Home

Citation: Lai Lu-Hua, Wang Le-Yu, Deng Qiao-Lin, Han Yu-Zhen, Ma Li-Bin, Xu Xiao-Jie, Tang You-Qi. Constraint Monte-Carlo Simulated Annealing:Application in Peptide Conformational Analysis in Solution[J]. Acta Physico-Chimica Sinica, ;1994, 10(10): 867-869. doi: 10.3866/PKU.WHXB19941001 shu

Constraint Monte-Carlo Simulated Annealing:Application in Peptide Conformational Analysis in Solution

1.
Institute of Physical Chemistry,Peking University,Beijing State Key Laboratory for Stable and Unstable Species,Beijing 100871

Received Date: 24 June 1994
Available Online: 15 October 1994

Distance geometry and molecular dynamics are currently employed in determining molecular structures with interatomic distances from NMR NOESY experiment. Because of the flexibility of peptide, distances obtained from NMR are usually not sufficient to confine its structure. Both distance geometry and molecular dynamics will bias in the conformational space at this circumstance. Constraint Monte Carlo simulated annealing was established to solve this problem. Distance constraints were included into the ECEPP/2 force field by introducing a harmonic energy term. Conformational analysis of a pentapeptide with eight interatomic distances from NMR was carried out as a test. By comparison of the 100 conformers obtained from constraint simulated annealing and the 100 conformers from distance geometry calculation, it was found that constraint simulated annealing can cover the outcomes of distance geometry and at the same time give more con-formers fitting to the experimental data. The result shows that constraint Monte-Carlo simulated annealing is more valid in constructing peptide structures from NMR distances than currently employed methods when no sufficient distances from NMR are available.
- Simulated annealing,
- Conformation,
- Peptide
1. [1]
  Jiaxi Xu , Yuan Ma . Influence of Hyperconjugation on the Stability and Stable Conformation of Ethane, Hydrazine, and Hydrogen Peroxide. University Chemistry, 2024, 39(11): 374-377. doi: 10.3866/PKU.DXHX202402049
2. [2]
  Peipei CUI , Xin LI , Yilin CHEN , Zhilin CHENG , Feiyan GAO , Xu GUO , Wenning YAN , Yuchen DENG . Transition metal coordination polymers with flexible dicarboxylate ligand: Synthesis, characterization, and photoluminescence property. Chinese Journal of Inorganic Chemistry, 2024, 40(11): 2221-2231. doi: 10.11862/CJIC.20240234
3. [3]
  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
4. [4]
  Zihan Lin , Wanzhen Lin , Fa-Jie Chen . Electrochemical Modifications of Native Peptides. University Chemistry, 2025, 40(3): 318-327. doi: 10.12461/PKU.DXHX202406089
5. [5]
  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
6. [6]
  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
7. [7]
  Xintian Xie , Sicong Ma , Yefei Li , Cheng Shang , Zhipan Liu . Application of Machine Learning Potential-based Theoretical Simulations in Undergraduate Teaching Laboratory Course Design. University Chemistry, 2025, 40(3): 140-147. doi: 10.12461/PKU.DXHX202405164
8. [8]
  Donghui PAN , Yuping XU , Xinyu WANG , Lizhen WANG , Junjie YAN , Dongjian SHI , Min YANG , Mingqing CHEN . Preparation and in vivo tracing of ⁶⁸Ga-labeled PM_2.5 mimetic particles for positron emission tomography imaging. Chinese Journal of Inorganic Chemistry, 2024, 40(4): 669-676. doi: 10.11862/CJIC.20230468
9. [9]
  Yaping Li , Sai An , Aiqing Cao , Shilong Li , Ming Lei . The Application of Molecular Simulation Software in Structural Chemistry Education: First-Principles Calculation of NiFe Layered Double Hydroxide. University Chemistry, 2025, 40(3): 160-170. doi: 10.12461/PKU.DXHX202405185

Get Citation

PDF

XML

Metrics

PDF Downloads(2210)
Abstract views(3332)
HTML views(120)

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