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Patel DK, Menon DV, Patel DH, Dave G. Linkers: A synergistic way for the synthesis of chimeric proteins. Protein Expr Purif 2021; 191:106012. [PMID: 34767950 DOI: 10.1016/j.pep.2021.106012] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/30/2021] [Accepted: 11/03/2021] [Indexed: 11/15/2022]
Abstract
In the cell, the protein domains are attached with the short oligopeptide, commonly known as linker peptide. Besides bridging, the linker assists in the domain-domain interaction and protein folding into the peculiar conformations. Linkers allow or control the movement of protein domains in the dynamic cellular environment. The recent advances in the recombinant DNA technology enable the construction of multiple gene constructs in an open reading frame. The express sequences can work in a cascade to cater for myriad functions. This trend has given momentum to incorporating bridge sequences (linker) that essentially separates the independent domains. According to the cellular need, the bridging partner can be spaced at a secure gap or requires attaching or interacting physically. The flexible or rigid linker can help to achieve such conformations in chimeric fusion proteins. The linker can improve solubility, proteolytic resistance and stability of such fusion proteins. Recently, linker aided protein switches and antibody-drug conjugates are gaining the attention of researchers worldwide. Here, we thoroughly reviewed the types of the linker, strategies for linker engineering and the composition of a linker.
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Affiliation(s)
- Dharti Keyur Patel
- PD Patel Institute of Applied Sciences, CHARUSAT, Changa, 388421, Gujarat, India
| | - Dhanya V Menon
- Tata Institute of Fundamental Research, NCBS, Bangalore, 560065, India
| | - Darshan H Patel
- Charotar Institute of Paramedical Sciences, CHARUSAT, Changa, 388421, Gujarat, India
| | - Gayatri Dave
- PD Patel Institute of Applied Sciences, CHARUSAT, Changa, 388421, Gujarat, India.
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Wang Y, Wang J, Li R, Shi Q, Xue Z, Zhang Y. ThreaDomEx: a unified platform for predicting continuous and discontinuous protein domains by multiple-threading and segment assembly. Nucleic Acids Res 2019; 45:W400-W407. [PMID: 28498994 PMCID: PMC5793814 DOI: 10.1093/nar/gkx410] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 04/28/2017] [Indexed: 12/21/2022] Open
Abstract
We develop a hierarchical pipeline, ThreaDomEx, for both continuous domain (CD) and discontinuous domain (DCD) structure predictions. Starting from a query sequence, ThreaDomEx first threads it through the PDB to identify multiple structure templates, where a profile of domain conservation score (DC-score) is derived for domain-segment assignment. To further detect DCDs that consist of separated segments along the sequence, a boundary-clustering algorithm is used to refine the DCD-linker locations. In case that the templates do not contain DCDs, a domain-segment assembly process, guided by symmetry comparison, is applied for further DCD detections. ThreaDomEx was tested a set of 1111 proteins and achieved a normalized domain overlap score of 89.3% compared to experimental data, which is significantly higher than other state-of-the-art methods. It also recalls 26.7% of DCDs with 72.7% precision on the proteins for which threading failed to detect any DCDs. The server provides facilities for users to interactively refine the domain models by adjusting DC-score threshold, deleting and adding domain linkers, and assembling domain segments, which are particularly helpful for the hard targets for which current methods have a low accuracy while human-expert knowledge and experimental insights can be used for refining models. ThreaDomEX server is available at http://zhanglab.ccmb.med.umich.edu/ThreaDomEx.
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Affiliation(s)
- Yan Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jian Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Ruiming Li
- School of Software, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Qiang Shi
- School of Software, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Zhidong Xue
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.,School of Software, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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Philippe D, Ababou A, Yang X, Ghosh R, Daviter T, Ladbury JE, Pfuhl M. Making Ends Meet: The Importance of the N- and C-Termini for the Structure, Stability, and Function of the Third SH3 Domain of CIN85. Biochemistry 2011; 50:3649-59. [DOI: 10.1021/bi1019644] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- D. Philippe
- Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN, U.K
| | - A. Ababou
- Department of Chemical and Biological Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, U.K
| | - X. Yang
- Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN, U.K
| | - R. Ghosh
- Department of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, U.K
| | - T. Daviter
- ISMB Biophysics Centre, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, U.K
| | - J. E. Ladbury
- Department of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, U.K
- Department of Biochemistry and Molecular Biology and Center for Biomolecular Structure and Function, University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77005, United States
| | - M. Pfuhl
- Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN, U.K
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