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Wang J, Lu X, Zhuge B, Zong H. Enhancing the catalytic efficiency of M32 carboxypeptidase by semi-rational design and its applications in food taste improvement. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:7375-7385. [PMID: 38666395 DOI: 10.1002/jsfa.13558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/02/2024] [Accepted: 04/26/2024] [Indexed: 05/09/2024]
Abstract
BACKGROUND Carboxypeptidase is an exopeptidase that hydrolyzes amino acids at the C-terminal end of the peptide chain and has a wide range of applications in food. However, in industrial applications, the relatively low catalytic efficiency of carboxypeptidases is one of the main limiting factors for industrialization. RESULTS The study has enhanced the catalytic efficiency of Bacillus megaterium M32 carboxypeptidase (BmeCPM32) through semi-rational design. Firstly, the specific activity of the optimal mutant, BmeCPM32-M2, obtained through single-site mutagenesis and combinatorial mutagenesis, was 2.2-fold higher than that of the wild type (187.9 versus 417.8 U mg-1), and the catalytic efficiency was 2.9-fold higher (110.14 versus 325.75 s-1 mmol-1). Secondly, compared to the wild type, BmeCPM32-M2 exhibited a 1.8-fold increase in half-life at 60 °C, with no significant changes in its enzymatic properties (optimal pH, optimal temperature). Finally, BmeCPM32-M2 significantly increased the umami intensity of soy protein isolate hydrolysate by 55% and reduced bitterness by 83%, indicating its potential in developing tasty protein components. CONCLUSION Our research has revealed that the strategy based on protein sequence evolution and computational residue mutation energy led to an improved catalytic efficiency of BmeCPM32. Molecular dynamics simulations have revealed that a smaller substrate binding pocket and increased enzyme-substrate affinity are the reasons for the enhanced catalytic efficiency. Furthermore the number of hydrogen bonds and solvent and surface area may contribute to the improvement of thermostability. Finally, the de-bittering effect of BmeCPM32-M2 in soy protein isolate hydrolysate suggests its potential in developing palatable protein components. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Jinjiang Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xinyao Lu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Bin Zhuge
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Hong Zong
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
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Naeemi SM, Aminzadeh S, Sari S, Nemati F, Naseroleslami M. In vitro and in silico characterization of a novel glutamate carboxypeptidase from Cohnella sp. A01. Biochimie 2023; 207:83-95. [PMID: 36493965 DOI: 10.1016/j.biochi.2022.12.003] [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: 03/02/2022] [Revised: 10/25/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
Glutamate carboxypeptidase is a bacterial enzyme of metallopeptidase superfamily. This enzyme is an exo-peptidase that catalyzes the hydrolysis of glutamate residues at the C-terminus of folic acid. The rCP302 is a novel zinc ion-dependent recombinant glutamate carboxypeptidase derived from a thermophilic bacterium, Cohnella sp. A01 (PTCC No: 1921). By simulating the structure of rCP302, analyzing its activity in various environmental settings, and contrasting it with that of related enzymes, we wanted to evaluate the heterologous production, purification, and characterization of this enzyme. The bioinformatics study showed that rCP302 had maximum similarity to M20 family of metallopeptidases. The purified rCP302 molecular weight was about 41.6 kDa. The optimum temperature and pH for the catalytic activity of rCP302 were 50 °C and 7.2, respectively. Fluorescence spectroscopy data elucidated the secondary structure of rCP302 and determined conformational changes caused by alterations in ambient conditions. Using folate as a substrate, Km and specific activity values were calculated as 0.108 μM and 687 μmol/min/mg, respectively. The enzyme activity was strongly inhibited when EDTA sequestered zinc ions. The half-life of this enzyme at 30 °C was 2012 min. Regarding the ability of rCP302 to degrade folic acid, and its long half-life at 37 °C, the normal temperature of many mammals, this enzyme can be introduced for further study for use in the pharmaceutical industry.
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Affiliation(s)
- Seyed Mahdi Naeemi
- Department of Molecular and Cellular Sciences, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Saeed Aminzadeh
- Bioprocess Engineering Group, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
| | - Soyar Sari
- Department of Molecular and Cellular Sciences, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Fahimeh Nemati
- Department of Biotechnoligy, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Maryam Naseroleslami
- Department of Molecular and Cellular Sciences, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
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Probing the Conformational States of Thimet Oligopeptidase in Solution. Int J Mol Sci 2022; 23:ijms23137297. [PMID: 35806299 PMCID: PMC9266445 DOI: 10.3390/ijms23137297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 02/06/2023] Open
Abstract
Thimet oligopeptidase (TOP) is a metallopeptidase involved in the metabolism of oligopeptides inside and outside cells of various tissues. It has been proposed that substrate or inhibitor binding in the TOP active site induces a large hinge-bending movement leading to a closed structure, in which the bound ligand is enclosed. The main goal of the present work was to study this conformational change, and fluorescence techniques were used. Four active TOP mutants were created, each equipped with a single-Trp residue (fluorescence donor) and a p-nitro-phenylalanine (pNF) residue as fluorescence acceptor at opposite sides of the active site. pNF was biosynthetically incorporated with high efficiency using the amber codon suppression technology. Inhibitor binding induced shorter Donor-Acceptor (D-A) distances in all mutants, supporting the view that a hinge-like movement is operative in TOP. The activity of TOP is known to be dependent on the ionic strength of the assay buffer and D-A distances were measured at different ionic strengths. Interestingly, a correlation between the D-A distance and the catalytic activity of TOP was observed: the highest activities corresponded to the shortest D-A distances. In this study for the first time the hinge-bending motion of a metallopeptidase in solution could be studied, yielding insight about the position of the equilibrium between the open and closed conformation. This information will contribute to a more detailed understanding of the mode of action of these enzymes, including therapeutic targets like neurolysin and angiotensin-converting enzyme 2 (ACE2).
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Fernandes GC, Sierra EGM, Brear P, Pereira MR, Lemos EGM. From Data Mining of Chitinophaga sp. Genome to Enzyme Discovery of a Hyperthermophilic Metallocarboxypeptidase. Microorganisms 2021; 9:393. [PMID: 33673011 PMCID: PMC7918520 DOI: 10.3390/microorganisms9020393] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 02/09/2021] [Accepted: 02/11/2021] [Indexed: 01/24/2023] Open
Abstract
For several centuries, microorganisms and enzymes have been used for many different applications. Although many enzymes with industrial applications have already been reported, different screening technologies, methods and approaches are constantly being developed in order to allow the identification of enzymes with even more interesting applications. In our work, we have performed data mining on the Chitinophaga sp. genome, a gram-negative bacterium isolated from a bacterial consortium of sugarcane bagasse isolated from an ethanol plant. The analysis of 8 Mb allowed the identification of the chtcp gene, previously annotated as putative Cht4039. The corresponding codified enzyme, denominated as ChtCP, showed the HEXXH conserved motif of family M32 from thermostable carboxypeptidases. After expression in E. coli, the recombinant enzyme was characterized biochemically. ChtCP showed the highest activity versus benziloxicarbonil Ala-Trp at pH 7.5, suggesting a preference for hydrophobic substrates. Surprisingly, the highest activity of ChtCP observed was between 55 °C and 75 °C, and 62% activity was still displayed at 100 °C. We observed that Ca2+, Ba2+, Mn2+ and Mg2+ ions had a positive effect on the activity of ChtCP, and an increase of 30 °C in the melting temperature was observed in the presence of Co2+. These features together with the structure of ChtCP at 1.2 Å highlight the relevance of ChtCP for further biotechnological applications.
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Affiliation(s)
- Gabriela Cabral Fernandes
- Department of Technology, São Paulo State University (UNESP), Jaboticabal, São Paulo State 14884-900, Brazil; (G.C.F.); (E.G.M.S.)
- Graduate Program in Agricultural and Livestock Microbiology, São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Jaboticabal, São Paulo State 14884-900, Brazil
| | - Elwi Guillermo Machado Sierra
- Department of Technology, São Paulo State University (UNESP), Jaboticabal, São Paulo State 14884-900, Brazil; (G.C.F.); (E.G.M.S.)
- Laboratorio de Investigación en Microbiología, Facultad de Ciencias Básicas y Biomédicas, Universidad Simón Bolívar, Barranquilla 080002, Colombia
| | - Paul Brear
- Department of Biochemistry, University of Cambridge, Cambridge CB21GA, UK;
| | - Mariana Rangel Pereira
- Department of Biochemistry, University of Cambridge, Cambridge CB21GA, UK;
- CAPES Foundation, Ministry of Education of Brazil, Brasília-DF 70.040-02, Brazil
| | - Eliana G. M. Lemos
- Department of Technology, São Paulo State University (UNESP), Jaboticabal, São Paulo State 14884-900, Brazil; (G.C.F.); (E.G.M.S.)
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Salas-Sarduy E, Landaburu LU, Carmona AK, Cazzulo JJ, Agüero F, Alvarez VE, Niemirowicz GT. Potent and selective inhibitors for M32 metallocarboxypeptidases identified from high-throughput screening of anti-kinetoplastid chemical boxes. PLoS Negl Trop Dis 2019; 13:e0007560. [PMID: 31329594 PMCID: PMC6675120 DOI: 10.1371/journal.pntd.0007560] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 08/01/2019] [Accepted: 06/18/2019] [Indexed: 11/18/2022] Open
Abstract
Enzymes of the M32 family are Zn-dependent metallocarboxypeptidases (MCPs) widely distributed among prokaryotic organisms and just a few eukaryotes including Trypanosoma brucei and Trypanosoma cruzi, the causative agents of sleeping sickness and Chagas disease, respectively. These enzymes are absent in humans and several functions have been proposed for trypanosomatid M32 MCPs. However, no synthetic inhibitors have been reported so far for these enzymes. Here, we present the identification of a set of inhibitors for TcMCP-1 and TbMCP-1 (two trypanosomatid M32 enzymes sharing 71% protein sequence identity) from the GlaxoSmithKline HAT and CHAGAS chemical boxes; two collections grouping 404 compounds with high antiparasitic potency, drug-likeness, structural diversity and scientific novelty. For this purpose, we adapted continuous fluorescent enzymatic assays to a medium-throughput format and carried out the screening of both collections, followed by the construction of dose-response curves for the most promising hits. As a result, 30 micromolar-range inhibitors were discovered for one or both enzymes. The best hit, TCMDC-143620, showed sub-micromolar affinity for TcMCP-1, inhibited TbMCP-1 in the low micromolar range and was inactive against angiotensin I-converting enzyme (ACE), a potential mammalian off-target structurally related to M32 MCPs. This is the first inhibitor reported for this family of MCPs and considering its potency and specificity, TCMDC-143620 seems to be a promissory starting point to develop more specific and potent chemical tools targeting M32 MCPs from trypanosomatid parasites.
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Affiliation(s)
- Emir Salas-Sarduy
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo Ugalde”–Universidad Nacional de San Martín–CONICET, San Martín, B1650HMP, Buenos Aires, Argentina
| | - Lionel Urán Landaburu
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo Ugalde”–Universidad Nacional de San Martín–CONICET, San Martín, B1650HMP, Buenos Aires, Argentina
| | - Adriana K. Carmona
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Juan José Cazzulo
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo Ugalde”–Universidad Nacional de San Martín–CONICET, San Martín, B1650HMP, Buenos Aires, Argentina
| | - Fernán Agüero
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo Ugalde”–Universidad Nacional de San Martín–CONICET, San Martín, B1650HMP, Buenos Aires, Argentina
| | - Vanina E. Alvarez
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo Ugalde”–Universidad Nacional de San Martín–CONICET, San Martín, B1650HMP, Buenos Aires, Argentina
| | - Gabriela T. Niemirowicz
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo Ugalde”–Universidad Nacional de San Martín–CONICET, San Martín, B1650HMP, Buenos Aires, Argentina
- * E-mail:
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Frasch AP, Bouvier LA, Oppenheimer FM, Juliano MA, Juliano L, Carmona AK, Cazzulo JJ, Niemirowicz GT. Substrate specificity profiling of M32 metallocarboxypeptidases from Trypanosoma cruzi and Trypanosoma brucei. Mol Biochem Parasitol 2018; 219:10-16. [DOI: 10.1016/j.molbiopara.2017.12.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 12/04/2017] [Accepted: 12/11/2017] [Indexed: 12/01/2022]
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Sharma B, Jamdar SN, Ghosh B, Yadav P, Kumar A, Kundu S, Goyal VD, Makde RD. Active site gate of M32 carboxypeptidases illuminated by crystal structure and molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1406-1415. [PMID: 28844748 DOI: 10.1016/j.bbapap.2017.07.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 07/21/2017] [Accepted: 07/24/2017] [Indexed: 01/09/2023]
Abstract
Enzyme gates are important dynamic features that regulate function. Study of these features is critical for understanding of enzyme mechanism. In this study, the active-site gate of M32 carboxypeptidases (M32CP) is illuminated. Only a handful of members of this family have been structurally and functionally characterized and various aspects of their activity and mechanism are yet not clarified. Here, crystal structure of putative M32CP from Deinococcus radiodurans (M32dr) was solved to 2.4Å resolution. Enzymatic assays confirmed its identity as a carboxypeptidase. Open and relatively closed conformations observed in the structure provided supporting evidence for previously hypothesized hinge motion in this family of enzymes. Molecular dynamics simulations of 1.5μs displayed distinct open and closed conformations revealing amplitude of the motion to be beyond what was observed in the crystal structure. Hinge region and anchoring region of this shell-type gate were identified. A small displacement of 3Å and a helical tilt of 9° propagated by the hinge region translates into a 10Å motion at the top of the gate. The dynamics of the gate was supported by our mutagenesis experiment involving formation of disulphide bond across helices of the gate. The nearly inactive mutant enzyme showed 65-fold increase in the enzymatic activity in presence of reducing agent. Further, while a previously proposed structural basis would have led to its classification in subfamily II, experimentally observed substrate length restriction places M32dr in subfamily I of M32CPs.
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Affiliation(s)
- Bhaskar Sharma
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India; Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Sahayog N Jamdar
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Biplab Ghosh
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Pooja Yadav
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Ashwani Kumar
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Venuka Durani Goyal
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India.
| | - Ravindra D Makde
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India.
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