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Timalsina B, Lee S, Kaang BK. Advances in the labelling and selective manipulation of synapses. Nat Rev Neurosci 2024; 25:668-687. [PMID: 39174832 DOI: 10.1038/s41583-024-00851-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2024] [Indexed: 08/24/2024]
Abstract
Synapses are highly specialized neuronal structures that are essential for neurotransmission, and they are dynamically regulated throughout the lifetime. Although accumulating evidence indicates that these structures are crucial for information processing and storage in the brain, their precise roles beyond neurotransmission are yet to be fully appreciated. Genetically encoded fluorescent tools have deepened our understanding of synaptic structure and function, but developing an ideal methodology to selectively visualize, label and manipulate synapses remains challenging. Here, we provide an overview of currently available synapse labelling techniques and describe their extension to enable synapse manipulation. We categorize these approaches on the basis of their conceptual bases and target molecules, compare their advantages and limitations and propose potential modifications to improve their effectiveness. These methods have broad utility, particularly for investigating mechanisms of synaptic function and synaptopathy.
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Affiliation(s)
- Binod Timalsina
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, South Korea
| | - Sangkyu Lee
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, South Korea
| | - Bong-Kiun Kaang
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, South Korea.
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2
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Majhi BK, Melis A. Recombinant protein synthesis and isolation of human interferon alpha-2 in cyanobacteria. BIORESOURCE TECHNOLOGY 2024; 400:130664. [PMID: 38583672 DOI: 10.1016/j.biortech.2024.130664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/01/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
Synechocystis sp. PCC 6803 (Synechocystis) is a unicellular photosynthetic microorganism that has been used as a model for photo-biochemical research. It comprises a potential cell factory for the generation of valuable bioactive compounds, therapeutic proteins, and possibly biofuels. Fusion constructs of recombinant proteins with the CpcA α-subunit or CpcB β-subunit of phycocyanin in Synechocystis have enabled true over-expression of several isoprenoid pathway enzymes and biopharmaceutical proteins to levels of 10-20 % of the total cellular protein. The present work employed the human interferon α-2 protein, as a study case of over-expression and downstream processing. It advanced the state of the art in the fusion constructs for protein overexpression technology by developing the bioresource for target protein separation from the fusion construct and isolation in substantially enriched or pure form. The work brings the cyanobacterial cell factory concept closer to meaningful commercial application for the photosynthetic production of useful recombinant proteins.
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Affiliation(s)
- Bharat K Majhi
- Department of Plant and Microbial Biology, 111 Koshland Hall, MC-3102, University of California, Berkeley, CA 94720-3102, USA
| | - Anastasios Melis
- Department of Plant and Microbial Biology, 111 Koshland Hall, MC-3102, University of California, Berkeley, CA 94720-3102, USA.
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3
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Georges RN, Ballut L, Octobre G, Comte A, Hecquet L, Charmantray F, Doumèche B. Structural determination and kinetic analysis of the transketolase from Vibrio vulnificus reveal unexpected cooperative behavior. Protein Sci 2024; 33:e4884. [PMID: 38145310 PMCID: PMC10868444 DOI: 10.1002/pro.4884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/07/2023] [Accepted: 12/20/2023] [Indexed: 12/26/2023]
Abstract
Vibrio vulnificus (vv) is a multidrug-resistant human bacterial pathogen whose prevalence is expected to increase over the years. Transketolases (TK), transferases catalyzing two reactions of the nonoxidative branch of the pentose-phosphate pathway and therefore linked to several crucial metabolic pathways, are potential targets for new drugs against this pathogen. Here, the vvTK is crystallized and its structure is solved at 2.1 Å. A crown of 6 histidyl residues is observed in the active site and expected to participate in the thiamine pyrophosphate (cofactor) activation. Docking of fructose-6-phosphate and ferricyanide used in the activity assay, suggests that both substrates can bind vvTK simultaneously. This is confirmed by steady-state kinetics showing a sequential mechanism, on the contrary to the natural transferase reaction which follows a substituted mechanism. Inhibition by the I38-49 inhibitor (2-(4-ethoxyphenyl)-1-(pyrimidin-2-yl)-1H-pyrrolo[2,3-b]pyridine) reveals for the first time a cooperative behavior of a TK and docking experiments suggest a previously undescribed binding site at the interface between the pyrophosphate and pyridinium domains.
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Affiliation(s)
| | - Lionel Ballut
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS-Université de Lyon, Lyon, France
| | | | - Arnaud Comte
- Univ Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Laurence Hecquet
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), Clermont-Ferrand, France
| | - Franck Charmantray
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), Clermont-Ferrand, France
| | - Bastien Doumèche
- Univ Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France
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Wang J, Xu Y, Wang X, Li J, Hua Z. Mechanism of Mutation-Induced Effects on the Catalytic Function of TEV Protease: A Molecular Dynamics Study. Molecules 2024; 29:1071. [PMID: 38474583 DOI: 10.3390/molecules29051071] [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: 01/27/2024] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Tobacco etch virus protease (TEVp) is wildly exploited for various biotechnological applications. These applications take advantage of TEVp's ability to cleave specific substrate sequences to study protein function and interactions. A major limitation of this enzyme is its relatively slow catalytic rate. In this study, MD simulations were conducted on TEV enzymes and known highly active mutants (eTEV and uTEV3) to explore the relationship between mutation, conformation, and catalytic function. The results suggest that mutations distant from the active site can influence the substrate-binding pocket through interaction networks. MD analysis of eTEV demonstrates that, by stabilizing the orientation of the substrate at the catalytic site, mutations that appropriately enlarge the substrate-binding pocket will be beneficial for Kcat, enhancing the catalytic efficiency of the enzyme. On the contrary, mutations in uTEV3 reduced the flexibility of the active pocket and increased the hydrogen bonding between the substrate and enzyme, resulting in higher affinity. At the same time, the MD simulation demonstrates that mutations outside of the active site residues could affect the dynamic movement of the binding pocket by altering residue networks and communication pathways, thereby having a profound impact on reactivity. These findings not only provide a molecular mechanistic explanation for the excellent mutants, but also serve as a guiding framework for rational computational design.
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Affiliation(s)
- Jingyao Wang
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Yicong Xu
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Xujian Wang
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Jiahuang Li
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, China
- Changzhou High-Tech Research Institute, Nanjing University, Changzhou 213164, China
| | - Zichun Hua
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, China
- Changzhou High-Tech Research Institute, Nanjing University, Changzhou 213164, China
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing 210023, China
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Parida PP, Saraswathi D, Mopidevi SM, Raran-Kurussi S. Advancing large-scale production of TEV protease through an innovative NT* tag-based fusion construct. Curr Res Struct Biol 2023; 6:100106. [PMID: 37822550 PMCID: PMC10563009 DOI: 10.1016/j.crstbi.2023.100106] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 09/29/2023] [Accepted: 09/29/2023] [Indexed: 10/13/2023] Open
Abstract
Tobacco etch virus Protease (TEVp), a cysteine protease, is renowned for its remarkable specific proteolysis, making it an invaluable tool for removing fusion tags from recombinant proteins. However, TEV protease's inherent insolubility limits its broad application. Fusion constructs like an N-terminal MBP fusion, known for its improved solubility, have been employed for TEVp production to address this issue. In this study, we fused the TEVp with the N-terminal domain of the spider silk protein, specifically utilizing a charge-reversed mutant (D40K/K65D) of the N-terminal domain of major ampullate spidroin-1 protein from Euprosthenops australis, referred to as NT*. This fusion construct contains a TEVp cleavage site, enabling intracellular self-processing and the release of a His7-tagged protease. The significant increase in soluble protein expression allowed us to purify approximately 90-100 mg of TEVp from a 1-L E. coli culture, surpassing previous findings by a considerable margin. The enzyme remained stable and catalytically active even after several months of storage in a deep freezer (-80 °C).
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Affiliation(s)
- Pragyan P. Parida
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Serilingampally, Hyderabad, 500046, Telangana, India
| | - Deepa Saraswathi
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Serilingampally, Hyderabad, 500046, Telangana, India
| | - Subbarao M.V. Mopidevi
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Serilingampally, Hyderabad, 500046, Telangana, India
| | - Sreejith Raran-Kurussi
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Serilingampally, Hyderabad, 500046, Telangana, India
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Paththamperuma C, Page RC. Fluorescence dequenching assay for the activity of TEV protease. Anal Biochem 2022; 659:114954. [PMID: 36265691 PMCID: PMC9662696 DOI: 10.1016/j.ab.2022.114954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/09/2022] [Accepted: 10/10/2022] [Indexed: 12/14/2022]
Abstract
Tobacco etch virus (TEV) protease is a widely used protease for fusion tag cleavage. Despite its widespread usage, an assay to quickly and easily quantify its activity in laboratory settings is still lacking. Thus, researchers may encounter inefficient cleavage of the desired fusion proteins due to poor activity of a given TEV protease preparation. Here, we describe the development and implementation of a fluorescence dequenching-based assay to quantify TEV protease activity and assess kinetic parameters. The peptide substrate used in this assay consists of a C-terminal TAMRA fluorophore, an N-terminal fluorescein fluorophore, and the canonical TEV protease recognition sequence. The assay is based on a reduction of fluorescence quenching of fluorescein upon cleavage by TEV protease. The substrate peptide was studied spectroscopically to assess feasibility and to propose a plausible mechanism of the assay. The assay was optimized and applied to obtain rapid assessments of TEV protease activity in purified samples and crude lysate extracts. The kinetic data obtained from improved TEV protease variants were compared with a traditional SDS-PAGE assay. Finally, the assay was applied to determine the optimum pH for TEV protease. Further, the study found that the assay is a rapid and simple approach to quantify TEV protease activity. The findings of the assay on crude lysate extracts, activity assay of TEV protease variants, and assessment of optimum pH for TEV protease reactions demonstrate the robust utility of the assay.
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Affiliation(s)
- Chathura Paththamperuma
- Department of Chemistry and Biochemistry, 651 East High Street, Miami University, Oxford, OH, 45056, United States
| | - Richard C Page
- Department of Chemistry and Biochemistry, 651 East High Street, Miami University, Oxford, OH, 45056, United States.
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Zlobin A, Golovin A. Between Protein Fold and Nucleophile Identity: Multiscale Modeling of the TEV Protease Enzyme-Substrate Complex. ACS OMEGA 2022; 7:40279-40292. [PMID: 36385818 PMCID: PMC9647873 DOI: 10.1021/acsomega.2c05201] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
The cysteine protease from the tobacco etch virus (TEVp) is a well-known and widely utilized enzyme. TEVp's chymotrypsin-like fold is generally associated with serine catalytic triads that differ in terms of a reaction mechanism from the most well-studied papain-like cysteine proteases. The question of what dominates the TEVp mechanism, nucleophile identity, or structural composition has never been previously addressed. Here, we use enhanced sampling multiscale modeling to uncover that TEVp combines the features of two worlds in such a way that potentially hampers its activity. We show that TEVp cysteine is strictly in the anionic form in a free enzyme similar to papain. Peptide binding shifts the equilibrium toward the nucleophile's protonated form, characteristic of chymotrypsin-like proteases, although the cysteinyl anion form is still present and interconversion is rapid. This way cysteine protonation generates enzyme states that are a diversion from the most effective course of action, with only 13.2% of Michaelis complex sub-states able to initiate the reaction. As a result, we propose an updated view on the reaction mechanism catalyzed by TEVp. We also demonstrate that AlphaFold is able to construct protease-substrate complexes with high accuracy. We propose that our findings open a way for its industrious use in enzymological tasks. Unique features of TEVp discovered in this work open a discussion on the evolutionary history and trade-offs of optimizing serine triad-associated folds to cysteine as a nucleophile.
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Affiliation(s)
- Alexander Zlobin
- Belozersky
Institute of Physico-Chemical Biology, Lomonosov
Moscow State University, 119991 Moscow, Russia
- Shemyakin
and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Andrey Golovin
- Belozersky
Institute of Physico-Chemical Biology, Lomonosov
Moscow State University, 119991 Moscow, Russia
- Shemyakin
and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Sirius
University of Science and Technology, 354340 Sochi, Russia
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Bayar E, Ren Y, Chen Y, Hu Y, Zhang S, Yu X, Fan J. Construction, Investigation and Application of TEV Protease Variants with Improved Oxidative Stability. J Microbiol Biotechnol 2021; 31:1732-1740. [PMID: 34528919 PMCID: PMC9705859 DOI: 10.4014/jmb.2106.06075] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/06/2021] [Accepted: 09/08/2021] [Indexed: 12/15/2022]
Abstract
Tobacco etch virus protease (TEVp) is a useful tool for removing fusion tags, but wild-type TEVp is less stable under oxidized redox state. In this work, we introduced and combined C19S, C110S and C130S into TEVp variants containing T17S, L56V, N68D, I77V and S135G to improve protein solubility, and S219V to inhibit self-proteolysis. The solubility and cleavage activity of the constructed variants in Escherichia coli strains including BL21(DE3), BL21(DE3)pLys, Rossetta(DE3) and Origami(DE3) under the same induction conditions were analyzed and compared. The desirable soluble amounts, activity, and oxidative stability were identified to be reluctantly favored in the TEVp. Unlike C19S, C110S and C130S hardly impacted on decreasing protein solubility in the BL21(DE3), but they contributed to improved tolerance to the oxidative redox state in vivo and in vitro. After two fusion proteins were cleaved by purified TEVp protein containing double mutations under the oxidized redox state, the refolded disulfide-rich bovine enterokinase catalytic domain or maize peroxidase with enhanced yields were released from the regenerated amorphous cellulose via affinity absorption of the cellulose-binding module as the affinity tag.
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Affiliation(s)
- Enkhtuya Bayar
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
| | - Yuanyuan Ren
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
| | - Yinghua Chen
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
| | - Yafang Hu
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
| | - Shuncheng Zhang
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
| | - Xuelian Yu
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
| | - Jun Fan
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China,Corresponding author Phone : +86-551-65786464 Fax : +86-551-65786021 E-mail:
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Denard CA, Paresi C, Yaghi R, McGinnis N, Bennett Z, Yi L, Georgiou G, Iverson BL. YESS 2.0, a Tunable Platform for Enzyme Evolution, Yields Highly Active TEV Protease Variants. ACS Synth Biol 2021; 10:63-71. [PMID: 33401904 DOI: 10.1021/acssynbio.0c00452] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Here we describe YESS 2.0, a highly versatile version of the yeast endoplasmic sequestration screening (YESS) system suitable for engineering and characterizing protein/peptide modifying enzymes such as proteases with desired new activities. By incorporating features that modulate gene transcription as well as substrate and enzyme spatial sequestration, YESS 2.0 achieves a significantly higher operational and dynamic range compared with the original YESS. To showcase the new advantages of YESS 2.0, we improved an already efficient TEV protease variant (TEV-EAV) to obtain a variant (eTEV) with a 2.25-fold higher catalytic efficiency, derived almost entirely from an increase in turnover rate (kcat). In our analysis, eTEV specifically digests a fusion protein in 2 h at a low 1:200 enzyme to substrate ratio. Structural modeling indicates that the increase in catalytic efficiency of eTEV is likely due to an enhanced interaction between the catalytic Cys151 with the P1 substrate residue (Gln). Furthermore, the modeling showed that the ENLYFQS peptide substrate is buried to a larger extent in the active site of eTEV compared with WT TEV. The new eTEV variant is functionally the fastest TEV variant reported to date and could potentially improve efficiency in any TEV application.
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Affiliation(s)
- Carl A. Denard
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Chelsea Paresi
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Rasha Yaghi
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Natalie McGinnis
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Zachary Bennett
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Li Yi
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Brent L. Iverson
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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Abdelkader EH, Otting G. NT*-HRV3CP: An optimized construct of human rhinovirus 14 3C protease for high-yield expression and fast affinity-tag cleavage. J Biotechnol 2021; 325:145-151. [PMID: 33166527 DOI: 10.1016/j.jbiotec.2020.11.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/28/2020] [Accepted: 11/01/2020] [Indexed: 12/20/2022]
Abstract
The human rhinovirus 14 3C protease (HRV3C protease), in fusion with glutathione S-transferase also referred to as PreScission™ protease, is a cysteine protease of particular interest for affinity tag removal from fusion proteins due to its stringent recognition sequence specificity (LEVLFQ/GX) and superior activity at low temperature. Here we report the expression, purification and use of a fusion construct of HRV3C protease, NT*-HRV3CP, that affords high expression yield in E. coli (over 300 mg/L cell culture), facile single-step purification, high solubility (>10 mg/mL) and excellent storage properties. NT*-HRV3CP cleaves affinity tags at 4 °C in minutes, making it an attractive tool for the production of recombinant proteins for biotechnological, industrial and pharmaceutical applications.
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Affiliation(s)
- Elwy H Abdelkader
- ARC Centre of Excellence in Innovations in Peptide and Protein Science, Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Gottfried Otting
- ARC Centre of Excellence in Innovations in Peptide and Protein Science, Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia.
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