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Abstract
The impacts of linkers on dynamics, expression, and activity of biomacromolecules are often overlooked. This may be due, in part, to the lack of facile methods for incorporation and analysis of linkers that vary iteratively in both length and sequence composition. The protaTETHER method addresses this gap by enabling the incorporation of focused linker libraries at potentially any region in a protein sequence. In this chapter, we describe the generation and incorporation of linkers in a PKAc-GFP fusion protein and provide methods for the application and evaluation of the protaTETHER process.
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53
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Abstract
Linker engineering constitutes a critical, yet frequently underestimated aspect in the construction of synthetic protein switches and sensors. Notably, systematic strategies to engineer linkers by predictive means remain largely elusive to date. This is primarily due to our insufficient understanding how the biophysical properties that underlie linker functions mediate the conformational transitions in artificially engineered protein switches and sensors. The construction of synthetic protein switches and sensors therefore heavily relies on experimental trial-and-error. Yet, methods for effectively generating linker diversity at the genetic level are scarce. Addressing this technical shortcoming, iterative functional linker cloning (iFLinkC) enables the combinatorial assembly of linker elements with functional domains from sequence verified repositories that are developed and stored in-house. The assembly process is highly scalable and given its recursive nature generates linker diversity in a combinatorial and exponential fashion based on a limited number of linker elements.
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54
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Vasilenko EA, Gorshkova EN, Astrakhantseva IV, Drutskaya MS, Tillib SV, Nedospasov SA, Mokhonov VV. The structure of myeloid cell-specific TNF inhibitors affects their biological properties. FEBS Lett 2020; 594:3542-3550. [PMID: 32865225 DOI: 10.1002/1873-3468.13913] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/25/2020] [Accepted: 07/06/2020] [Indexed: 11/05/2022]
Abstract
Spatial organization and conformational changes of antibodies may significantly affect their biological functions. We assessed the effect of mutual organization of the two VH H domains within bispecific antibodies recognizing human TNF and the surface molecules of murine myeloid cells (F4/80 or CD11b) on TNF retention and inhibition. TNF-neutralizing properties in vitro and in vivo of MYSTI-2 and MYSTI-3 antibodies were compared with new variants with interchanged VH H domains and different linker sequences. The most effective structure of MYSTI-2 and MYSTI-3 proteins required the Ser/Gly-containing 'superflexible' linker. The orientation of the modules was crucial for the activity of the proteins, but not for MYSTI-3 with the Pro/Gln-containing 'semi-rigid' linker. Our results may contribute toward the development of more effective drug prototypes.
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Affiliation(s)
| | | | - Irina V Astrakhantseva
- Lobachevsky State University, Nizhny Novgorod, Russia.,Sirius University of Science and Technology, Sochi, Russia
| | - Marina S Drutskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sergei V Tillib
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sergei A Nedospasov
- Sirius University of Science and Technology, Sochi, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Lomonosov Moscow State University, Moscow, Russia
| | - Vladislav V Mokhonov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Blokhina Scientific Research Institute of Epidemiology and Microbiology of Nizhny Novgorod, Nizhny Novgorod, Russia
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55
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Jin X, Li Q, Wang Y, Zhang W, Xu R, Li J, Du G, Kang Z. Optimizing the sulfation-modification system for scale preparation of chondroitin sulfate A. Carbohydr Polym 2020; 246:116570. [PMID: 32747242 DOI: 10.1016/j.carbpol.2020.116570] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 11/29/2022]
Abstract
Chondroitin sulfate (CS) extracted from animal tissues has been widely used as nutraceutical and pharmaceutical products for osteoarthritis treatment. Here we developed an efficient sulfation-modification system for large scale preparation of CSA in vitro. First, the expression level of C4ST was improved by 30 times with fusion of the chaperone SUMO. Then, glycerol as a protein stabilizer was found to improve rat AST IV stability during the regeneration of cofactor PAPS. Then peptide linkers or protein scaffolds were employed to assemble AST IV and C4ST into artificial complexes to bring the enzymes and PAPS spatially closer and enhance the catalytic efficiency of chondroitin sulfation. Eventually, the system was scaled up to 1 L system and 15 g chondroitin was converted to CSA in 24 h, with a 98 % conversion. The present study made a step further towards the industrial production of CSA with different sulfation degrees.
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Affiliation(s)
- Xuerong Jin
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Qing Li
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Yang Wang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Weijiao Zhang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Ruirui Xu
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Jianghua Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Guocheng Du
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Zhen Kang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China.
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56
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Gräwe A, Ranglack J, Weyrich A, Stein V. iFLinkC: an iterative functional linker cloning strategy for the combinatorial assembly and recombination of linker peptides with functional domains. Nucleic Acids Res 2020; 48:e24. [PMID: 31925441 PMCID: PMC7039005 DOI: 10.1093/nar/gkz1210] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 12/10/2019] [Accepted: 12/18/2019] [Indexed: 02/02/2023] Open
Abstract
Recent years have witnessed increasing efforts to engineer artificial biological functions through recombination of modular-organized toolboxes of protein scaffolds and parts. A critical, yet frequently neglected aspect concerns the identity of peptide linkers or spacers connecting individual domains which remain poorly understood and challenging to assemble. Addressing these limitations, iFlinkC comprises a highly scalable DNA assembly process that facilitates the combinatorial recombination of functional domains with linkers of varying length and flexibility, thereby overcoming challenges with high GC-content and the repeat nature of linker elements. The capacity of iFLinkC is demonstrated in the construction of synthetic protease switches featuring PDZ-FN3-based affinity clamps and single-chain FKBP12-FRB receptors as allosteric inputs. Library screening experiments demonstrate that linker space is highly plastic as the induction of allosterically regulated protease switches can vary from >150-fold switch-ON to >13-fold switch-OFF solely depending on the identity of the connecting linkers and relative orientation of functional domains. In addition, Pro-rich linkers yield the most potent switches contradicting the conventional use of flexible Gly-Ser linkers. Given the ease and efficiency how functional domains can be readily recombined with any type of linker, iFLinkC is anticipated to be widely applicable to the assembly of any type of fusion protein.
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Affiliation(s)
- Alexander Gräwe
- Fachbereich Biologie, Technische Universität Darmstadt, 64287 Darmstadt, Germany.,Centre for Synthetic Biology, Technische Universität Darmstadt, 64283 Darmstadt, Germany
| | - Jan Ranglack
- Fachbereich Biologie, Technische Universität Darmstadt, 64287 Darmstadt, Germany.,Centre for Synthetic Biology, Technische Universität Darmstadt, 64283 Darmstadt, Germany
| | - Anastasia Weyrich
- Fachbereich Biologie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Viktor Stein
- Fachbereich Biologie, Technische Universität Darmstadt, 64287 Darmstadt, Germany.,Centre for Synthetic Biology, Technische Universität Darmstadt, 64283 Darmstadt, Germany
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57
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Chen LC, Wang E, Tai CS, Chiu YC, Li CW, Lin YR, Lee TH, Huang CW, Chen JC, Chen WL. Improving the reproducibility, accuracy, and stability of an electrochemical biosensor platform for point-of-care use. Biosens Bioelectron 2020; 155:112111. [PMID: 32217334 DOI: 10.1016/j.bios.2020.112111] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/12/2020] [Accepted: 02/18/2020] [Indexed: 11/15/2022]
Abstract
Electrochemical biosensors possess numerous desirable qualities for target detection, such as portability and ease of use, and are often considered for point-of-care (POC) development. Label-free affinity electrochemical biosensors constructed with semiconductor manufacturing technology (SMT)-produced electrodes and a streptavidin biomediator currently display the highest reproducibility, accuracy, and stability in modern biosensors. However, such biosensors still do not meet POC guidelines regarding these three characteristics. The purpose of this research was to resolve the limitations in reproducibility and accuracy caused by problems with production of the biosensors, with the aim of developing a platform capable of producing devices that exceed POC standards. SMT production settings were optimized and bioreceptor immobilization was improved through the use of a unique linker, producing a biosensor with exceptional reproducibility, impressive accuracy, and high stability. Importantly, the three characteristics of the sensors produced using the proposed platform all meet POC standards set by the Clinical and Laboratory Standards Institute (CLSI). This suggests possible approval of the biosensors for POC development. Furthermore, the detection range of the platform was demonstrated by constructing biosensors capable of detecting common POC targets, including circulating tumor cells (CTCs), DNA/RNA, and curcumin, and the devices were optimized for POC use. Overall, the platform developed in this study shows high potential for production of POC biosensors.
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Affiliation(s)
- Lung-Chieh Chen
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan; Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, Taiwan
| | - Erick Wang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Chun-San Tai
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan; Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, Taiwan
| | - Yuan-Chen Chiu
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan; Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, Taiwan
| | - Chang-Wei Li
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan; AllBio Life Inc, Taichung, Taiwan
| | - Yan-Ren Lin
- Department of Emergency Medicine, Changhua Christian Hospital, Changhua, Taiwan; School of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Tsung-Han Lee
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan; Department of Emergency Medicine, Changhua Christian Hospital, Changhua, Taiwan
| | - Ching-Wen Huang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan; Department of Emergency, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan; Division of Thoracic Surgery, Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Jung-Chih Chen
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan; Institute of Biomedical Engineering, National Chiao Tung University, Hsinchu, Taiwan
| | - Wen Liang Chen
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan.
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58
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Meng D, Wang J, You C. The properties of the linker in a mini-scaffoldin influence the catalytic efficiency of scaffoldin-mediated enzyme complexes. Enzyme Microb Technol 2020; 133:109460. [DOI: 10.1016/j.enzmictec.2019.109460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/27/2019] [Accepted: 10/31/2019] [Indexed: 10/25/2022]
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59
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Structural and evolutionary approaches to the design and optimization of fluorescence-based small molecule biosensors. Curr Opin Struct Biol 2019; 57:31-38. [DOI: 10.1016/j.sbi.2019.01.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/10/2019] [Accepted: 01/23/2019] [Indexed: 11/21/2022]
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60
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Wu Y, Yan P, Liu X, Wang Z, Tang YJ, Chen T, Zhao X. Combinatorial expression of different β-carotene hydroxylases and ketolases in Escherichia coli for increased astaxanthin production. J Ind Microbiol Biotechnol 2019; 46:1505-1516. [PMID: 31297712 DOI: 10.1007/s10295-019-02214-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 07/04/2019] [Indexed: 01/10/2023]
Abstract
In natural produced bacteria, β-carotene hydroxylase (CrtZ) and β-carotene ketolase (CrtW) convert β-carotene into astaxanthin. To increase astaxanthin production in heterologous strain, simple and effective strategies based on the co-expression of CrtZ and CrtW were applied in E. coli. First, nine artificial operons containing crtZ and crtW genes from different sources were constructed and, respectively, introduced into E. coli ZF237T, a β-carotene producing host. Among the nine resulting strains, five accumulated detectable amounts of astaxanthin ranging from 0.49 to 8.07 mg/L. Subsequently, the protein fusion CrtZ to CrtW using optimized peptide linkers further increased the astaxanthin production. Strains expressing fusion proteins with CrtZ rather than CrtW attached to the N-terminus accumulated much more astaxanthin. The astaxanthin production of the best strain ZF237T/CrtZAs-(GS)1-WBs was 127.6% and 40.2% higher than that of strains ZF237T/crtZAsWBs and ZF237T/crtZBsWPs, respectively. The strategies depicted here also will be useful for the heterologous production of other natural products.
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Affiliation(s)
- Yuanqing Wu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Panpan Yan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Xuewei Liu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Zhiwen Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Ya-Jie Tang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China.,Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan, 430068, People's Republic of China
| | - Tao Chen
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.
| | - Xueming Zhao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
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61
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Zhao W, Liu S, Du G, Zhou J. An efficient expression tag library based on self-assembling amphipathic peptides. Microb Cell Fact 2019; 18:91. [PMID: 31133014 PMCID: PMC6535861 DOI: 10.1186/s12934-019-1142-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 05/17/2019] [Indexed: 11/10/2022] Open
Abstract
Background Self-assembling amphipathic peptides (SAPs) may improve protein production or induce the formation of inclusion bodies by fusing them to the N-terminus of proteins. However, they do not function uniformly well with all target enzymes and systematic research on how the composition of SAPs influence the production of fusion protein is still limited. Results To improve the efficiency of SAPs, we studied factors that might be involved in SAP-mediated protein production using S1 (AEAEAKAK)2 as the original SAP and green fluorescent protein (GFP) as the reporter. The results indicate that hydrophobicity and net charges of SAPs play a key role in protein expression. As hydrophobicity regulation tend to cause the formation of insoluble inclusion bodies of protein, an expression tag library composed of SAPs, which varied in net charge (from + 1 to + 20), was constructed based on the random amplification of S1nv1 (ANANARAR)10. The efficiency of the library was validated by polygalacturonate lyase (PGL), lipoxygenase (LOX), l-asparaginase (ASN) and transglutaminase (MTG). To accelerate preliminary screening, each enzyme was fused at the C-terminus with GFP. Among the four enzyme fusions, the SAPs with + 2 – + 6 net charges were optimal for protein expression. Finally, application of the library improved the expression of PGL, LOX, ASN, and MTG by 8.3, 3.5, 2.64, and 3.68-fold relative to that of the corresponding wild-type enzyme, respectively. Conclusions This is the first report to study key factors of SAPs as an expression tag to enhance recombinant enzyme production. The SAP library could be used as a novel plug-and-play protein-engineering method to screen for enzymes or proteins with enhanced production. Electronic supplementary material The online version of this article (10.1186/s12934-019-1142-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Weixin Zhao
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China.,School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Song Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China. .,School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Guocheng Du
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China.,School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
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62
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An efficient thermostabilization strategy based on self-assembling amphipathic peptides for fusion tags. Enzyme Microb Technol 2019; 121:68-77. [DOI: 10.1016/j.enzmictec.2018.11.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 11/13/2018] [Accepted: 11/16/2018] [Indexed: 11/20/2022]
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63
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Kaliamurthi S, Selvaraj G, Chinnasamy S, Wang Q, Nangraj AS, Cho WC, Gu K, Wei DQ. Exploring the Papillomaviral Proteome to Identify Potential Candidates for a Chimeric Vaccine against Cervix Papilloma Using Immunomics and Computational Structural Vaccinology. Viruses 2019; 11:E63. [PMID: 30650527 PMCID: PMC6357041 DOI: 10.3390/v11010063] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/03/2019] [Accepted: 01/10/2019] [Indexed: 02/06/2023] Open
Abstract
The human papillomavirus (HPV) 58 is considered to be the second most predominant genotype in cervical cancer incidents in China. HPV type-restriction, non-targeted delivery, and the highcost of existing vaccines necessitate continuing research on the HPV vaccine. We aimed to explore the papillomaviral proteome in order to identify potential candidates for a chimeric vaccine against cervix papilloma using computational immunology and structural vaccinology approaches. Two overlapped epitope segments (23⁻36) and (29⁻42) from the N-terminal region of the HPV58 minor capsid protein L2 are selected as capable of inducing both cellular and humoral immunity. In total, 318 amino acid lengths of the vaccine construct SGD58 contain adjuvants (Flagellin and RS09), two Th epitopes, and linkers. SGD58 is a stable protein that is soluble, antigenic, and non-allergenic. Homology modeling and the structural refinement of the best models of SGD58 and TLR5 found 96.8% and 93.9% favored regions in Rampage, respectively. The docking results demonstrated a HADDOCK score of -62.5 ± 7.6, the binding energy (-30 kcal/mol) and 44 interacting amino acid residues between SGD58-TLR5 complex. The docked complex are stable in 100 ns of simulation. The coding sequences of SGD58 also show elevated gene expression in Escherichia coli with 1.0 codon adaptation index and 59.92% glycine-cysteine content. We conclude that SGD58 may prompt the creation a vaccine against cervix papilloma.
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Affiliation(s)
- Satyavani Kaliamurthi
- Center of Interdisciplinary Science-Computational Life Sciences, College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China.
- College of Chemistry, Chemical Engineering and Environment, Henan University of Technology, Zhengzhou 450001, China.
| | - Gurudeeban Selvaraj
- Center of Interdisciplinary Science-Computational Life Sciences, College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China.
- College of Chemistry, Chemical Engineering and Environment, Henan University of Technology, Zhengzhou 450001, China.
| | - Sathishkumar Chinnasamy
- The State Key Laboratory of Microbial Metabolism, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Qiankun Wang
- The State Key Laboratory of Microbial Metabolism, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Asma Sindhoo Nangraj
- The State Key Laboratory of Microbial Metabolism, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - William Cs Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong.
| | - Keren Gu
- Center of Interdisciplinary Science-Computational Life Sciences, College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China.
- College of Chemistry, Chemical Engineering and Environment, Henan University of Technology, Zhengzhou 450001, China.
| | - Dong-Qing Wei
- Center of Interdisciplinary Science-Computational Life Sciences, College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China.
- The State Key Laboratory of Microbial Metabolism, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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64
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Abstract
One approach to bringing enzymes together for multienzyme biocatalysis is genetic fusion. This enables the production of multifunctional enzymes that can be used for whole-cell biotransformations or for in vitro (cascade) reactions. In some cases and in some aspects, such as expression and conversions, the fused enzymes outperform a combination of the individual enzymes. In contrast, some enzyme fusions are greatly compromised in activity and/or expression. In this Minireview, we give an overview of studies on fusions between two or more enzymes that were used for biocatalytic applications, with a focus on oxidative enzymes. Typically, the enzymes are paired to facilitate cofactor recycling or cosubstrate supply. In addition, different linker designs are briefly discussed. Although enzyme fusion is a promising tool for some biocatalytic applications, future studies could benefit from integrating the findings of previous studies in order to improve reliability and effectiveness.
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Affiliation(s)
- Friso S. Aalbers
- Molecular Enzymology GroupUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Marco W. Fraaije
- Molecular Enzymology GroupUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
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65
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Wang Z, Zhang T, Long L, Ding S. Altering the linker in processive GH5 endoglucanase 1 modulates lignin binding and catalytic properties. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:332. [PMID: 30568732 PMCID: PMC6297974 DOI: 10.1186/s13068-018-1333-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/07/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND The non-productive adsorption of cellulases onto lignin in biomass is a key issue for the biofuel process economy. It would be helpful to reduce the inhibitory effect of lignin on enzymatic hydrolysis by engineering weak lignin-binding cellulases. Cellulase linkers are highly divergent in their lengths, compositions, and glycosylations. Numerous studies have revealed that linkers can facilitate optimal interactions between structured domains. Recently, efforts have focused on the contributions and mechanisms of carbohydrate-binding modules and catalytic domains that affect lignin affinity and processivity of cellulases, but our understanding of the effects of the linker regions on lignin adsorption and processivity of GH5 processive endoglucanases is still limited. RESULTS Eight GH5 endoglucanase 1 variants of varying length, flexibility, and sequence in the linker region were constructed. Their characteristics were then compared to the wild-type enzyme (EG1). Remarkably, significant differences in the lignin adsorption profiles and processivities were observed for EG1 and other variants. Our studies suggest that either the length or the specific amino acid composition of the linker has a prominent influence on the lignin-binding affinity of the enzymes. Comparatively, the processivity may depend primarily on the length of the linker and less so on the specific amino acid composition. EG1-ApCel5A, a variant with better performance in enzymatic hydrolysis in the presence of lignin, was obtained by replacing a longer, flexible linker. In total, up to between 28.2 and 30.1% more reducing sugars were generated from filter paper by EG1-ApCel5A in the presence of lignin compared to EG1. CONCLUSIONS Our results highlight the relevance of the linker region in the lignin adsorption and processivity of a processive endoglucanase. Our findings suggest that the linker region may be used as a target for the design of more active and weaker lignin-binding cellulases.
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Affiliation(s)
- Zhen Wang
- The Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Tianrui Zhang
- The Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Liangkun Long
- The Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Shaojun Ding
- The Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
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66
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Evaluation on the efficacy and immunogenicity of recombinant DNA plasmids expressing S gene from porcine epidemic diarrhea virus and VP7 gene from porcine rotavirus. Braz J Microbiol 2018; 50:279-286. [PMID: 30637649 PMCID: PMC6863295 DOI: 10.1007/s42770-018-0022-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 10/02/2018] [Indexed: 12/30/2022] Open
Abstract
Porcine rotavirus (PoRV) and porcine epidemic diarrhea virus (PEDV) usually co-infect pigs in modern large-scale piggery, which both can cause severe diarrhea in newborn piglets and lead to significant economic losses to the pig industry. The VP7 protein is the main coat protein of PoRV, and the S protein is the main structural protein of PEDV, which are capable of inducing neutralizing antibodies in vivo. In this study, a DNA vaccine pPI-2.EGFP.VP7.S co-expressing VP7 protein of PoRV and S protein of PEDV was constructed. Six 8-week-old mice were immunized with the recombinant plasmid pPI-2.EGFP.VP7.S. The high humoral immune responses (virus specific antibody) and cellular immune responses (IFN-γ, IL-4, and spleen lymphocyte proliferation) were evaluated. The immune effect through intramuscular injection increased with plasmid dose when compared with subcutaneous injection. The immune-enhancing effect of IFN-α adjuvant was excellent compared with pig spleen transfer factor and IL-12 adjuvant. These results demonstrated that pPI-2.EGFP.VP7.S possess the immunological functions of the VP7 proteins of PoRV and S proteins of PEDV, indicating that pPI-2.EGFP.VP7.S is a candidate vaccine for porcine rotaviral infection (PoR) and porcine epidemic diarrhea (PED).
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67
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Norris JL, Hughes RM. protaTETHER - a method for the incorporation of variable linkers in protein fusions reveals impacts of linker flexibility in a PKAc-GFP fusion protein. FEBS Open Bio 2018; 8:1029-1042. [PMID: 29928581 PMCID: PMC5986021 DOI: 10.1002/2211-5463.12414] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 02/12/2018] [Accepted: 03/01/2018] [Indexed: 11/11/2022] Open
Abstract
Protein fusions are of fundamental importance in the study of cellular biology and the elucidation of cell signaling pathways, and the importance of linkers for the proper function of protein fusions is well documented in the literature. However, there are few convenient methods available to experimentalists for the systematic implementation of linkers in protein fusions. In this work, we describe a universal approach to the creation and insertion of focused linker libraries into protein fusions. This process, deemed protaTETHER, utilizes reiterative oligomer design, PCR-mediated linker library generation, and restriction enzyme-free cloning methods in a straightforward, three-step cloning process. We utilize a fusion between the catalytic subunit of cAMP-dependent protein kinase A (PKAc) and green fluorescent protein (GFP) for the development of the protaTETHER method, implementing small linker libraries that vary by length, sequence, and predicted secondary structural elements. We analyze the impact of linker length and sequence on the expression, activity, and subcellular localization of the PKAc-GFP fusions, and use these results to select a PKAc-GFP fusion construct with robust expression and enzymatic activity. Based upon the results of both biochemical experiments and molecular modeling, we determine that linker flexibility is more important than linker length for optimal kinase activity and expression.
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68
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Blank M, Schweiger P. Surface display for metabolic engineering of industrially important acetic acid bacteria. PeerJ 2018; 6:e4626. [PMID: 29637028 PMCID: PMC5890722 DOI: 10.7717/peerj.4626] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 03/26/2018] [Indexed: 11/20/2022] Open
Abstract
Acetic acid bacteria have unique metabolic characteristics that suit them for a variety of biotechnological applications. They possess an arsenal of membrane-bound dehydrogenases in the periplasmic space that are capable of regiospecific and enantioselective partial oxidations of sugars, alcohols, and polyols. The resulting products are deposited directly into the medium where they are easily recovered for use as pharmaceutical precursors, industrial chemicals, food additives, and consumer products. Expression of extracytoplasmic enzymes to augment the oxidative capabilities of acetic acid bacteria is desired but is challenging due to the already crowded inner membrane. To this end, an original surface display system was developed to express recombinant enzymes at the outer membrane of the model acetic acid bacterium Gluconobacter oxydans. Outer membrane porin F (OprF) was used to deliver alkaline phosphatase (PhoA) to the cell surface. Constitutive high-strength p264 and moderate-strength p452 promoters were used to direct expression of the surface display system. This system was demonstrated for biocatalysis in whole-cell assays with the p264 promoter having a twofold increase in PhoA activity compared to the p452 promoter. Proteolytic cleavage of PhoA from the cell surface confirmed proper delivery to the outer membrane. Furthermore, a linker library was constructed to optimize surface display. A rigid (EAAAK)1 linker led to the greatest improvement, increasing PhoA activity by 69%. This surface display system could be used both to extend the capabilities of acetic acid bacteria in current biotechnological processes, and to broaden the potential of these microbes in the production of value-added products.
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Affiliation(s)
- Marshal Blank
- Biology Department, Missouri State University, Springfield, MO, USA
| | - Paul Schweiger
- Department of Microbiology, University of Wisconsin-La Crosse, La Crosse, WI, USA
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69
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Yagi S, Akanuma S, Yamagishi A. Creation of artificial protein-protein interactions using α-helices as interfaces. Biophys Rev 2018; 10:411-420. [PMID: 29214605 PMCID: PMC5899712 DOI: 10.1007/s12551-017-0352-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 11/15/2017] [Indexed: 12/31/2022] Open
Abstract
Designing novel protein-protein interactions (PPIs) with high affinity is a challenging task. Directed evolution, a combination of randomization of the gene for the protein of interest and selection using a display technique, is one of the most powerful tools for producing a protein binder. However, the selected proteins often bind to the target protein at an undesired surface. More problematically, some selected proteins bind to their targets even though they are unfolded. Current state-of-the-art computational design methods have successfully created novel protein binders. These computational methods have optimized the non-covalent interactions at interfaces and thus produced artificial protein complexes. However, to date there are only a limited number of successful examples of computationally designed de novo PPIs. De novo design of coiled-coil proteins has been extensively performed and, therefore, a large amount of knowledge of the sequence-structure relationship of coiled-coil proteins has been accumulated. Taking advantage of this knowledge, de novo design of inter-helical interactions has been used to produce artificial PPIs. Here, we review recent progress in the in silico design and rational design of de novo PPIs and the use of α-helices as interfaces.
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Affiliation(s)
- Sota Yagi
- Department of Applied Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Satoshi Akanuma
- Faculty of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama, 359-1192, Japan
| | - Akihiko Yamagishi
- Department of Applied Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan.
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70
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Caparco AA, Bommarius AS, Champion JA. Effect of peptide linker length and composition on immobilization and catalysis of leucine zipper‐enzyme fusion proteins. AIChE J 2018. [DOI: 10.1002/aic.16150] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Adam A. Caparco
- School of Chemical and Biomolecular Engineering, Petit Institute for Bioengineering and BioscienceGeorgia Institute of TechnologyAtlanta GA 30332
| | - Andreas S. Bommarius
- School of Chemical and Biomolecular Engineering, Petit Institute for Bioengineering and BioscienceGeorgia Institute of TechnologyAtlanta GA 30332
| | - Julie A. Champion
- School of Chemical and Biomolecular Engineering, Petit Institute for Bioengineering and BioscienceGeorgia Institute of TechnologyAtlanta GA 30332
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71
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Ji Y, Lu Y, Yan Y, Liu X, Su N, Zhang C, Bi S, Xing XH. Design of Fusion Proteins for Efficient and Soluble Production of Immunogenic Ebola Virus Glycoprotein in Escherichia coli. Biotechnol J 2018; 13:e1700627. [PMID: 29500882 DOI: 10.1002/biot.201700627] [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] [Received: 10/31/2017] [Revised: 01/30/2018] [Indexed: 11/08/2022]
Abstract
The Ebola hemorrhagic fever caused by Ebola virus is an extremely dangerous disease, and effective therapeutic agents are still lacking. Platforms for the efficient production of vaccines are crucial to ensure quick response against an Ebola virus outbreak. Ebola virus glycoprotein (EbolaGP) on the virion surface is responsible for membrane binding and virus entry, thus becoming the key target for vaccine development. However, heterologous expression of this protein still faces engineering challenges such as low production levels and insoluble aggregation. Here, the authors design and compare various fusion strategies, attaching great importance to the solubility-enhancing effect, and tag removal process. It is found that a C-terminal intein-based tag greatly enhances the solubility of EbolaGP and allows one-step chromatographic purification of the untagged EbolaGP through thiol-catalyzed self-cleavage. The purified untagged EbolaGP alone or with Freund's adjuvant are highly immunogenic, as confirmed in a mouse model. Consequently, the present study puts forward a new strategy for the efficient and soluble expression of untagged immunogenic EbolaGP. The intein-based protein fusion approach may be of importance for the large-scale production of Ebola virus subunit vaccine.
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Affiliation(s)
- Yang Ji
- MOE Key Laboratory of Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, P. R. China
| | - Yuan Lu
- MOE Key Laboratory of Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, P. R. China
| | - Yishu Yan
- MOE Key Laboratory of Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, P. R. China
| | - Xinxin Liu
- Bio-Cell Co. Ltd., Beijing, 100085, P. R. China
| | - Nan Su
- Bio-Cell Co. Ltd., Beijing, 100085, P. R. China
| | - Chong Zhang
- MOE Key Laboratory of Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, P. R. China.,Centre for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, P. R. China
| | - Shengli Bi
- Institute of Virology Disease Control, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xin-Hui Xing
- MOE Key Laboratory of Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, P. R. China.,Centre for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, P. R. China
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72
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Pinheiro AM, Carreira A, Ferreira RB, Monteiro S. Fusion proteins towards fungi and bacteria in plant protection. MICROBIOLOGY (READING, ENGLAND) 2018; 164:11-19. [PMID: 29239714 PMCID: PMC5892777 DOI: 10.1099/mic.0.000592] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/04/2017] [Indexed: 02/06/2023]
Abstract
In agriculture, although fungi are considered the foremost problem, infections by bacteria also cause significant economical losses. The presence of different diseases in crops often leads to a misuse of the proper therapeutic, or the combination of different diseases forces the use of more than one pesticide. This work concerns the development of a 'super-Blad': a chimeric protein consisting of Blad polypeptide, the active ingredient of a biological fungicide already on the market, and two selected peptides, SP10-5 and Sub5, proven to possess biological potential as antibacterial agents. The resulting chimeric protein obtained from the fusion of Blad with SP10-5 not only maintained strong antibacterial activity, especially against Xanthomonas spp. and Pseudomonas syringae, but was also able to retain the ability to inhibit the growth of both yeast and filamentous fungi. However, the antibacterial activity of Sub5 was considerably diminished when fused with Blad, which seems to indicate that not all fusion proteins behave equally. These newly designed drugs can be considered promising compounds for use in plant protection. A deeper and focused development of an appropriate formulation may result in a potent biopesticide that can replace, per se, two conventional chemistries with less impact on the environment.
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Affiliation(s)
- Ana Margarida Pinheiro
- LEAF – Linking Landscape, Environment, Agriculture and Food Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal
| | - Alexandra Carreira
- CEV, SA, Parque Industrial de Cantanhede/Biocant-Park, lote 120, 3060-197 Cantanhede, Portugal
| | - Ricardo B. Ferreira
- LEAF – Linking Landscape, Environment, Agriculture and Food Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal
| | - Sara Monteiro
- LEAF – Linking Landscape, Environment, Agriculture and Food Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal
- CEV, SA, Parque Industrial de Cantanhede/Biocant-Park, lote 120, 3060-197 Cantanhede, Portugal
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73
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van Rosmalen M, Krom M, Merkx M. Tuning the Flexibility of Glycine-Serine Linkers To Allow Rational Design of Multidomain Proteins. Biochemistry 2017; 56:6565-6574. [PMID: 29168376 PMCID: PMC6150656 DOI: 10.1021/acs.biochem.7b00902] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
![]()
Flexible
polypeptide linkers composed of glycine and serine are
important components of engineered multidomain proteins. We have previously
shown that the conformational properties of Gly-Gly-Ser repeat linkers
can be quantitatively understood by comparing experimentally determined
Förster resonance energy transfer (FRET) efficiencies of ECFP-linker-EYFP
proteins to theoretical FRET efficiencies calculated using wormlike
chain and Gaussian chain models. Here we extend this analysis to include
linkers with different glycine contents. We determined the FRET efficiencies
of ECFP-linker-EYFP proteins with linkers ranging in length from 25
to 73 amino acids and with glycine contents of 33.3% (GSSGSS), 16.7%
(GSSSSSS), and 0% (SSSSSSS). The FRET efficiency decreased with an
increasing linker length and was overall lower for linkers with less
glycine. Modeling the linkers using the WLC model revealed that the
experimentally observed FRET efficiencies were consistent with persistence
lengths of 4.5, 4.8, and 6.2 Å for the GSSGSS, GSSSSS, and SSSSSS
linkers, respectively. The observed increase in linker stiffness with
reduced glycine content is much less pronounced than that predicted
by a classical model developed by Flory and co-workers. We discuss
possible reasons for this discrepancy as well as implications for
using the stiffer linkers to control the effective concentrations
of connected domains in engineered multidomain proteins.
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Affiliation(s)
- Martijn van Rosmalen
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Mike Krom
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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74
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Hoffmann D, Ebrahimi M, Gerlach D, Salzig D, Czermak P. Reassessment of inclusion body-based production as a versatile opportunity for difficult-to-express recombinant proteins. Crit Rev Biotechnol 2017; 38:729-744. [DOI: 10.1080/07388551.2017.1398134] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Daniel Hoffmann
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany
| | - Mehrdad Ebrahimi
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany
| | - Doreen Gerlach
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Project group Bioresources, Giessen, Germany
| | - Denise Salzig
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany
| | - Peter Czermak
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Project group Bioresources, Giessen, Germany
- Faculty of Biology and Chemistry, Justus Liebig University, Giessen, Germany
- Department of Chemical Engineering, Kansas State University, Manhattan, KS, USA
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75
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Jiang M, Zhang L, Wang F, Zhang J, Liu G, Gao B, Wei D. Novel Application of Magnetic Protein: Convenient One-Step Purification and Immobilization of Proteins. Sci Rep 2017; 7:13329. [PMID: 29042612 PMCID: PMC5645317 DOI: 10.1038/s41598-017-13648-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 09/26/2017] [Indexed: 12/04/2022] Open
Abstract
Recently, a magnetic protein was discovered, and a multimeric magnetosensing complex was validated, which may form the basis of magnetoreception. In this study, the magnetic protein was firstly used in biotechnology application, and a novel convenient one-step purification and immobilization method was established. A universal vector and three linker patterns were developed for fusion expression of magnetic protein and target protein. The magnetic protein was absorbed by iron beads, followed by target protein aggregation, purification, and immobilization. GFP, employed as a reporter protein, was successfully purified from cell lysate. Subsequently, three enzymes (lipase, α-L-arabinofuranosidase, pullulanase) with different molecular sizes testified the versatility of this magnetic-based approach. The specific activities of the purified enzymes were distinctly higher than those of the traditionally purified enzymes using affinity chromatography. The lipase immobilized on iron beads presented improved thermostability and enhanced pH tolerance compared to the free enzyme. The immobilized lipase could be easily recovered and reused for maximum utilization. After 20 cycles of reutilization, the magnetically immobilized lipase retained 71% of its initial activity. This investigation may help introduce magnetic protein into biotechnology applications, and the one-step purification and immobilization method may serve to illustrate an economically viable process for industry.
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Affiliation(s)
- Min Jiang
- State Key Lab of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Lujia Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China
| | - Fengqing Wang
- State Key Lab of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Jie Zhang
- School of Physics and Materials Science, East China Normal University, Shanghai, 200062, China
| | - Guosong Liu
- State Key Lab of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Bei Gao
- State Key Lab of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Dongzhi Wei
- State Key Lab of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
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76
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Liu B, Åberg C, van Eerden FJ, Marrink SJ, Poolman B, Boersma AJ. Design and Properties of Genetically Encoded Probes for Sensing Macromolecular Crowding. Biophys J 2017; 112:1929-1939. [PMID: 28494963 DOI: 10.1016/j.bpj.2017.04.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 03/27/2017] [Accepted: 04/04/2017] [Indexed: 10/19/2022] Open
Abstract
Cells are highly crowded with proteins and polynucleotides. Any reaction that depends on the available volume can be affected by macromolecular crowding, but the effects of crowding in cells are complex and difficult to track. Here, we present a set of Förster resonance energy transfer (FRET)-based crowding-sensitive probes and investigate the role of the linker design. We investigate the sensors in vitro and in vivo and by molecular dynamics simulations. We find that in vitro all the probes can be compressed by crowding, with a magnitude that increases with the probe size, the crowder concentration, and the crowder size. We capture the role of the linker in a heuristic scaling model, and we find that compression is a function of size of the probe and volume fraction of the crowder. The FRET changes observed in Escherichia coli are more complicated, where FRET-increases and scaling behavior are observed solely with probes that contain the helices in the linker. The probe with the highest sensitivity to crowding in vivo yields the same macromolecular volume fractions as previously obtained from cell dry weight. The collection of new probes provides more detailed readouts on the macromolecular crowding than a single sensor.
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Affiliation(s)
- Boqun Liu
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Christoffer Åberg
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Floris J van Eerden
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Siewert J Marrink
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands.
| | - Arnold J Boersma
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands.
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77
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Ruan H, Chen X, Xie C, Li B, Ying M, Liu Y, Zhang M, Zhang X, Zhan C, Lu W, Lu W. Stapled RGD Peptide Enables Glioma-Targeted Drug Delivery by Overcoming Multiple Barriers. ACS APPLIED MATERIALS & INTERFACES 2017; 9:17745-17756. [PMID: 28497694 DOI: 10.1021/acsami.7b03682] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Malignant glioma, the most frequent and aggressive central nervous system (CNS) tumor, severely threatens human health. One reason for its poor prognosis and short survival is the presence of the blood-brain barrier (BBB) and blood-brain tumor barrier (BBTB), which restrict the penetration of therapeutics into the brain at different stages of glioma. Herein, inspired by the peptide stapling technique, we designed a cyclic RGD ligand via an all-hydrocarbon staple (stapled RGD, sRGD) to facilitate BBB penetration while retaining the capacity of BBTB penetration and targeting ability to glioma cells. As expected, sRGD-modified micelles were able to penetrate the in vitro BBB model while retaining the glioma targeted capability. The results of the in vivo imaging studies further revealed that this nanocarrier could not only efficiently transverse the intact BBB of normal mice, but also could specifically target glioma cells of intracranial glioma-bearing nude mice. Furthermore, Paclitaxel-loaded sRGD-modified micelles exhibited improved antiglioma efficacy in vitro and significantly prolonged survival time of glioma-bearing nude mice. Overall, this sRGD peptide showed potency for glioma-targeted drug delivery by overcoming multiple barriers.
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Affiliation(s)
- Huitong Ruan
- Key Laboratory of Smart Drug Delivery of the Ministry of Education (Fudan University), & Department of Pharmaceutics, School of Pharmacy, Fudan University , Shanghai 201203, P.R. China
| | - Xishan Chen
- Key Laboratory of Smart Drug Delivery of the Ministry of Education (Fudan University), & Department of Pharmaceutics, School of Pharmacy, Fudan University , Shanghai 201203, P.R. China
| | - Cao Xie
- Key Laboratory of Smart Drug Delivery of the Ministry of Education (Fudan University), & Department of Pharmaceutics, School of Pharmacy, Fudan University , Shanghai 201203, P.R. China
| | - Beibei Li
- Key Laboratory of Smart Drug Delivery of the Ministry of Education (Fudan University), & Department of Pharmaceutics, School of Pharmacy, Fudan University , Shanghai 201203, P.R. China
| | | | - Yu Liu
- Key Laboratory of Smart Drug Delivery of the Ministry of Education (Fudan University), & Department of Pharmaceutics, School of Pharmacy, Fudan University , Shanghai 201203, P.R. China
| | - Mingfei Zhang
- Key Laboratory of Smart Drug Delivery of the Ministry of Education (Fudan University), & Department of Pharmaceutics, School of Pharmacy, Fudan University , Shanghai 201203, P.R. China
| | - Xuesai Zhang
- Key Laboratory of Smart Drug Delivery of the Ministry of Education (Fudan University), & Department of Pharmaceutics, School of Pharmacy, Fudan University , Shanghai 201203, P.R. China
| | | | - Wuyuan Lu
- Institute of Human Virology & Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine , Baltimore, Maryland 21201, United States
| | - Weiyue Lu
- Key Laboratory of Smart Drug Delivery of the Ministry of Education (Fudan University), & Department of Pharmaceutics, School of Pharmacy, Fudan University , Shanghai 201203, P.R. China
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University , Shanghai 200433, P.R. China
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78
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Bioavailability of immobilized epidermal growth factor: Covalent versus noncovalent grafting. Biointerphases 2017; 12:010501. [PMID: 28325051 DOI: 10.1116/1.4978871] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In an effort to rationalize and optimize an antiapoptotic coating combining chondroitin sulfate (CS) and epidermal growth factor (EGF) for vascular applications, the authors here report the comparison of two grafting strategies aiming to display EGF in an oriented fashion on CS. For that purpose, the authors produced, purified, and characterized a chimeric protein corresponding to EGF that was N-terminally fused to a cysteine and a coil peptide. The chimera was covalently immobilized via its free thiol group or captured via coiled-coil interactions at the surface of a biosensor or on a chondroitin sulfate coating in multiwell plates, mimicking the coating that was previously developed by them for stent-graft surfaces. The interactions of grafted EGF with the soluble domain of its receptor or the impact of grafted EGF upon vascular smooth muscle survival in proapoptotic conditions indicated that the coiled-coil based tethering was the best approach to display EGF. These results, combined to direct enzyme-linked immunosorbent assay measurements, indicated that the coiled-coil tethering approach allowed increasing the amount of bioavailable EGF when compared to covalent coupling, rather than the total amount of grafted EGF, while using much lower concentrations of tagged EGF during incubation.
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79
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Quin MB, Wallin KK, Zhang G, Schmidt-Dannert C. Spatial organization of multi-enzyme biocatalytic cascades. Org Biomol Chem 2017; 15:4260-4271. [DOI: 10.1039/c7ob00391a] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Multi-enzyme cascades provide a wealth of valuable chemicals. Efficiency of reaction schemes can be improved by spatial organization of biocatalysts. This review will highlight various methods of spatial organization of biocatalysts: fusion, immobilization, scaffolding and encapsulation.
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Affiliation(s)
- M. B. Quin
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
| | - K. K. Wallin
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
| | - G. Zhang
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
| | - C. Schmidt-Dannert
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
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80
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Rizk M, Antranikian G, Elleuche S. Influence of Linker Length Variations on the Biomass-Degrading Performance of Heat-Active Enzyme Chimeras. Mol Biotechnol 2016; 58:268-79. [PMID: 26921187 DOI: 10.1007/s12033-016-9925-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Plant cell walls are composed of complex polysaccharides such as cellulose and hemicellulose. In order to efficiently hydrolyze cellulose, the synergistic action of several cellulases is required. Some anaerobic cellulolytic bacteria form multienzyme complexes, namely cellulosomes, while other microorganisms produce a portfolio of diverse enzymes that work in synergistic fashion. Molecular biological methods can mimic such effects through the generation of artificial bi- or multifunctional fusion enzymes. Endoglucanase and β-glucosidase from extremely thermophilic anaerobic bacteria Fervidobacterium gondwanense and Fervidobacterium islandicum, respectively, were fused end-to-end in an approach to optimize polysaccharide degradation. Both enzymes are optimally active at 90 °C and pH 6.0-7.0 representing excellent candidates for fusion experiments. The direct linkage of both enzymes led to an increased activity toward the substrate specific for β-glucosidase, but to a decreased activity of endoglucanase. However, these enzyme chimeras were superior over 1:1 mixtures of individual enzymes, because combined activities resulted in a higher final product yield. Therefore, such fusion enzymes exhibit promising features for application in industrial bioethanol production processes.
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Affiliation(s)
- Mazen Rizk
- Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, 21073, Hamburg, Germany
| | - Garabed Antranikian
- Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, 21073, Hamburg, Germany
| | - Skander Elleuche
- Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, 21073, Hamburg, Germany.
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81
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Luna-Pineda VM, Reyes-Grajeda JP, Cruz-Córdova A, Saldaña-Ahuactzi Z, Ochoa SA, Maldonado-Bernal C, Cázares-Domínguez V, Moreno-Fierros L, Arellano-Galindo J, Hernández-Castro R, Xicohtencatl-Cortes J. Dimeric and Trimeric Fusion Proteins Generated with Fimbrial Adhesins of Uropathogenic Escherichia coli. Front Cell Infect Microbiol 2016; 6:135. [PMID: 27843814 PMCID: PMC5087080 DOI: 10.3389/fcimb.2016.00135] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/04/2016] [Indexed: 12/29/2022] Open
Abstract
Urinary tract infections (UTIs) are associated with high rates of morbidity and mortality worldwide, and uropathogenic Escherichia coli (UPEC) is the main etiologic agent. Fimbriae assembled on the bacterial surface are essential for adhesion to the urinary tract epithelium. In this study, the FimH, CsgA, and PapG adhesins were fused to generate biomolecules for use as potential target vaccines against UTIs. The fusion protein design was generated using bioinformatics tools, and template fusion gene sequences were synthesized by GenScript in the following order fimH-csgA-papG-fimH-csgA (fcpfc) linked to the nucleotide sequence encoding the [EAAAK]5 peptide. Monomeric (fimH, csgA, and papG), dimeric (fimH-csgA), and trimeric (fimH-csgA-papG) genes were cloned into the pLATE31 expression vector and generated products of 1040, 539, 1139, 1442, and 2444 bp, respectively. Fusion protein expression in BL21 E. coli was induced with 1 mM IPTG, and His-tagged proteins were purified under denaturing conditions and refolded by dialysis using C-buffer. Coomassie blue-stained SDS-PAGE gels and Western blot analysis revealed bands of 29.5, 11.9, 33.9, 44.9, and 82.1 kDa, corresponding to FimH, CsgA, PapG, FC, and FCP proteins, respectively. Mass spectrometry analysis by MALDI-TOF/TOF revealed specific peptides that confirmed the fusion protein structures. Dynamic light scattering analysis revealed the polydispersed state of the fusion proteins. FimH, CsgA, and PapG stimulated the release of 372–398 pg/mL IL-6; interestingly, FC and FCP stimulated the release of 464.79 pg/mL (p ≤ 0.018) and 521.24 pg/mL (p ≤ 0.002) IL-6, respectively. In addition, FC and FCP stimulated the release of 398.52 pg/mL (p ≤ 0.001) and 450.40 pg/mL (p ≤ 0.002) IL-8, respectively. High levels of IgA and IgG antibodies in human sera reacted against the fusion proteins, and under identical conditions, low levels of IgA and IgG antibodies were detected in human urine. Rabbit polyclonal antibodies generated against FimH, CsgA, PapG, FC, and FCP blocked the adhesion of E. coli strain CFT073 to HTB5 bladder cells. In conclusion, the FC and FCP proteins were highly stable, demonstrated antigenic properties, and induced cytokine release (IL-6 and IL-8); furthermore, antibodies generated against these proteins showed protection against bacterial adhesion.
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Affiliation(s)
- Víctor M Luna-Pineda
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México "Federico Gómez"Ciudad de México, Mexico; Instituto de Fisiología Celular, Universidad Nacional Autónoma de MéxicoCiudad de México, Mexico
| | | | - Ariadnna Cruz-Córdova
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México "Federico Gómez" Ciudad de México, Mexico
| | - Zeus Saldaña-Ahuactzi
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México "Federico Gómez"Ciudad de México, Mexico; Instituto de Fisiología Celular, Universidad Nacional Autónoma de MéxicoCiudad de México, Mexico
| | - Sara A Ochoa
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México "Federico Gómez" Ciudad de México, Mexico
| | - Carmen Maldonado-Bernal
- Laboratorio de Investigación de Inmunología y Proteómica, Hospital Infantil de México "Federico Gómez", Dirección De Investigación Ciudad de México, Mexico
| | - Vicenta Cázares-Domínguez
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México "Federico Gómez" Ciudad de México, Mexico
| | - Leticia Moreno-Fierros
- Unidad de Biomedicina, Laboratorio de Inmunidad en Mucosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México Tlalnepantla, Mexico
| | - José Arellano-Galindo
- Departamento de Infectología, Hospital Infantil de México "Federico Gómez" Ciudad de México, Mexico
| | - Rigoberto Hernández-Castro
- Departamento de Ecología de Agentes Patógenos, Hospital General "Dr. Manuel Gea González" Ciudad de México, Mexico
| | - Juan Xicohtencatl-Cortes
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México "Federico Gómez" Ciudad de México, Mexico
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82
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Milano T, Angelaccio S, Tramonti A, Di Salvo ML, Contestabile R, Pascarella S. Structural properties of the linkers connecting the N- and C- terminal domains in the MocR bacterial transcriptional regulators. BIOCHIMIE OPEN 2016; 3:8-18. [PMID: 29450126 PMCID: PMC5801912 DOI: 10.1016/j.biopen.2016.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 07/10/2016] [Indexed: 12/03/2022]
Abstract
Peptide inter-domain linkers are peptide segments covalently linking two adjacent domains within a protein. Linkers play a variety of structural and functional roles in naturally occurring proteins. In this work we analyze the sequence properties of the predicted linker regions of the bacterial transcriptional regulators belonging to the recently discovered MocR subfamily of the GntR regulators. Analyses were carried out on the MocR sequences taken from the phyla Actinobacteria, Firmicutes, Alpha-, Beta- and Gammaproteobacteria. The results suggest that MocR linkers display phylum-specific characteristics and unique features different from those already described for other classes of inter-domain linkers. They show an average length significantly higher: 31.8 ± 14.3 residues reaching a maximum of about 150 residues. Compositional propensities displayed general and phylum-specific trends. Pro is dominating in all linkers. Dyad propensity analysis indicate Pro–Pro as the most frequent amino acid pair in all linkers. Physicochemical properties of the linker regions were assessed using amino acid indices relative to different features: in general, MocR linkers are flexible, hydrophilic and display propensity for β-turn or coil conformations. Linker sequences are hypervariable: only similarities between MocR linkers from organisms related at the level of species or genus could be found with sequence searches. The results shed light on the properties of the linker regions of the new MocR subfamily of bacterial regulators and may provide knowledge-based rules for designing artificial linkers with desired properties. An overview of the structural properties of MocR inter-domain linkers is reported. Linker length distribution is heterogeneous in different phyla. Linkers are flexible, hydrophilic and have coil conformation propensity. Pro and Pro–Pro dyads are very frequent in all the linkers. MocR linkers display a few properties different from those reported for other linkers.
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Affiliation(s)
- Teresa Milano
- Dipartimento di Scienze biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, 00185 Roma, Italy
| | - Sebastiana Angelaccio
- Dipartimento di Scienze biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, 00185 Roma, Italy
| | - Angela Tramonti
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, 00185 Roma, Italy
| | - Martino Luigi Di Salvo
- Dipartimento di Scienze biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, 00185 Roma, Italy
| | - Roberto Contestabile
- Dipartimento di Scienze biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, 00185 Roma, Italy
| | - Stefano Pascarella
- Dipartimento di Scienze biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, 00185 Roma, Italy
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83
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Kirubakaran P, Pfeiferová L, Boušová K, Bednarova L, Obšilová V, Vondrášek J. Artificial proteins as allosteric modulators of PDZ3 and SH3 in two-domain constructs: A computational characterization of novel chimeric proteins. Proteins 2016; 84:1358-74. [DOI: 10.1002/prot.25082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 05/24/2016] [Accepted: 05/30/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Palani Kirubakaran
- Institute of Organic Chemistry and Biochemistry ASCR; v.v.i, Flemingovo náměstí 2, Prague 6, 166 10 Czech Republic
| | - Lucie Pfeiferová
- Institute of Organic Chemistry and Biochemistry ASCR; v.v.i, Flemingovo náměstí 2, Prague 6, 166 10 Czech Republic
| | - Kristýna Boušová
- Institute of Organic Chemistry and Biochemistry ASCR; v.v.i, Flemingovo náměstí 2, Prague 6, 166 10 Czech Republic
- Institute of Physiology ASCR; v.v.i, Videnska 1083, 14220 Prague 4 Czech Republic
| | - Lucie Bednarova
- Institute of Organic Chemistry and Biochemistry ASCR; v.v.i, Flemingovo náměstí 2, Prague 6, 166 10 Czech Republic
| | - Veronika Obšilová
- Institute of Physiology ASCR; v.v.i, Videnska 1083, 14220 Prague 4 Czech Republic
| | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry ASCR; v.v.i, Flemingovo náměstí 2, Prague 6, 166 10 Czech Republic
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84
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Sanyal S, Coker DF, MacKernan D. How flexible is a protein: simple estimates using FRET microscopy. MOLECULAR BIOSYSTEMS 2016; 12:2988-91. [DOI: 10.1039/c6mb00410e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A simple numerical procedure to measure the flexibility of linker proteins used in unimolecular FRET probes.
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