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Journal of Biomolecular Structure and Dynamics Volume 33, 2015 - Issue 5
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Molecular dynamics study of segment peptides of Bax, Bim, and Mcl-1 BH3 domain of the apoptosis-regulating proteins bound to the anti-apoptotic Mcl-1 protein

Run-Ning ZhaoInstitute of Applied Mathematics and Physics, Shanghai Dianji University, Shanghai201306, P.R. China
,
Song FanDepartment of Urology and Anhui Geriatric Institute, The First Affiliated Hospital of Anhui Medical University, Hefei230025, China
,
Ju-Guang HanNational Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei230029, P.R. ChinaCorrespondence[email protected]
&
Guang LiuNational Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei230029, P.R. China
Pages 1067-1081 | Received 23 Jan 2014, Accepted 26 May 2014, Published online: 30 Jun 2014

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Ajit Kumar Rai & Neeraj Kumar Satija. (2023) A comparative analysis of daunorubicin and its metabolite daunorubicinol interaction with apoptotic and drug resistance proteins using in silico approach. Journal of Biomolecular Structure and Dynamics 41:20, pages 10737-10749.
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Hui Zhong, Yan-Jun Zhang & Xiao-Bin Shan. (2019) Exploring binding modes of the selected inhibitors to phosphodiesterase delta by all-atom molecular dynamics simulations and free energy calculations. Journal of Biomolecular Structure and Dynamics 37:9, pages 2415-2429.
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Yantao Chen, Jun Wang, Jian Zhang & Wei Wang. (2018) Binding modes of Bcl-2 homology 3 (BH3) peptides with anti-apoptotic protein A1 and redesign of peptide inhibitors: a computational study. Journal of Biomolecular Structure and Dynamics 36:15, pages 3967-3977.
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Jing-Na Ding, Yan-Jun Zhang, Hui Zhong, Cheng-Cheng Ao & Ju-Guang Han. (2018) A simulation investigation on interaction mechanism between Ebola nucleoprotein and VP35 peptide. Journal of Biomolecular Structure and Dynamics 36:4, pages 1009-1028.
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Ting-Ting Feng, Yan-Jun Zhang, H. Chen, Song Fan & Ju-Guang Han. (2016) The binding mechanism of a novel nicotinamide isostere inhibiting with TNKSs: a molecular dynamic simulation and binding free energy calculation. Journal of Biomolecular Structure and Dynamics 34:3, pages 517-528.
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Articles from other publishers (7)

Esther Wolf, Cristina Lento, Jinyue Pu, Bryan C. Dickinson & Derek J. Wilson. (2023) Innate Conformational Dynamics Drive Binding Specificity in Anti-Apoptotic Proteins Mcl-1 and Bcl-2. Biochemistry 62:11, pages 1619-1630.
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Dakshinamurthy Sivakumar & Sangwook Wu. (2022) Classical and Machine Learning Methods for Protein - Ligand Binding Free Energy Estimation. Current Drug Metabolism 23:4, pages 252-259.
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Changhao Wang, D'Artagnan Greene, Li Xiao, Ruxi Qi & Ray Luo. (2018) Recent Developments and Applications of the MMPBSA Method. Frontiers in Molecular Biosciences 4.
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Jade Fogha, Bogdan Marekha, Marcella De Giorgi, Anne Sophie Voisin-Chiret, Sylvain Rault, Ronan Bureau & Jana Sopkova-de Oliveira Santos. (2017) Toward Understanding Mcl-1 Promiscuous and Specific Binding Mode. Journal of Chemical Information and Modeling 57:11, pages 2885-2895.
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Yan-Jun Zhang, Jing-Na Ding, Hui Zhong & Ju-Guang Han. (2017) Exploration micromechanism of VP35 IID interaction and recognition dsRNA: A molecular dynamics simulation. Proteins: Structure, Function, and Bioinformatics 85:6, pages 1008-1023.
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Yan-Jun Zhang, Jing-Na Ding, Hui Zhong, Chang-Ping Sun & Ju-Guang Han. (2017) Molecular dynamics exploration of the binding mechanism and properties of single-walled carbon nanotube to WT and mutant VP35 FBP region of Ebola virus. Journal of Biological Physics 43:1, pages 149-165.
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Jing-Na Ding, Yan-Jun Zhang, Hui Zhong, Cheng-Cheng Ao, Jing Li & Ju-Guang Han. (2017) An all-atom molecular dynamics study of the anti-interferon signaling of Ebola virus: interaction mechanisms of EBOV VP24 binding to Karyopherin alpha5. Molecular BioSystems 13:5, pages 1031-1045.
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