Home

Citation: WU Xiao-Min, ZU Yuan-Gang, YANG Zhi-Wei, FU Yu-Jie, ZHOU Li-Jun, YANG Gang. Temperature-Controlled Molecular Dynamics Studies on the Folding Mechanism of the Tubulin Active Peptides[J]. Acta Physico-Chimica Sinica, ;2009, 25(04): 773-782. doi: 10.3866/PKU.WHXB20090333 shu

Temperature-Controlled Molecular Dynamics Studies on the Folding Mechanism of the Tubulin Active Peptides

1.
Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, P. R. China

Received Date: 11 November 2008
Available Online: 23 January 2009

Using temperature controlled and normal temperature molecular dynamics methods, an in-depth study
was undertaken on the folding mechanismof the tubulin active peptide (Pep1-28). The total simulation time was 380.0 ns. We found a clear folding pathway by gradually decreasing the temperature using temperature controlled molecular dynamics simulations. Noticeable folding was observed at about 550 K and reversible folding and unfolding mechanisms were determined as U(>1200 K)←→←→I1(1200-1000 K)←→I2(800 K)←→I3(600 K)←→I4(450 K)←→F1(400 K)←→F2 (300 K), where U is an unfolded conformation and I1, I2, I3, and I4 are four important intermediates in the folding process. F1 and F2 are two folded conformations with similar structures. Conformational transformation and the folding process take place very quickly in normal temperature molecular dynamics, causing great difficulty in observing effective and stable intermediate conformations. The normal temperature molecular dynamics folds into a local energy minimum with the structure having severe discrepancies with that of the temperature controlled (300 K). The energy difference between these two folded structures was calculated to be as high as 297.53 kJ·mol-1. Therefore, the temperature controlled molecular dynamics method can provide direct and reliable proof for folding and unfolding by presenting the important intermediate conformations and can also induce folding towards the global lowest-energy conformation by crossing over high energy barriers.
- Tubulin,
- Temperature-controlled molecular dynamics,
- Conformational analysis,
- Folding mechanism,
- Intermediates
1. [1]
  Yaling Chen . Basic Theory and Competitive Exam Analysis of Dynamic Isotope Effect. University Chemistry, 2024, 39(8): 403-410. doi: 10.3866/PKU.DXHX202311093
2. [2]
  Yan Li , Xinze Wang , Xue Yao , Shouyun Yu . Kinetic Resolution Enabled by Photoexcited Chiral Copper Complex-Mediated Alkene E→Z Isomerization: A Comprehensive Chemistry Experiment for Undergraduate Students. University Chemistry, 2024, 39(5): 1-10. doi: 10.3866/PKU.DXHX202309053
3. [3]
  Shule Liu . Application of SPC/E Water Model in Molecular Dynamics Teaching Experiments. University Chemistry, 2024, 39(4): 338-342. doi: 10.3866/PKU.DXHX202310029
4. [4]
  Jinfu Ma , Hui Lu , Jiandong Wu , Zhongli Zou . Teaching Design of Electrochemical Principles Course Based on “Cognitive Laws”: Kinetics of Electron Transfer Steps. University Chemistry, 2024, 39(3): 174-177. doi: 10.3866/PKU.DXHX202309052
5. [5]
  Yeyun Zhang , Ling Fan , Yanmei Wang , Zhenfeng Shang . Development and Application of Kinetic Reaction Flasks in Physical Chemistry Experimental Teaching. University Chemistry, 2024, 39(4): 100-106. doi: 10.3866/PKU.DXHX202308044
6. [6]
  Xuzhen Wang , Xinkui Wang , Dongxu Tian , Wei Liu . Enhancing the Comprehensive Quality and Innovation Abilities of Graduate Students through a “Student-Centered, Dual Integration and Dual Drive” Teaching Model: A Case Study in the Course of Chemical Reaction Kinetics. University Chemistry, 2024, 39(6): 160-165. doi: 10.3866/PKU.DXHX202401074
7. [7]
  Dexin Tan , Limin Liang , Baoyi Lv , Huiwen Guan , Haicheng Chen , Yanli Wang . Exploring Reverse Teaching Practices in Physical Chemistry Experiment Courses: A Case Study on Chemical Reaction Kinetics. University Chemistry, 2024, 39(11): 79-86. doi: 10.12461/PKU.DXHX202403048
8. [8]
  Yiying Yang , Dongju Zhang . Elucidating the Concepts of Thermodynamic Control and Kinetic Control in Chemical Reactions through Theoretical Chemistry Calculations: A Computational Chemistry Experiment on the Diels-Alder Reaction. University Chemistry, 2024, 39(3): 327-335. doi: 10.3866/PKU.DXHX202309074
9. [9]
  Yue Wu , Jun Li , Bo Zhang , Yan Yang , Haibo Li , Xian-Xi Zhang . Research on Kinetic and Thermodynamic Transformations of Organic-Inorganic Hybrid Materials for Fluorescent Anti-Counterfeiting Application information: Introducing a Comprehensive Chemistry Experiment. University Chemistry, 2024, 39(6): 390-399. doi: 10.3866/PKU.DXHX202403028
10. [10]
  You Wu , Chang Cheng , Kezhen Qi , Bei Cheng , Jianjun Zhang , Jiaguo Yu , Liuyang Zhang . ZnO/D-A共轭聚合物S型异质结高效光催化产H₂O₂及其电荷转移动力学研究. Acta Physico-Chimica Sinica, 2024, 40(11): 2406027-. doi: 10.3866/PKU.WHXB202406027
11. [11]
  Pingping Zhu , Yongjun Xie , Yuanping Yi , Yu Huang , Qiang Zhou , Shiyan Xiao , Haiyang Yang , Pingsheng He . Excavation and Extraction of Ideological and Political Elements for the Virtual Simulation Experiments at Molecular Level: Taking the Project “the Simulation and Computation of Conformation, Morphology and Dimensions of Polymer Chains” as an Example. University Chemistry, 2024, 39(2): 83-88. doi: 10.3866/PKU.DXHX202309063
12. [12]
  Zizheng LU , Wanyi SU , Qin SHI , Honghui PAN , Chuanqi ZHAO , Chengfeng HUANG , Jinguo PENG . Surface state behavior of W doped BiVO₄ photoanode for ciprofloxacin degradation. Chinese Journal of Inorganic Chemistry, 2024, 40(3): 591-600. doi: 10.11862/CJIC.20230225
13. [13]
  Zeyu XU , Anlei DANG , Bihua DENG , Xiaoxin ZUO , Yu LU , Ping YANG , Wenzhu YIN . Evaluation of the efficacy of graphene oxide quantum dots as an ovalbumin delivery platform and adjuvant for immune enhancement. Chinese Journal of Inorganic Chemistry, 2024, 40(6): 1065-1078. doi: 10.11862/CJIC.20240099
14. [14]
  Xinyi Hong , Tailing Xue , Zhou Xu , Enrong Xie , Mingkai Wu , Qingqing Wang , Lina Wu . Non-Site-Specific Fluorescent Labeling of Proteins as a Chemical Biology Experiment. University Chemistry, 2024, 39(4): 351-360. doi: 10.3866/PKU.DXHX202310010
15. [15]
  Wenyan Dan , Weijie Li , Xiaogang Wang . The Technical Analysis of Visual Software ShelXle for Refinement of Small Molecular Crystal Structure. University Chemistry, 2024, 39(3): 63-69. doi: 10.3866/PKU.DXHX202302060
16. [16]
  Haiping Wang . A Streamlined Method for Drawing Lewis Structures Using the Valence State of Outer Atoms. University Chemistry, 2024, 39(8): 383-388. doi: 10.12461/PKU.DXHX202401073
17. [17]
  Zhonghua Xi , Xuanfeng Kong , Jinyue Yang , Bin Liu , Tingyu Zhu , Hui Zhang , Wenwei Zhang . Construction of Public Teaching Instrument Platform and Exploration of Opening Mechanism. University Chemistry, 2024, 39(7): 200-206. doi: 10.12461/PKU.DXHX202405123
18. [18]
  Zhilian Liu , Wengui Wang , Hongxiao Yang , Yu Cui , Shoufeng Wang . Ideological and Political Education Design for the Synthesis of Irinotecan Drug Intermediate 7-Ethyl Camptothecin. University Chemistry, 2024, 39(2): 89-93. doi: 10.3866/PKU.DXHX202306012
19. [19]
  Jiarong Feng , Yejie Duan , Chu Chu , Dezhen Xie , Qiu'e Cao , Peng Liu . Preparation and Application of a Streptomycin Molecularly Imprinted Electrochemical Sensor: A Suggested Comprehensive Analytical Chemical Experiment. University Chemistry, 2024, 39(8): 295-305. doi: 10.3866/PKU.DXHX202401016
20. [20]
  Huan LI , Shengyan WANG , Long Zhang , Yue CAO , Xiaohan YANG , Ziliang WANG , Wenjuan ZHU , Wenlei ZHU , Yang ZHOU . Growth mechanisms and application potentials of magic-size clusters of groups Ⅱ-Ⅵ semiconductors. Chinese Journal of Inorganic Chemistry, 2024, 40(8): 1425-1441. doi: 10.11862/CJIC.20240088

Get Citation

PDF

XML

Metrics

PDF Downloads(1525)
Abstract views(3464)
HTML views(0)

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