1
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Zhao C, Rong Y, Shi S, Gao WC, Zhang C. A novel method for synthesizing authentic SARS-CoV-2 main protease. Protein Expr Purif 2024; 222:106531. [PMID: 38852715 DOI: 10.1016/j.pep.2024.106531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/01/2024] [Accepted: 06/07/2024] [Indexed: 06/11/2024]
Abstract
The SARS-CoV-2 main protease (Mpro) plays a crucial role in virus amplification and is an ideal target for antiviral drugs. Currently, authentic Mpro is prepared through two rounds of proteolytic cleavage. In this method, Mpro carries a self-cleavage site at the N-terminus and a protease cleavage site followed by an affinity tag at the C-terminus. This article proposes a novel method for producing authentic Mpro through single digestion. Mpro was constructed by fusing a His tag containing TEV protease cleavage sites at the N-terminus. The expressed recombinant protein was digested by TEV protease, and the generated protein had a decreased molecular weight and significantly increased activity, which was consistent with that of authentic Mpro generated by the previous method. These findings indicated that authentic Mpro was successfully obtained. Moreover, the substrate specificity of Mpro was investigated. Mpro had a strong preference for Phe at position the P2, which suggested that the S2 subsite was an outstanding target for designing inhibitors. This article also provides a reference for the preparation of Mpro for sudden coronavirus infection in the future.
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Affiliation(s)
- Cheng Zhao
- College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, 030024, People's Republic of China.
| | - Yi Rong
- College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, 030024, People's Republic of China
| | - Shuyuan Shi
- College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, 030024, People's Republic of China
| | - Wen-Chao Gao
- College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, 030024, People's Republic of China
| | - Chaofeng Zhang
- College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, 030024, People's Republic of China.
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2
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Golda M, Hoffka G, Cherry S, Tropea JE, Lountos GT, Waugh DS, Wlodawer A, Tőzsér J, Mótyán JA. P1' specificity of the S219V/R203G mutant tobacco etch virus protease. Proteins 2024; 92:1085-1096. [PMID: 38666764 PMCID: PMC11303109 DOI: 10.1002/prot.26693] [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: 02/22/2024] [Revised: 03/26/2024] [Accepted: 04/08/2024] [Indexed: 08/07/2024]
Abstract
Proteases that recognize linear amino acid sequences with high specificity became indispensable tools of recombinant protein technology for the removal of various fusion tags. Due to its stringent sequence specificity, the catalytic domain of the nuclear inclusion cysteine protease of tobacco etch virus (TEV PR) is also a widely applied reagent for enzymatic removal of fusion tags. For this reason, efforts have been made to improve its stability and modify its specificity. For example, P1' autoproteolytic cleavage-resistant mutant (S219V) TEV PR was found not only to be nearly impervious to self-inactivation, but also exhibited greater stability and catalytic efficiency than the wild-type enzyme. An R203G substitution has been reported to further relax the P1' specificity of the enzyme, however, these results were obtained from crude intracellular assays. Until now, there has been no rigorous comparison of the P1' specificity of the S219V and S219V/R203G mutants in vitro, under carefully controlled conditions. Here, we compare the P1' amino acid preferences of these single and double TEV PR mutants. The in vitro analysis was performed by using recombinant protein substrates representing 20 P1' variants of the consensus TENLYFQ*SGT cleavage site, and synthetic oligopeptide substrates were also applied to study a limited set of the most preferred variants. In addition, the enzyme-substrate interactions were analyzed in silico. The results indicate highly similar P1' preferences for both enzymes, many side-chains can be accommodated by the S1' binding sites, but the kinetic assays revealed lower catalytic efficiency for the S219V/R203G than for the S219V mutant.
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Affiliation(s)
- Mária Golda
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Gyula Hoffka
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Debrecen, Hungary
| | - Scott Cherry
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Joseph E. Tropea
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - George T. Lountos
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - David S. Waugh
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Alexander Wlodawer
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - József Tőzsér
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - János András Mótyán
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
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3
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Fan X, He H, Wang T, Xu P, Zhang F, Hu S, Yun Y, Mei M, Zhang G, Yi L. Characterizing interactions of endoplasmic reticulum resident proteins in situ through the YST-PPI method. Biotechnol J 2024; 19:e2400346. [PMID: 39212204 DOI: 10.1002/biot.202400346] [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: 05/25/2024] [Revised: 08/14/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024]
Abstract
The mutual interactions of endoplasmic reticulum (ER) resident proteins in the ER maintain its functions, prompting the protein folding, modification, and transportation. Here, a new method, named YST-PPI (YESS-based Split fast TEV protease system for Protein-Protein Interaction) was developed, targeting the characterization of protein interactions in ER. YST-PPI method integrated the YESS system, split-TEV technology, and endoplasmic reticulum retention signal peptide (ERS) to provide an effective strategy for studying ER in situ PPIs in a fast and quantitative manner. The interactions among 15 ER-resident proteins, most being identified molecular chaperones, of S. cerevisiae were explored using the YST-PPI system, and their interaction network map was constructed, in which more than 74 interacting resident protein pairs were identified. Our studies also showed that Lhs1p plays a critical role in regulating the interactions of most of the ER-resident proteins, except the Sil1p, indicating its potential role in controlling the ER molecular chaperones. Moreover, the mutual interaction revealed by our studies further confirmed that the ER-resident proteins perform their functions in a cooperative way and a multimer complex might be formed during the process.
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Affiliation(s)
- Xian Fan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative, Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Huahua He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative, Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Ting Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative, Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Pan Xu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative, Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Faying Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative, Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Shantong Hu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yueli Yun
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative, Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Meng Mei
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative, Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Guimin Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative, Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Li Yi
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative, Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
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4
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Beaumont LP, Mehalko J, Johnson A, Wall VE, Esposito D. Unexpected tobacco etch virus (TEV) protease cleavage of recombinant human proteins. Protein Expr Purif 2024; 220:106488. [PMID: 38679188 PMCID: PMC11129917 DOI: 10.1016/j.pep.2024.106488] [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: 02/08/2024] [Revised: 04/10/2024] [Accepted: 04/24/2024] [Indexed: 05/01/2024]
Abstract
The tobacco etch virus (TEV) protease is a commonly used reagent for removal of solubility and purification tags from recombinant proteins and is cited as being highly specific for its canonical cleavage site. Flexibility in some amino acids within this recognition sequence has been described in the literature but researchers generally assume few native human proteins will carry off-target sequences for TEV cleavage. We report here the aberrant cleavage of three human proteins with non-canonical TEV protease cleavage sites and identify broader sequence specificity rules that can be used to predict unwanted cleavage of recombinant proteins. Using these rules, 456 human proteins were identified that could be substrates for unwanted TEV protease cleavage.
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Affiliation(s)
- Lauren P Beaumont
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Jennifer Mehalko
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Adam Johnson
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Vanessa E Wall
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Dominic Esposito
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
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5
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Sanfaçon H, Skern T. AlphaFold modeling of nepovirus 3C-like proteinases provides new insights into their diverse substrate specificities. Virology 2024; 590:109956. [PMID: 38052140 DOI: 10.1016/j.virol.2023.109956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/10/2023] [Accepted: 11/24/2023] [Indexed: 12/07/2023]
Abstract
The majority of picornaviral 3C proteinases (3Cpro) cleavage sites possess glutamine at the P1 position. Plant nepovirus 3C-like proteinases (3CLpro) show however much broader specificity, cleaving not only after glutamine, but also after several basic and hydrophobic residues. To investigate this difference, we employed AlphaFold to generate structural models of twelve selected 3CLpro, representing six substrate specificities. Generally, we observed favorable correlations between the architecture and charge of nepovirus proteinase S1 subsites and their ability to accept or restrict larger residues. The models identified a conserved aspartate residue close to the P1 residue in the S1 subsites of all nepovirus proteinases examined, consistent with the observed strong bias against negatively-charged residues at the P1 position of nepovirus cleavage sites. Finally, a cramped S4 subsite along with the presence of two unique histidine and serine residues explains the strict requirement of the grapevine fanleaf virus proteinase for serine at the P4 position.
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Affiliation(s)
- Hélène Sanfaçon
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, 4200 Highway 97, V0H 1Z0, Summerland, BC, Canada.
| | - Tim Skern
- Department of Medical Biochemistry, Max Perutz Labs, Vienna Biocenter, Medical University of Vienna, A-1030, Vienna, Austria.
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6
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Sumida K, Núñez-Franco R, Kalvet I, Pellock SJ, Wicky BIM, Milles LF, Dauparas J, Wang J, Kipnis Y, Jameson N, Kang A, De La Cruz J, Sankaran B, Bera AK, Jiménez-Osés G, Baker D. Improving Protein Expression, Stability, and Function with ProteinMPNN. J Am Chem Soc 2024; 146:2054-2061. [PMID: 38194293 PMCID: PMC10811672 DOI: 10.1021/jacs.3c10941] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 01/10/2024]
Abstract
Natural proteins are highly optimized for function but are often difficult to produce at a scale suitable for biotechnological applications due to poor expression in heterologous systems, limited solubility, and sensitivity to temperature. Thus, a general method that improves the physical properties of native proteins while maintaining function could have wide utility for protein-based technologies. Here, we show that the deep neural network ProteinMPNN, together with evolutionary and structural information, provides a route to increasing protein expression, stability, and function. For both myoglobin and tobacco etch virus (TEV) protease, we generated designs with improved expression, elevated melting temperatures, and improved function. For TEV protease, we identified multiple designs with improved catalytic activity as compared to the parent sequence and previously reported TEV variants. Our approach should be broadly useful for improving the expression, stability, and function of biotechnologically important proteins.
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Affiliation(s)
- Kiera
H. Sumida
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Reyes Núñez-Franco
- Center
for Cooperative Research in Biosciences, Basque Research and Technology Alliance, Derio 48160, Spain
| | - Indrek Kalvet
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
- Howard
Hughes Medical Institute, University of
Washington, Seattle, Washington 98195, United States
| | - Samuel J. Pellock
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Basile I. M. Wicky
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Lukas F. Milles
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Justas Dauparas
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Jue Wang
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Yakov Kipnis
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
- Howard
Hughes Medical Institute, University of
Washington, Seattle, Washington 98195, United States
| | - Noel Jameson
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Alex Kang
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Joshmyn De La Cruz
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Banumathi Sankaran
- Berkeley
Center for Structural Biology, Molecular Biophysics, and Integrated
Bioimaging, Lawrence Berkeley Laboratory, Berkeley, California 94720, United States
| | - Asim K. Bera
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Gonzalo Jiménez-Osés
- Center
for Cooperative Research in Biosciences, Basque Research and Technology Alliance, Derio 48160, Spain
- Ikerbasque,
Basque Foundation for Science, Bilbao 48013, Spain
| | - David Baker
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
- Howard
Hughes Medical Institute, University of
Washington, Seattle, Washington 98195, United States
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7
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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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8
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Lu C, Lubin JH, Sarma VV, Stentz SZ, Wang G, Wang S, Khare SD. Prediction and design of protease enzyme specificity using a structure-aware graph convolutional network. Proc Natl Acad Sci U S A 2023; 120:e2303590120. [PMID: 37729196 PMCID: PMC10523478 DOI: 10.1073/pnas.2303590120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 08/14/2023] [Indexed: 09/22/2023] Open
Abstract
Site-specific proteolysis by the enzymatic cleavage of small linear sequence motifs is a key posttranslational modification involved in physiology and disease. The ability to robustly and rapidly predict protease-substrate specificity would also enable targeted proteolytic cleavage by designed proteases. Current methods for predicting protease specificity are limited to sequence pattern recognition in experimentally derived cleavage data obtained for libraries of potential substrates and generated separately for each protease variant. We reasoned that a more semantically rich and robust model of protease specificity could be developed by incorporating the energetics of molecular interactions between protease and substrates into machine learning workflows. We present Protein Graph Convolutional Network (PGCN), which develops a physically grounded, structure-based molecular interaction graph representation that describes molecular topology and interaction energetics to predict enzyme specificity. We show that PGCN accurately predicts the specificity landscapes of several variants of two model proteases. Node and edge ablation tests identified key graph elements for specificity prediction, some of which are consistent with known biochemical constraints for protease:substrate recognition. We used a pretrained PGCN model to guide the design of protease libraries for cleaving two noncanonical substrates, and found good agreement with experimental cleavage results. Importantly, the model can accurately assess designs featuring diversity at positions not present in the training data. The described methodology should enable the structure-based prediction of specificity landscapes of a wide variety of proteases and the construction of tailor-made protease editors for site-selectively and irreversibly modifying chosen target proteins.
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Affiliation(s)
- Changpeng Lu
- Institute for Quantitative Biomedicine, Rutgers–The State University of New Jersey, Piscataway, NJ08854
| | - Joseph H. Lubin
- Department of Chemistry and Chemical Biology, Rutgers–The State University of New Jersey, Piscataway, NJ08854
| | - Vidur V. Sarma
- Institute for Quantitative Biomedicine, Rutgers–The State University of New Jersey, Piscataway, NJ08854
| | | | - Guanyang Wang
- Department of Statistics, Rutgers–The State University of New Jersey, Piscataway, NJ08854
| | - Sijian Wang
- Institute for Quantitative Biomedicine, Rutgers–The State University of New Jersey, Piscataway, NJ08854
- Department of Statistics, Rutgers–The State University of New Jersey, Piscataway, NJ08854
| | - Sagar D. Khare
- Institute for Quantitative Biomedicine, Rutgers–The State University of New Jersey, Piscataway, NJ08854
- Department of Chemistry and Chemical Biology, Rutgers–The State University of New Jersey, Piscataway, NJ08854
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9
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Hu J, Chang N, Hong C, Liu J, Zeng F, Gao H. A new method for studying the orientation of membrane proteins in plants based on the release of a fluorescent protein tag by TEV protease. PLANT COMMUNICATIONS 2023; 4:100602. [PMID: 37060178 PMCID: PMC10504556 DOI: 10.1016/j.xplc.2023.100602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/08/2023] [Accepted: 04/12/2023] [Indexed: 05/29/2023]
Affiliation(s)
- Jinglei Hu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Ning Chang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Conghao Hong
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Jia Liu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Fang Zeng
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Hongbo Gao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
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10
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Chen SY, Feilen LP, Chávez-Gutiérrez L, Steiner H, Zacharias M. Enzyme-substrate hybrid β-sheet controls geometry and water access to the γ-secretase active site. Commun Biol 2023; 6:670. [PMID: 37355752 PMCID: PMC10290658 DOI: 10.1038/s42003-023-05039-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023] Open
Abstract
γ-Secretase is an aspartyl intramembrane protease that cleaves the amyloid precursor protein (APP) involved in Alzheimer's disease pathology and other transmembrane proteins. Substrate-bound structures reveal a stable hybrid β-sheet immediately following the substrate scissile bond consisting of β1 and β2 from the enzyme and β3 from the substrate. Molecular dynamics simulations and enhanced sampling simulations demonstrate that the hybrid β-sheet stability is strongly correlated with the formation of a stable cleavage-compatible active geometry and it also controls water access to the active site. The hybrid β-sheet is only stable for substrates with 3 or more C-terminal residues beyond the scissile bond. The simulation model allowed us to predict the effect of Pro and Phe mutations that weaken the formation of the hybrid β-sheet which were confirmed by experimental testing. Our study provides a direct explanation why γ-secretase preferentially cleaves APP in steps of 3 residues and how the hybrid β-sheet facilitates γ-secretase proteolysis.
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Affiliation(s)
- Shu-Yu Chen
- Center of Functional Protein Assemblies, Technical University of Munich, Garching, Germany
| | - Lukas P Feilen
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Lucía Chávez-Gutiérrez
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
- Department of Neurosciences, Leuven Research Institute for Neuroscience and Disease (LIND), KU Leuven, Leuven, Belgium
| | - Harald Steiner
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Biomedical Center (BMC), Division of Metabolic Biochemistry, Faculty of Medicine, LMU Munich, Germany
| | - Martin Zacharias
- Center of Functional Protein Assemblies, Technical University of Munich, Garching, Germany.
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11
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Rodamilans B, Hadersdorfer J, Berki Z, García B, Neumüller M, García JA. The Mechanism of Resistance of EUROPEAN Plum to Plum pox virus Mediated by Hypersensitive Response Is Linked to VIRAL NIa and Its Protease Activity. PLANTS (BASEL, SWITZERLAND) 2023; 12:1609. [PMID: 37111834 PMCID: PMC10147044 DOI: 10.3390/plants12081609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/21/2023] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
Plum pox virus (PPV) infects Prunus trees across the globe, causing the serious Sharka disease. Breeding programs in the past 20 years have been successful, generating plum varieties hypersensitive to PPV that show resistance in the field. Recently, a single tree displaying typical PPV symptoms was detected in an orchard of resistant plums. The tree was eradicated, and infected material was propagated under controlled conditions to study the new PPV isolate. Performing overlapping PCR analysis, the viral sequence was reconstructed, cloned and tested for infectivity in different 'Jojo'-based resistant plums. The results confirmed that the isolate, named PPV-D 'Herrenberg' (PPVD-H), was able to infect all these varieties. Analyses of chimeras between PPVD-H and a PPV-D standard isolate (PPVD) revealed that the NIa region of PPD-H, carrying three amino acid changes, was enough to break the resistance of these plums. Experiments with single and double mutants showed that all changes were essential to preserve the escaping phenotype. Additionally, one of the changes at the VPg-NIapro junction suggested the involvement of controlled endopeptidase cleavage in the viral response. Transient expression experiments in Nicotiana benthamiana confirmed that NIa cleavage in PPVD-H was reduced, compared to PPVD, linking the observed behavior to an NIa cleavage modulation.
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Affiliation(s)
- Bernardo Rodamilans
- Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, Darwin 3, 28049 Madrid, Spain
| | - Johannes Hadersdorfer
- School of Life Sciences Weihenstephan, Technical University of Munich, Dürnast 2, D-85354 Freising, Germany
| | - Zita Berki
- Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, Darwin 3, 28049 Madrid, Spain
| | - Beatriz García
- Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, Darwin 3, 28049 Madrid, Spain
| | - Michael Neumüller
- Bavarian Centre of Pomology and Fruit Breeding, Am Süßbach 1, D-85399 Hallbergmoos, Germany
| | - Juan Antonio García
- Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, Darwin 3, 28049 Madrid, Spain
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12
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Lu C, Lubin JH, Sarma VV, Stentz SZ, Wang G, Wang S, Khare SD. Prediction and Design of Protease Enzyme Specificity Using a Structure-Aware Graph Convolutional Network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.16.528728. [PMID: 36824945 PMCID: PMC9949123 DOI: 10.1101/2023.02.16.528728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Site-specific proteolysis by the enzymatic cleavage of small linear sequence motifs is a key post-translational modification involved in physiology and disease. The ability to robustly and rapidly predict protease substrate specificity would also enable targeted proteolytic cleavage - editing - of a target protein by designed proteases. Current methods for predicting protease specificity are limited to sequence pattern recognition in experimentally-derived cleavage data obtained for libraries of potential substrates and generated separately for each protease variant. We reasoned that a more semantically rich and robust model of protease specificity could be developed by incorporating the three-dimensional structure and energetics of molecular interactions between protease and substrates into machine learning workflows. We present Protein Graph Convolutional Network (PGCN), which develops a physically-grounded, structure-based molecular interaction graph representation that describes molecular topology and interaction energetics to predict enzyme specificity. We show that PGCN accurately predicts the specificity landscapes of several variants of two model proteases: the NS3/4 protease from the Hepatitis C virus (HCV) and the Tobacco Etch Virus (TEV) proteases. Node and edge ablation tests identified key graph elements for specificity prediction, some of which are consistent with known biochemical constraints for protease:substrate recognition. We used a pre-trained PGCN model to guide the design of TEV protease libraries for cleaving two non-canonical substrates, and found good agreement with experimental cleavage results. Importantly, the model can accurately assess designs featuring diversity at positions not present in the training data. The described methodology should enable the structure-based prediction of specificity landscapes of a wide variety of proteases and the construction of tailor-made protease editors for site-selectively and irreversibly modifying chosen target proteins.
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Affiliation(s)
- Changpeng Lu
- Institute for Quantitative Biomedicine, Rutgers - The State University of New Jersey, Piscataway, NJ
| | - Joseph H. Lubin
- Department of Chemistry & Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, NJ
| | - Vidur V. Sarma
- Institute for Quantitative Biomedicine, Rutgers - The State University of New Jersey, Piscataway, NJ
| | | | - Guanyang Wang
- Department of Statistics, Rutgers - The State University of New Jersey, Piscataway, NJ
| | - Sijian Wang
- Institute for Quantitative Biomedicine, Rutgers - The State University of New Jersey, Piscataway, NJ
- Department of Statistics, Rutgers - The State University of New Jersey, Piscataway, NJ
| | - Sagar D. Khare
- Institute for Quantitative Biomedicine, Rutgers - The State University of New Jersey, Piscataway, NJ
- Department of Chemistry & Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, NJ
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13
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Li W. Distinct enzymatic strategies for de novo generation of disulfide bonds in membranes. Crit Rev Biochem Mol Biol 2023; 58:36-49. [PMID: 37098102 PMCID: PMC10460286 DOI: 10.1080/10409238.2023.2201404] [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: 01/02/2023] [Revised: 04/02/2023] [Accepted: 04/06/2023] [Indexed: 04/26/2023]
Abstract
Disulfide bond formation is a catalyzed reaction essential for the folding and stability of proteins in the secretory pathway. In prokaryotes, disulfide bonds are generated by DsbB or VKOR homologs that couple the oxidation of a cysteine pair to quinone reduction. Vertebrate VKOR and VKOR-like enzymes have gained the epoxide reductase activity to support blood coagulation. The core structures of DsbB and VKOR variants share the architecture of a four-transmembrane-helix bundle that supports the coupled redox reaction and a flexible region containing another cysteine pair for electron transfer. Despite considerable similarities, recent high-resolution crystal structures of DsbB and VKOR variants reveal significant differences. DsbB activates the cysteine thiolate by a catalytic triad of polar residues, a reminiscent of classical cysteine/serine proteases. In contrast, bacterial VKOR homologs create a hydrophobic pocket to activate the cysteine thiolate. Vertebrate VKOR and VKOR-like maintain this hydrophobic pocket and further evolved two strong hydrogen bonds to stabilize the reaction intermediates and increase the quinone redox potential. These hydrogen bonds are critical to overcome the higher energy barrier required for epoxide reduction. The electron transfer process of DsbB and VKOR variants uses slow and fast pathways, but their relative contribution may be different in prokaryotic and eukaryotic cells. The quinone is a tightly bound cofactor in DsbB and bacterial VKOR homologs, whereas vertebrate VKOR variants use transient substrate binding to trigger the electron transfer in the slow pathway. Overall, the catalytic mechanisms of DsbB and VKOR variants have fundamental differences.
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Affiliation(s)
- Weikai Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
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14
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Panigrahi R, Kailasam S. Mapping allosteric pathway in NIa-Pro using computational approach. QUANTITATIVE BIOLOGY 2023. [DOI: 10.15302/j-qb-022-0296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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15
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Winckler LI, Dissmeyer N. TEV protease cleavage in generation of artificial substrate proteins bearing neo-N-termini. Methods Enzymol 2023. [PMID: 37532397 DOI: 10.1016/bs.mie.2023.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
Abstract
The tobacco etch virus (TEV) protease is widely used in in vitro and in vivo approaches for the removal of affinity tags from fusion proteins or the generation of proteins with a desired N-terminal amino acid. Processing of fusion proteins by the TEV protease can either be achieved by encoding the TEV protease and its recognition site on one construct (self-cleavage) or on two different constructs (co-expression). Here, we compare the efficiency of the self-splitting approach to the co-expression approach.
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16
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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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17
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Cleveland JD, Taslimi A, Liu Q, Van Keuren AM, Churchill MEA, Tucker CL. Reprogramming the Cleavage Specificity of Botulinum Neurotoxin Serotype B1. ACS Synth Biol 2022; 11:3318-3329. [PMID: 36153971 PMCID: PMC9907380 DOI: 10.1021/acssynbio.2c00235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Proteases with reprogrammed specificity for nonnative substrates are highly desired in synthetic biology and biomedicine. However, generating reprogrammed proteases that are orthogonal and highly specific for a new target has been a major challenge. In this work, we sought to expand the versatility of protease systems by engineering an orthogonal botulinum neurotoxin serotype B (BoNT/B) protease that recognizes an orthogonal substrate. We designed and validated an orthogonal BoNT/B protease system in mammalian cells, combining mutations in the protease with compensatory mutations in the protease substrate and incorporating a truncated target sequence and then demonstrated use of this orthogonal BoNT/B protease-substrate combination to regulate complex transcriptional circuitry in mammalian cells. Transposing this platform into yeast, we demonstrated utility of this approach for in vivo protease evolution. We tested this platform with the newly designed orthogonal protease and then used it in a high-throughput screen to identify novel orthogonal protease/protease substrate combinations. While carrying out this work, we also generated new cleavage reporters that could be used to report botulinum toxin protease activity in mammalian cells using simple fluorescent readouts. We envision that these approaches will expand the applications of botulinum protease in new directions and aid in the development of new reprogrammed proteases.
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Affiliation(s)
- Joseph D. Cleveland
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045 USA
| | - Amir Taslimi
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045 USA
| | - Qi Liu
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045 USA
| | - Anna M. Van Keuren
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045 USA
| | - Mair E. A. Churchill
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045 USA
| | - Chandra L. Tucker
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045 USA
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18
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Eastman KS, Kincannon WM, Bandarian V. Leveraging Substrate Promiscuity of a Radical S-Adenosyl-L-methionine RiPP Maturase toward Intramolecular Peptide Cross-Linking Applications. ACS CENTRAL SCIENCE 2022; 8:1209-1217. [PMID: 36032765 PMCID: PMC9413430 DOI: 10.1021/acscentsci.2c00501] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Indexed: 05/05/2023]
Abstract
Radical S-adenosyl-l-methionine (RS) enzymes operate on a variety of substrates and catalyze a wide range of complex radical-mediated transformations. Radical non-α-carbon thioether peptides (ranthipeptides) are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs). The RS enzyme PapB catalyzes the formation of thioether cross-links between Cys/Asp (or Cys/Glu) residues located in six Cys-X3-Asp/Glu motifs. In this report, using a minimal substrate that contains a single cross-link motif, we explore the substrate scope of the PapB and show that the enzyme is highly promiscuous and will accept a variety of Cys-X n -Asp sequences where n = 0-6. Moreover, we show that the enzyme will introduce in-line and nested thioether cross-links independently in peptide sequences that contain two motifs derived from the wild-type sequence. Additionally, the enzyme accepts peptides that contain d-amino acids at either the Cys or the Asp position. These observations are leveraged to produce a thioether cyclized analogue of the FDA-approved therapeutic agent octreotide, with a Cys-Glu cross-link replacing the disulfide that is found in the drug. These findings highlight the remarkable substrate tolerance of PapB and show the utility of RS RiPP maturases in biotechnological applications.
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Affiliation(s)
- Karsten
A. S. Eastman
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt
Lake City, Utah 84112, United States
| | | | - Vahe Bandarian
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt
Lake City, Utah 84112, United States
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19
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Protein Fusion Strategies for Membrane Protein Stabilization and Crystal Structure Determination. CRYSTALS 2022. [DOI: 10.3390/cryst12081041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Crystal structures of membrane proteins are highly desired for their use in the mechanistic understanding of their functions and the designing of new drugs. However, obtaining the membrane protein structures is difficult. One way to overcome this challenge is with protein fusion methods, which have been successfully used to determine the structures of many membrane proteins, including receptors, enzymes and adhesion molecules. Existing fusion strategies can be categorized into the N or C terminal fusion, the insertion fusion and the termini restraining. The fusions facilitate protein expression, purification, crystallization and phase determination. Successful applications often require further optimization of protein fusion linkers and interactions, whose design can be facilitated by a shared helix strategy and by AlphaFold prediction in the future.
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20
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Abstract
Proteins have shown promise as therapeutics and diagnostics, but their effectiveness is limited by our inability to spatially target their activity. To overcome this limitation, we developed a computationally guided method to design inactive proenzymes or zymogens, which are activated through cleavage by a protease. Since proteases are differentially expressed in various tissues and disease states, including cancer, these proenzymes could be targeted to the desired microenvironment. We tested our method on the therapeutically relevant protein carboxypeptidase G2 (CPG2). We designed Pro-CPG2s that are inhibited by 80 to 98% and are partially to fully reactivatable following protease treatment. The developed methodology, with further refinements, could pave the way for routinely designing protease-activated protein-based therapeutics and diagnostics that act in a spatially controlled manner. Confining the activity of a designed protein to a specific microenvironment would have broad-ranging applications, such as enabling cell type-specific therapeutic action by enzymes while avoiding off-target effects. While many natural enzymes are synthesized as inactive zymogens that can be activated by proteolysis, it has been challenging to redesign any chosen enzyme to be similarly stimulus responsive. Here, we develop a massively parallel computational design, screening, and next-generation sequencing-based approach for proenzyme design. For a model system, we employ carboxypeptidase G2 (CPG2), a clinically approved enzyme that has applications in both the treatment of cancer and controlling drug toxicity. Detailed kinetic characterization of the most effectively designed variants shows that they are inhibited by ∼80% compared to the unmodified protein, and their activity is fully restored following incubation with site-specific proteases. Introducing disulfide bonds between the pro- and catalytic domains based on the design models increases the degree of inhibition to 98% but decreases the degree of restoration of activity by proteolysis. A selected disulfide-containing proenzyme exhibits significantly lower activity relative to the fully activated enzyme when evaluated in cell culture. Structural and thermodynamic characterization provides detailed insights into the prodomain binding and inhibition mechanisms. The described methodology is general and could enable the design of a variety of proproteins with precise spatial regulation.
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21
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Mobbs GW, Aziz AA, Dix SR, Blackburn GM, Sedelnikova SE, Minshull TC, Dickman MJ, Baker PJ, Nathan S, Raih MF, Rice DW. Molecular basis of specificity and deamidation of eIF4A by Burkholderia Lethal Factor 1. Commun Biol 2022; 5:272. [PMID: 35347220 PMCID: PMC8960835 DOI: 10.1038/s42003-022-03186-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 02/17/2022] [Indexed: 12/22/2022] Open
Abstract
Burkholderiapseudomallei lethal factor 1 (BLF1) exhibits site-specific glutamine deamidase activity against the eukaryotic RNA helicase, eIF4A, thereby blocking mammalian protein synthesis. The structure of a complex between BLF1 C94S and human eIF4A shows that the toxin binds in the cleft between the two RecA-like eIF4A domains forming interactions with residues from both and with the scissile amide of the target glutamine, Gln339, adjacent to the toxin active site. The RecA-like domains adopt a radically twisted orientation compared to other eIF4A structures and the nature and position of conserved residues suggests this may represent a conformation associated with RNA binding. Comparison of the catalytic site of BLF1 with other deamidases and cysteine proteases reveals that they fall into two classes, related by pseudosymmetry, that present either the re or si faces of the target amide/peptide to the nucleophilic sulfur, highlighting constraints in the convergent evolution of their Cys-His active sites. The crystal structure of the toxin from the pathogenic bacterium Burkholderia pseudomallei in complex with its target, human eIF4A, provides insights into substrate specificity and may facilitate the design of inhibitors for the treatment of melioidosis.
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22
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Mero HR, Lyantagaye SL, Bongcam-Rudloff E. Cassava Brown Streak Viruses express second 6-kilodalton (6K2) protein with varied polarity and three dimensional (3D) structures: Basis for trait discrepancy between the virus species. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 98:105219. [PMID: 35066168 DOI: 10.1016/j.meegid.2022.105219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 12/15/2021] [Accepted: 01/17/2022] [Indexed: 10/19/2022]
Abstract
Cassava Brown Streak Virus (CBSV) and Ugandan Cassava Brown Streak Virus (UCBSV) are the two among six virus species speculated to cause the most catastrophic Brown Streak Disease of Cassava (CBSD) in Africa and Asia. Cassava Brown Streak Virus (CBSV) is hard to breed resistance for compared to Ugandan Cassava Brown Streak Virus (UCBSV) species. This is exemplified by incidences of CBSV species rather than UCBSV species in elite breeding line, KBH 2006/0026 at Bagamoyo, Tanzania. It is not yet understood as to why CBSV species could breakdown CBSD-resistance in the KBH 2006/0026 unlike the UCBSV species. This marks the first in silico study conducted to understand molecular basis for the trait discrepancy between CBSV and UCBSV species from structural biology view point. Following ab initio modelling and analysis of physical-chemical properties of second 6-kilodalton (6K2) protein encoded by CBSV and UCBSV species, using ROBETTA server and Protein Parameters tool, respectively we report that; three dimensional (3D) structures and polarity of the protein differs significantly between the two virus species. (95% and 5%) and (85% and 15%) strains of 20 CBSV and 20 UCBSV species respectively, expressed the protein in homo-trimeric and homo-tetrameric forms, correspondingly. 95% and 85% of studied strain population of the two virus species expressed hydrophilic and hydrophobic 6K2, respectively. Based on findings of the curent study, we hypothesize that; (i) The hydrophilic 6K2 expressed by the CBSV species, favour its faster systemic movement via vascular tissues of cassava host and hence result into higher tissue titres than the UCBSV species encoding hydrophobic form of the protein. t and (ii) The hydrophilic 6K2 expressed byCBSV species have additional interaction advantage with Nuclear Inclusion b protease domain (NIb) and Viral genome-linked protein (VPg), components of Virus Replication Complex (VRC) and hence contributing to faster replication of viral genome than the hydrophobic 6K2 expressed by the UCBSV species. Experimental studies are needed to resolve the 3D structures of the 6K2, VPg and NIb and comprehend complex molecular interactions between them. We suggest that, the 6K2 gene should be targeted for improvement of RNA interference (RNAi)-directed transgenesis of virus-resistant cassava as a more effective way to control the CBSD besides breeding.
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Affiliation(s)
- Herieth Rhodes Mero
- University of Dar es Salaam, Mkwawa University College of Education (MUCE), P. O. Box 2513, Iringa, Tanzania; Swedish University of Agricultural Sciences (SLU), SLU-Global Bioinformatics Centre, Department of Animal Breeding and Genetics, P. 0. BOX 7054, 750 07 Uppsala, Sweden.
| | | | - Erik Bongcam-Rudloff
- Swedish University of Agricultural Sciences (SLU), SLU-Global Bioinformatics Centre, Department of Animal Breeding and Genetics, P. 0. BOX 7054, 750 07 Uppsala, Sweden
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23
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Improved yield, stability, and cleavage reaction of a novel tobacco etch virus protease mutant. Appl Microbiol Biotechnol 2022; 106:1475-1492. [DOI: 10.1007/s00253-022-11786-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 11/02/2022]
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24
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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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25
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Ogushi S, Rattani A, Godwin J, Metson J, Schermelleh L, Nasmyth K. Loss of sister kinetochore co-orientation and peri-centromeric cohesin protection after meiosis I depends on cleavage of centromeric REC8. Dev Cell 2021; 56:3100-3114.e4. [PMID: 34758289 PMCID: PMC8629431 DOI: 10.1016/j.devcel.2021.10.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/28/2021] [Accepted: 10/18/2021] [Indexed: 11/27/2022]
Abstract
Protection of peri-centromeric (periCEN) REC8 cohesin from Separase and sister kinetochore (KT) attachment to microtubules emanating from the same spindle pole (co-orientation) ensures that sister chromatids remain associated after meiosis I. Both features are lost during meiosis II, resulting in sister chromatid disjunction and the production of haploid gametes. By transferring spindle-chromosome complexes (SCCs) between meiosis I and II in mouse oocytes, we discovered that both sister KT co-orientation and periCEN cohesin protection depend on the SCC, and not the cytoplasm. Moreover, the catalytic activity of Separase at meiosis I is necessary not only for converting KTs from a co- to a bi-oriented state but also for deprotection of periCEN cohesion, and cleavage of REC8 may be the key event. Crucially, selective cleavage of REC8 in the vicinity of KTs is sufficient to destroy co-orientation in univalent chromosomes, albeit not in bivalents where resolution of chiasmata may also be required.
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Affiliation(s)
- Sugako Ogushi
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; The Hakubi Center for Advanced Research, Kyoto University, Kyoto 606-8501, Japan.
| | - Ahmed Rattani
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Jonathan Godwin
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Jean Metson
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | | | - Kim Nasmyth
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
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26
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Hu J, Chen Y, Ren Y, Xiao W, Hu Y, Yu X, Fan J. Combination of the mutations for improving activity of TEV protease in inclusion bodies. Bioprocess Biosyst Eng 2021; 44:2129-2139. [PMID: 34036441 DOI: 10.1007/s00449-021-02589-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/12/2021] [Indexed: 11/28/2022]
Abstract
Tobacco etch virus protease (TEVp) is an enzymatic reagent to remove fusion tag, but additional purification steps are required for removing the TEVp after cleavage reaction is finished. Use of carrier-free and dependent TEVp immobilizates can eliminate protease contamination. In this work, we identified that, among the four constructed missense variants, the insoluble variant with the highest activity was correspondent with the soluble one tested formerly. The activities of the insoluble 15 codon variants were assayed and the variant with highest activity was selected. The K45F and/or E106G mutations have been reported on slightly improving protein stability of the wild-type TEVp, but only E106G mutation enhanced soluble production and activity of the selected TEVp variant, and it increased soluble amounts of two codon variants with the impaired folding. The decreased activity and use efficiency of the optimized TEVp variant in inclusion bodies was balanced by the determined high level production, lower leaking amounts of the protein, the enhanced resistance to the limited proteolysis mediated by protease K and trypsin, and the increased inhibition of auto-cleavage, as comparison to those of the immobilized soluble one. Thus, the TEVp construct is a potential alternate for simplifying protein purification protocols after tag-removal.
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Affiliation(s)
- Jiong Hu
- School of Life Science, Anhui Agricultural University, 130, Changjiang West Road, Hefei, 230036, Anhui Province, People's Republic of China
| | - Yinghua Chen
- School of Life Science, Anhui Agricultural University, 130, Changjiang West Road, Hefei, 230036, Anhui Province, People's Republic of China
| | - Yuanyuan Ren
- School of Life Science, Anhui Agricultural University, 130, Changjiang West Road, Hefei, 230036, Anhui Province, People's Republic of China
| | - Wenjun Xiao
- School of Life Science, Anhui Agricultural University, 130, Changjiang West Road, Hefei, 230036, Anhui Province, People's Republic of China
| | - Yafang Hu
- School of Life Science, Anhui Agricultural University, 130, Changjiang West Road, Hefei, 230036, Anhui Province, People's Republic of China
| | - Xuelian Yu
- School of Life Science, Anhui Agricultural University, 130, Changjiang West Road, Hefei, 230036, Anhui Province, People's Republic of China
| | - Jun Fan
- School of Life Science, Anhui Agricultural University, 130, Changjiang West Road, Hefei, 230036, Anhui Province, People's Republic of China.
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27
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Chen S, Lovell S, Lee S, Fellner M, Mace PD, Bogyo M. Identification of highly selective covalent inhibitors by phage display. Nat Biotechnol 2021; 39:490-498. [PMID: 33199876 PMCID: PMC8043995 DOI: 10.1038/s41587-020-0733-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 10/09/2020] [Indexed: 12/20/2022]
Abstract
Molecules that covalently bind macromolecular targets have found widespread applications as activity-based probes and as irreversibly binding drugs. However, the general reactivity of the electrophiles needed for covalent bond formation makes control of selectivity difficult. There is currently no rapid, unbiased screening method to identify new classes of covalent inhibitors from highly diverse pools of candidate molecules. Here we describe a phage display method to directly screen for ligands that bind to protein targets through covalent bond formation. This approach makes use of a reactive linker to form cyclic peptides on the phage surface while simultaneously introducing an electrophilic 'warhead' to covalently react with a nucleophile on the target. Using this approach, we identified cyclic peptides that irreversibly inhibited a cysteine protease and a serine hydrolase with nanomolar potency and exceptional specificity. This approach should enable rapid, unbiased screening to identify new classes of highly selective covalent inhibitors for diverse molecular targets.
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Affiliation(s)
- Shiyu Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Scott Lovell
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sumin Lee
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthias Fellner
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Peter D Mace
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
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28
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Vatansever EC, Yang KS, Drelich AK, Kratch KC, Cho CC, Kempaiah KR, Hsu JC, Mellott DM, Xu S, Tseng CTK, Liu WR. Bepridil is potent against SARS-CoV-2 in vitro. Proc Natl Acad Sci U S A 2021; 118:e2012201118. [PMID: 33597253 PMCID: PMC7958448 DOI: 10.1073/pnas.2012201118] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Guided by a computational docking analysis, about 30 Food and Drug Administration/European Medicines Agency (FDA/EMA)-approved small-molecule medicines were characterized on their inhibition of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro). Of these small molecules tested, six displayed a concentration that inhibits response by 50% (IC50) value below 100 μM in inhibiting Mpro, and, importantly, three, that is, pimozide, ebastine, and bepridil, are basic molecules that potentiate dual functions by both raising endosomal pH to interfere with SARS-CoV-2 entry into the human cell host and inhibiting Mpro in infected cells. A live virus-based modified microneutralization assay revealed that bepridil possesses significant anti-SARS-CoV-2 activity in both Vero E6 and A459/ACE2 cells in a dose-dependent manner with low micromolar effective concentration, 50% (EC50) values. Therefore, the current study urges serious considerations of using bepridil in COVID-19 clinical tests.
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Affiliation(s)
- Erol C Vatansever
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Kai S Yang
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Aleksandra K Drelich
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555
| | - Kaci C Kratch
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Chia-Chuan Cho
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843
| | | | - Jason C Hsu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555
| | - Drake M Mellott
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Shiqing Xu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Chien-Te K Tseng
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555;
- Center of Biodefense and Emerging Disease, University of Texas Medical Branch, Galveston, TX 77555
| | - Wenshe Ray Liu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843;
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
- Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030
- Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX 77030
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, College Station, TX 77843
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29
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Engineering subtilisin proteases that specifically degrade active RAS. Commun Biol 2021; 4:299. [PMID: 33674772 PMCID: PMC7935941 DOI: 10.1038/s42003-021-01818-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 02/10/2021] [Indexed: 12/18/2022] Open
Abstract
We describe the design, kinetic properties, and structures of engineered subtilisin proteases that degrade the active form of RAS by cleaving a conserved sequence in switch 2. RAS is a signaling protein that, when mutated, drives a third of human cancers. To generate high specificity for the RAS target sequence, the active site was modified to be dependent on a cofactor (imidazole or nitrite) and protease sub-sites were engineered to create a linkage between substrate and cofactor binding. Selective proteolysis of active RAS arises from a 2-step process wherein sub-site interactions promote productive binding of the cofactor, enabling cleavage. Proteases engineered in this way specifically cleave active RAS in vitro, deplete the level of RAS in a bacterial reporter system, and also degrade RAS in human cell culture. Although these proteases target active RAS, the underlying design principles are fundamental and will be adaptable to many target proteins.
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30
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Palani SN, Sankaranarayanan R, Tennyson J. Comparative study of potyvirid NIa proteases and their cleavage sites. Arch Virol 2021; 166:1141-1149. [PMID: 33599826 DOI: 10.1007/s00705-021-04997-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/27/2020] [Indexed: 10/22/2022]
Abstract
Nuclear inclusion a protease (NIaPro), a major protease of potyvirids, processes its cognate viral polyprotein at distinct cleavage sites. Although Potyviridae is the largest family of the realm Riboviria, the individual NIaPro enzymes and their cleavage sites are believed to be species-specific. In the present study, the NIaPro amino acid sequences of 165 potyvirids of 10 genera and their 1154 cleavage sites were compared to understand their genus/species-specificity and functional regulation. Of these, the NIaPro of macluraviruses, maintains a constant length of 217 amino acids, while those of other genera allow variation. In particular, poaceviruses exhibited a broad range of NIaPro amino acid sequence lengths. Alignment of 162 NIaPro amino acid sequences showed that the N- and C-terminal regions allow variations, while the central region, with the catalytic triad and S1 subsite, are highly conserved. NIaPro cleavage sites are composed of seven amino acids (heptapeptide) denoted as P6-P5-P4-P3-P2-P1/P1'. A survey of 1154 cleavage sites showed that the P1 position is predominantly occupied by Gln/Glu, as is seen in picornaviruses. The P6 (Glu), P4 (Val/Cys/Gln), P2 (His/Tyr/Leu), and P1' (Ser/Ala/Gly/Met) positions are predominantly occupied by genus-specific residues, while P5 and P3 are not genus-specific. The 6K2-VPg and VPg-NIaPro junctions possess Glu at the P1 position in order to maintain latency.
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31
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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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32
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Patil AB, Dalvi VS, Azeez A, Krishna B, Mishra AA, Sane PV. Cloning, expression and characterization of P1 and NIa proteases from banana bract mosaic virus (BBrMV). Protein Expr Purif 2020; 180:105811. [PMID: 33347949 DOI: 10.1016/j.pep.2020.105811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/21/2020] [Accepted: 12/15/2020] [Indexed: 10/22/2022]
Abstract
Banana bract mosaic virus (BBrMV) causes the banana bract mosaic disease in banana. It belongs to the genus Potyvirus within the family Potyviridae. To the best of our knowledge apart from BBrMV coat protein gene, there are no reports on cloning, expression and characterization of any other genes from BBrMV. In this study, the BBrMV P1 and NIa protease genes were amplified from BBrMV infected banana plant cultivar Nendran and were cloned into the protein expression vector pET28b. Recombinant plasmids were transferred to BL21-CodonPlus (DE3)-RP cells and the IPTG (Isopropyl β-d-1-thiogalactopyranoside) induced BBrMV P1 and NIa proteins with molecular weights of 42 and 32 KDa respectively were purified on Ni-NTA resin column under denaturing conditions using 8 M urea. BBrMV P1 and NIa purified proteins were detected by Western blot using anti-histidine antibody. The activity of both P1 and NIa proteases in native form was analyzed through in-gel zymographic assay. The activities of both the proteases were strongly inhibited by PMSF, suggesting that both the proteases are the serine type proteases. Interestingly both the proteases showed a temperature optimum of 50 °C while the pH optimum was 8. Both proteases lost their activity when incubated at 70 °C for 1 h. This is the first report of expression, purification and characterization of BBrMV P1 and NIa proteases.
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Affiliation(s)
- Atul B Patil
- Plant Virology Lab, Jain R&D, Jain Hills, Jain Irrigation Systems Limited, Shirsoli Road, Post Box No # 72, Jalgaon, 425001, Maharashtra State, India.
| | - Vijayendra S Dalvi
- Plant Virology Lab, Jain R&D, Jain Hills, Jain Irrigation Systems Limited, Shirsoli Road, Post Box No # 72, Jalgaon, 425001, Maharashtra State, India.
| | - Abdul Azeez
- College of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, 906-487-1885, USA.
| | - Bal Krishna
- Plant Molecular Biology Lab, Jain R&D, Jain Hills, Jain Irrigation Systems Limited, Shirsoli Road, Post Box No# 72, Jalgaon, 425001, Maharashtra State, India.
| | - Akhilesh A Mishra
- Plant Virology Lab, Jain R&D, Jain Hills, Jain Irrigation Systems Limited, Shirsoli Road, Post Box No # 72, Jalgaon, 425001, Maharashtra State, India.
| | - Prafullachandra V Sane
- Plant Virology Lab, Jain R&D, Jain Hills, Jain Irrigation Systems Limited, Shirsoli Road, Post Box No # 72, Jalgaon, 425001, Maharashtra State, India.
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33
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Mohammadian N, Mohammadian H, Moazen F, Pakdel MH, Jahanian-Najafabadi A, Mir Mohammad Sadeghi H. Optimization of solvent media to solubilize TEV protease using response surface method. Res Pharm Sci 2020; 15:331-339. [PMID: 33312211 PMCID: PMC7714021 DOI: 10.4103/1735-5362.293511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 01/20/2020] [Accepted: 08/16/2020] [Indexed: 11/04/2022] Open
Abstract
Background and purpose Tobacco etch virus (TEV) protease, a 27 KDa protein, consists of the catalytic domain of nuclear inclusion a (NIa) protein produced by Tobacco etch virus. Because of its unique sequence, TEV protease is used for purging fusion tags from proteins. It also has many advantages such as stability and activity in a board range of temperature and pH and overproduction in Escherichia coli and these benefits make this protease valuable. Despite all these benefits, TEV protease has problems like low solubility (less than 1 mg/mL). There are methods for enhancing protein solubility and in this study, the effect of additives during cell lysis was studied. Experimental approach Eleven different additives that made twelve different lysis buffers were used and their effect on TEV protease solubility analyzed by Plackett-Burman and response surface methodology methods. Findings / Results Three best effective additives on TEV solubility (L-proline, sodium selenite, and CuCl2) were selected according to software analysis and the best concentration of them was applied to optimize TEV protease solubility. Conclusion and implications The obtained results provided the composition of an optimum solvent for obtaining soluble TEV protease.
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Affiliation(s)
- Niloufar Mohammadian
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Hossein Mohammadian
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Fatemeh Moazen
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Mohammad Hosein Pakdel
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, I.R. Iran
| | - Ali Jahanian-Najafabadi
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Hamid Mir Mohammad Sadeghi
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
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34
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Liu S, Li S, Yang Y, Li W. Termini restraining of small membrane proteins enables structure determination at near-atomic resolution. SCIENCE ADVANCES 2020; 6:eabe3717. [PMID: 33355146 PMCID: PMC11205269 DOI: 10.1126/sciadv.abe3717] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/04/2020] [Indexed: 06/12/2023]
Abstract
Small membrane proteins are difficult targets for structural characterization. Here, we stabilize their folding by restraining their amino and carboxyl termini with associable protein entities, exemplified by the two halves of a superfolder GFP. The termini-restrained proteins are functional and show improved stability during overexpression and purification. The reassembled GFP provides a versatile scaffold for membrane protein crystallization, enables diffraction to atomic resolution, and facilitates crystal identification, phase determination, and density modification. This strategy gives rise to 14 new structures of five vertebrate proteins from distinct functional families, bringing a substantial expansion to the structural database of small membrane proteins. Moreover, a high-resolution structure of bacterial DsbB reveals that this thiol oxidoreductase is activated through a catalytic triad, similar to cysteine proteases. Overall, termini restraining proves exceptionally effective for stabilization and structure determination of small membrane proteins.
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Affiliation(s)
- Shixuan Liu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Shuang Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yihu Yang
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Weikai Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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35
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Cachero S, Gkantia M, Bates AS, Frechter S, Blackie L, McCarthy A, Sutcliffe B, Strano A, Aso Y, Jefferis GSXE. BAcTrace, a tool for retrograde tracing of neuronal circuits in Drosophila. Nat Methods 2020; 17:1254-1261. [PMID: 33139893 PMCID: PMC7610425 DOI: 10.1038/s41592-020-00989-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 10/05/2020] [Indexed: 11/26/2022]
Abstract
Animal behavior is encoded in neuronal circuits in the brain. To elucidate the function of these circuits, it is necessary to identify, record from and manipulate networks of connected neurons. Here we present BAcTrace (Botulinum Activated Tracer), a genetically encoded, retro-grade, transsynaptic labelling system. BAcTrace is based on C. botulinum neurotoxin A, Botox, which we have engineered to travel retrogradely between neurons to activate an otherwise silent transcription factor. We validate BAcTrace at three neuronal connections in the Drosophila olfactory system. We show that BAcTrace-mediated labeling allows electrophysiological recordings of connected neurons. Finally, in a challenging circuit with highly divergent connections, BAcTrace correctly identifies 12 out of 16 connections, which were previously observed by electron microscopy.
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Affiliation(s)
- Sebastian Cachero
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK.
| | - Marina Gkantia
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Alexander S Bates
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Shahar Frechter
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Laura Blackie
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK.,MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Amy McCarthy
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK.,Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK
| | - Ben Sutcliffe
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Alessio Strano
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK.,Department of Cancer and Developmental Biology & Zayed Centre for Research into Rare Disease in Children, University College London, London, UK
| | - Yoshinori Aso
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
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36
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Sabharwal P, Savithri HS. Functional Characterization of Pepper Vein Banding Virus-Encoded Proteins and Their Interactions: Implications in Potyvirus Infection. Viruses 2020; 12:v12091037. [PMID: 32957699 PMCID: PMC7551749 DOI: 10.3390/v12091037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/20/2020] [Accepted: 07/22/2020] [Indexed: 11/16/2022] Open
Abstract
Pepper vein banding virus (PVBV) is a distinct species in the Potyvirus genus which infects economically important plants in several parts of India. Like other potyviruses, PVBV encodes multifunctional proteins, with several interaction partners, having implications at different stages of the potyviral infection. In this review, we summarize the functional characterization of different PVBV-encoded proteins with an emphasis on their interaction partners governing the multifunctionality of potyviral proteins. Intrinsically disordered domains/regions of these proteins play an important role in their interactions with other proteins. Deciphering the function of PVBV-encoded proteins and their interactions with cognitive partners will help in understanding the putative mechanisms by which the potyviral proteins are regulated at different stages of the viral life-cycle. This review also discusses PVBV virus-like particles (VLPs) and their potential applications in nanotechnology. Further, virus-like nanoparticle-cell interactions and intracellular fate of PVBV VLPs are also discussed.
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37
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Lakshmanan A, Jin Z, Nety SP, Sawyer DP, Lee-Gosselin A, Malounda D, Swift MB, Maresca D, Shapiro MG. Acoustic biosensors for ultrasound imaging of enzyme activity. Nat Chem Biol 2020; 16:988-996. [PMID: 32661379 PMCID: PMC7713704 DOI: 10.1038/s41589-020-0591-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 06/12/2020] [Indexed: 12/19/2022]
Abstract
Visualizing biomolecular and cellular processes inside intact living organisms is a major goal of chemical biology. However, existing molecular biosensors, based primarily on fluorescent emission, have limited utility in this context due to the scattering of light by tissue. In contrast, ultrasound can easily image deep tissue with high spatiotemporal resolution, but lacks the biosensors needed to connect its contrast to the activity of specific biomolecules such as enzymes. To overcome this limitation, we introduce the first genetically encodable acoustic biosensors-molecules that 'light up' in ultrasound imaging in response to protease activity. These biosensors are based on a unique class of air-filled protein nanostructures called gas vesicles, which we engineered to produce nonlinear ultrasound signals in response to the activity of three different protease enzymes. We demonstrate the ability of these biosensors to be imaged in vitro, inside engineered probiotic bacteria, and in vivo in the mouse gastrointestinal tract.
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Affiliation(s)
- Anupama Lakshmanan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Zhiyang Jin
- Division of Engineering and Applied Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Suchita P Nety
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Daniel P Sawyer
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Audrey Lee-Gosselin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Dina Malounda
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Mararet B Swift
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - David Maresca
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Imaging Physics, Delft University of Technology, Delft, Netherlands
| | - Mikhail G Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
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38
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Vatansever EC, Yang K, Kratch KC, Drelich A, Cho CC, Mellott DM, Xu S, Tseng CTK, Liu WR. Bepridil is potent against SARS-CoV-2 In Vitro. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32511370 PMCID: PMC7263498 DOI: 10.1101/2020.05.23.112235] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Guided by a computational docking analysis, about 30 FDA/EMA-approved small molecule medicines were characterized on their inhibition of the SARS-CoV-2 main protease (MPro). Of these tested small molecule medicines, six displayed an IC50 value in inhibiting MPro below 100 μM. Three medicines pimozide, ebastine, and bepridil are basic small molecules. Their uses in COVID-19 patients potentiate dual functions by both raising endosomal pH to slow SARS-CoV-2 entry into the human cell host and inhibiting MPro in infected cells. A live virus-based microneutralization assay showed that bepridil inhibited cytopathogenic effect induced by SARS-CoV-2 in Vero E6 cells completely at and dose-dependently below 5 μM and in A549 cells completely at and dose-dependently below 6.25 μM. Therefore, the current study urges serious considerations of using bepridil in COVID-19 clinical tests.
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Affiliation(s)
- Erol C Vatansever
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Kai Yang
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Kaci C Kratch
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Aleksandra Drelich
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Chia-Chuan Cho
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Drake M Mellott
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Shiqing Xu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Chien-Te K Tseng
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Wenshe Ray Liu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA.,Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA.,Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, College Station, TX 77843, USA
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Attri P, Choi S, Kim M, Shiratani M, Cho AE, Lee W. Influence of alkyl chain substitution of ammonium ionic liquids on the activity and stability of tobacco etch virus protease. Int J Biol Macromol 2020; 155:439-446. [DOI: 10.1016/j.ijbiomac.2020.03.175] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 02/06/2023]
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Proteus: An algorithm for proposing stabilizing mutation pairs based on interactions observed in known protein 3D structures. BMC Bioinformatics 2020; 21:275. [PMID: 32611389 PMCID: PMC7330979 DOI: 10.1186/s12859-020-03575-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 05/28/2020] [Indexed: 11/10/2022] Open
Abstract
Background Protein engineering has many applications for industry, such as the development of new drugs, vaccines, treatment therapies, food, and biofuel production. A common way to engineer a protein is to perform mutations in functionally essential residues to optimize their function. However, the discovery of beneficial mutations for proteins is a complex task, with a time-consuming and high cost for experimental validation. Hence, computational approaches have been used to propose new insights for experiments narrowing the search space and reducing the costs. Results In this study, we developed Proteus (an acronym for Protein Engineering Supporter), a new algorithm for proposing mutation pairs in a target 3D structure. These suggestions are based on contacts observed in other known structures from Protein Data Bank (PDB). Proteus’ basic assumption is that if a non-interacting pair of amino acid residues in the target structure is exchanged to an interacting pair, this could enhance protein stability. This trade is only allowed if the main-chain conformation of the residues involved in the contact is conserved. Furthermore, no steric impediment is expected between the proposed mutations and the surrounding protein atoms. To evaluate Proteus, we performed two case studies with proteins of industrial interests. In the first case study, we evaluated if the mutations suggested by Proteus for four protein structures enhance the number of inter-residue contacts. Our results suggest that most mutations proposed by Proteus increase the number of interactions into the protein. In the second case study, we used Proteus to suggest mutations for a lysozyme protein. Then, we compared Proteus’ outcomes to mutations with available experimental evidence reported in the ProTherm database. Four mutations, in which our results agree with the experimental data, were found. This could be initial evidence that changes in the side-chain of some residues do not cause disturbances that harm protein structure stability. Conclusion We believe that Proteus could be used combined with other methods to give new insights into the rational development of engineered proteins. Proteus user-friendly web-based tool is available at <http://proteus.dcc.ufmg.br>.
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Mohammadian H, Mahnam K, Sadeghi HM, Ganjalikhany MR, Akbari V. Rational design of a new mutant of tobacco etch virus protease in order to increase the in vitro solubility. Res Pharm Sci 2020; 15:164-173. [PMID: 32582356 PMCID: PMC7306250 DOI: 10.4103/1735-5362.283816] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/30/2019] [Accepted: 03/16/2020] [Indexed: 12/13/2022] Open
Abstract
Background and purpose: Tobacco etch virus (TEV) protease is a protease with high sequence specificity which is useful for the cleavage of fusion proteins. A major limitation of this enzyme is its relatively poor solubility. This study aimed to investigate the effects of some suggested mutations by online tools and molecular dynamics simulation to improve the solubility of TEV protease in vitro. Experimental approach: We designed a rational multi-stage process to determine the solubilizing mutations of TEV protease. At the first stage, all the possible mutations were predicted using online tools such as PoPMuSiC and Eris servers, in which five mutations include N23F, N23L, Q74L, Q74V, and Q74I were suggested for further studies. In the next step, the three dimensional structure of the wild type (WT) and the best mutations were subjected to molecular dynamic simulations to evaluate the dynamic behaviour of the obtained structures. The selected mutation was introduced into the structure using site-directed mutagenesis and expressed in Escherichia coli BL21DE3. After purification, solubility and activity of the purified mutant and WT-TEV proteases were assayed. Findings /Results: By considering the analysis of various factors such as structural and solubility properties, one mutant, N23F, was selected for in vitro studies which led to a 1.5 times increase in the solubility compared to the WT while its activity was decreased somewhat. Conclusion and implications: We propose N23F mutation, according to computational and experimental analyses for TEV proteases which resulted in a 150% increase in solubility compared to the WT.
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Affiliation(s)
- Hossein Mohammadian
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran.,Isfahan Pharmaceutical Sciences Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Karim Mahnam
- Department of Biology, Faculty of Sciences, University of Shahrekord, Shahrekord, I.R. Iran.,Nanotechnology Research Centre, Shahrekord University, Shahrekord, I.R. Iran
| | - Hamid Mirmohammad Sadeghi
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran.,Isfahan Pharmaceutical Sciences Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | | | - Vajihe Akbari
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran.,Isfahan Pharmaceutical Sciences Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
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42
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Nam H, Hwang BJ, Choi DY, Shin S, Choi M. Tobacco etch virus (TEV) protease with multiple mutations to improve solubility and reduce self-cleavage exhibits enhanced enzymatic activity. FEBS Open Bio 2020; 10:619-626. [PMID: 32129006 PMCID: PMC7137792 DOI: 10.1002/2211-5463.12828] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/13/2020] [Accepted: 02/28/2020] [Indexed: 01/27/2023] Open
Abstract
Tobacco etch virus (TEV) protease is a 27‐kDa catalytic domain of the polyprotein nuclear inclusion a (NIa) in TEV, which recognizes the specific amino acid sequence ENLYFQG/S and cleaves between Q and G/S. Despite its substrate specificity, its use is limited by its autoinactivation through self‐cleavage and poor solubility during purification. It was previously reported that T17S/N68D/I77V mutations improve the solubility and yield of TEV protease and S219 mutations provide protection against self‐cleavage. In this study, we isolated TEV proteases with S219N and S219V mutations in the background of T17S, N68D, and I77V without the inclusion body, and measured their enzyme kinetics. The kcat of two isolated S219N and S219V mutants in the background of T17S, N68D, and I77V mutations was highly increased compared to that of the control, and S219N was twofold faster than S219V without Km change. This result indicates that combination of these mutations can further enhance TEV activity.
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Affiliation(s)
- Heejin Nam
- Interdisciplinary Program of Bioenergy and Biomaterials Graduate School, College of Engineering, Chonnam National University, Gwangju, South Korea
| | - Beom J Hwang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | | | - Sooim Shin
- Interdisciplinary Program of Bioenergy and Biomaterials Graduate School, College of Engineering, Chonnam National University, Gwangju, South Korea.,Department of Bioengineering and Biotechnology, College of Engineering, Chonnam National University, Gwangju, South Korea
| | - Moonsung Choi
- Department of Optometry, College of Energy and Biotechnology, Seoul National University of Science and Technology, South Korea.,Convergence Institute of Biomaterials and Bioengineering, Seoul National University of Science and Technology, South Korea
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43
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Denesyuk AI, Johnson MS, Salo-Ahen OMH, Uversky VN, Denessiouk K. NBCZone: Universal three-dimensional construction of eleven amino acids near the catalytic nucleophile and base in the superfamily of (chymo)trypsin-like serine fold proteases. Int J Biol Macromol 2020; 153:399-411. [PMID: 32151723 PMCID: PMC7124590 DOI: 10.1016/j.ijbiomac.2020.03.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 10/25/2022]
Abstract
(Chymo)trypsin-like serine fold proteases belong to the serine/cysteine proteases found in eukaryotes, prokaryotes, and viruses. Their catalytic activity is carried out using a triad of amino acids, a nucleophile, a base, and an acid. For this superfamily of proteases, we propose the existence of a universal 3D structure comprising 11 amino acids near the catalytic nucleophile and base - Nucleophile-Base Catalytic Zone (NBCZone). The comparison of NBCZones among 169 eukaryotic, prokaryotic, and viral (chymo)trypsin-like proteases suggested the existence of 15 distinct groups determined by the combination of amino acids located at two "key" structure-functional positions 54T and 55T near the catalytic base His57T. Most eukaryotic and prokaryotic proteases fell into two major groups, [ST]A and TN. Usually, proteases of [ST]A group contain a disulfide bond between cysteines Cys42T and Cys58T of the NBCZone. In contrast, viral proteases were distributed among seven groups, and lack this disulfide bond. Furthermore, only the [ST]A group of eukaryotic proteases contains glycine at position 43T, which is instrumental for activation of these enzymes. In contrast, due to the side chains of residues at position 43T prokaryotic and viral proteases do not have the ability to carry out the structural transition of the eukaryotic zymogen-zyme type.
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Affiliation(s)
- Alexander I Denesyuk
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 142290 Pushchino, Russia; Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland.
| | - Mark S Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Outi M H Salo-Ahen
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland; Pharmaceutical Sciences Laboratory, Pharmacy, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Vladimir N Uversky
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 142290 Pushchino, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland; Pharmaceutical Sciences Laboratory, Pharmacy, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
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44
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Fan X, Li X, Zhou Y, Mei M, Liu P, Zhao J, Peng W, Jiang ZB, Yang S, Iverson BL, Zhang G, Yi L. Quantitative Analysis of the Substrate Specificity of Human Rhinovirus 3C Protease and Exploration of Its Substrate Recognition Mechanisms. ACS Chem Biol 2020; 15:63-73. [PMID: 31613083 DOI: 10.1021/acschembio.9b00539] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Human rhinovirus 3C protease (HRV 3C-P) is a high-value commercial cysteine protease that could specifically recognize the short peptide sequence of LEVLFQ↓GP. In here, a strategy based on our previous Yeast Endoplasmic Reticulum Sequestration Screening (YESS) approach was developed in Saccharomyces cerevisiae, a model microorganism, to fully characterize the substrate specificity of a typical human virus protease, HRV 3C-P, in a quantitative and fast manner. Our results demonstrated that HRV 3C-P had very high specificity at P1 and P1' positions, only recognizing Gln/Glu at the P1 position and Gly/Ala/Cys/Ser at the P1' position, respectively. Comparably, it exhibited efficient recognition of most residues at the P2' position, except Trp. Further biochemical characterization through site mutagenesis, enzyme structural modeling, and comparison with other 3C proteases indicated that the S1 pocket of HRV 3C-P was constituted by neutral and basic amino acids, in which His160 and Thr141 specifically interacted with Gln or Glu residues at the substrate P1 position. Additionally, the stringent S1' pocket determined its unique property of only accommodating residues without or with short side chains. Based on our characterization, LEVLFQ↓GM was identified as a more favorable substrate than the original LEVLFQ↓GP at high temperature, which might be caused by the conversion of random coils to β-turns in HRV 3C-P along with the temperature increase. Our studies prompted a further understanding of the substrate specificity and recognition mechanism of HRV 3C-P. Besides, the YESS-PSSC combined with the enzyme modeling strategy in this study provides a general strategy for deciphering the substrate specificities of proteases.
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Affiliation(s)
- Xian Fan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences , Hubei University , Wuhan , 430062 , China
| | - Xinzhi Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences , Hubei University , Wuhan , 430062 , China
| | - Yu Zhou
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences , Hubei University , Wuhan , 430062 , China
| | - Meng Mei
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences , Hubei University , Wuhan , 430062 , China
| | - Pi Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin 300308 , China
| | - Jing Zhao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences , Hubei University , Wuhan , 430062 , China
| | - Wenfang Peng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences , Hubei University , Wuhan , 430062 , China
| | - Zheng-Bing Jiang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences , Hubei University , Wuhan , 430062 , China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences , Hubei University , Wuhan , 430062 , China
| | - Brent L Iverson
- Department of Chemistry , University of Texas , Austin , Texas 78712 , United States
| | - Guimin Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences , Hubei University , Wuhan , 430062 , China
| | - Li Yi
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences , Hubei University , Wuhan , 430062 , China
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45
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Belluzo BS, Abriata LA, Giannini E, Mihovilcevic D, Dal Peraro M, Llarrull LI. An experiment-informed signal transduction model for the role of the Staphylococcus aureus MecR1 protein in β-lactam resistance. Sci Rep 2019; 9:19558. [PMID: 31862951 PMCID: PMC6925264 DOI: 10.1038/s41598-019-55923-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 12/04/2019] [Indexed: 11/13/2022] Open
Abstract
The treatment of hospital- and community-associated infections by methicillin-resistant Staphylococcus aureus (MRSA) is a perpetual challenge. This Gram-positive bacterium is resistant specifically to β-lactam antibiotics, and generally to many other antibacterial agents. Its resistance mechanisms to β-lactam antibiotics are activated only when the bacterium encounters a β-lactam. This activation is regulated by the transmembrane sensor/signal transducer proteins BlaR1 and MecR1. Neither the transmembrane/metalloprotease domain, nor the complete MecR1 and BlaR1 proteins, are isolatable for mechanistic study. Here we propose a model for full-length MecR1 based on homology modeling, residue coevolution data, a new extensive experimental mapping of transmembrane topology, partial structures, molecular simulations, and available NMR data. Our model defines the metalloprotease domain as a hydrophilic transmembrane chamber effectively sealed by the apo-sensor domain. It proposes that the amphipathic helices inserted into the gluzincin domain constitute the route for transmission of the β-lactam-binding event in the extracellular sensor domain, to the intracellular and membrane-embedded zinc-containing active site. From here, we discuss possible routes for subsequent activation of proteolytic action. This study provides the first coherent model of the structure of MecR1, opening routes for future functional investigations on how β-lactam binding culminates in the proteolytic degradation of MecI.
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Affiliation(s)
- Bruno S Belluzo
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, 27 de Febrero 210 bis, 2000, Rosario, Argentina
| | - Luciano A Abriata
- Laboratory for Biomolecular Modeling - École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland
| | - Estefanía Giannini
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, 27 de Febrero 210 bis, 2000, Rosario, Argentina
| | - Damila Mihovilcevic
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, 27 de Febrero 210 bis, 2000, Rosario, Argentina
| | - Matteo Dal Peraro
- Laboratory for Biomolecular Modeling - École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland
| | - Leticia I Llarrull
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, 27 de Febrero 210 bis, 2000, Rosario, Argentina. .,Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, 2000, Rosario, Argentina.
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46
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Directed evolution improves the catalytic efficiency of TEV protease. Nat Methods 2019; 17:167-174. [PMID: 31819267 PMCID: PMC7004888 DOI: 10.1038/s41592-019-0665-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 10/25/2019] [Indexed: 11/08/2022]
Abstract
Tobacco etch virus protease (TEV) is one of the most widely used proteases in biotechnology because of its exquisite sequence specificity. A limitation, however, is its slow catalytic rate. We developed a generalizable yeast-based platform for directed evolution of protease catalytic properties. Protease activity is read out via proteolytic release of a membrane-anchored transcription factor, and we temporally regulate access to TEV's cleavage substrate using a photosensory LOV domain. By gradually decreasing light exposure time, we enriched faster variants of TEV over multiple rounds of selection. Our TEV-S153N mutant (uTEV1Δ), when incorporated into the calcium integrator FLARE, improved the signal/background ratio by 27-fold, and enabled recording of neuronal activity in culture with 60-s temporal resolution. Given the widespread use of TEV in biotechnology, both our evolved TEV mutants and the directed-evolution platform used to generate them could be beneficial across a wide range of applications.
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Abstract
Synthesis and regulation of lipid levels and identities is critical for a wide variety of cellular functions, including structural and morphological properties of organelles, energy storage, signaling, and stability and function of membrane proteins. Proteolytic cleavage events regulate and/or influence some of these lipid metabolic processes and as a result help modulate their pleiotropic cellular functions. Proteins involved in lipid regulation are proteolytically cleaved for the purpose of their relocalization, processing, turnover, and quality control, among others. The scope of this review includes proteolytic events governing cellular lipid dynamics. After an initial discussion of the classic example of sterol regulatory element-binding proteins, our focus will shift to the mitochondrion, where a range of proteolytic events are critical for normal mitochondrial phospholipid metabolism and enforcing quality control therein. Recently, mitochondrial phospholipid metabolic pathways have been implicated as important for the proliferative capacity of cancers. Thus, the assorted proteases that regulate, monitor, or influence the activity of proteins that are important for phospholipid metabolism represent attractive targets to be manipulated for research purposes and clinical applications.
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Affiliation(s)
- Pingdewinde N. Sam
- Department of Physiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Erica Avery
- Department of Physiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Steven M. Claypool
- Department of Physiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
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48
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Drabek AA, Loparo JJ, Blacklow SC. A Flow-Extension Tethered Particle Motion Assay for Single-Molecule Proteolysis. Biochemistry 2019; 58:2509-2518. [PMID: 30946563 PMCID: PMC6607913 DOI: 10.1021/acs.biochem.9b00106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Regulated proteolysis of signaling proteins under mechanical tension enables cells to communicate with their environment in a variety of developmental and physiologic contexts. The role of force in inducing proteolytic sensitivity has been explored using magnetic tweezers at the single-molecule level with bead-tethered assays, but such efforts have been limited by challenges in ensuring that beads not be restrained by multiple tethers. Here, we describe a multiplexed assay for single-molecule proteolysis that overcomes the multiple-tether problem using a flow-extension strategy on a microscope equipped with magnetic tweezers. Particle tracking and computational sorting of flow-induced displacements allow assignment of tethered substrates to singly captured and multiply tethered bins, with the fraction of fully mobile, single-tether substrates depending inversely on the concentration of substrate loaded on the coverslip. Computational exclusion of multiple-tether beads enables robust assessment of on-target proteolysis by the highly specific tobacco etch virus protease and the more promiscuous metalloprotease ADAM17. This method should be generally applicable to a wide range of proteases and readily extensible to robust evaluation of proteolytic sensitivity as a function of applied magnetic force.
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Affiliation(s)
- Andrew A. Drabek
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Joseph J. Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Stephen C. Blacklow
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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49
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Kanitz M, Blanck S, Heine A, Gulyaeva AA, Gorbalenya AE, Ziebuhr J, Diederich WE. Structural basis for catalysis and substrate specificity of a 3C-like cysteine protease from a mosquito mesonivirus. Virology 2019; 533:21-33. [PMID: 31078932 PMCID: PMC7111312 DOI: 10.1016/j.virol.2019.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 04/30/2019] [Accepted: 05/01/2019] [Indexed: 01/05/2023]
Abstract
Cavally virus (CavV) is a mosquito-borne plus-strand RNA virus in the family Mesoniviridae (order Nidovirales). We present X-ray structures for the CavV 3C-like protease (3CLpro), as a free enzyme and in complex with a peptide aldehyde inhibitor mimicking the P4-to-P1 residues of a natural substrate. The 3CLpro structure (refined to 1.94 Å) shows that the protein forms dimers. The monomers are comprised of N-terminal domains I and II, which adopt a chymotrypsin-like fold, and a C-terminal α-helical domain III. The catalytic Cys-His dyad is assisted by a complex network of interactions involving a water molecule that mediates polar contacts between the catalytic His and a conserved Asp located in the domain II-III junction and is suitably positioned to stabilize the developing positive charge of the catalytic His in the transition state during catalysis. The study also reveals the structural basis for the distinct P2 Asn-specific substrate-binding pocket of mesonivirus 3CLpros. First structure of a 3CLpro of an invertebrate RNA virus. Structural basis of the unique substrate specificity defined by Asn at the P2 position of mesonivirus 3CLpro substrates. Emerging role of a conserved Asp residue that assists the Cys-His catalytic dyad in vertebrate and invertebrate 3CLpros.
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Affiliation(s)
- Manuel Kanitz
- Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany; Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany
| | - Sandra Blanck
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Andreas Heine
- Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany
| | - Anastasia A Gulyaeva
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Alexander E Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany.
| | - Wibke E Diederich
- Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany; Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany.
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50
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Ceccarelli DF, Ivantsiv S, Mullin AA, Coyaud E, Manczyk N, Maisonneuve P, Kurinov I, Zhao L, Go C, Gingras AC, Raught B, Cordes S, Sicheri F. FAM105A/OTULINL Is a Pseudodeubiquitinase of the OTU-Class that Localizes to the ER Membrane. Structure 2019; 27:1000-1012.e6. [PMID: 31056421 DOI: 10.1016/j.str.2019.03.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 02/23/2019] [Accepted: 03/27/2019] [Indexed: 12/16/2022]
Abstract
Pseudoenzymes have been identified across a diverse range of enzyme classes and fulfill important cellular functions. Examples of pseudoenzymes exist within ubiquitin conjugating and deubiquitinase (DUB) protein families. Here we characterize FAM105A/OTULINL, the only putative pseudodeubiquitinase of the ovarian tumor protease (OTU domain) family in humans. The crystal structure of FAM105A revealed that the OTU domain possesses structural deficiencies in both active site and substrate-binding infrastructure predicted to impair normal DUB function. We confirmed the absence of catalytic function against all ubiquitin linkages and an inability of FAM105A to bind ubiquitin compared with catalytically active FAM105B/OTULIN. FAM105A co-localized with KDEL markers and Lamin B1 at the endoplasmic reticulum (ER) and nuclear envelope, respectively. Accordingly, the FAM105A interactome exhibited significant enrichment in proteins localized to the ER/outer nuclear, Golgi and vesicular membranes. In light of undetectable deubiquitinase activity, we posit that FAM105A/OTULINL functions through its ability to mediate protein-protein interactions.
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Affiliation(s)
- Derek F Ceccarelli
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Sofiia Ivantsiv
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Amber Anne Mullin
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Noah Manczyk
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Pierre Maisonneuve
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Igor Kurinov
- Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Argonne, IL 60439, USA
| | - Liang Zhao
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Chris Go
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Anne-Claude Gingras
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.
| | - Sabine Cordes
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Frank Sicheri
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
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