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Yasuzawa Y, Shibuya R, Senga Y, Miyafusa T, Honda S. Determination of the optimal connector length to enhance stability of backbone-circularized granulocyte colony-stimulating factor. FEBS Open Bio 2023; 13:1910-1921. [PMID: 37574212 PMCID: PMC10549227 DOI: 10.1002/2211-5463.13692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 07/19/2023] [Accepted: 08/11/2023] [Indexed: 08/15/2023] Open
Abstract
Improving protein stability is important for industrial applications, and one promising method for achieving this is backbone circularization. As connector length affects stability, predicting and elucidating a more stable connector length is necessary for development of the backbone circularization method. However, the relationship between connector length and protein stability has not been completely elucidated. Here, we determined the most stable connector length for granulocyte colony-stimulating factor by changing one residue at a time to produce connector length variants and then measuring their thermal stability. Analysis of the local structures obtained from the predicted structures of the circularized variants revealed that an approach using helix length, dihedral backbone angle, and number of unbonded hydrogen bond donors and acceptors is suitable for identifying connector lengths with higher stability.
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Affiliation(s)
- Yosuke Yasuzawa
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier SciencesThe University of TokyoJapan
| | - Risa Shibuya
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier SciencesThe University of TokyoJapan
- Biomedical Research InstituteNational Institute of Advanced Industrial Science and Technology (AIST)TsukubaJapan
| | - Yukako Senga
- Biomedical Research InstituteNational Institute of Advanced Industrial Science and Technology (AIST)TsukubaJapan
| | - Takamitsu Miyafusa
- Biomedical Research InstituteNational Institute of Advanced Industrial Science and Technology (AIST)TsukubaJapan
- Bioproduction Research InstituteNational Institute of Advanced Industrial Science and Technology (AIST)TsukubaJapan
| | - Shinya Honda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier SciencesThe University of TokyoJapan
- Biomedical Research InstituteNational Institute of Advanced Industrial Science and Technology (AIST)TsukubaJapan
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Hamdan SH, Maiangwa J, Nezhad NG, Ali MSM, Normi YM, Shariff FM, Rahman RNZRA, Leow TC. Knotting terminal ends of mutant T1 lipase with disulfide bond improved structure rigidity and stability. Appl Microbiol Biotechnol 2023; 107:1673-1686. [PMID: 36752811 DOI: 10.1007/s00253-023-12396-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 12/22/2022] [Accepted: 01/17/2023] [Indexed: 02/09/2023]
Abstract
Lipase biocatalysts offer unique properties which are often impaired by low thermal and methanol stability. In this study, the rational design was employed to engineer a disulfide bond in the protein structure of Geobacillus zalihae T1 lipase in order to improve its stability. The selection of targeted disulfide bond sites was based on analysis of protein spatial configuration and change of Gibbs free energy. Two mutation points (S2C and A384C) were generated to rigidify the N-terminal and C-terminal regions of T1 lipase. The results showed the mutant 2DC lipase improved methanol stability from 35 to 40% (v/v) after 30 min of pre-incubation. Enhancement in thermostability for the mutant 2DC lipase at 70 °C and 75 °C showed higher half-life at 70 °C and 75 °C for 30 min and 52 min, respectively. The mutant 2DC lipase maintained the same optimum temperature (70 °C) as T1 lipase, while thermally induced unfolding showed the mutant maintained higher rigidity. The kcat/Km values demonstrated a relatively small difference between the T1 lipase (WT) and 2DC lipase (mutant). The kcat/Km (s-1 mM-1) of the T1 and 2DC showed values of 13,043 ± 224 and 13,047 ± 312, respectively. X-ray diffraction of 2DC lipase crystal structure with a resolution of 2.04 Å revealed that the introduced single disulfide bond did not lower initial structural interactions within the residues. Enhanced methanol and thermal stability are suggested to be strongly related to the newly disulfide bridge formation and the enhanced compactness and rigidity of the mutant structure. KEY POINTS: • Protein engineering via rational design revealed relative improved enzymatic performance. • The presence of disulfide bond impacts on the rigidity and structural function of proteins. • X-ray crystallography reveals structural changes accompanying protein modification.
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Affiliation(s)
- Siti Hajar Hamdan
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia Serdang, UPM Serdang, 43400, Selangor, Malaysia
- Enzyme Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia Serdang, UPM Serdang, 43400, Selangor, Malaysia
| | - Jonathan Maiangwa
- Department of Microbiology, Faculty of Science, Kaduna State University, PMB 2336, Kaduna, Nigeria
| | - Nima Ghahremani Nezhad
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia Serdang, UPM Serdang, 43400, Selangor, Malaysia
- Enzyme Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia Serdang, UPM Serdang, 43400, Selangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia Serdang, UPM Serdang, 43400, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia Serdang, UPM Serdang, 43400, Selangor, Malaysia
| | - Yahaya M Normi
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia Serdang, UPM Serdang, 43400, Selangor, Malaysia
- Enzyme Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia Serdang, UPM Serdang, 43400, Selangor, Malaysia
| | - Fairolniza Mohd Shariff
- Enzyme Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia Serdang, UPM Serdang, 43400, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, UPM Serdang, 43400, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia Serdang, UPM Serdang, 43400, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, UPM Serdang, 43400, Selangor, Malaysia
| | - Thean Chor Leow
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia Serdang, UPM Serdang, 43400, Selangor, Malaysia.
- Enzyme Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia Serdang, UPM Serdang, 43400, Selangor, Malaysia.
- Institute of Bioscience, Universiti Putra Malaysia Serdang, UPM Serdang, 43400, Selangor, Malaysia.
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Hayes HC, Luk LYP, Tsai YH. Approaches for peptide and protein cyclisation. Org Biomol Chem 2021; 19:3983-4001. [PMID: 33978044 PMCID: PMC8114279 DOI: 10.1039/d1ob00411e] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/01/2021] [Indexed: 12/26/2022]
Abstract
The cyclisation of polypeptides can play a crucial role in exerting biological functions, maintaining stability under harsh conditions and conferring proteolytic resistance, as demonstrated both in nature and in the laboratory. To date, various approaches have been reported for polypeptide cyclisation. These approaches range from the direct linkage of N- and C- termini to the connection of amino acid side chains, which can be applied both in reaction vessels and in living systems. In this review, we categorise the cyclisation approaches into chemical methods (e.g. direct backbone cyclisation, native chemical ligation, aldehyde-based ligations, bioorthogonal reactions, disulphide formation), enzymatic methods (e.g. subtiligase variants, sortases, asparaginyl endopeptidases, transglutaminases, non-ribosomal peptide synthetases) and protein tags (e.g. inteins, engineered protein domains for isopeptide bond formation). The features of each approach and the considerations for selecting an appropriate method of cyclisation are discussed.
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Affiliation(s)
- Heather C Hayes
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Louis Y P Luk
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK and Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT.
| | - Yu-Hsuan Tsai
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK and Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen 518132, China.
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Makabe K. Molecular basis of flexible peptide recognition by an antibody. J Biochem 2020; 167:343-345. [PMID: 32027351 DOI: 10.1093/jb/mvaa017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 01/19/2020] [Indexed: 11/12/2022] Open
Abstract
Antibodies can recognize various types of antigens with high specificity and affinity and peptide is one of their major targets. Understanding an antibody's molecular recognition mechanism for peptide is important for developing clones with a higher specificity and affinity. Here, the author reviews recent progresses in flexible peptide recognition by an antibody using several biophysical techniques, including X-ray crystallography, molecular dynamics simulations and calorimetric measurements. A set of two reports highlight the importance of intramolecular hydrogen bonds that form in an unbound flexible state. Such intramolecular hydrogen bonds restrict the fluctuation of the peptide and reduce the conformational entropy, resulting in the destabilization of the unbound state and increasing the binding affinity by increasing the free energy change. These detailed analyses will aid in the antibody design in the future.
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Affiliation(s)
- Koki Makabe
- Graduate School of Science and Engineering, Yamagata University, 4-3-16 Jyonan, Yonezawa, Yamagata 992-8510, Japan
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