
  Sanmei Wang , Yong Zhou , Hengxin Fang , Chunyang Nie , Chang Q Sun , Biao Wang . Constant-potential simulation of electrocatalytic N₂ reduction over atomic metal-N-graphene catalysts. Chinese Chemical Letters, 2025, 36(3): 110476-. doi: 10.1016/j.cclet.2024.110476
17. [17]
  Rongjun Zhao , Tai Wu , Yong Hua , Yude Wang . Improving performance of perovskite solar cells enabled by defects passivation and carrier transport dynamics regulation via organic additive. Chinese Chemical Letters, 2025, 36(2): 109587-. doi: 10.1016/j.cclet.2024.109587
18. [18]
  Mengjia Luo , Yi Qiu , Zhengyang Zhou . Exploring temperature-driven phase dynamics of phosphate: The periodic to incommensurately modulated long-range ordered phase transition in CsCdPO4. Chinese Journal of Structural Chemistry, 2025, 44(1): 100446-100446. doi: 10.1016/j.cjsc.2024.100446
19. [19]
  Caihong Mao , Yanfeng He , Xiaohan Wang , Yan Cai , Xiaobo Hu . Synthesis and molecular recognition characteristics of a tetrapodal benzene cage. Chinese Chemical Letters, 2024, 35(8): 109362-. doi: 10.1016/j.cclet.2023.109362
20. [20]
  Cheng-Da Zhao , Huan Yao , Shi-Yao Li , Fangfang Du , Li-Li Wang , Liu-Pan Yang . Amide naphthotubes: Biomimetic macrocycles for selective molecular recognition. Chinese Chemical Letters, 2024, 35(4): 108879-. doi: 10.1016/j.cclet.2023.108879

Get Citation

PDF

XML

Metrics

PDF Downloads(0)
Abstract views(599)
HTML views(28)

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