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Ma X, Zhao Y, He C, Zhou X, Qi H, Wang Y, Chen C, Wang D, Li J, Ke Y, Wang J, Xu H. Ordered Packing of β-Sheet Nanofibrils into Nanotubes: Multi-hierarchical Assembly of Designed Short Peptides. NANO LETTERS 2021; 21:10199-10207. [PMID: 34870987 DOI: 10.1021/acs.nanolett.1c02944] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Although it is well-known proteins and their complexes are hierarchically organized and highly ordered structures, it remains a major challenge to replicate their hierarchical self-assembly process and to fabricate multihierarchical architectures with well-defined shapes and monodisperse characteristic sizes via peptide self-assembly. Here we describe an amphiphilic short peptide Ac-I3GGHK-NH2 that first preassembles into thin, left-handed β-sheet nanofibrils, followed by their ordered packing into right-handed nanotubes. The key intermediate morphology and structures featuring the hierarchical process are simultaneously demonstrated. Further mechanistic exploration with the variants Ac-I3GGGK-NH2, Ac-I3GGFK-NH2, and Ac-I3GGDHDK-NH2 reveals the vital role of multiple His-His side chain interactions between nanofibrils in mediating higher-order assembly and architectures. Altogether, our findings not only advance current understanding of hierarchical assembly of peptides and proteins but also afford a paradigm of how to take advantage of side chain interactions to construct higher-order assemblies with enhanced complexities.
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Affiliation(s)
- Xiaoyue Ma
- State Key Laboratory of Heavy Oil Processing and Center for Biotechnology and Bioengineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Yurong Zhao
- State Key Laboratory of Heavy Oil Processing and Center for Biotechnology and Bioengineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Chunyong He
- Spallation Neutron Source Science Center, Dalang, Dongguan 523803, China
- Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing 100049, China
| | - Xing Zhou
- Qingdao West Coast New Area Marine Development Bureau, 59 Shuilingshan Road, Qingdao 266400, China
| | - Hao Qi
- State Key Laboratory of Heavy Oil Processing and Center for Biotechnology and Bioengineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Yan Wang
- State Key Laboratory of Heavy Oil Processing and Center for Biotechnology and Bioengineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Cuixia Chen
- State Key Laboratory of Heavy Oil Processing and Center for Biotechnology and Bioengineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Dong Wang
- State Key Laboratory of Heavy Oil Processing and Center for Biotechnology and Bioengineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Jie Li
- State Key Laboratory of Heavy Oil Processing and Center for Biotechnology and Bioengineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Yubin Ke
- Spallation Neutron Source Science Center, Dalang, Dongguan 523803, China
- Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing 100049, China
| | - Jiqian Wang
- State Key Laboratory of Heavy Oil Processing and Center for Biotechnology and Bioengineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Hai Xu
- State Key Laboratory of Heavy Oil Processing and Center for Biotechnology and Bioengineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
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Hema K, Ahamad S, Joon HK, Pandey R, Gupta D. Atomic Resolution Homology Models and Molecular Dynamics Simulations of Plasmodium falciparum Tubulins. ACS OMEGA 2021; 6:17510-17522. [PMID: 34278137 PMCID: PMC8280665 DOI: 10.1021/acsomega.1c01988] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 05/21/2021] [Indexed: 05/14/2023]
Abstract
Microtubules are tubulin polymers present in the eukaryotic cytoskeleton essential for structural stability and cell division that are also roadways for intracellular transport of vesicles and organelles. In the human malaria parasite Plasmodium falciparum, apart from providing structural stability and cell division, microtubules also facilitate important biological activities crucial for parasite survival in hosts, such as egression and motility. Hence, parasite structures and processes involving microtubules are among the most important drug targets for discovering much-needed novel Plasmodium inhibitors. The current study aims to construct reliable and high-quality 3D models of α-, β-, and γ-tubulins using various modeling techniques. We identified a common binding pocket specific to Plasmodium α-, β-, and γ-tubulins. Molecular dynamics simulations confirmed the stability of the Plasmodium tubulin 3D structures. The models generated in the present study may be used for protein-protein and protein-drug interaction investigations targeted toward designing malaria parasite tubulin-specific inhibitors.
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Affiliation(s)
| | | | | | | | - Dinesh Gupta
- . Mobile: +91 9312304662. Office: +91 11 26742184
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