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Petkov P, Marinova R, Kochev V, Ilieva N, Lilkova E, Litov L. Computational study of solution behavior of magainin 2 monomers. J Biomol Struct Dyn 2018; 37:1231-1240. [PMID: 29557267 DOI: 10.1080/07391102.2018.1454850] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Antimicrobial peptides (AMPs) play crucial role as mediators of the primary host defense against microbial invasion. They are considered a promising alternative to antibiotics for multidrug resistant bacterial strains. For complete understanding of the antimicrobial defense mechanism, a detailed knowledge of the dynamics of peptide-membrane interactions, including atomistic studies on AMPs geometry and both peptide and membrane structural changes during the whole process is a prerequisite. We aim at clarifying the conformation dynamics of small linear AMPs in solution as a first step of in silico protocol for establishing a correspondence between certain amino-acid sequence motifs, secondary-structure elements, conformational dynamics in solution and the intensity and mode of interaction with the bacterial membrane. To this end, we use molecular dynamics simulations augmented by well-tempered metadynamics to study the free-energy landscape of two AMPs with close primary structure and different antibacterial activity - the native magainin 2 (MG2) and an analog (MG2m, with substitutions F5Y and F16W) in aqueous solution. We observe that upon solvation, the initial α-helical structures change differently. The native form remains structured, with three shorter α-helical motifs, connected by random coils, while the synthetic analog tends predominantly to a disordered conformation. Our results indicate the importance of the side-chains at positions 5 and 16 for maintaining the solvated peptide conformation. They also provide a modeling background for recent experimental observations, relating the higher α-helical content in solution (peptide pre-folding) in the case of small linear AMPs to a lower antibacterial activity.
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Key Words
- AA, Amino Acid
- AAS, Amino Acid Sequence
- AMP, Antimicrobial Peptides
- CV, Collective Variable
- FF, Force Field
- MD, Molecular Dynamics
- MG2, Magainin 2
- MG2m, (F5Y, F16W)-magainin 2 analog
- PC, Principal Component
- PCA, Principal Component Analysis
- PMF, Potential of Mean Force
- antimicrobial peptides (AMPs)
- computational study
- conformational dynamics
- free-energy landscape
- magainin 2 (MG2)
- molecular dynamics simulations
- point mutation
- solvated peptide behavior
- well-tempered metadynamics
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Affiliation(s)
- P Petkov
- a Faculty of Physics , Sofia University "St. Kl. Ohridski" , Sofia , Bulgaria
| | - R Marinova
- a Faculty of Physics , Sofia University "St. Kl. Ohridski" , Sofia , Bulgaria
| | - V Kochev
- a Faculty of Physics , Sofia University "St. Kl. Ohridski" , Sofia , Bulgaria
| | - N Ilieva
- b Institute of Information and Communication Technologies , Bulgarian Academy of Sciences , Sofia , Bulgaria
| | - E Lilkova
- b Institute of Information and Communication Technologies , Bulgarian Academy of Sciences , Sofia , Bulgaria
| | - L Litov
- a Faculty of Physics , Sofia University "St. Kl. Ohridski" , Sofia , Bulgaria
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Wang Q, Wen B, Yan G, Wei J, Xie L, Xu S, Jiang D, Wang T, Lin L, Zi J, Zhang J, Zhou R, Zhao H, Ren Z, Qu N, Lou X, Sun H, Du C, Chen C, Zhang S, Tan F, Xian Y, Gao Z, He M, Chen L, Zhao X, Xu P, Zhu Y, Yin X, Shen H, Zhang Y, Jiang J, Zhang C, Li L, Chang C, Ma J, Yan G, Yao J, Lu H, Ying W, Zhong F, He QY, Liu S. Qualitative and Quantitative Expression Status of the Human Chromosome 20 Genes in Cancer Tissues and the Representative Cell Lines. J Proteome Res 2012; 12:151-61. [DOI: 10.1021/pr3008336] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Quanhui Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101318, China
- BGI-Shenzhen, Shenzhen 518083, China
| | - Bo Wen
- BGI-Shenzhen, Shenzhen 518083, China
| | - Guangrong Yan
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou 510632, China
| | - Junying Wei
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206,
China
- National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Liqi Xie
- Institutes of Biomedical Sciences
and Department of Chemistry, Fudan University, Shanghai 200032, China
| | | | | | | | - Liang Lin
- BGI-Shenzhen, Shenzhen 518083, China
| | - Jin Zi
- BGI-Shenzhen, Shenzhen 518083, China
| | - Ju Zhang
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101318, China
| | - Ruo Zhou
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Zhe Ren
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Xiaomin Lou
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101318, China
| | - Haidan Sun
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101318, China
| | | | | | - Shenyan Zhang
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101318, China
| | | | | | - Zhibo Gao
- BGI-Shenzhen, Shenzhen 518083, China
| | | | | | - Xiaohang Zhao
- State Key Laboratory of Molecular Oncology, Cancer Institute & Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206,
China
- National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Yunping Zhu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206,
China
- National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Xingfeng Yin
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou 510632, China
| | - Huali Shen
- Institutes of Biomedical Sciences
and Department of Chemistry, Fudan University, Shanghai 200032, China
| | - Yang Zhang
- Institutes of Biomedical Sciences
and Department of Chemistry, Fudan University, Shanghai 200032, China
| | - Jing Jiang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206,
China
- National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Chengpu Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206,
China
- National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Liwei Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206,
China
- National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Cheng Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206,
China
- National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Jie Ma
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206,
China
- National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Guoquan Yan
- Institutes of Biomedical Sciences
and Department of Chemistry, Fudan University, Shanghai 200032, China
| | - Jun Yao
- Institutes of Biomedical Sciences
and Department of Chemistry, Fudan University, Shanghai 200032, China
| | - Haojie Lu
- Institutes of Biomedical Sciences
and Department of Chemistry, Fudan University, Shanghai 200032, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206,
China
- National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Fan Zhong
- Institutes of Biomedical Sciences
and Department of Chemistry, Fudan University, Shanghai 200032, China
| | - Qing-Yu He
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou 510632, China
| | - Siqi Liu
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101318, China
- BGI-Shenzhen, Shenzhen 518083, China
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