1
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Poddar S, Yu J. Angiotensin-Converting Enzyme and Renin-Inhibitory Activities of Protein Hydrolysates Produced by Alcalase Hydrolysis of Peanut Protein. Int J Mol Sci 2024; 25:7463. [PMID: 39000571 PMCID: PMC11242875 DOI: 10.3390/ijms25137463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 07/16/2024] Open
Abstract
Hypertension is a major controllable risk factor associated with cardiovascular disease (CVD) and overall mortality worldwide. Most people with hypertension must take medications that are effective in blood pressure management but cause many side effects. Thus, it is important to explore safer antihypertensive alternatives to regulate blood pressure. In this study, peanut protein concentrate (PPC) was hydrolyzed with 3-5% Alcalase for 3-10 h. The in vitro angiotensin-converting enzyme (ACE) and renin-inhibitory activities of the resulting peanut protein hydrolysate (PPH) samples and their fractions of different molecular weight ranges were determined as two measures of their antihypertensive potentials. The results show that the crude PPH produced at 4% Alcalase for 6 h of hydrolysis had the highest ACE-inhibitory activity with IC50 being 5.45 mg/mL. The PPH samples produced with 3-5% Alcalase hydrolysis for 6-8 h also displayed substantial renin-inhibitory activities, which is a great advantage over the animal protein-derived bioactive peptides or hydrolysate. Remarkably higher ACE- and renin-inhibitory activities were observed in fractions smaller than 5 kDa with IC50 being 0.85 and 1.78 mg/mL. Hence, the PPH and its small molecular fraction produced under proper Alcalase hydrolysis conditions have great potential to serve as a cost-effective anti-hypertensive ingredient for blood pressure management.
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Affiliation(s)
- Sukanya Poddar
- Food and Nutritional Sciences Program, Department of Family and Consumer Sciences, North Carolina Agricultural and Technical State University, Greensboro, NC 27411, USA
| | - Jianmei Yu
- Food and Nutritional Sciences Program, Department of Family and Consumer Sciences, North Carolina Agricultural and Technical State University, Greensboro, NC 27411, USA
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2
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Guicherd M, Ben Khaled M, Guéroult M, Nomme J, Dalibey M, Grimaud F, Alvarez P, Kamionka E, Gavalda S, Noël M, Vuillemin M, Amillastre E, Labourdette D, Cioci G, Tournier V, Kitpreechavanich V, Dubois P, André I, Duquesne S, Marty A. An engineered enzyme embedded into PLA to make self-biodegradable plastic. Nature 2024; 631:884-890. [PMID: 39020178 DOI: 10.1038/s41586-024-07709-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/12/2024] [Indexed: 07/19/2024]
Abstract
Plastic production reached 400 million tons in 2022 (ref. 1), with packaging and single-use plastics accounting for a substantial amount of this2. The resulting waste ends up in landfills, incineration or the environment, contributing to environmental pollution3. Shifting to biodegradable and compostable plastics is increasingly being considered as an efficient waste-management alternative4. Although polylactide (PLA) is the most widely used biosourced polymer5, its biodegradation rate under home-compost and soil conditions remains low6-8. Here we present a PLA-based plastic in which an optimized enzyme is embedded to ensure rapid biodegradation and compostability at room temperature, using a scalable industrial process. First, an 80-fold activity enhancement was achieved through structure-based rational engineering of a new hyperthermostable PLA hydrolase. Second, the enzyme was uniformly dispersed within the PLA matrix by means of a masterbatch-based melt extrusion process. The liquid enzyme formulation was incorporated in polycaprolactone, a low-melting-temperature polymer, through melt extrusion at 70 °C, forming an 'enzymated' polycaprolactone masterbatch. Masterbatch pellets were integrated into PLA by melt extrusion at 160 °C, producing an enzymated PLA film (0.02% w/w enzyme) that fully disintegrated under home-compost conditions within 20-24 weeks, meeting home-composting standards. The mechanical and degradation properties of the enzymated film were compatible with industrial packaging applications, and they remained intact during long-term storage. This innovative material not only opens new avenues for composters and biomethane production but also provides a feasible industrial solution for PLA degradation.
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Affiliation(s)
- M Guicherd
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- Carbios, Clermont-Ferrand, France
| | - M Ben Khaled
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - M Guéroult
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- Carbios, Clermont-Ferrand, France
| | - J Nomme
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | | | | | - P Alvarez
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - E Kamionka
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - S Gavalda
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- Carbios, Clermont-Ferrand, France
| | - M Noël
- Carbiolice, Clermont-Ferrand, France
| | - M Vuillemin
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - E Amillastre
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - D Labourdette
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - G Cioci
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | | | - V Kitpreechavanich
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - P Dubois
- Center of Innovation and Research in Materials & Polymers, University of Mons, Mons, Belgium
| | - I André
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - S Duquesne
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - A Marty
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
- Carbios, Clermont-Ferrand, France.
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3
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Cannon JA, Zhou Y, Qualey LT, Reynolds TB. Surface-associated residues in subtilisins contribute to poly-L-lactic acid depolymerization via enzyme adsorption. Microb Biotechnol 2024; 17:e14473. [PMID: 38877615 PMCID: PMC11178483 DOI: 10.1111/1751-7915.14473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/22/2024] [Accepted: 04/14/2024] [Indexed: 06/16/2024] Open
Abstract
Poly-L-lactic acid (PLLA) is currently the most abundant bioplastic; however, limited environmental biodegradability and few recycling options diminish its value as a biodegradable commodity. Enzymatic recycling is one strategy for ensuring circularity of PLLA, but this approach requires a thorough understanding of enzymatic mechanisms and protein engineering strategies to enhance activity. In this study, we engineer PLLA depolymerizing subtilisin enzymes originating from Bacillus species to elucidate the molecular mechanisms dictating their PLLA depolymerization activity and to improve their function. The surface-associated amino acids of two closely related subtilisin homologues originating from Bacillus subtilis (BsAprE) and Bacillus pumilus (BpAprE) were compared, as they were previously engineered to have nearly identical active sites, but still varied greatly in PLLA depolymerizing activity. Further analysis identified several surface-associated amino acids in BpAprE that lead to enhanced PLLA depolymerization activity when engineered into BsAprE. In silico protein modelling demonstrated increased enzyme surface hydrophobicity in engineered BsAprE variants and revealed a structural motif favoured for PLLA depolymerization. Experimental evidence suggests that increases in activity are associated with enhanced polymer binding as opposed to substrate specificity. These data highlight enzyme adsorption as a key factor in PLLA depolymerization by subtilisins.
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Affiliation(s)
- Jordan A Cannon
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville, Tennessee, USA
| | - Yue Zhou
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville, Tennessee, USA
| | - Luke T Qualey
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville, Tennessee, USA
| | - Todd B Reynolds
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville, Tennessee, USA
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4
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Martinez M, Bouillon A, Brûlé S, Raynal B, Haouz A, Alzari PM, Barale JC. Prodomain-driven enzyme dimerization: a pH-dependent autoinhibition mechanism that controls Plasmodium Sub1 activity before merozoite egress. mBio 2024; 15:e0019824. [PMID: 38386597 PMCID: PMC10936178 DOI: 10.1128/mbio.00198-24] [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: 01/25/2024] [Accepted: 01/31/2024] [Indexed: 02/24/2024] Open
Abstract
Malaria symptoms are associated with the asexual multiplication of Plasmodium falciparum within human red blood cells (RBCs) and fever peaks coincide with the egress of daughter merozoites following the rupture of the parasitophorous vacuole (PV) and the RBC membranes. Over the last two decades, it has emerged that the release of competent merozoites is tightly regulated by a complex cascade of events, including the unusual multi-step activation mechanism of the pivotal subtilisin-like protease 1 (Sub1) that takes place in three different cellular compartments and remains poorly understood. Following an initial auto-maturation in the endoplasmic reticulum (ER) between its pro- and catalytic domains, the Sub1 prodomain (PD) undergoes further cleavages by the parasite aspartic protease plasmepsin X (PmX) within acidic secretory organelles that ultimately lead to full Sub1 activation upon discharge into the PV. Here, we report the crystal structure of full-length P. falciparum Sub1 (PfS1FL) and demonstrate, through structural, biochemical, and biophysical studies, that the atypical Plasmodium-specific Sub1 PD directly promotes the assembly of inactive enzyme homodimers at acidic pH, whereas Sub1 is primarily monomeric at neutral pH. Our results shed new light into the finely tuned Sub1 spatiotemporal activation during secretion, explaining how PmX processing and full activation of Sub1 can occur in different cellular compartments, and uncover a robust mechanism of pH-dependent subtilisin autoinhibition that plays a key role in P. falciparum merozoites egress from infected host cells.IMPORTANCEMalaria fever spikes are due to the rupture of infected erythrocytes, allowing the egress of Plasmodium sp. merozoites and further parasite propagation. This fleeting tightly regulated event involves a cascade of enzymes, culminating with the complex activation of the subtilisin-like protease 1, Sub1. Differently than other subtilisins, Sub1 activation strictly depends upon the processing by a parasite aspartic protease within acidic merozoite secretory organelles. However, Sub1 biological activity is required in the pH neutral parasitophorous vacuole, to prime effectors involved in the rupture of the vacuole and erythrocytic membranes. Here, we show that the unusual, parasite-specific Sub1 prodomain is directly responsible for its acidic-dependent dimerization and autoinhibition, required for protein secretion, before its full activation at neutral pH in a monomeric form. pH-dependent Sub1 dimerization defines a novel, essential regulatory element involved in the finely tuned spatiotemporal activation of the egress of competent Plasmodium merozoites.
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Affiliation(s)
- Mariano Martinez
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Anthony Bouillon
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Sébastien Brûlé
- Plate-forme de Biophysique Moleculaire-C2RT, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Bertrand Raynal
- Plate-forme de Biophysique Moleculaire-C2RT, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Ahmed Haouz
- Plate-forme de Cristallographie-C2RT, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Pedro M. Alzari
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Jean-Christophe Barale
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
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5
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Falkenberg F, Kohn S, Bott M, Bongaerts J, Siegert P. Biochemical characterisation of a novel broad pH spectrum subtilisin from Fictibacillus arsenicus DSM 15822 T. FEBS Open Bio 2023; 13:2035-2046. [PMID: 37649135 PMCID: PMC10626276 DOI: 10.1002/2211-5463.13701] [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: 04/25/2023] [Revised: 08/23/2023] [Accepted: 08/29/2023] [Indexed: 09/01/2023] Open
Abstract
Subtilisins from microbial sources, especially from the Bacillaceae family, are of particular interest for biotechnological applications and serve the currently growing enzyme market as efficient and novel biocatalysts. Biotechnological applications include use in detergents, cosmetics, leather processing, wastewater treatment and pharmaceuticals. To identify a possible candidate for the enzyme market, here we cloned the gene of the subtilisin SPFA from Fictibacillus arsenicus DSM 15822T (obtained through a data mining-based search) and expressed it in Bacillus subtilis DB104. After production and purification, the protease showed a molecular mass of 27.57 kDa and a pI of 5.8. SPFA displayed hydrolytic activity at a temperature optimum of 80 °C and a very broad pH optimum between 8.5 and 11.5, with high activity up to pH 12.5. SPFA displayed no NaCl dependence but a high NaCl tolerance, with decreasing activity up to concentrations of 5 m NaCl. The stability enhanced with increasing NaCl concentration. Based on its substrate preference for 10 synthetic peptide 4-nitroanilide substrates with three or four amino acids and its phylogenetic classification, SPFA can be assigned to the subgroup of true subtilisins. Moreover, SPFA exhibited high tolerance to 5% (w/v) SDS and 5% H2 O2 (v/v). The biochemical properties of SPFA, especially its tolerance of remarkably high pH, SDS and H2 O2 , suggest it has potential for biotechnological applications.
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Affiliation(s)
- Fabian Falkenberg
- Institute of Nano‐ and BiotechnologiesAachen University of Applied SciencesJülichGermany
| | - Sophie Kohn
- Institute of Nano‐ and BiotechnologiesAachen University of Applied SciencesJülichGermany
| | - Michael Bott
- Institute of Bio‐ and Geosciences, IBG‐1: BiotechnologyForschungszentrum JülichGermany
| | - Johannes Bongaerts
- Institute of Nano‐ and BiotechnologiesAachen University of Applied SciencesJülichGermany
| | - Petra Siegert
- Institute of Nano‐ and BiotechnologiesAachen University of Applied SciencesJülichGermany
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6
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Shettar SS, Bagewadi ZK, Kolvekar HN, Yunus Khan T, Shamsudeen SM. Optimization of subtilisin production from Bacillus subtilis strain ZK3 and biological and molecular characterization of synthesized subtilisin capped nanoparticles. Saudi J Biol Sci 2023; 30:103807. [PMID: 37744003 PMCID: PMC10514557 DOI: 10.1016/j.sjbs.2023.103807] [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: 08/03/2023] [Revised: 08/22/2023] [Accepted: 09/01/2023] [Indexed: 09/26/2023] Open
Abstract
The increase and dissemination of multi-drug resistant bacteria have presented a major healthcare challenge, making bacterial infections a significant concern. The present research contributes towards the production of bioactive subtilisin from a marine soil isolate Bacillus subtilis strain ZK3. Custard apple seed powder (raw carbon) and mustard oil cake (raw nitrogen) sources showed a pronounced effect on subtilisin production. A 7.67-fold enhancement in the production was evidenced after optimization with central composite design-response surface methodology. Subtilisin capped silver (AgNP) and zinc oxide (ZnONP) nanoparticles were synthesized and characterized by UV-Visible spectroscopy. Subtilisin and its respective nanoparticles revealed significant biological properties such as, antibacterial activity against all tested pathogenic strains with potential against Escherichia coli and Pseudomonas aeruginosa. Prospective antioxidant behavior of subtilisin, AgNP and ZnONP was evidenced through radical scavenging assays with ABTS and DPPH. Subtilisin, AgNP and ZnONP revealed cytotoxic effect against cancerous breast cell lines MCF-7 with IC50of 83.48, 3.62 and 7.57 µg/mL respectively. Characterizations of nanoparticles were carried out by Fourier transform infrared spectroscopy, scanning electron microscopy with energy dispersive X-ray, X-ray diffraction, thermogravimetric analysis and atomic force microscopy analysis to elucidate the structure, surface and thermostability properties. The study proposes the potential therapeutic applications of subtilisin and its nanoparticles, a way forward for further exploration in the field of healthcare.
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Affiliation(s)
- Shreya S. Shettar
- Department of Biotechnology, KLE Technological University, Hubballi, Karnataka 580031, India
| | - Zabin K. Bagewadi
- Department of Biotechnology, KLE Technological University, Hubballi, Karnataka 580031, India
| | - Harsh N. Kolvekar
- Department of Biotechnology, KLE Technological University, Hubballi, Karnataka 580031, India
| | - T.M. Yunus Khan
- Department of Mechanical Engineering, College of Engineering, King Khalid University, Abha 61421, Saudi Arabia
| | - Shaik Mohamed Shamsudeen
- Department of Diagnostic Dental Science and Oral Biology, College of Dentistry, King Khalid University, Abha 61421, Saudi Arabia
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7
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Ma Z, Mu K, Zhu J, Xiao M, Wang L, Jiang X. Molecular dynamics simulations identify the topological weak spots of a protease CN2S8A. J Mol Graph Model 2023; 124:108571. [PMID: 37487372 DOI: 10.1016/j.jmgm.2023.108571] [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: 05/10/2023] [Revised: 07/06/2023] [Accepted: 07/19/2023] [Indexed: 07/26/2023]
Abstract
Thermophilic enzymes are highly desired in industrial applications due to their efficient catalytic activity at high temperature. However, most enzymes exhibit inferior thermostability and it remains challenging to identify the optimal sites for designing mutations to improve protein stability. To tackle this issue, we integrated topological analysis and all-atom molecular dynamics simulations to efficiently pinpoint the thermally-unstable regions in protein structures. Using a protease CN2S8A as the model, we analyzed the intramolecular hydrogen bonding interactions between adjacent secondary structure elements, and then identified the topological weak spots of CN2S8A where weak hydrogen bonding interactions were formed. To examine the role of these sites in protein structural stability, we designed three virtual mutations at different weak spots and characterized the effects of these mutations on the structural properties of CN2S8A. The results showed that all three mutations increased the protein structural stability. In conclusion, these findings provide a novel method to identify the topological weak spots of proteins, with implications in the rational design of biocatalysts with superior thermostability.
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Affiliation(s)
- Zhenyu Ma
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China
| | - Kaijie Mu
- Biomedicine Discovery Institute, Monash University, Melbourne, 3500, Australia
| | - Jingyi Zhu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Min Xiao
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xukai Jiang
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China.
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8
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Bahun M, Poklar Ulrih N. High selectivity of the hyperthermophilic subtilase propeptide domain toward inhibition of its cognate protease. Microbiol Spectr 2023; 11:e0148723. [PMID: 37655909 PMCID: PMC10580911 DOI: 10.1128/spectrum.01487-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 07/04/2023] [Indexed: 09/02/2023] Open
Abstract
Microbial extracellular subtilases are highly active proteolytic enzymes commonly used in commercial applications. These subtilases are synthesized in their inactive proform, which matures into the active protease under the control of the propeptide domain. In mesophilic bacterial prosubtilases, the propeptide functions as both an obligatory chaperone and an inhibitor of the subtilase catalytic domain. In contrast, the propeptides of hyperthermophilic archaeal prosubtilases act mainly as tight inhibitors and are not essential for subtilase folding. It is unclear whether this stronger inhibitory activity of hyperthermophilic propeptides results in their higher selectivity toward their cognate subtilases, in contrast to promiscuous mesophilic propeptides. Here, we showed that the propeptide of pernisine, a hyperthermostable archaeal subtilase, strongly interacts with and inhibits pernisine, but not the homologous subtilisin Carlsberg and proteinase K. Instead, the pernisine propeptide was readily degraded by subtilisin Carlsberg and proteinase K. In addition, the catalytic domain of unprocessed propernisine was also susceptible to degradation but became proteolytically stable after autoprocessing of propernisine into the inactive, noncovalent complex propeptide:pernisine. This allowed efficient transactivation of the autoprocessed complex propeptide:pernisine through degradation of pernisine propeptide by subtilisin Carlsberg and proteinase K at mesophilic temperature. Moreover, we demonstrated that active pernisine molecules are inhibited by the propeptide that is released after pernisine-catalyzed degradation of the unprocessed propernisine catalytic domain. This highlights the high inhibitory potency of the hyperthermophilic propeptide toward its cognate subtilase and its importance in regulating subtilase maturation, to prevent the degradation of the unprocessed subtilase precursors by the prematurely activated molecules. IMPORTANCE Many microorganisms secrete proteases into their environment to degrade protein substrates for their growth. The important group of these extracellular enzymes are subtilases, which are also widely used in practical applications. These subtilases are inhibited by their propeptide domain, which is degraded during the prosubtilase maturation process. Here, we showed that the propeptide of pernisine, a prion-degrading subtilase from the hyperthermophilic archaeon, strongly inhibits pernisine with extraordinarily high binding affinity. This interaction proved to be highly selective, as pernisine propeptide was rapidly degraded by mesophilic pernisine homologs. This in turn allowed rapid transactivation of propernisine by mesophilic subtilases at lower temperatures, which might simplify the procedures for preparation of active pernisine for commercial use. The results reported in this study suggest that the hyperthermophilic subtilase propeptide evolved to function as tight and selective regulator of maturation of the associated prosubtilase to prevent its premature activation under high temperatures.
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Affiliation(s)
- Miha Bahun
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Nataša Poklar Ulrih
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Ljubljana, Slovenia
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9
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Mohd Azrin NA, Mohamad Ali MS, Raja Abd Rahman RNZ, Mohd Shariff F, Ahmad Kamarudin NH, Muhd Noor ND. Effect of cysteine mutation at Ca 2+ coordinating residues to the autolysis, folding and hydrophobicity of full length and mature Rand protease: molecular dynamics simulation and essential dynamics. J Biomol Struct Dyn 2023:1-13. [PMID: 37608543 DOI: 10.1080/07391102.2023.2249105] [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: 04/10/2023] [Accepted: 08/12/2023] [Indexed: 08/24/2023]
Abstract
Rand protease is a serine protease that shared common characteristics with members of the MEROPS S8 subtilisin family. It is thermostable, highly stable in organic solvent and broad in specificity. Many structures of homologous protein solved by X-ray crystallography and NMR have been deposited to Protein Data Bank (PDB) which allowed this study to rely on structure prediction by deep learning to build three-dimensional (3D) structure of full length and mature Rand protease (flRP and mRP). In silico cysteine mutation to 7 predicted high affinity Ca2+ coordinating residues were introduced, and the mutants were subjected to molecular dynamics simulation to study its effect on flRP and mRP. MD simulation showed a marked increase in flexibility of the pro-peptide segment indicating the impact of single cysteine substitution at high affinity Ca2+ coordinating residues to autolysis of flRP. MD simulation for mRP reaffirmed the role of Ca2+ coordinating sites in providing stability to Rand protease. In addition, these residues also affect the autolysis, folding and hydrophobicity of RP. Essential dynamics observed large contribution of the first few eigenvectors of flRP, mRP and their high affinity Ca2+ coordinating residues mutants to the TMSF values which indicates that these values account for a large portion of the overall atomic fluctuations. These results have given a more comprehensive understanding on the role of cysteine substituted Ca2+ coordinating surface loop to the structure of flRP and mRP which are important in contributing to the structural stability of subtilisin.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nur Aliyah Mohd Azrin
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Selangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Selangor, Malaysia
- Department of Biochemistry, Universiti Putra Malaysia, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Selangor, Malaysia
- Department of Microbiology, Universiti Putra Malaysia, Selangor, Malaysia
| | - Fairolniza Mohd Shariff
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Selangor, Malaysia
- Department of Microbiology, Universiti Putra Malaysia, Selangor, Malaysia
| | - Nor Hafizah Ahmad Kamarudin
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Selangor, Malaysia
- Centre of Foundation Studies for Agricultural Science, Universiti Putra Malaysia, Selangor, Malaysia
| | - Noor Dina Muhd Noor
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Selangor, Malaysia
- Department of Biochemistry, Universiti Putra Malaysia, Selangor, Malaysia
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10
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Begum W, Saha B, Mandal U. A comprehensive review on production of bio-surfactants by bio-degradation of waste carbohydrate feedstocks: an approach towards sustainable development. RSC Adv 2023; 13:25599-25615. [PMID: 37649573 PMCID: PMC10463011 DOI: 10.1039/d3ra05051c] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 08/17/2023] [Indexed: 09/01/2023] Open
Abstract
The advancement of science and technology demands chemistry which is safer, smarter and green by nature. The sustainability of science thus requires well-behaved alternates that best suit the demand. Bio-surfactants are surface active compounds, established to affect surface chemistry. In general, microbial bio-surfactants are a group of structurally diverse molecules produced by different microbes. A large number of bio-surfactants are produced during hydrocarbon degradation by hydrocarbonoclistic microorganisms during their own growth on carbohydrates and the production rate is influenced by the rate of degradation of carbohydrates. The production of such biological surfactants is thus of greater importance. This write up is a dedicated review to update the existing knowledge of inexpensive carbohydrate sources as substrates, microorganisms and technologies of biosurfactant production. This is an economy friendly as well as sustainable approach which will facilitate achieving some sustainable development goals. The production is dependent on the fermentation strategies, different factors of the microbial culture broth and downstream processing; these all have been elaborately presented in this article.
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Affiliation(s)
- Wasefa Begum
- Department of Chemistry, The University of Burdwan Golapbag West Bengal 713104 India
| | - Bidyut Saha
- Department of Chemistry, The University of Burdwan Golapbag West Bengal 713104 India
| | - Ujjwal Mandal
- Department of Chemistry, The University of Burdwan Golapbag West Bengal 713104 India
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Wang X, Dong T, Zhou Q, Tong L, Zheng J, Qin X, Wang X, Wang Y, Yao B, Huang H, Luo H. Improving the Activity and Stability of Serine Protease ThAPT3 by Alleviating Self-Cleavage and Its Application in Deproteinization of Shrimp Shells. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:7777-7790. [PMID: 37161941 DOI: 10.1021/acs.jafc.3c01618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The self-cleavage properties of proteases result in low activity and instability, which limit their industrial application. In this study, the serine protease ThAPT3 from Torrubiella hemipterigena was successfully expressed in Komagataella phaffii. We investigated the self-degradation mechanism of ThAPT3 and presented a rational strategy to alleviate self-cleavage. A major self-degradation site (Leu238-Met239) and a primary autolysis region were identified. The autolysis regions (loop18, α8-helix, and loop19) were redesigned and optimized using loop transplantation, energy calculations, surface cavity optimization, and loop anchoring. A triple-superposition mutant, ThAPT3-M9 (M239GKDGAVAAGLC250 → M239TLNRTTAANAC250/A251E/A254Q/R259L/A267E/S280N), was obtained. Compared to the wild type, the autolysis of M9 was significantly alleviated, and its half-life at 60 °C was increased approximately 39-fold (from 1.6 to 62.4 min). The optimal temperature and specific activity of M9 increased by 5 °C (from 60 to 65 °C) and 62% (4985 vs 3078 U/mg), respectively. M9 showed significant advantages in shrimp shell deproteinization.
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Affiliation(s)
- Xiao Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tao Dong
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Qiao Zhou
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, Shaanxi 712100, China
| | - Lige Tong
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jie Zheng
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xing Qin
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaolu Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yaru Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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12
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Falkenberg F, Voß L, Bott M, Bongaerts J, Siegert P. New robust subtilisins from halotolerant and halophilic Bacillaceae. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12553-w. [PMID: 37160606 DOI: 10.1007/s00253-023-12553-w] [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: 03/21/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 05/11/2023]
Abstract
The aim of the present study was the characterisation of three true subtilisins and one phylogenetically intermediate subtilisin from halotolerant and halophilic microorganisms. Considering the currently growing enzyme market for efficient and novel biocatalysts, data mining is a promising source for novel, as yet uncharacterised enzymes, especially from halophilic or halotolerant Bacillaceae, which offer great potential to meet industrial needs. Both halophilic bacteria Pontibacillus marinus DSM 16465T and Alkalibacillus haloalkaliphilus DSM 5271T and both halotolerant bacteria Metabacillus indicus DSM 16189 and Litchfieldia alkalitelluris DSM 16976T served as a source for the four new subtilisins SPPM, SPAH, SPMI and SPLA. The protease genes were cloned and expressed in Bacillus subtilis DB104. Purification to apparent homogeneity was achieved by ethanol precipitation, desalting and ion-exchange chromatography. Enzyme activity could be observed between pH 5.0-12.0 with an optimum for SPPM, SPMI and SPLA around pH 9.0 and for SPAH at pH 10.0. The optimal temperature for SPMI and SPLA was 70 °C and for SPPM and SPAH 55 °C and 50 °C, respectively. All proteases showed high stability towards 5% (w/v) SDS and were active even at NaCl concentrations of 5 M. The four proteases demonstrate potential for future biotechnological applications. KEY POINTS: • Halophilic and halotolerant Bacillaceae are a valuable source of new subtilisins. • Four new subtilisins were biochemically characterised in detail. • The four proteases show potential for future biotechnological applications.
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Affiliation(s)
- Fabian Falkenberg
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428, Jülich, Germany
| | - Leonie Voß
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428, Jülich, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Johannes Bongaerts
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428, Jülich, Germany
| | - Petra Siegert
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428, Jülich, Germany.
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13
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Luo J, Song C, Cui W, Han L, Zhou Z. Counteraction of stability-activity trade-off of Nattokinase through flexible region shifting. Food Chem 2023; 423:136241. [PMID: 37178594 DOI: 10.1016/j.foodchem.2023.136241] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 04/16/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
The widespread trade-off between stability and activity severely limits enzyme evolution. Although some progresses have been made to overcome this limitation, the counteraction mechanism for enzyme stability-activity trade-off remains obscure. Here, we clarified the counteraction mechanism of the Nattokinase stability-activity trade-off. A combinatorial mutant M4 was obtained by multi-strategy engineering, exhibiting a 20.7-fold improved half-life; meanwhile, the catalytic efficiency was doubled. Molecular dynamics simulation revealed that an obvious flexible region shifting in the structure of mutant M4 was occurred. The flexible region shifting which contributed to maintain the global structural flexibility, was considered to be the key factor for counteracting the stability-activity trade-off. Further analysis illustrated that the flexible region shifting was driven by region dynamical networks reshaping. This work provided deep insight into the counteraction mechanism of enzyme stability-activity trade-off, suggesting that flexible region shifting would be an effective strategy for enzyme evolution through computational protein engineering.
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Affiliation(s)
- Jie Luo
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Chenshuo Song
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wenjing Cui
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Laichuang Han
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.
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14
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Cannon JA, Reynolds TB. Synergistic Mutations Create Bacillus Subtilisin Variants with Enhanced Poly-l-Lactic Acid Depolymerization Activity. Biomacromolecules 2023; 24:1141-1154. [PMID: 36780360 DOI: 10.1021/acs.biomac.2c01198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
Enzymatic recycling of poly-l-lactic acid (PLLA) plastic has recently become an area of interest; however, investigation of enzymatic mechanisms and engineering strategies to improve activity remains limited. In this study, we have identified a subtilisin from Bacillus pumilus that has the ability to depolymerize high-molecular-weight PLLA. We performed a comparative, mutational analysis of this enzyme with a less active homologue from Bacillus subtilis to determine residues favored for activity. Our results demonstrate that both enzymes contain residues favored for PLLA depolymerization, with the generation of several hyperactive variants. In silico modeling suggests that increases in activity are due to opening of the binding pockets and increased surface hydrophobicity. Combinations of hyperactive mutations have synergistic effects with the generation of subtilisin variants with 830- and 184-fold increases in activity for B. subtilis and B. pumilus subtilisins, respectively. One B. pumilus subtilisin variant can visibly dissolve high-molecular-weight PLLA films.
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Affiliation(s)
- Jordan A Cannon
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville, Tennessee 37996, United States
| | - Todd B Reynolds
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville, Tennessee 37996, United States
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15
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Diez-Galán A, Cobos R, Ibañez A, Calvo-Peña C, Coque JJR. Biodegradation of Pine Processionary Caterpillar Silk Is Mediated by Elastase- and Subtilisin-like Proteases. Int J Mol Sci 2022; 23:ijms232315253. [PMID: 36499578 PMCID: PMC9741414 DOI: 10.3390/ijms232315253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Pine processionary caterpillar nests are made from raw silk. Fibroin protein is the main component of silk which, in the case of pine processionary caterpillar, has some unusual properties such as a higher resistance to chemical hydrolysis. Isolation of microorganisms naturally present in silk nests led to identification of Bacillus licheniformis and Pseudomonas aeruginosa strains that in a defined minimal medium were able to carry out extensive silk biodegradation. A LasB elastase-like protein from P. aeruginosa was shown to be involved in silk biodegradation. A recombinant form of this protein expressed in Escherichia coli and purified by affinity chromatography was able to efficiently degrade silk in an in vitro assay. However, silk biodegradation by B. licheniformis strain was mediated by a SubC subtilisin-like protease. Homologous expression of a subtilisin Carlsberg encoding gene (subC) allowed faster degradation compared to the biodegradation kinetics of a wildtype B. licheniformis strain. This work led to the identification of new enzymes involved in biodegradation of silk materials, a finding which could lead to possible applications for controlling this pest and perhaps have importance from sanitary and biotechnological points of view.
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Garofalo SF, Cavallini N, Demichelis F, Savorani F, Mancini G, Fino D, Tommasi T. From tuna viscera to added-value products: A circular approach for fish-waste recovery by green enzymatic hydrolysis. FOOD AND BIOPRODUCTS PROCESSING 2022. [DOI: 10.1016/j.fbp.2022.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Falkenberg F, Bott M, Bongaerts J, Siegert P. Phylogenetic survey of the subtilase family and a data-mining-based search for new subtilisins from Bacillaceae. Front Microbiol 2022; 13:1017978. [PMID: 36225363 PMCID: PMC9549277 DOI: 10.3389/fmicb.2022.1017978] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 08/30/2022] [Indexed: 11/30/2022] Open
Abstract
The subtilase family (S8), a member of the clan SB of serine proteases are ubiquitous in all kingdoms of life and fulfil different physiological functions. Subtilases are divided in several groups and especially subtilisins are of interest as they are used in various industrial sectors. Therefore, we searched for new subtilisin sequences of the family Bacillaceae using a data mining approach. The obtained 1,400 sequences were phylogenetically classified in the context of the subtilase family. This required an updated comprehensive overview of the different groups within this family. To fill this gap, we conducted a phylogenetic survey of the S8 family with characterised holotypes derived from the MEROPS database. The analysis revealed the presence of eight previously uncharacterised groups and 13 subgroups within the S8 family. The sequences that emerged from the data mining with the set filter parameters were mainly assigned to the subtilisin subgroups of true subtilisins, high-alkaline subtilisins, and phylogenetically intermediate subtilisins and represent an excellent source for new subtilisin candidates.
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Affiliation(s)
- Fabian Falkenberg
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Jülich, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Johannes Bongaerts
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Jülich, Germany
| | - Petra Siegert
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Jülich, Germany
- *Correspondence: Petra Siegert,
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