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Dušeková E, Berta M, Sedláková D, Řeha D, Dzurillová V, Shaposhnikova A, Fadaei F, Tomková M, Minofar B, Sedlák E. Specific anion effect on properties of HRV 3C protease. Biophys Chem 2022; 287:106825. [PMID: 35597150 DOI: 10.1016/j.bpc.2022.106825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/19/2022] [Accepted: 05/07/2022] [Indexed: 12/12/2022]
Abstract
Specific salts effect is intensively studied from the prospective of modification of different physico-chemical properties of biomacromolecules. Limited knowledge of the specific salts effect on enzymes led us to address the influence of five sodium anions: sulfate, phosphate, chloride, bromide, and perchlorate, on catalytic and conformational properties of human rhinovirus-14 (HRV) 3C protease. The enzyme conformation was monitored by circular dichroism spectrum (CD) and by tyrosines fluorescence. Stability and flexibility of the enzyme have been analyzed by CD in the far-UV region, differential scanning calorimetry and molecular dynamics simulations, respectively. We showed significant influence of the anions on the enzyme properties in accordance with the Hofmeister effect. The HRV 3C protease in the presence of kosmotropic anions, in contrast with chaotropic anions, exhibits increased stability, rigidity. Correlations of stabilization effect of anions on the enzyme with their charge density and the rate constant of the enzyme with the viscosity B-coefficients of anions suggest direct interaction of the anions with HRV 3C protease. The role of stabilization and decreased fluctuation of the polypeptide chain of HRV 3C protease on its activation in the presence of kosmotropic anions is discussed within the frame of the macromolecular rate theory.
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Affiliation(s)
- Eva Dušeková
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia
| | - Martin Berta
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia
| | - Dagmar Sedláková
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia; Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Košice, Slovakia
| | - David Řeha
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31A, 37005 České Budějovice, Czech Republic
| | - Veronika Dzurillová
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia
| | - Anastasiia Shaposhnikova
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31A, 37005 České Budějovice, Czech Republic; Laboratory of Structural Biology and Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Zámek 136, 37333 Nové Hrady, Czech Republic
| | - Fatemeh Fadaei
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31A, 37005 České Budějovice, Czech Republic; Laboratory of Structural Biology and Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Zámek 136, 37333 Nové Hrady, Czech Republic
| | - Mária Tomková
- Centre for Interdisciplinary Biosciences, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia
| | - Babak Minofar
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31A, 37005 České Budějovice, Czech Republic.
| | - Erik Sedlák
- Centre for Interdisciplinary Biosciences, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia.
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Gregory KP, Elliott GR, Wanless EJ, Webber GB, Page AJ. A quantum chemical molecular dynamics repository of solvated ions. Sci Data 2022; 9:430. [PMID: 35864118 PMCID: PMC9304403 DOI: 10.1038/s41597-022-01527-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/30/2022] [Indexed: 12/29/2022] Open
Abstract
The importance of ion-solvent interactions in predicting specific ion effects in contexts ranging from viral activity through to electrolyte viscosity cannot be underestimated. Moreover, investigations of specific ion effects in nonaqueous systems, highly relevant to battery technologies, biochemical systems and colloid science, are severely limited by data deficiency. Here, we report IonSolvR – a collection of more than 3,000 distinct nanosecond-scale ab initio molecular dynamics simulations of ions in aqueous and non-aqueous solvent environments at varying effective concentrations. Density functional tight binding (DFTB) is used to detail the solvation structure of up to 55 solutes in 28 different protic and aprotic solvents. DFTB is a fast quantum chemical method, and as such enables us to bridge the gap between efficient computational scaling and maintaining accuracy, while using an internally-consistent simulation technique. We validate the database against experimental data and provide guidance for accessing individual IonSolvR records. Measurement(s) | solvation structure | Technology Type(s) | quantum chemistry computational method • Molecular Dynamics |
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Affiliation(s)
- Kasimir P Gregory
- Discipline of Chemistry, School of Environmental & Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia.,Department of Materials Physics, Research School of Physics, Australian National University, Canberra, ACT, 0200, Australia
| | - Gareth R Elliott
- Discipline of Chemistry, School of Environmental & Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Erica J Wanless
- Discipline of Chemistry, School of Environmental & Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Grant B Webber
- Discipline of Chemical Engineering, School of Engineering, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Alister J Page
- Discipline of Chemistry, School of Environmental & Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia.
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3
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Dušeková E, Garajová K, Yavaşer R, Tomková M, Sedláková D, Dzurillová V, Kulik N, Fadaei F, Shaposhnikova A, Minofar B, Sedlák E. Modulation of global stability, ligand binding and catalytic properties of trypsin by anions. Biophys Chem 2022; 288:106856. [PMID: 35872468 DOI: 10.1016/j.bpc.2022.106856] [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: 05/08/2022] [Revised: 07/02/2022] [Accepted: 07/13/2022] [Indexed: 12/01/2022]
Abstract
Specific salts effect is well-known on stability and solubility of proteins, however, relatively limited knowledge is known regarding the effect on catalytic properties of enzymes. Here, we examined the effect of four sodium anions on thermal stability and catalytic properties of trypsin and binding of the fluorescent probe, p-aminobenzamidine (PAB), to the enzyme. We show that the specific anions effect on trypsin properties agrees with the localization of the anions in the Hofmeister series. Thermal stability of trypsin, Tm, the affinity of the fluorescent probe to the binding site, Kd, and the rate constant, kcat, of trypsin-catalyzed hydrolysis of the substrate N-benzoyl-L-arginine ethyl ester (BAEE) increase with increasing kosmotropic character of anions in the order: perchlorate<bromide<chloride<sulfate, while the value of Michaelis constant, KM, decreases. Correlations between the values of Tm, Kd for PAB, kcat, and KM for BAEE in the presence of 1 M studied salts suggest interrelation among these parameters of the enzyme. Global stabilization as well as increased rigidity of trypsin is accompanied by strengthening of interaction with fluorescent probe PAB and in accordance with decreasing values of KM for the substrate BAEE. Strong correlations between parameters characterizing the trypsin properties with the charge densities of anions clearly indicate direct electrostatic interaction as a basis of the specific anion effect on the conformational and functional properties of the enzyme.
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Affiliation(s)
- Eva Dušeková
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia
| | - Katarína Garajová
- Department of Biochemistry, Faculty of Science, P. J. Šafárik University in Košice, Moyzesova 11, 04154 Košice, Slovakia
| | - Rukiye Yavaşer
- Department of Biochemistry, Faculty of Science, P. J. Šafárik University in Košice, Moyzesova 11, 04154 Košice, Slovakia; Chemistry Department, Faculty of Arts and Science, Aydın Adnan Menderes University, 09010 Aydın, Turkey
| | - Mária Tomková
- Center for Interdisciplinary Biosciences, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia
| | - Dagmar Sedláková
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Košice, Slovakia
| | - Veronika Dzurillová
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia
| | - Natalia Kulik
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31A, 37005 České Budějovice, Czech Republic
| | - Fatemeh Fadaei
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31A, 37005 České Budějovice, Czech Republic; Laboratory of Structural Biology and Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Zámek 136, 37333 Nové Hrady, Czech Republic
| | - Anastasiia Shaposhnikova
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31A, 37005 České Budějovice, Czech Republic; Laboratory of Structural Biology and Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Zámek 136, 37333 Nové Hrady, Czech Republic
| | - Babak Minofar
- Laboratory of Structural Biology and Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Zámek 136, 37333 Nové Hrady, Czech Republic.
| | - Erik Sedlák
- Center for Interdisciplinary Biosciences, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia.
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Gregory KP, Elliott GR, Robertson H, Kumar A, Wanless EJ, Webber GB, Craig VSJ, Andersson GG, Page AJ. Understanding specific ion effects and the Hofmeister series. Phys Chem Chem Phys 2022; 24:12682-12718. [PMID: 35543205 DOI: 10.1039/d2cp00847e] [Citation(s) in RCA: 87] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Specific ion effects (SIE), encompassing the Hofmeister Series, have been known for more than 130 years since Hofmeister and Lewith's foundational work. SIEs are ubiquitous and are observed across the medical, biological, chemical and industrial sciences. Nevertheless, no general predictive theory has yet been able to explain ion specificity across these fields; it remains impossible to predict when, how, and to what magnitude, a SIE will be observed. In part, this is due to the complexity of real systems in which ions, counterions, solvents and cosolutes all play varying roles, which give rise to anomalies and reversals in anticipated SIEs. Herein we review the historical explanations for SIE in water and the key ion properties that have been attributed to them. Systems where the Hofmeister series is perturbed or reversed are explored, as is the behaviour of ions at the liquid-vapour interface. We discuss SIEs in mixed electrolytes, nonaqueous solvents, and in highly concentrated electrolyte solutions - exciting frontiers in this field with particular relevance to biological and electrochemical applications. We conclude the perspective by summarising the challenges and opportunities facing this SIE research that highlight potential pathways towards a general predictive theory of SIE.
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Affiliation(s)
- Kasimir P Gregory
- Discipline of Chemistry, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales 2308, Australia. .,Department of Materials Physics, Research School of Physics, Australian National University, Canberra, ACT 0200, Australia
| | - Gareth R Elliott
- Discipline of Chemistry, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales 2308, Australia.
| | - Hayden Robertson
- Discipline of Chemistry, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales 2308, Australia.
| | - Anand Kumar
- Flinders Institute of Nanoscale Science and Technology, College of Science and Engineering, Flinders University, South Australia 5001, Australia
| | - Erica J Wanless
- Discipline of Chemistry, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales 2308, Australia.
| | - Grant B Webber
- School of Engineering, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Vincent S J Craig
- Department of Materials Physics, Research School of Physics, Australian National University, Canberra, ACT 0200, Australia
| | - Gunther G Andersson
- Flinders Institute of Nanoscale Science and Technology, College of Science and Engineering, Flinders University, South Australia 5001, Australia
| | - Alister J Page
- Discipline of Chemistry, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales 2308, Australia.
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5
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Enhanced activity and stability of protein-glutaminase by Hofmeister effects. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2021.112054] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Gregory KP, Wanless EJ, Webber GB, Craig VSJ, Page AJ. The electrostatic origins of specific ion effects: quantifying the Hofmeister series for anions. Chem Sci 2021; 12:15007-15015. [PMID: 34976339 PMCID: PMC8612401 DOI: 10.1039/d1sc03568a] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/15/2021] [Indexed: 12/23/2022] Open
Abstract
Life as we know it is dependent upon water, or more specifically salty water. Without dissolved ions, the interactions between biological molecules are insufficiently complex to support life. This complexity is intimately tied to the variation in properties induced by the presence of different ions. These specific ion effects, widely known as Hofmeister effects, have been known for more than 100 years. They are ubiquitous throughout the chemical, biological and physical sciences. The origin of these effects and their relative strengths is still hotly debated. Here we reconsider the origins of specific ion effects through the lens of Coulomb interactions and establish a foundation for anion effects in aqueous and non-aqueous environments. We show that, for anions, the Hofmeister series can be explained and quantified by consideration of site-specific electrostatic interactions. This can simply be approximated by the radial charge density of the anion, which we have calculated for commonly reported ions. This broadly quantifies previously unpredictable specific ion effects, including those known to influence solution properties, virus activities and reaction rates. Furthermore, in non-aqueous solvents, the relative magnitude of the anion series is dependent on the Lewis acidity of the solvent, as measured by the Gutmann Acceptor Number. Analogous SIEs for cations bear limited correlation with their radial charge density, highlighting a fundamental asymmetry in the origins of specific ion effects for anions and cations, due to competing non-Coulombic phenomena.
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Affiliation(s)
- Kasimir P Gregory
- Discipline of Chemistry, School of Environmental and Life Sciences, The University of Newcastle Callaghan New South Wales 2308 Australia
| | - Erica J Wanless
- Discipline of Chemistry, School of Environmental and Life Sciences, The University of Newcastle Callaghan New South Wales 2308 Australia
| | - Grant B Webber
- School of Engineering, The University of Newcastle Callaghan New South Wales 2308 Australia
| | - Vincent S J Craig
- Department of Applied Mathematics, Research School of Physics, Australian National University Canberra ACT 0200 Australia
| | - Alister J Page
- Discipline of Chemistry, School of Environmental and Life Sciences, The University of Newcastle Callaghan New South Wales 2308 Australia
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7
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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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8
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Xu H, Wang Q, Zhang Z, Yi L, Ma L, Zhai C. A simplified method to remove fusion tags from a xylanase of Bacillus sp. HBP8 with HRV 3C protease. Enzyme Microb Technol 2019; 123:15-20. [PMID: 30686346 DOI: 10.1016/j.enzmictec.2019.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 10/19/2018] [Accepted: 01/04/2019] [Indexed: 02/06/2023]
Abstract
Human rhinovirus 3C protease (HRV 3C protease) is commonly used as a tool to remove fusion tags from recombinant proteins in gene engineering due to its distinguished specificity and high activity at low temperature. This paper is aimed to simplify the strategy of removing epitope tags from target proteins with HRV 3C protease. Fusion proteins composed of a xylanase from Bacillus sp. HBP8 (xylHB) and double tags (MBP/Nus and 6×His, with an HRV 3C protease recognition site between them) were applied as substrates. To perform the cleavage and purification, strains expressing HRV 3C protease and the substrates were mixed before (co-fermentation method) or after (post-fermentation method) inducing with IPTG, followed by cell disruption and incubation at 4℃, overnight for cleavage. The soluble cytoplasmic fraction was added to Ni-NTA resin to recover the cleaved target protein. Because the process was carried out in the cell lysate, it was named as cell lysate purification system based on HRV 3C protease (CLP3C). Our data indicated small number of cells expressing HRV 3C protease was enough to remove the fusion tags efficiently with both co-fermentation and post-fermentation methods. More importantly, the tags were cleaved precisely with no obvious non-specific degradation to the target protein. Hence, active xylanase was recovered easily with this strategy.
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Affiliation(s)
- Hu Xu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, People's Republic of China; School of Chucai honors, Hubei University, Wuhan, People's Republic of China
| | - Qian Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, People's Republic of China; School of Chucai honors, Hubei University, Wuhan, People's Republic of China
| | - Zhiwei Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, People's Republic of China
| | - Li Yi
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, People's Republic of China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, People's Republic of China
| | - Chao Zhai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, People's Republic of China.
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9
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Bumbak F, Bathgate RAD, Scott DJ, Gooley PR. Expression and Purification of a Functional E. coli 13CH 3-Methionine-Labeled Thermostable Neurotensin Receptor 1 Variant for Solution NMR Studies. Methods Mol Biol 2019; 1947:31-55. [PMID: 30969410 DOI: 10.1007/978-1-4939-9121-1_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Escherichia coli (E. coli) is the most widely used expression host for recombinant proteins due to high expression yields and straightforward molecular cloning. Directed evolution of G protein-coupled receptors (GPCRs) has made several of these difficult to express membrane proteins amenable to prokaryotic expression. Here, we describe a protocol for near complete 13CH3-methionine labeling of a thermostable neurotensin receptor 1 (enNTS1) variant in E. coli for solution NMR-based dynamics studies. Our expression strategy utilizes methionine biosynthesis pathway inhibition forcing E. coli to incorporate exogenous methionine with 96% efficiency at expression levels of 2.6 mg enNTS1 per liter of expression culture containing 50 mg of 13CH3-methionine. We also provide a 3-step purification protocol that produces final yields of 0.6 mg of functional Apo-state enNTS1.
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Affiliation(s)
- Fabian Bumbak
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, Australia.,Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia.,The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Ross A D Bathgate
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, Australia.,The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Daniel J Scott
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, Australia.,The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Paul R Gooley
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, Australia. .,Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia.
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10
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Dušeková E, Garajová K, Yavaşer R, Varhač R, Sedlák E. Hofmeister effect on catalytic properties of chymotrypsin is substrate-dependent. Biophys Chem 2018; 243:8-16. [DOI: 10.1016/j.bpc.2018.10.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 09/30/2018] [Accepted: 10/09/2018] [Indexed: 12/26/2022]
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11
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Liu J, Cheng R, Wu H, Li S, Wang PG, DeGrado WF, Rozovsky S, Wang L. Building and Breaking Bonds via a Compact S-Propargyl-Cysteine to Chemically Control Enzymes and Modify Proteins. Angew Chem Int Ed Engl 2018; 57:12702-12706. [PMID: 30118570 PMCID: PMC6169525 DOI: 10.1002/anie.201806197] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/30/2018] [Indexed: 02/03/2023]
Abstract
Analogous to reversible post-translational protein modifications, the ability to attach and subsequently remove modifications on proteins would be valuable for protein and biological research. Although bioorthogonal functionalities have been developed to conjugate or cleave protein modifications, they are introduced into proteins on separate residues and often with bulky side chains, limiting their use to one type of control and primarily protein surface. Here we achieved dual control on one residue by genetically encoding S-propargyl-cysteine (SprC), which has bioorthogonal alkyne and propargyl groups in a compact structure, permitting usage in protein interior in addition to surface. We demonstrated its incorporation at the dimer interface of glutathione transferase for in vivo crosslinking via thiol-yne click chemistry, and at the active site of human rhinovirus 3C protease for masking and then turning on enzyme activity via Pd-cleavage of SprC into Cys. In addition, we installed biotin onto EGFP via Sonogashira coupling of SprC and then tracelessly removed it via Pd cleavage. SprC is small in size, commercially available, nontoxic, and allows for bond building and breaking on a single residue. Genetically encoded SprC will be valuable for chemically controlling proteins with an essential Cys and for reversible protein modifications.
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Affiliation(s)
- Jun Liu
- Dr. J. Liu, Dr. H. Wu, S. Li, Prof. W. F. DeGrado, and Prof. L. Wang University of California, San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA, 94158
| | - Rujin Cheng
- R. Cheng, and Prof. S. Rozovsky.University of Delaware, Department of Chemistry and Biochemistry, Newark, DE, 19716
| | - Haifan Wu
- Dr. J. Liu, Dr. H. Wu, S. Li, Prof. W. F. DeGrado, and Prof. L. Wang University of California, San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA, 94158
| | - Shanshan Li
- Dr. J. Liu, Dr. H. Wu, S. Li, Prof. W. F. DeGrado, and Prof. L. Wang University of California, San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA, 94158
- S. Li, Prof. P.G. Wang Department of Chemistry and Center for Therapeutics and Diagnostics, Georgia State University, Atlanta, Georgia 30302
| | - Peng G. Wang
- S. Li, Prof. P.G. Wang Department of Chemistry and Center for Therapeutics and Diagnostics, Georgia State University, Atlanta, Georgia 30302
| | - William F. DeGrado
- Dr. J. Liu, Dr. H. Wu, S. Li, Prof. W. F. DeGrado, and Prof. L. Wang University of California, San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA, 94158
| | - Sharon Rozovsky
- R. Cheng, and Prof. S. Rozovsky.University of Delaware, Department of Chemistry and Biochemistry, Newark, DE, 19716
| | - Lei Wang
- Dr. J. Liu, Dr. H. Wu, S. Li, Prof. W. F. DeGrado, and Prof. L. Wang University of California, San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA, 94158
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12
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Roed NK, Viola CM, Kristensen O, Schluckebier G, Norrman M, Sajid W, Wade JD, Andersen AS, Kristensen C, Ganderton TR, Turkenburg JP, De Meyts P, Brzozowski AM. Structures of insect Imp-L2 suggest an alternative strategy for regulating the bioavailability of insulin-like hormones. Nat Commun 2018; 9:3860. [PMID: 30242155 PMCID: PMC6155051 DOI: 10.1038/s41467-018-06192-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 08/16/2018] [Indexed: 12/30/2022] Open
Abstract
The insulin/insulin-like growth factor signalling axis is an evolutionary ancient and highly conserved hormonal system involved in the regulation of metabolism, growth and lifespan in animals. Human insulin is stored in the pancreas, while insulin-like growth factor-1 (IGF-1) is maintained in blood in complexes with IGF-binding proteins (IGFBP1-6). Insect insulin-like polypeptide binding proteins (IBPs) have been considered as IGFBP-like structural and functional homologues. Here, we report structures of the Drosophila IBP Imp-L2 in its free form and bound to Drosophila insulin-like peptide 5 and human IGF-1. Imp-L2 contains two immunoglobulin-like fold domains and its architecture is unrelated to human IGFBPs, suggesting a distinct strategy for bioavailability regulation of insulin-like hormones. Similar hormone binding modes may exist in other insect vectors, as the IBP sequences are highly conserved. Therefore, these findings may open research routes towards a rational interference of transmission of diseases such as malaria, dengue and yellow fevers.
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Affiliation(s)
| | - Cristina M Viola
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York, YO10 5DD, UK
| | - Ole Kristensen
- Department of Drug Design and Pharmacology, University of Copenhagen, DK-2100, Copenhagen Ø, Denmark
| | - Gerd Schluckebier
- Global Research, Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Maaloev, Denmark
| | - Mathias Norrman
- Global Research, Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Maaloev, Denmark
| | - Waseem Sajid
- Global Research, Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Maaloev, Denmark
| | - John D Wade
- Florey Institute of Neuroscience & Mental Health, University of Melbourne, Parkville, VIC, 3010, Australia
- School of Chemistry, University of Melbourne, Parkville, VIC, 3010, Australia
| | | | - Claus Kristensen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2100, Copenhagen N, Denmark
| | - Timothy R Ganderton
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York, YO10 5DD, UK
| | - Johan P Turkenburg
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York, YO10 5DD, UK
| | - Pierre De Meyts
- Global Research, Novo Nordisk A/S, Novo Nordisk Park 1, 2760, Maaloev, Denmark
- Department of Cell Signalling, de Duve Institute, B-1200, Brussels, Belgium
| | - Andrzej M Brzozowski
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York, YO10 5DD, UK.
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13
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Liu J, Cheng R, Wu H, Li S, Wang PG, DeGrado WF, Rozovsky S, Wang L. Building and Breaking Bonds via a Compact S‐Propargyl‐Cysteine to Chemically Control Enzymes and Modify Proteins. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jun Liu
- University of California, San Francisco Department of Pharmaceutical Chemistry San Francisco CA 94158 USA
| | - Rujin Cheng
- University of Delaware Department of Chemistry and Biochemistry Newark DE 19716 USA
| | - Haifan Wu
- University of California, San Francisco Department of Pharmaceutical Chemistry San Francisco CA 94158 USA
| | - Shanshan Li
- University of California, San Francisco Department of Pharmaceutical Chemistry San Francisco CA 94158 USA
- Department of Chemistry and Center for Therapeutics and Diagnostics Georgia State University Atlanta GA 30302 USA
| | - Peng G. Wang
- Department of Chemistry and Center for Therapeutics and Diagnostics Georgia State University Atlanta GA 30302 USA
| | - William F. DeGrado
- University of California, San Francisco Department of Pharmaceutical Chemistry San Francisco CA 94158 USA
| | - Sharon Rozovsky
- University of Delaware Department of Chemistry and Biochemistry Newark DE 19716 USA
| | - Lei Wang
- University of California, San Francisco Department of Pharmaceutical Chemistry San Francisco CA 94158 USA
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14
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Garajová K, Balogová A, Dušeková E, Sedláková D, Sedlák E, Varhač R. Correlation of lysozyme activity and stability in the presence of Hofmeister series anions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:281-288. [DOI: 10.1016/j.bbapap.2016.11.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/01/2016] [Accepted: 11/28/2016] [Indexed: 01/01/2023]
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15
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Ullah R, Shah MA, Tufail S, Ismat F, Imran M, Iqbal M, Mirza O, Rhaman M. Activity of the Human Rhinovirus 3C Protease Studied in Various Buffers, Additives and Detergents Solutions for Recombinant Protein Production. PLoS One 2016; 11:e0153436. [PMID: 27093053 PMCID: PMC4836831 DOI: 10.1371/journal.pone.0153436] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 03/29/2016] [Indexed: 11/18/2022] Open
Abstract
Proteases are widely used to remove affinity and solubility tags from recombinant proteins to avoid potential interference of these tags with the structure and function of the fusion partner. In recent years, great interest has been seen in use of the human rhinovirus 3C protease owing to its stringent sequence specificity and enhanced activity. Like other proteases, activity of the human rhinovirus 3C protease can be affected in part by the buffer components and additives that are generally employed for purification and stabilization of proteins, hence, necessitate their removal by tedious and time-consuming procedures before proteolysis can occur. To address this issue, we examined the effect of elution buffers used for common affinity based purifications, salt ions, stability/solubility and reducing agents, and detergents on the activity of the human rhinovirus 3C protease using three different fusion proteins at 4°C, a temperature of choice for purification of many proteins. The results show that the human rhinovirus 3C protease performs better at 4°C than the frequently used tobacco etch virus protease and its activity was insensitive to most of the experimental conditions tested. Though number of fusion proteins tested is limited, we expect that these finding will facilitate the use of the human rhinovirus 3C protease in recombinant protein production for pharmaceutical and biotechnological applications.
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Affiliation(s)
- Raheem Ullah
- Drug Discovery and Structural Biology group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, P.O. Nilore, Islamabad, Pakistan
| | - Majid Ali Shah
- Drug Discovery and Structural Biology group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, P.O. Nilore, Islamabad, Pakistan
| | - Soban Tufail
- Drug Discovery and Structural Biology group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Fouzia Ismat
- Drug Discovery and Structural Biology group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Muhammad Imran
- Drug Discovery and Structural Biology group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Mazhar Iqbal
- Drug Discovery and Structural Biology group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, P.O. Nilore, Islamabad, Pakistan
| | - Osman Mirza
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Moazur Rhaman
- Drug Discovery and Structural Biology group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, P.O. Nilore, Islamabad, Pakistan
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16
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An overview of enzymatic reagents for the removal of affinity tags. Protein Expr Purif 2011; 80:283-93. [PMID: 21871965 PMCID: PMC3195948 DOI: 10.1016/j.pep.2011.08.005] [Citation(s) in RCA: 251] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 08/04/2011] [Accepted: 08/05/2011] [Indexed: 11/20/2022]
Abstract
Although they are often exploited to facilitate the expression and purification of recombinant proteins, every affinity tag, whether large or small, has the potential to interfere with the structure and function of its fusion partner. For this reason, reliable methods for removing affinity tags are needed. Only enzymes have the requisite specificity to be generally useful reagents for this purpose. In this review, the advantages and disadvantages of some commonly used endo- and exoproteases are discussed in light of the latest information.
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17
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Gouvea IE, Santos JAN, Burlandy FM, Tersariol ILS, da Silva EE, Juliano MA, Juliano L, Cunha RLOR. Poliovirus 3C proteinase inhibition by organotelluranes. Biol Chem 2011; 392:587-91. [PMID: 21521074 DOI: 10.1515/bc.2011.059] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
The 3C proteinase, essential for human poliovirus (PV) replication, has unique characteristics as its three-dimensional structure resembles chymotrypsin, but its catalytic nucleophile is a cysteine SH group rather than the OH group of serine. Here, we describe the use of tellurium compounds as inhibitors of PV3C proteinase. A rapid, stoichiometric and covalent inactivation of PV3C was observed with both a chloro-telluroxetane and a bis-vinylic organotellurane. These compounds also inhibit human cathepsins B, L, S, and K with second order rate constants higher than those obtained for PV3C. Chloro-telluroxetane inhibits replication of PV in human embryonic rhabdomyosarcoma cells in the low micromolar range and below the toxic level for the host cells. Bis-vinylic organotellurane is more effective as antiviral agent but reduces the cell viability by 20% at 10 μm, a concentration almost completely inhibiting virus growth. This is the first description of inhibition of viral 3C proteinase with antiviral property by this class of compounds.
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Affiliation(s)
- Iuri E Gouvea
- Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio,100, São Paulo, SP 04044-020, Brazil
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18
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Okamoto DN, Oliveira LC, Kondo MY, Cezari MH, Szeltner Z, Juhász T, Juliano MA, Polgár L, Juliano L, Gouvea IE. Increase of SARS-CoV 3CL peptidase activity due to macromolecular crowding effects in the milieu composition. Biol Chem 2010; 391:1461-8. [DOI: 10.1515/bc.2010.145] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The 3C-like peptidase of the severe acute respiratory syndrome virus (SARS-CoV) is strictly required for viral replication, thus being a potential target for the development of antiviral agents. In contrast to monomeric picornavirus 3C peptidases, SARS-CoV 3CLpro exists in equilibrium between the monomer and dimer forms in solution, and only the dimer is proteolytically active in dilute buffer solutions. In this study, the increase of SARS-CoV 3CLpro peptidase activity in presence of kosmotropic salts and crowding agents is described. The activation followed the Hofmeister series of anions, with two orders of magnitude enhancement in the presence of Na2SO4, whereas the crowding agents polyethylene glycol and bovine serum albumin increased the hydrolytic rate up to 3 times. Kinetic determinations of the monomer dimer dissociation constant (K
d) indicated that activation was a result of a more active dimer, without significant changes in K
d values. The activation was found to be independent of substrate length and was derived from both k
cat increase and K
m decrease. The viral peptidase activation described here could be related to the crowded intracellular environment and indicates a further fine-tuning mechanism for biological control, particularly in the microenvironment of the vesicles that are induced in host cells during positive strand RNA virus infection.
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19
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Okamoto DN, Kondo MY, Santos JA, Nakajima S, Hiraga K, Oda K, Juliano MA, Juliano L, Gouvea IE. Kinetic analysis of salting activation of a subtilisin-like halophilic protease. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:367-73. [DOI: 10.1016/j.bbapap.2008.10.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Revised: 10/13/2008] [Accepted: 10/23/2008] [Indexed: 10/21/2022]
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20
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Jaulent AM, Fahy AS, Knox SR, Birtley JR, Roqué-Rosell N, Curry S, Leatherbarrow RJ. A continuous assay for foot-and-mouth disease virus 3C protease activity. Anal Biochem 2007; 368:130-7. [PMID: 17631855 DOI: 10.1016/j.ab.2007.05.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2007] [Revised: 05/22/2007] [Accepted: 05/29/2007] [Indexed: 11/29/2022]
Abstract
Foot-and-mouth disease virus is a highly contagious pathogen that spreads rapidly among livestock and is capable of causing widespread agricultural and economic devastation. The virus genome is translated to produce a single polypeptide chain that subsequently is cleaved by viral proteases into mature protein products, with one protease, 3C(pro), carrying out the majority of the cleavages. The highly conserved nature of this protease across different viral strains and its crucial role in viral maturation and replication make it a very desirable target for inhibitor design. However, the lack of a convenient and high-throughput assay has been a hindrance in the characterization of potential inhibitors. In this article, we report the development of a continuous assay with potential for high throughput using fluorescence resonance energy transfer-based peptide substrates. Several peptide substrates containing the 3C-specific cleavage site were synthesized, varying both the positions and separation of the fluorescent donor and quencher groups. The best substrate, with a specificity constant k(cat)/K(M) of 57.6+/-2.0M(-1) s(-1), was used in inhibition assays to further characterize the protease's activity against a range of commercially available inhibitors. The inhibition profile of the enzyme showed characteristics of both cysteine and serine proteases, with the chymotrypsin inhibitor TPCK giving stoichiometric inhibition of the enzyme and allowing active site titration of the 3C(pro).
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Affiliation(s)
- Agnès M Jaulent
- Department of Chemistry, Imperial College, South Kensington Campus, London SW7 2AZ, UK
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21
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Greaves R, Warwicker J. Active site identification through geometry-based and sequence profile-based calculations: burial of catalytic clefts. J Mol Biol 2005; 349:547-57. [PMID: 15882869 DOI: 10.1016/j.jmb.2005.04.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2005] [Revised: 03/30/2005] [Accepted: 04/08/2005] [Indexed: 12/30/2022]
Abstract
Electrostatics calculations with proteins that are uniformly charged over volume can aid enzyme/non-enzyme discrimination. For known enzymes, such methods locate active sites to within 5% on the enzyme surface, in 77% of a test set. We now report that removing the dielectric boundary improves active site location to 80%, with optimal discrimination between enzymes and non-enzymes of around 80% specificity and 80% sensitivity. This calculation quantifies burial of solvent-accessible regions. Many of the true enzymes incorrectly assigned as non-enzymes have active sites at subunit boundaries. These are missed in monomer-based calculations. Catalytic and non-catalytic antibodies are studied in this context of active/binding site burial. Whilst catalytic antibodies, on average, have marginally higher active site burial than non-catalytic antibodies, these values are generally smaller than for non-antibody enzymes, possibly contributing to their relatively low turnover. Prediction of active site location improves further when sequence profile-based weights replace the uniform charge distribution, so that a combination of burial and amino acid conservation is assessed. Accuracy rises to 93% of active sites to within 5%, in the test set, for the optimal profile weights scheme. The equivalent value in a separate validation set is 89% to within 5%. Enzyme/non-enzyme and enzyme functional site predictions are made for structural genomics proteins, suggesting that a substantial majority of these are non-enzymes.
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Affiliation(s)
- Richard Greaves
- Faculty of Life Sciences, Jackson's Mill, University of Manchester, P.O. Box 88, Sackville Street, Manchester M60 1QD, UK
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22
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Affiliation(s)
- Liang Tong
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA.
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23
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Wang QM, Peery RB, Johnson RB, Alborn WE, Yeh WK, Skatrud PL. Identification and characterization of a monofunctional glycosyltransferase from Staphylococcus aureus. J Bacteriol 2001; 183:4779-85. [PMID: 11466281 PMCID: PMC99532 DOI: 10.1128/jb.183.16.4779-4785.2001] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A gene (mgt) encoding a monofunctional glycosyltransferase (MGT) from Staphylococcus aureus has been identified. This first reported gram-positive MGT shared significant homology with several MGTs from gram-negative bacteria and the N-terminal glycosyltransferase domain of class A high-molecular-mass penicillin-binding proteins from different species. S. aureus MGT contained an N-terminal hydrophobic domain perhaps involved with membrane association. It was expressed in Escherichia coli cells as a truncated protein lacking the hydrophobic domain and purified to homogeneity. Analysis by circular dichroism revealed that secondary structural elements of purified truncated S. aureus MGT were consistent with predicted structural elements, indicating that the protein might exhibit the expected folding. In addition, purified S. aureus MGT catalyzed incorporation of UDP-N-acetylglucosamine into peptidoglycan, proving that it was enzymatically active. MGT activity was inhibited by moenomycin A, and the reaction product was sensitive to lysozyme treatment. Moreover, a protein matching the calculated molecular weight of S. aureus MGT was identified from an S. aureus cell lysate using antibodies developed against purified MGT. Taken together, our results suggest that this enzyme is natively present in S. aureus cells and that it may play a role in bacterial cell wall biosynthesis.
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Affiliation(s)
- Q M Wang
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, USA.
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