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Ungaro VA, Fairbanks JPA, Rossi LM, Machini MT. Fe 3O 4@silica-thermolysin: A robust, advantageous, and reusable microbial nanobiocatalyst for proteolysis and milk-clotting. Int J Biol Macromol 2024; 278:134503. [PMID: 39111503 DOI: 10.1016/j.ijbiomac.2024.134503] [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: 04/05/2024] [Revised: 08/02/2024] [Accepted: 08/03/2024] [Indexed: 08/25/2024]
Abstract
Thermolysin (TLN) is a microbial highly-priced thermostable metallo-endoprotease with complementary substrate specificity to those of proteases widely used in science and industry for protein digestion and milk-clotting. This study is the first to immobilize TLN on aminated superparamagnetic nanoparticles (Fe3O4@silica-NH2) aiming for higher stability, recoverability, reusability, and applicability in proteolysis and as a microbial rennet-like milk-clotting enzyme. The nanobiocatalyst developed (Fe3O4@silica-TLN) displays hydrolytic activity on a synthetic TLN substrate and, apparently, was fully recovered from reaction media by magnetic decantation. More importantly, Fe3O4@silica-TLN retains TLN catalytic properties in the presence of calcium ions even after exposure to 60 °C for 48 h, storage at 4 °C for 80 days and room temperature for 42 days, use in proteolyses, and in milk-clotting for up to 11 cycles. Its proteolytic activity on bovine milk casein in 24 h furnished 84 peptides, of which 29 are potentially bioactive. Also, Fe3O4@silica-TLN catalyzed the digestion of bovine serum albumin. In conclusion, Fe3O4@silica-TLN showed to be a new, less autolytic, thermostable, non-toxic, magnetically-separable, and reusable nanobiocatalyst with highly attractive properties for both science (peptide/protein chemistry and structure, proteomic studies, and the search for new bioactive peptides) and food industry (cheese manufacture).
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Affiliation(s)
- Vitor A Ungaro
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - João P A Fairbanks
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Liane M Rossi
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - M Teresa Machini
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil.
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2
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Singh A, Chakraborty J, Pal S, Das D. Site-selective peptide bond hydrolysis and ligation in water by short peptide-based assemblies. Proc Natl Acad Sci U S A 2024; 121:e2321396121. [PMID: 39042686 PMCID: PMC11295027 DOI: 10.1073/pnas.2321396121] [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: 12/05/2023] [Accepted: 06/20/2024] [Indexed: 07/25/2024] Open
Abstract
The evolution of complex chemical inventory from Darwin's nutrient-rich warm pond necessitated rudimentary yet efficient catalytic folds. Short peptides and their self-organized microstructures, ranging from spherical colloids to amyloidogenic aggregates might have played a crucial role in the emergence of contemporary catalytic entities. However, the question of how short peptide fragments had functions akin to contemporary complex enzymes to catalyze cleavage and formation of highly stable peptide bonds that constitute the backbone of all proteins remains an unresolved yet fundamentally important question in terms of the origins of enzymes. We report short-peptide-based spherical assemblies that demonstrated residue-specific cleavage and formation of peptide bonds of diverse peptide-based substrates under aqueous environment. Despite the short sequence length, the assemblies utilized the synergistic collaboration of four residues which included the catalytic triad of extant serine proteases with a nonproteinogenic amino acid (quinone moiety), to facilitate proteolysis, ligation, and a three-step (hydrolysis-ligation-hydrolysis) cascade. Such short-peptide-based catalytic assemblies argue for their candidacy as the earliest protein folds and open up avenues for biotechnological applications.
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Affiliation(s)
- Abhishek Singh
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur741246, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research, Kolkata, Mohanpur741246, India
| | - Janardan Chakraborty
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur741246, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research, Kolkata, Mohanpur741246, India
| | - Sumit Pal
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur741246, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research, Kolkata, Mohanpur741246, India
| | - Dibyendu Das
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur741246, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research, Kolkata, Mohanpur741246, India
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3
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Filippova TA, Masamrekh RA, Khudoklinova YY, Shumyantseva VV, Kuzikov AV. The multifaceted role of proteases and modern analytical methods for investigation of their catalytic activity. Biochimie 2024; 222:169-194. [PMID: 38494106 DOI: 10.1016/j.biochi.2024.03.006] [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: 09/25/2023] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 03/19/2024]
Abstract
We discuss the diverse functions of proteases in the context of their biotechnological and medical significance, as well as analytical approaches used to determine the functional activity of these enzymes. An insight into modern approaches to studying the kinetics and specificity of proteases, based on spectral (absorption, fluorescence), mass spectrometric, immunological, calorimetric, and electrochemical methods of analysis is given. We also examine in detail electrochemical systems for determining the activity and specificity of proteases. Particular attention is given to exploring innovative electrochemical systems based on the detection of the electrochemical oxidation signal of amino acid residues, thereby eliminating the need for extra redox labels in the process of peptide synthesis. In the review, we highlight the main prospects for the further development of electrochemical systems for the study of biotechnologically and medically significant proteases, which will enable the miniaturization of the analytical process for determining the catalytic activity of these enzymes.
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Affiliation(s)
- Tatiana A Filippova
- Institute of Biomedical Chemistry, 10 bld. 8, Pogodinskaya str., 119121, Moscow, Russia; Pirogov Russian National Research Medical University, 1, Ostrovityanova Street, Moscow, 117513, Russia
| | - Rami A Masamrekh
- Institute of Biomedical Chemistry, 10 bld. 8, Pogodinskaya str., 119121, Moscow, Russia; Pirogov Russian National Research Medical University, 1, Ostrovityanova Street, Moscow, 117513, Russia
| | - Yulia Yu Khudoklinova
- Pirogov Russian National Research Medical University, 1, Ostrovityanova Street, Moscow, 117513, Russia
| | - Victoria V Shumyantseva
- Institute of Biomedical Chemistry, 10 bld. 8, Pogodinskaya str., 119121, Moscow, Russia; Pirogov Russian National Research Medical University, 1, Ostrovityanova Street, Moscow, 117513, Russia
| | - Alexey V Kuzikov
- Institute of Biomedical Chemistry, 10 bld. 8, Pogodinskaya str., 119121, Moscow, Russia; Pirogov Russian National Research Medical University, 1, Ostrovityanova Street, Moscow, 117513, Russia.
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4
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Edson CB, Liu M, Totsingan F, O’Berg E, Salvucci J, Dao U, Khare SD, Gross RA. Monomer Choice Influences N-Acryloyl Amino Acid Grafter Conversion via Protease Catalysis. Biomacromolecules 2023; 24:1798-1809. [PMID: 36996092 PMCID: PMC10139737 DOI: 10.1021/acs.biomac.3c00029] [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] [Indexed: 03/31/2023]
Abstract
End-capped peptides modified with reactive functional groups on the N-terminus provide a route to prepare peptide-polymer conjugates for a broad range of applications. Unfortunately, current chemical methods to construct modified peptides rely largely on solid-phase peptide synthesis (SPPS), which lacks green preparative characteristics and is costly, thus limiting its applicability to specialty applications such as regenerative medicine. This work evaluates N-terminally modified N-acryloyl-glutamic acid diethyl ester, N-acryloyl-leucine ethyl ester, and N-acryloyl-alanine ethyl ester as grafters and papain as the protease for the direct addition of amino acid ethyl ester (AA-OEt) monomers via protease-catalyzed peptide synthesis (PCPS) and the corresponding formation of N-acryloyl-functionalized oligopeptides in a one-pot aqueous reaction. It was hypothesized that by building N-acryloyl grafters from AA-OEt monomers that are known to be good substrates for papain in PCPS, the corresponding grafters would yield high grafter conversions, high ratio of grafter-oligopeptide to free NH2-oligopeptide, and high overall yield. However, this work demonstrates based on the grafter/monomers studied herein that the dominant factor in N-acryloyl-AA-OEt grafter conversion is the co-monomer used in co-oligomerizations. Computational modeling using Rosetta qualitatively recapitulates the results and provides insight into the structural and energetic bases underlying substrate selectivity. The findings herein expand our knowledge of factors that determine the efficiency of preparing N-acryloyl-terminated oligopeptides by PCPS that could provide practical routes to peptide macromers for conjugation to polymers and surfaces for a broad range of applications.
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Affiliation(s)
- Cody B. Edson
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8 St. Troy, NY 12180
| | - Melinda Liu
- Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Filbert Totsingan
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8 St. Troy, NY 12180
| | - Evan O’Berg
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8 St. Troy, NY 12180
| | - John Salvucci
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8 St. Troy, NY 12180
| | - Uyen Dao
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8 St. Troy, NY 12180
| | - Sagar D. Khare
- Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Richard A. Gross
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8 St. Troy, NY 12180
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5
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Wang F, Li C, Wang H, Yu L, Zhang F, Linhardt RJ. Amphiphilic O(Phe-r-Glu) oligopeptides randomly polymerized via papain exhibiting a pH-insensitive emulsification property. Colloids Surf A Physicochem Eng Asp 2023. [DOI: 10.1016/j.colsurfa.2023.131141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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6
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Purohit MK, Rathore DS, Koladiya G, Pandey S, Singh SP. Comparative analysis of the catalysis and stability of the native, recombinant and metagenomic alkaline proteases in organic solvents. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:80968-80982. [PMID: 35725880 DOI: 10.1007/s11356-022-21411-7] [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: 12/11/2021] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
The effect of organic solvents on alkaline proteases was assessed for native, recombinant, and metagenomically derived alkaline proteases. Their stability and the effects of physicochemical parameters were studied in the presence of hexane. The native enzyme was comparatively more resistant against the organic solvents than the recombinant counterparts. On the other hand, the metagenomically derived alkaline protease was minimally resistant against solvents. A similar trend was apparent for the stability of enzyme in organic solvents. The novelty of this study lies in the fact that the majority of the studies on the solvent tolerance have focused on the mesophilic enzymes, while those from the haloalkaliphilic bacteria have received little attention. The comparative tolerance of the native, recombinant, and metagenomic alkaline proteases against the organic solvent has practical importance. The phylogenetic relatedness among the various protease sequences will be described.
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Affiliation(s)
- Megha K Purohit
- Department of Biosciences, UGC-CAS, Saurashtra University, Rajkot, 360 005, India
- Current Address: DNA Investigating Laboratory, Toronto, ON, Canada
| | - Dalip Singh Rathore
- Department of Biosciences, UGC-CAS, Saurashtra University, Rajkot, 360 005, India
| | - Gopi Koladiya
- Department of Biosciences, UGC-CAS, Saurashtra University, Rajkot, 360 005, India
| | | | - Satya P Singh
- Department of Biosciences, UGC-CAS, Saurashtra University, Rajkot, 360 005, India.
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7
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Fryszkowska A, An C, Alvizo O, Banerjee G, Canada KA, Cao Y, DeMong D, Devine PN, Duan D, Elgart DM, Farasat I, Gauthier DR, Guidry EN, Jia X, Kong J, Kruse N, Lexa KW, Makarov AA, Mann BF, Milczek EM, Mitchell V, Nazor J, Neri C, Orr RK, Orth P, Phillips EM, Riggins JN, Schafer WA, Silverman SM, Strulson CA, Subramanian N, Voladri R, Yang H, Yang J, Yi X, Zhang X, Zhong W. A chemoenzymatic strategy for site-selective functionalization of native peptides and proteins. Science 2022; 376:1321-1327. [PMID: 35709255 DOI: 10.1126/science.abn2009] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The emergence of new therapeutic modalities requires complementary tools for their efficient syntheses. Availability of methodologies for site-selective modification of biomolecules remains a long-standing challenge, given the inherent complexity and the presence of repeating residues that bear functional groups with similar reactivity profiles. We describe a bioconjugation strategy for modification of native peptides relying on high site selectivity conveyed by enzymes. We engineered penicillin G acylases to distinguish among free amino moieties of insulin (two at amino termini and an internal lysine) and manipulate cleavable phenylacetamide groups in a programmable manner to form protected insulin derivatives. This enables selective and specific chemical ligation to synthesize homogeneous bioconjugates, improving yield and purity compared to the existing methods, and generally opens avenues in the functionalization of native proteins to access biological probes or drugs.
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Affiliation(s)
- Anna Fryszkowska
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Chihui An
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Oscar Alvizo
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | | | - Keith A Canada
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Yang Cao
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Duane DeMong
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Paul N Devine
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Da Duan
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - David M Elgart
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Iman Farasat
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Donald R Gauthier
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Erin N Guidry
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Xiujuan Jia
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Jongrock Kong
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Nikki Kruse
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Katrina W Lexa
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Alexey A Makarov
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Benjamin F Mann
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Erika M Milczek
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Vesna Mitchell
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Jovana Nazor
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Claudia Neri
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Robert K Orr
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Peter Orth
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Eric M Phillips
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - James N Riggins
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Wes A Schafer
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Steven M Silverman
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | | | | | - Rama Voladri
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Hao Yang
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Jie Yang
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Xiang Yi
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Xiyun Zhang
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Wendy Zhong
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
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8
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Wu J, Gao J, Lin J, Cui C, Li L, He S, Brennan C. Preparation and Taste Characteristics of Kokumi N-Lactoyl Phenylalanine in the Presence of Phenylalanine and Lactate. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:5396-5407. [PMID: 35452224 DOI: 10.1021/acs.jafc.2c00530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
N-l-Lactoyl phenylalanine (N-l-lactoyl-Phe) has been identified as a taste-active contributor in many fermented foods. However, its preparation, taste property, and content in foodstuffs are little known to date. In the current study, two preparation technologies of N-l-lactoyl-Phe including heating and enzymatic methods were investigated. Other investigations include its taste property and quantification in several fermented foods. The results indicated that the heating preparation and enzymatic preparation only produced N-l-lactoyl-Phe instead of N-d-lactoyl-Phe in the presence of l-lactate/d-lactate and l-phenylalanine (Phe). A high yield (58.0% ± 0.7%) of N-l-lactoyl-Phe was achieved under the following conditions: Phe, lactate, CaO, and water at molar ratios of 1:8:0.3:9 kept at 100 °C for 3 h. With nine enzymes, a maximum yield of 21.2% ± 0.3% was achieved in the aqueous solution under mild operating conditions: 0.18 M Phe, 0.90 M lactate, 5 g/L Debitrase HYW 20, pH 8, and 55 °C for 24 h. The sensory evaluation revealed that N-l-lactoyl-Phe in water enhanced the salty and umami intensity. It also enhanced the thickness, mouthfulness, and continuity of salt solution, model broth, and chicken broth, revealing that N-l-lactoyl-Phe was a kokumi-active compound. The kokumi thresholds of N-l-lactoyl-Phe in these solutions were 50, 50, and 25 mg/L, respectively. N-l-Lactoyl-Phe was quantified in traditional Chinese fermented foods as 30.12 ± 0.28 mg/kg in preserved pickles, 14.11 ± 0.14 mg/kg in soybean paste, 4.87 ± 0.16 mg/kg in fermented bean, 0.71 ± 0.11 mg/kg in rice vinegar, and 20.34 ± 0.18 mg/kg in soy sauce. These results revealed the potential of N-l-lactoyl-Phe as a taste enhancer, presenting a new opportunity for the food industry.
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Affiliation(s)
- Jing Wu
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, National R&D Center for Aquatic Product Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Jingrong Gao
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Junjie Lin
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Chun Cui
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Laihao Li
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, National R&D Center for Aquatic Product Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Shan He
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, China
- Flinders Institute for Nanoscale Science and Technology, College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Charles Brennan
- School of Science STEM College, RMIT University, Melbourne 3000, Australia
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9
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Mutations in the regulatory regions result in increased streptomycin resistance and keratinase synthesis in Bacillus thuringiensis. Arch Microbiol 2021; 203:5387-5396. [PMID: 34390357 DOI: 10.1007/s00203-021-02525-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 12/29/2022]
Abstract
Keratinases are a group of proteases of great industrial significance. To take full advantage of Bacillus species as an inherent superior microbial producer of proteases, we performed the ribosome engineering to improve the keratinase synthesis capacity of the wild-type Bacillus thuringiensis by inducing streptomycin resistance. Mutant Bt(Str-O) was identified as a stable keratinase overproducer. Comparative characterization of the two strains revealed that, although the resistance to Streptomycin increased by eight-fold in MIC, the mutant's resistance to other commonly used antibiotics was not affected. Furthermore, the mutant exhibited an enhanced keratinase synthesis (1.5-fold) when cultured in a liquid LB medium. In the whole feather degradation experiment, the mutant could secret twofold keratinase into the medium, reaching 640 U/mL per 107 CFU. By contrast, no significant differences were found in the scanning electron microscopic analysis and spore formation experiment. To understand the genetic factors causing these phenotypic changes, we cloned and analyzed the rpsL gene. No mutation was observed. We subsequently determined the genome sequences of the two strains. Comparing the rpsL gene revealed that the emergence of streptomycin resistance was not necessarily dependent on the mutation(s) in the generally recognized "hotspot." Genome-wide analysis showed that the phenotypic changes of the mutant were the collective consequence of the genetic variations occurring in the regulatory regions and the non-coding RNA genes. This study demonstrated the importance of genetic changes in regulatory regions and the effectiveness of irrational ribosome engineering in creating prokaryotic microbial mutants without sufficient genetic information.
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10
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Deiana L, Rafi AA, Naidu VR, Tai CW, Bäckvall JE, Córdova A. Artificial plant cell walls as multi-catalyst systems for enzymatic cooperative asymmetric catalysis in non-aqueous media. Chem Commun (Camb) 2021; 57:8814-8817. [PMID: 34382975 DOI: 10.1039/d1cc02878b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The assembly of cellulose-based artificial plant cell wall (APCW) structures that contain different types of catalysts is a powerful strategy for the development of cascade reactions. Here we disclose an APCW catalytic system containing a lipase enzyme and nanopalladium particles that transform a racemic amine into the corresponding enantiomerically pure amide in high yield via a dynamic kinetic resolution.
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Affiliation(s)
- Luca Deiana
- Department of Natural Sciences, Mid Sweden University, Holmgatan 10, 85 179 Sundsvall, Sweden.
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11
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Wang T, Liang C, Xiao S, Li L, Xu H, An Y, Zheng M, Liu L. A Thermostable Aluminum-Tolerant Protease Produced by Feather-Degrading Bacillus thuringiensis Isolated from Tea Plantation. Protein Pept Lett 2021; 28:563-572. [PMID: 33143609 DOI: 10.2174/0929866527666201103153309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 09/22/2020] [Accepted: 09/30/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Proteases with keratinolytic activity are widely used in biotechnologies. The feather-degrading Bacillus thuringensis isolated from soil sample of a tea plantation produced high level of extracellular keratinase. OBJECTIVE This study aimed to analyze the properties by biochemical and enzymological methods to gain information for better utilization of the enzyme. METHODS The enzyme was purified with ion exchange and size exclusion chromatography. The substrate preference, optimal pH and temperature, and the effects of organic solvents and ions were checked. Circular dichroism was performed to compare the secondary structures of the native and apo-enzyme. RESULTS The enzyme worked best at 50°C, and it was an acidic serine protease with an optimal pH of 6.2. Ions Ca2+ and Mg2+ were essential for its activity. Organic solvents and other metal ions generally deactivated the enzyme in a concentration-dependent manner. However, Mn2+ and DMSO, which were frequently reported as inhibitors of protease, could activate the enzyme at low concentration (0.01 to 2 mmol/L of Mn2+; DMSO <2%, v/v). The enzyme exhibited high resistance to Al3+, which might be explained by the soil properties of its host's residence. Circular dichroism confirmed the contribution of ions to the structure and activity. CONCLUSION The enzyme was a thermostable aluminum-tolerant serine protease with unique biochemical properties.
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Affiliation(s)
- Tianwen Wang
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang 464000, China
| | - Chen Liang
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang 464000, China
| | - Sha Xiao
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang 464000, China
| | - Li Li
- Fujian Provincial University Engineering Research Center of Industrial Biocatalysis, College of Chemistry and Materials Science, Fujian Normal University, Fuzhou 350007, China
| | - Hongju Xu
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang 464000, China
| | - Yafei An
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang 464000, China
| | - Mengyuan Zheng
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang 464000, China
| | - Lu Liu
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang 464000, China
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12
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Shi K, Cao L, Liu F, Xie S, Wang S, Huang Y, Lei C, Nie Z. Amplified and label-free electrochemical detection of a protease biomarker by integrating proteolysis-triggered transcription. Biosens Bioelectron 2021; 190:113372. [PMID: 34116447 DOI: 10.1016/j.bios.2021.113372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/14/2021] [Accepted: 05/20/2021] [Indexed: 10/25/2022]
Abstract
Cell-free synthetic biology provides a promising strategy for developing high-performance biosensors by integrating with advanced testing technologies. However, the combination of synthetic biology with electrochemical testing techniques is still underdeveloped. Here, we proposed an electrochemical biosensor for the label-free and ultrasensitive detection of target protease biomarker by coupling a protease-responsive RNA polymerase (PR) for signal amplification. Taking tumor biomarker matrix metalloprotease-2 (MMP-2) as a model protease, we employed PR to transduce each proteolysis reaction mediated by MMP-2 into multiple programmable RNA outputs that can be captured by the DNA probes immobilized on a gold electrode. Moreover, the captured RNAs are designed to contain a guanine-rich sequence that can form G-quadruplex and bind to hemin in the presence of potassium ions. In this scenario, the activity of MMP-2 is converted and amplified into the electrochemical signals of hemin. Under the optimal conditions, this PR-based electrochemical biosensor enabled the sensitive detection of MMP-2 in a wide linear dynamic range from 10 fM to 1.0 nM, with a limit of detection of 7.1 fM. Moreover, the proposed biosensor was further applied in evaluating MMP-2 activities in different cell cultures and human tissue samples, demonstrating its potential in the analysis of protease biomarkers in complex clinical samples.
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Affiliation(s)
- Kai Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China
| | - Lei Cao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China
| | - Fang Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China
| | - Shiyi Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China
| | - Shuo Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China
| | - Yan Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China.
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China
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13
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Ahmadi S, Salehi M, Ausi S. Kinetic and thermodynamic study of aspartic protease extracted from Withania coagulans. Int Dairy J 2021. [DOI: 10.1016/j.idairyj.2020.104960] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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14
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Dong L, Qi S, Jia J, Zhang Y, Hu Y. Enantioselective resolution of (±)-1-phenylethyl acetate using the immobilized extracellular proteases from deep-sea Bacillus sp. DL-1. BIOCATAL BIOTRANSFOR 2021. [DOI: 10.1080/10242422.2021.1897579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Lu Dong
- Guangdong Key Laboratory of Marine Materia Medical, South China Sea Institute of Oceanology, Chinese Academy of Sciences, CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangzhou, PR China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, PR China
| | - Shujuan Qi
- The Affiliated Traditional Chinese Medicine Hospital of Guangzhou Medical University, Guangzhou, PR China
| | - Jianwei Jia
- International College, Guangzhou University of Chinese Medicine, Guangzhou, PR China
| | - Yun Zhang
- Guangdong Key Laboratory of Marine Materia Medical, South China Sea Institute of Oceanology, Chinese Academy of Sciences, CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangzhou, PR China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, PR China
- Equipment Public Service Center, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, PR China
| | - Yunfeng Hu
- Guangdong Key Laboratory of Marine Materia Medical, South China Sea Institute of Oceanology, Chinese Academy of Sciences, CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangzhou, PR China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, PR China
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15
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Abstract
Historically, ligase activity by proteases was theoretically derived due to their catalyst nature, and it was experimentally observed as early as around 1900. Initially, the digestive proteases, such as pepsin, chymotrypsin, and trypsin were employed to perform in vitro syntheses of small peptides. Protease-catalyzed ligation is more efficient than peptide bond hydrolysis in organic solvents, representing control of the thermodynamic equilibrium. Peptide esters readily form acyl intermediates with serine and cysteine proteases, followed by peptide bond synthesis at the N-terminus of another residue. This type of reaction is under kinetic control, favoring aminolysis over hydrolysis. Although only a few natural peptide ligases are known, such as ubiquitin ligases, sortases, and legumains, the principle of proteases as general catalysts could be adapted to engineer some proteases accordingly. In particular, the serine proteases subtilisin and trypsin were converted to efficient ligases, which are known as subtiligase and trypsiligase. Together with sortases and legumains, they turned out to be very useful in linking peptides and proteins with a great variety of molecules, including biomarkers, sugars or building blocks with non-natural amino acids. Thus, these engineered enzymes are a promising branch for academic research and for pharmaceutical progress.
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16
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Ultra-high throughput screening for novel protease specificities. Methods Enzymol 2020. [PMID: 32943144 DOI: 10.1016/bs.mie.2020.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The screening of large libraries of enzyme variants remains an essential tool in evolving biocatalysts toward improved properties for applications in medicine, chemistry, and a broad variety of other fields. Over the last decades, the technology for conducting systematic screens of arrayed members of a library of enzyme variants has made great strides in terms of increasing throughput and reducing assay volume. Here, we describe in detail an alternative to arrayed analysis, which is a screen based on density shifts in result of changed enzyme function, which allows highly parallelized screening. Specifically, we link changes in protease substrate specificity in vivo to the production of an alternative reporter protein, catalase. Depending on the catalase expression level, microcolonies of library bacteria with active protease variants contained in polymeric droplets generate an oxygen bubble, which causes a density shift in the droplet and enables it to float.
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17
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Improvement of enzymatic performance of Asclepias curassavica L. proteases by immobilization. Application to the synthesis of an antihypertensive peptide. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.05.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Gimenez-Dejoz J, Tsuchiya K, Tateishi A, Motoda Y, Kigawa T, Asano Y, Numata K. Computational study on the polymerization reaction of d-aminopeptidase for the synthesis of d-peptides. RSC Adv 2020; 10:17582-17592. [PMID: 35515590 PMCID: PMC9053604 DOI: 10.1039/d0ra01138j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/28/2020] [Indexed: 02/02/2023] Open
Abstract
Almost all natural proteins are composed exclusively of l-amino acids, and this chirality influences their properties, functions, and selectivity. Proteases can recognize proteins composed of l-amino acids but display lower selectivity for their stereoisomers, d-amino acids. Taking this as an advantage, d-amino acids can be used to develop polypeptides or biobased materials with higher biostability. Chemoenzymatic peptide synthesis is a technique that uses proteases as biocatalysts to synthesize polypeptides, and d-stereospecific proteases can be used to synthesize polypeptides incorporating d-amino acids. However, engineered proteases with modified catalytic activities are required to allow the incorporation of d-amino acids with increased efficiency. To understand the stereospecificity presented by proteases and their involvement in polymerization reactions, we studied d-aminopeptidase. This enzyme displays the ability to efficiently synthesize poly d-alanine-based peptides under mild conditions. To elucidate the mechanisms involved in the unique specificity of d-aminopeptidase, we performed quantum mechanics/molecular mechanics simulations of its polymerization reaction and determined the energy barriers presented by the chiral substrates. The enzyme faces higher activation barriers for the acylation and aminolysis reactions with the l-stereoisomer than with the d-substrate (10.7 and 17.7 kcal mol-1 higher, respectively). The simulation results suggest that changes in the interaction of the substrate with Asn155 influence the stereospecificity of the polymerization reaction.
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Affiliation(s)
- Joan Gimenez-Dejoz
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science 2-1 Hirosawa Wako-shi Saitama 351-0198 Japan
| | - Kousuke Tsuchiya
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science 2-1 Hirosawa Wako-shi Saitama 351-0198 Japan
| | - Ayaka Tateishi
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science 2-1 Hirosawa Wako-shi Saitama 351-0198 Japan
| | - Yoko Motoda
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science 2-1 Hirosawa Wako-shi Saitama 351-0198 Japan
| | - Takanori Kigawa
- Laboratory for Cellular Structural Biology, RIKEN Center for Biosystems Dynamics Research 1-7-22 Suehiro-cho, Tsurumi Yokohama 230-0045 Japan
| | - Yasuhisa Asano
- Biotechnology Research Center, Department of Biotechnology, Toyama Prefectural University 5180 Kurokawa Imizu Toyama 939-0398 Japan
| | - Keiji Numata
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science 2-1 Hirosawa Wako-shi Saitama 351-0198 Japan
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19
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Centore R, Totsingan F, Amason AC, Lyons S, Zha RH, Gross RA. Self-Assembly-Assisted Kinetically Controlled Papain-Catalyzed Formation of mPEG- b-Phe(Leu) x. Biomacromolecules 2020; 21:493-507. [PMID: 31820938 DOI: 10.1021/acs.biomac.9b01237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Self-assembling peptide materials are promising next-generation materials with applications that include tissue engineering scaffolds, drug delivery, bionanomedicine, and enviro-responsive materials. Despite these advances, synthetic methods to form peptides and peptide-polymer conjugates still largely rely on solid-phase peptide synthesis (SPPS) and N-carboxyanhydride ring-opening polymerization (NCA-ROP), while green methods remain largely undeveloped. This work demonstrates a protease-catalyzed peptide synthesis (PCPS) capable of directly grafting leucine ethyl ester (Leu-OEt) from the C-terminus of a methoxy poly(ethylene glycol)-phenylalanine ethyl ester macroinitiator in a one-pot, aqueous reaction. By using the natural tendency of the growing hydrophobic peptide segment to self-assemble, a large narrowing of the (Leu)x distributions for both mPEG45-b-Phe(Leu)x and oligo(Leu)x coproducts, relative to oligo(Leu)x synthesized in the absence of a macroinitiator (mPEG45-Phe-OEt), was achieved. A mechanism is described where in situ β-sheet coassembly of mPEG45-b-Phe(Leu)x and oligo(Leu)x coproducts during polymerization prevents peptide hydrolysis, providing a means to control the degree of polymerization (DP) and dispersity of diblock (Leu)x segments (matrix-assisted laser desorption time-of-flight (MALDI-TOF) x = 5.1, dispersity ≤ 1.02). The use of self-assembly to control the uniformity of peptides synthesized by PCPS paves the way for precise peptide block copolymer architectures with various polymer backbones and amino acid compositions synthesized by a green process.
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20
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Khalil AB, Qarawi S, Sivakumar N. Genomic comparison of anoxybacillus flavithermus AK1, a thermophilic bacteria, with other strains. Enzyme Microb Technol 2019; 131:109385. [PMID: 31615674 DOI: 10.1016/j.enzmictec.2019.109385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 11/30/2022]
Abstract
From ecological and industrial perspectives, Anoxybacillus flavithermus species that lives in a thermophilic environment, are extremely important bacteria due to their potential in producing highly interesting compounds and enzymes. In order to understand the genetic makeup of these thermophiles, we have performed a comparative genomics study of 12 genome-sequenced strains of Anoxybacillus flavithermus bacteria. The genome size of Anoxybacillus flavithermus strains is from 2.5Mbp to 3.7Mbp and on average containing a low percentage of G + C genomic content (˜41.9%). We show that, on the basis of the total gene-content, Anoxybacillus flavithermus strains are grouped in three different subgroups. In the future, it would be interesting to explore these strain subgroups to further understand the lifestyle of thermophilic bacteria. Focussing on the Anoxybacillus flavithermus AK1 strain, which was isolated from a Hot Spring in Saudi Arabia and closely related to A. flavithermus NBRC strain, we identified a unique list of 75 genes specific to AK1 strain, of which 63 of them have homologs in other taxonomically related species. We speculate that these AK1-specific genes might be resulted due to horizontal gene transfer from other bacteria in order to adapt to the extreme environmental conditions. Moreover, we predicted three potential secondary metabolite gene clusters in the AK1 strain that further need to be experimentally characterised. Genomic annotation, secondary metabolite gene clusters and outcomes of the strain genomic comparisons from this study would be the basis for the strain-specific mathematical model for exploiting the metabolism for the industrial and ecological applications.
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Affiliation(s)
- Amjad B Khalil
- Department of Life Sciences, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia.
| | - Sami Qarawi
- Biosciences Core Lab, King Abdullah University of Science and Technology, Thuwal, Jeddah, Saudi Arabia
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21
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Gimenez-Dejoz J, Tsuchiya K, Numata K. Insights into the Stereospecificity in Papain-Mediated Chemoenzymatic Polymerization from Quantum Mechanics/Molecular Mechanics Simulations. ACS Chem Biol 2019; 14:1280-1292. [PMID: 31063345 DOI: 10.1021/acschembio.9b00259] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chemoenzymatic peptide synthesis is an efficient and clean method to generate polypeptides for new applications in the fields of biomedical and functional materials. However, this enzyme-mediated synthesis is dependent on the reaction rate of the protease biocatalyst, which is essentially determined by the natural substrate specificity of the enzyme. Papain, one of the most studied cysteine proteases, is extensively used for the chemoenzymatic synthesis of new polypeptides. Similar to most proteases, papain displays high stereospecificity toward l-amino acids, with limited reactivity for the d-stereoisomer counterparts. However, the incorporation of d-amino acids into peptides is a promising approach to increase their biostability by conferring intrinsic resistance to proteolysis. Herein, we determined the stereospecific-limiting step of the papain-mediated polymerization reaction with the chiral substrates l/d-alanine ethyl ester (Ala-OEt). Afterward, we used Quantum Mechanics/Molecular Mechanics (QM/MM) simulations to study the catalytic mechanism at atomic level of detail and investigate the origin of its stereospecificity. The experimental and computational results show that papain is able to attack both l- and d-stereoisomers of Ala-OEt, forming an enzyme-substrate intermediate, and that the two reactions display a similar activation barrier. Moreover, we found that the reduced catalytic activity of papain in the polymerization of d-amino acids arises from the aminolysis step of the reaction, in which l-Ala-OEt displays a significantly lower free-energy barrier (12 kcal/mol) than d-Ala-OEt (30 kcal/mol). Further simulations suggest that the main factor affecting the polymerization of d-amino acids is the configuration of the d-acyl-intermediate enzyme, and in particular the orientation of its methyl group, which hinders the nucleophilic attack by other monomers and thus the formation of polypeptides.
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Affiliation(s)
- Joan Gimenez-Dejoz
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Kousuke Tsuchiya
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Keiji Numata
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
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22
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Razzaq A, Shamsi S, Ali A, Ali Q, Sajjad M, Malik A, Ashraf M. Microbial Proteases Applications. Front Bioeng Biotechnol 2019; 7:110. [PMID: 31263696 PMCID: PMC6584820 DOI: 10.3389/fbioe.2019.00110] [Citation(s) in RCA: 190] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/01/2019] [Indexed: 11/13/2022] Open
Abstract
The use of chemicals around the globe in different industries has increased tremendously, affecting the health of people. The modern world intends to replace these noxious chemicals with environmental friendly products for the betterment of life on the planet. Establishing enzymatic processes in spite of chemical processes has been a prime objective of scientists. Various enzymes, specifically microbial proteases, are the most essentially used in different corporate sectors, such as textile, detergent, leather, feed, waste, and others. Proteases with respect to physiological and commercial roles hold a pivotal position. As they are performing synthetic and degradative functions, proteases are found ubiquitously, such as in plants, animals, and microbes. Among different producers of proteases, Bacillus sp. are mostly commercially exploited microbes for proteases. Proteases are successfully considered as an alternative to chemicals and an eco-friendly indicator for nature or the surroundings. The evolutionary relationship among acidic, neutral, and alkaline proteases has been analyzed based on their protein sequences, but there remains a lack of information that regulates the diversity in their specificity. Researchers are looking for microbial proteases as they can tolerate harsh conditions, ways to prevent autoproteolytic activity, stability in optimum pH, and substrate specificity. The current review focuses on the comparison among different proteases and the current problems faced during production and application at the industrial level. Deciphering these issues would enable us to promote microbial proteases economically and commercially around the world.
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Affiliation(s)
- Abdul Razzaq
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Sadia Shamsi
- School of Medicine, Medical Sciences and Nutrition, The Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Arfan Ali
- 1-FB, Genetics, Four Brothers Group, Lahore, Pakistan
| | - Qurban Ali
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Sajjad
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Arif Malik
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Ashraf
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
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23
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Simon AH, Liebscher S, Aumüller TH, Treblow D, Bordusa F. Application of a Dual Internally Quenched Fluorogenic Substrate in Screening for D-Arginine Specific Proteases. Front Microbiol 2019; 10:711. [PMID: 31001242 PMCID: PMC6456654 DOI: 10.3389/fmicb.2019.00711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 03/21/2019] [Indexed: 11/13/2022] Open
Abstract
The application of D-stereospecific proteases (DSPs) in resolution of racemic amino acids and in the semisynthesis of proteins has been a successful strategy. The main limitation for a broader application is, however, the accessibility of suitable DSPs covering multiple substrate specificities. To identify DSPs with novel primary substrate preferences, a fast specificity screening method using the easily accessible internally quenched fluorogenic substrate aminobenzoyl-D-arginyl-D-alanyl-p-nitroanilide was developed. By monitoring both UV/vis-absorbance and fluorescence signals at the same time it allows to detect two distinct D-amino acid substrate specificities simultaneously and separately with respect to the individual specificities. In order to identify novel DSP specificities for synthesis applications, DSPs specific for D-arginine were of special interest due to their potential ability as catalysts for substrate mimetics-mediated peptide and protein ligations. D-alanine in the substrate served as positive control and reference based on its known acceptance by numerous DSPs. In silico analysis suggested that DSPs are predominantly present in gram-positive microorganisms, therefore this study focused on the bacilli strains Bacillus thuringiensis and Bacillus subtilis as potential hosts of D-Arg-specific DSPs. While protease activities toward D-alanine were found in both organisms, a novel and so far unknown D-arginine specific DSP was detected within the culture supernatant of B. thuringiensis. Enrichment of this activity via cation exchange and size exclusion chromatography allowed isolation and further characterization of this novel enzyme consisting of a molecular mass of 37.7 kDa and an enzymatic activity of 8.3 U mg-1 for cleaving the D-Arg|D-Ala bond in the detecting substrate. Independent experiments also showed that the identified enzyme shows similarities to the class of penicillin binding proteins. In future applications this enzyme will be a promising starting point for the development of novel strategies for the semisynthesis of all-L-proteins.
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Affiliation(s)
- Andreas H Simon
- Institute of Biochemistry/Biotechnology, Charles Tanford Protein Centre, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Sandra Liebscher
- Institute of Biochemistry/Biotechnology, Charles Tanford Protein Centre, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Tobias H Aumüller
- Max Planck Research Unit for Enzymology of Protein Folding, Halle, Germany
| | - Dennis Treblow
- Institute of Biochemistry/Biotechnology, Charles Tanford Protein Centre, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Frank Bordusa
- Institute of Biochemistry/Biotechnology, Charles Tanford Protein Centre, Martin-Luther-University Halle-Wittenberg, Halle, Germany
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24
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Wang F, Zhu J, Yan T, Pei X, Zhang F, Linhardt RJ. Amphiphilic bromelain-synthesized oligo-phenylalanine grafted with methoxypolyethylene glycol possessing stabilizing thermo-responsive emulsion properties. J Colloid Interface Sci 2019; 538:1-14. [PMID: 30481653 DOI: 10.1016/j.jcis.2018.11.082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 11/16/2018] [Accepted: 11/22/2018] [Indexed: 12/20/2022]
Abstract
A thermo-responsive amphiphile was developed from oligo-phenylalanine [oligo(Phe)]. The hydrophobic moiety of the amphiphile, oligo(Phe) was synthesized via reverse hydrolysis catalyzed by bromelain in dimethyl sulfoxide and dioxane solutions. The production of oligo(Phe) increased by 80.7% by screening suitable reaction conditions. The average degree of polymerization of oligo(Phe) was determined to be four by 1H NMR. By grafting with aldehyde-ended methoxypolyethylene glycol (mPEG), oligo(Phe) was converted to amphiphilic oligo(Phe)-mPEG. The surface tension of oligo(Phe)-mPEG solution increased with decreasing chain length of the mPEG moiety. Cytotoxicity studies showed oligo(Phe)-mPEGs are biocompatible. On varying temperature, a reversible phase transition of oligo(Phe)-mPEG solutions could be observed. N-octane-in-water emulsions and 0.5% beta-carotene containing squalene-in-water emulsions stabilized by oligo(Phe)-mPEGs occurred at 25 °C but de-emulsification took place at >40 °C. Emulsification could be restored once the separated mixture cooled and re-homogenized. The emulsification/de-emulsification cycling could be repeated many times. The time required for de-emulsification decreased with elevated temperature but increased with a reduced concentration of oligo(Phe)-mPEGs and a reduction in the chain length of the mPEG moiety.
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Affiliation(s)
- Feng Wang
- School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122, China.
| | - Jinwen Zhu
- School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122, China
| | - Tingting Yan
- School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122, China
| | - Xiaomei Pei
- School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122, China
| | - Fuming Zhang
- Department of Chemistry and Chemical Biology, Departments of Chemical and Biological Engineering, Biology and Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Robert J Linhardt
- Department of Chemistry and Chemical Biology, Departments of Chemical and Biological Engineering, Biology and Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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25
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Abstract
Site-specific incorporation of artificial functionalities into protein targets is an important tool in both basic and applied research and can be a major challenge to protein chemists. Chemical labeling methods often targeting multiple positions within a protein and therefore suffer from lack of specificity. Enzymatic protein modification is an attractive alternative due to the inherent regioselectivity and stereoselectivity of enzymes. In this contribution we describe the application of the highly specific trypsin variant named trypsiligase for the site-specific modification of virtual any target protein. We present two general routes of modification resulting in either N- or C-terminal functionalized protein products. Both reaction regimes proceed under mild and bioorthogonal conditions in a short period of time which result in homogeneously modified proteins bearing the artificial functionality exclusively at the desired position. We detail protocols for the expression and purification of trypsiligase as well as the construction of peptide or acyl donor ester probes used as substrates for the biocatalyst. In addition, we provide instructions how to perform the ultimate bioconjugation reactions and finally render assistance for the qualitative and quantitative analysis of the reaction course and outcome.
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Affiliation(s)
- Sandra Liebscher
- Charles-Tanford-Protein Center, Institute of Biochemistry/Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Frank Bordusa
- Charles-Tanford-Protein Center, Institute of Biochemistry/Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle, Germany.
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26
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Abstract
Site-specific incorporation of nonproteinogenic functionalities into protein targets is an important tool in both basic and applied research and represents a major challenge to protein chemists. Chemical labeling methods often target multiple positions within a protein and therefore suffer from a lack of specificity. Enzymatic protein modification is an attractive alternative due to the inherent regioselectivity and stereoselectivity of enzymes. In this chapter we describe the application of the highly specific trypsin variant trypsiligase for the site-specific modification of virtual any target protein. We present two general routes of modification resulting in either N- or C-terminal functionalized protein products. Reactions rapidly proceed under mild conditions and result in homogeneously modified proteins bearing the artificial functionality exclusively at the desired position. We detail protocols for the expression and purification of trypsiligase as well as the synthesis of peptide (ester) substrates. In addition, we provide instructions for the bioconjugation reactions and for the qualitative and quantitative analysis of reaction progress and efficiency.
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27
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Yin DY, Pan J, Zhu J, Liu YY, Xu JH. A green-by-design bioprocess forl-carnosine production integrating enzymatic synthesis with membrane separation. Catal Sci Technol 2019. [DOI: 10.1039/c9cy01622h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This simple and clean bioprocess enables the economically attractive and environmentally benign production of the bioactive dipeptidel-Car.
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Affiliation(s)
- Dong-Ya Yin
- State Key Laboratory of Bioreactor Engineering
- East China University of Science and Technology
- Shanghai 200237
- P.R. China
| | - Jiang Pan
- State Key Laboratory of Bioreactor Engineering
- East China University of Science and Technology
- Shanghai 200237
- P.R. China
| | - Jie Zhu
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- P.R. China
| | - You-Yan Liu
- College of Chemistry and Chemical Engineering
- Guangxi University
- Nanning 530004
- P.R. China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering
- East China University of Science and Technology
- Shanghai 200237
- P.R. China
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28
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Elsner C, Lohan M, Griebel J, Decker U. Photo-stimulated leaving group isomerization of acyl donor esters in protease-catalyzed hydrolysis reactions. BIOCATAL BIOTRANSFOR 2018. [DOI: 10.1080/10242422.2018.1427739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
| | - Marcus Lohan
- Leibniz Institute of Surface Engineering, Leipzig, Germany
| | - Jan Griebel
- Leibniz Institute of Surface Engineering, Leipzig, Germany
| | - Ulrich Decker
- Leibniz Institute of Surface Engineering, Leipzig, Germany
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29
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Sharifzadeh G, Hosseinkhani H. Biomolecule-Responsive Hydrogels in Medicine. Adv Healthc Mater 2017; 6. [PMID: 29057617 DOI: 10.1002/adhm.201700801] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/17/2017] [Indexed: 12/19/2022]
Abstract
Recent advances and applications of biomolecule-responsive hydrogels, namely, glucose-responsive hydrogels, protein-responsive hydrogels, and nucleic-acid-responsive hydrogels are highlighted. However, achieving the ultimate purpose of using biomolecule-responsive hydrogels in preclinical and clinical areas is still at the very early stage and calls for more novel designing concepts and advance ideas. On the way toward the real/clinical application of biomolecule-responsive hydrogels, plenty of factors should be extensively studied and examined under both in vitro and in vivo conditions. For example, biocompatibility, biointegration, and toxicity of biomolecule-responsive hydrogels should be carefully evaluated. From the living body's point of view, biocompatibility is seriously depended on the interactions at the tissue/polymer interface. These interactions are influenced by physical nature, chemical structure, surface properties, and degradation of the materials. In addition, the developments of advanced hydrogels with tunable biological and mechanical properties which cause no/low side effects are of great importance.
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Affiliation(s)
- Ghorbanali Sharifzadeh
- Department of Polymer Engineering; Faculty of Chemical Engineering; Universiti Teknologi Malaysia; 81310 Johor Malaysia
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30
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Białkowska AM, Morawski K, Florczak T. Extremophilic proteases as novel and efficient tools in short peptide synthesis. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/s10295-017-1961-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Abstract
The objective of this review is to outline the crucial role that peptides play in various sectors, including medicine. Different ways of producing these compounds are discussed with an emphasis on the benefits offered by industrial enzyme biotechnology. This paper describes mechanisms of peptide bond formation using a range of proteases with different active site structures. Importantly, these enzymes may be further improved chemically and/or genetically to make them better suited for their various applications and process conditions. The focus is on extremophilic proteases, whose potential does not seem to have been fully appreciated to date. The structure of these proteins is somewhat different from that of the common commercially available enzymes, making them effective at high salinity and high or low temperatures, which are often favorable to peptide synthesis. Examples of such enzymes include halophilic, thermophilic, and psychrophilic proteases; this paper also mentions some promising catalytic proteins which require further study in this respect.
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Affiliation(s)
- Aneta M Białkowska
- 0000 0004 0620 0652 grid.412284.9 Institute of Technical Biochemistry Lodz University of Technology Stefanowskiego Street 4/10 90-924 Lodz Poland
| | - Krzysztof Morawski
- 0000 0004 0620 0652 grid.412284.9 Institute of Technical Biochemistry Lodz University of Technology Stefanowskiego Street 4/10 90-924 Lodz Poland
| | - Tomasz Florczak
- 0000 0004 0620 0652 grid.412284.9 Institute of Technical Biochemistry Lodz University of Technology Stefanowskiego Street 4/10 90-924 Lodz Poland
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31
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Tsuchiya K, Numata K. Chemoenzymatic Synthesis of Polypeptides for Use as Functional and Structural Materials. Macromol Biosci 2017; 17. [PMID: 28722358 DOI: 10.1002/mabi.201700177] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 06/20/2017] [Indexed: 12/13/2022]
Abstract
Polypeptides inspired by the natural functional and structural proteins present in living systems are promising materials for various fields in terms of their versatile functionality and physical properties. Designing and synthesizing mimetic sequences of specific peptide motifs in proteins are important for exploring the functionality of natural proteins. Chemoenzymatic polymerization, which utilizes aminolysis (i.e., the reverse reaction of hydrolysis catalyzed by proteases), is a useful technique for synthesizing artificial polypeptide materials and has several advantages, including facile synthesis protocols, environmental friendliness, scalability, and atom economy. In this review, recent progress in chemoenzymatic polypeptide synthesis for the production of functional and structural materials for various applications is summarized in conjunction with the current status of technical challenges in the field.
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Affiliation(s)
- Kousuke Tsuchiya
- Enzyme Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Keiji Numata
- Enzyme Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
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32
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Abstract
The formation of well-defined protein bioconjugates is critical for many studies and technologies in chemical biology. Tried-and-true methods for accomplishing this typically involve the targeting of cysteine residues, but the rapid growth of contemporary bioconjugate applications has required an expanded repertoire of modification techniques. One very powerful set of strategies involves the modification of proteins at their N termini, as these positions are typically solvent exposed and provide chemically distinct sites for many protein targets. Several chemical techniques can be used to modify N-terminal amino acids directly or convert them into unique functional groups for further ligations. A growing number of N-terminus-specific enzymatic ligation strategies have provided additional possibilities. This Perspective provides an overview of N-terminal modification techniques and the chemical rationale governing each. Examples of specific N-terminal protein conjugates are provided, along with their uses in a number of diverse biological applications.
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33
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Wu X, Yang C, Ge J. Green synthesis of enzyme/metal-organic framework composites with high stability in protein denaturing solvents. BIORESOUR BIOPROCESS 2017; 4:24. [PMID: 28596935 PMCID: PMC5438438 DOI: 10.1186/s40643-017-0154-8] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 05/11/2017] [Accepted: 05/12/2017] [Indexed: 01/24/2023] Open
Abstract
OBJECTIVES Enzyme/metal-organic framework composites with high stability in protein denaturing solvents were reported in this study. RESULTS Encapsulation of enzyme in metal-organic frameworks (MOFs) via co-precipitation process was realized, and the generality of the synthesis was validated by using cytochrome c, horseradish peroxidase, and Candida antarctica lipase B as model enzymes. The stability of encapsulated enzyme was greatly increased after immobilization on MOFs. Remarkably, when exposed to protein denaturing solvents including dimethyl sulfoxide, dimethyl formamide, methanol, and ethanol, the enzyme/MOF composites still preserved almost 100% of activity. In contrast, free enzymes retained no more than 20% of their original activities at the same condition. This study shows the extraordinary protecting effect of MOF shell on increasing enzyme stability at extremely harsh conditions. CONCLUSION The enzyme immobilized in MOF exhibited enhanced thermal stability and high tolerance towards protein denaturing organic solvents.
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Affiliation(s)
- Xiaoling Wu
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
| | - Cheng Yang
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
| | - Jun Ge
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
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34
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Wieczorek R, Adamala K, Gasperi T, Polticelli F, Stano P. Small and Random Peptides: An Unexplored Reservoir of Potentially Functional Primitive Organocatalysts. The Case of Seryl-Histidine. Life (Basel) 2017; 7:E19. [PMID: 28397774 PMCID: PMC5492141 DOI: 10.3390/life7020019] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 04/03/2017] [Accepted: 04/05/2017] [Indexed: 12/11/2022] Open
Abstract
Catalysis is an essential feature of living systems biochemistry, and probably, it played a key role in primordial times, helping to produce more complex molecules from simple ones. However, enzymes, the biocatalysts par excellence, were not available in such an ancient context, and so, instead, small molecule catalysis (organocatalysis) may have occurred. The best candidates for the role of primitive organocatalysts are amino acids and short random peptides, which are believed to have been available in an early period on Earth. In this review, we discuss the occurrence of primordial organocatalysts in the form of peptides, in particular commenting on reports about seryl-histidine dipeptide, which have recently been investigated. Starting from this specific case, we also mention a peptide fragment condensation scenario, as well as other potential roles of peptides in primordial times. The review actually aims to stimulate further investigation on an unexplored field of research, namely one that specifically looks at the catalytic activity of small random peptides with respect to reactions relevant to prebiotic chemistry and early chemical evolution.
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Affiliation(s)
- Rafal Wieczorek
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Katarzyna Adamala
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Tecla Gasperi
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy.
| | - Fabio Polticelli
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy.
- National Institute of Nuclear Physics, Roma Tre Section, Via della Vasca Navale 84, 00146 Rome, Italy.
| | - Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Campus Ecotekne (S.P. 6 Lecce-Monteroni), 73100 Lecce, Italy.
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35
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Effect of enzyme load and catalyst particle size on the diffusional restrictions in reactions of synthesis and hydrolysis catalyzed by α-chymotrypsin immobilized into glyoxal-agarose. Process Biochem 2017. [DOI: 10.1016/j.procbio.2016.12.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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36
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Nuijens T, Toplak A, Quaedflieg PJLM, Drenth J, Wu B, Janssen DB. Engineering a Diverse Ligase Toolbox for Peptide Segment Condensation. Adv Synth Catal 2016. [DOI: 10.1002/adsc.201600774] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Timo Nuijens
- EnzyPep B.V.; Brightlands Campus; Urmonderbaan 22 6167 RD Geleen The Netherlands
| | - Ana Toplak
- EnzyPep B.V.; Brightlands Campus; Urmonderbaan 22 6167 RD Geleen The Netherlands
- Biotransformation and Biocatalysis, Groningen Biomolecular Science and Biotechnology Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | | | - Jeroen Drenth
- Biotransformation and Biocatalysis, Groningen Biomolecular Science and Biotechnology Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Bian Wu
- Biotransformation and Biocatalysis, Groningen Biomolecular Science and Biotechnology Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
- Present address: CAS Key Laboratory of Microbial Physiology and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, China, and State Key Laboratory of Transduction Technology; Chinese Academy of Sciences; China
| | - Dick B. Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Science and Biotechnology Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
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37
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Patil U, Mokashe N, Chaudhari A. Detergent-compatible, organic solvent-tolerant alkaline protease from Bacillus circulans MTCC 7942: Purification and characterization. Prep Biochem Biotechnol 2016; 46:56-64. [PMID: 25356983 DOI: 10.1080/10826068.2014.979205] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Proteases are now recognized as the most indispensable industrial biocatalyst owing to their diverse microbial sources and innovative applications. In the present investigation, a thermostable, organic solvent-tolerant, alkaline serine protease from Bacillus circulans MTCC 7942, was purified and characterized. The protease was purified to 37-fold by a three-step purification scheme with 39% recovery. The optimum pH and temperature for protease was 10 and 60 °C, respectively. The apparent molecular mass of the purified enzyme was 43 kD as revealed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The Km and Vmax values using casein-substrate were 3.1 mg/mL and 1.8 µmol/min, respectively. The protease remained stable in the presence of organic solvents with higher (>3.2) log P value (cyclohexane, n-octane, n-hexadecane, n-decane, and n-dodecane), as compared to organic solvents with lower (<3.2) log P value (acetone, butanol, benzene, chloroform, toluene). Remarkably, the protease showed profound stability even in the presence of organic solvents with less log P values (glycerol, dimethyl sulfate [DMSO], p-xylene), indicating the possibility of nonaqueous enzymatic applications. Also, protease activity was improved in the presence of metal ions (Ca(2+), Mg(2+), Mn(2+)); enhanced by biosurfactants; hardly affected by bleaching agents, oxidizing agents, and chemical surfactants; and stable in commercial detergents. In addition, a protease-detergent formulation effectively washed out egg and blood stains as compared to detergent alone. The protease was suitable for various commercial applications like processing of gelatinous film and as a compatible additive to detergent formulation with its operative utility in hard water.
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Affiliation(s)
- Ulhas Patil
- a Department of Microbiology , R. C. Patel A. C. S. College , Shirpur , India
| | - Narendra Mokashe
- a Department of Microbiology , R. C. Patel A. C. S. College , Shirpur , India
| | - Ambalal Chaudhari
- b School of Life Sciences , North Maharashtra University , Jalgaon , India
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38
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Toplak A, Nuijens T, Quaedflieg PJLM, Wu B, Janssen DB. Peptiligase, an Enzyme for Efficient Chemoenzymatic Peptide Synthesis and Cyclization in Water. Adv Synth Catal 2016. [DOI: 10.1002/adsc.201600017] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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39
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Cummings CS, Murata H, Matyjaszewski K, Russell AJ. Polymer-Based Protein Engineering Enables Molecular Dissolution of Chymotrypsin in Acetonitrile. ACS Macro Lett 2016; 5:493-497. [PMID: 35607221 DOI: 10.1021/acsmacrolett.6b00137] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
While most effective in aqueous environments, enzymes are also able to catalyze reactions in essentially anhydrous organic media. Enzyme activity in organic solvents is limited as a result of inefficient substrate binding, lack of solubility, and inactivation by hydrophilic anhydrous solvents. With these facts in mind, atom transfer radical polymerization was used to synthesize chymotrypsin-poly(2-(dimethylamino)ethyl methacrylate) (CT-pDMAEMA) conjugates designed to be soluble and active in acetonitrile. CT-pDMAEMA solubility in organic solvents and the rate of CT-pDMAEMA-catalyzed transesterification in acetonitrile were examined at a range of water (0-15 M) and propanol (0.01-5 M) concentrations. The conjugates were soluble at the molecular scale in several organic solvents, exhibited good substrate binding with N-acetyl l-phenylalanine thiophenylester (KM as low as 17 mM), and had an activity (peak activity 330 μM/min/mg enzyme) many orders of magnitude higher than that of the insoluble native enzyme.
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Affiliation(s)
- Chad S. Cummings
- Center
for Polymer-based Protein Engineering, ICES, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
- Department
of Biomedical Engineering, Scott Hall 4N201, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Hironobu Murata
- Center
for Polymer-based Protein Engineering, ICES, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Krzysztof Matyjaszewski
- Center
for Polymer-based Protein Engineering, ICES, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
- Department
of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Alan J. Russell
- Center
for Polymer-based Protein Engineering, ICES, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
- Department
of Biomedical Engineering, Scott Hall 4N201, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
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40
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Tsuchiya K, Numata K. Papain-Catalyzed Chemoenzymatic Synthesis of Telechelic Polypeptides Using Bis(Leucine Ethyl Ester) Initiator. Macromol Biosci 2016; 16:1001-8. [DOI: 10.1002/mabi.201600005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 01/27/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Kousuke Tsuchiya
- Enzyme Research Team; Biomass Engineering Research Division; RIKEN Center for Sustainable Resource Science; 2-1 Hirosawa Wako, Saitama 351-0198 Japan
| | - Keiji Numata
- Enzyme Research Team; Biomass Engineering Research Division; RIKEN Center for Sustainable Resource Science; 2-1 Hirosawa Wako, Saitama 351-0198 Japan
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41
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Chen S, Land H, Berglund P, Humble MS. Stabilization of an amine transaminase for biocatalysis. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2015.11.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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42
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Shoda SI, Uyama H, Kadokawa JI, Kimura S, Kobayashi S. Enzymes as Green Catalysts for Precision Macromolecular Synthesis. Chem Rev 2016; 116:2307-413. [PMID: 26791937 DOI: 10.1021/acs.chemrev.5b00472] [Citation(s) in RCA: 303] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The present article comprehensively reviews the macromolecular synthesis using enzymes as catalysts. Among the six main classes of enzymes, the three classes, oxidoreductases, transferases, and hydrolases, have been employed as catalysts for the in vitro macromolecular synthesis and modification reactions. Appropriate design of reaction including monomer and enzyme catalyst produces macromolecules with precisely controlled structure, similarly as in vivo enzymatic reactions. The reaction controls the product structure with respect to substrate selectivity, chemo-selectivity, regio-selectivity, stereoselectivity, and choro-selectivity. Oxidoreductases catalyze various oxidation polymerizations of aromatic compounds as well as vinyl polymerizations. Transferases are effective catalysts for producing polysaccharide having a variety of structure and polyesters. Hydrolases catalyzing the bond-cleaving of macromolecules in vivo, catalyze the reverse reaction for bond forming in vitro to give various polysaccharides and functionalized polyesters. The enzymatic polymerizations allowed the first in vitro synthesis of natural polysaccharides having complicated structures like cellulose, amylose, xylan, chitin, hyaluronan, and chondroitin. These polymerizations are "green" with several respects; nontoxicity of enzyme, high catalyst efficiency, selective reactions under mild conditions using green solvents and renewable starting materials, and producing minimal byproducts. Thus, the enzymatic polymerization is desirable for the environment and contributes to "green polymer chemistry" for maintaining sustainable society.
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Affiliation(s)
- Shin-ichiro Shoda
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University , Aoba-ku, Sendai 980-8579, Japan
| | - Hiroshi Uyama
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University , Yamadaoka, Suita 565-0871, Japan
| | - Jun-ichi Kadokawa
- Department of Chemistry, Biotechnology, and Chemical Engineering, Graduate School of Science and Engineering, Kagoshima University , Korimoto, Kagoshima 890-0065, Japan
| | - Shunsaku Kimura
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University , Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Shiro Kobayashi
- Center for Fiber & Textile Science, Kyoto Institute of Technology , Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
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43
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Ageitos JM, Yazawa K, Tateishi A, Tsuchiya K, Numata K. The Benzyl Ester Group of Amino Acid Monomers Enhances Substrate Affinity and Broadens the Substrate Specificity of the Enzyme Catalyst in Chemoenzymatic Copolymerization. Biomacromolecules 2015; 17:314-23. [PMID: 26620763 DOI: 10.1021/acs.biomac.5b01430] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The chemoenzymatic polymerization of amino acid monomers by proteases involves a two-step reaction: the formation of a covalent acyl-intermediate complex between the protease and the carboxyl ester group of the monomer and the subsequent deacylation of the complex by aminolysis to form a peptide bond. Although the initiation with the ester group of the monomer is an important step, the influence of the ester group on the polymerization has not been studied in detail. Herein, we studied the effect of the ester groups (methyl, ethyl, benzyl, and tert-butyl esters) of alanine and glycine on the synthesis of peptides using papain as the catalyst. Alanine and glycine were selected as monomers because of their substantially different affinities toward papain. The efficiency of the polymerization of alanine and glycine benzyl esters was much greater than that of the other esters. The benzyl ester group therefore allowed papain to equally polymerize alanine and glycine, even though the affinity of alanine toward papain is substantially higher. The characterization of the copolymers of alanine and glycine in terms of the secondary structure and thermal properties revealed that the thermal stability of the peptides depends on the amino acid composition and resultant secondary structure. The current results indicate that the nature of the ester group drastically affects the polymerization efficiency and broadens the substrate specificity of the protease.
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Affiliation(s)
- Jose Manuel Ageitos
- Enzyme Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Kenjiro Yazawa
- Enzyme Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Ayaka Tateishi
- Enzyme Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Kousuke Tsuchiya
- Enzyme Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Keiji Numata
- Enzyme Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
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44
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Ma Y, Sato R, Li Z, Numata K. Chemoenzymatic Synthesis of Oligo(L-cysteine) for Use as a Thermostable Bio-Based Material. Macromol Biosci 2015; 16:151-9. [PMID: 26388290 DOI: 10.1002/mabi.201500255] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 08/13/2015] [Indexed: 11/06/2022]
Abstract
Oligomerization of thiol-unprotected L-cysteine ethyl ester (Cys-OEt) catalyzed by proteinase K in aqueous solution has been used to synthesize oligo(L-cysteine) (OligoCys) with a well-defined chemical structure and relatively large degree of polymerization (DP) up to 16-17 (average 8.8). By using a high concentration of Cys-OEt, 78.0% free thiol content was achieved. The thermal properties of OligoCys are stable, with no glass transition until 200 °C, and the decomposition temperature could be increased by oxidation. Chemoenzymatically synthesized OligoCys has great potential for use as a thermostable bio-based material with resistance to oxidation.
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Affiliation(s)
- Yinan Ma
- Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Ryota Sato
- Enzyme Research Team, Biomass Engineering Program Cooperation Division, Center for Sustainable Resource Science, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Zhibo Li
- Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China. .,School of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Keiji Numata
- Enzyme Research Team, Biomass Engineering Program Cooperation Division, Center for Sustainable Resource Science, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.
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45
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Toplak A, Nuijens T, Quaedflieg PJ, Wu B, Janssen DB. Peptide synthesis in neat organic solvents with novel thermostable proteases. Enzyme Microb Technol 2015; 73-74:20-8. [DOI: 10.1016/j.enzmictec.2015.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 02/24/2015] [Accepted: 03/03/2015] [Indexed: 11/30/2022]
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46
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N-lactoyl-amino acids are ubiquitous metabolites that originate from CNDP2-mediated reverse proteolysis of lactate and amino acids. Proc Natl Acad Sci U S A 2015; 112:6601-6. [PMID: 25964343 DOI: 10.1073/pnas.1424638112] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Despite technological advances in metabolomics, large parts of the human metabolome are still unexplored. In an untargeted metabolomics screen aiming to identify substrates of the orphan transporter ATP-binding cassette subfamily C member 5 (ABCC5), we identified a class of mammalian metabolites, N-lactoyl-amino acids. Using parallel protein fractionation in conjunction with shotgun proteomics on fractions containing N-lactoyl-Phe-forming activity, we unexpectedly found that a protease, cytosolic nonspecific dipeptidase 2 (CNDP2), catalyzes their formation. N-lactoyl-amino acids are ubiquitous pseudodipeptides of lactic acid and amino acids that are rapidly formed by reverse proteolysis, a process previously considered to be negligible in vivo. The plasma levels of these metabolites strongly correlate with plasma levels of lactate and amino acid, as shown by increased levels after physical exercise and in patients with phenylketonuria who suffer from elevated Phe levels. Our approach to identify unknown metabolites and their biosynthesis has general applicability in the further exploration of the human metabolome.
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Ageitos JM, Chuah JA, Numata K. Chemo-Enzymatic Synthesis of Linear and Branched Cationic Peptides: Evaluation as Gene Carriers. Macromol Biosci 2015; 15:990-1003. [PMID: 25828913 DOI: 10.1002/mabi.201400487] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 01/30/2015] [Indexed: 11/08/2022]
Abstract
Cationic peptides such as poly(l-lysine) and poly(l-arginine) are important tools for gene delivery since they can efficiently condense DNA. It is difficult to produce cationic peptides by recombinant bacterial expression, and its chemical synthesis requires several steps of protection/deprotection and toxic agents. Chemo-enzymatic synthesis of peptides is a clean chemistry technique that allows fast production under mild conditions. With the aim to simplify the production of cationic peptides, the present work develops an enzymatic reaction which enables the synthesis of linear cationic peptides and, through terminal functionalization with tris(2-aminoethyl)amine, of branched cationic peptide conjugates, which show improved DNA complex formation. Cytotoxicity and transfection efficiency of all the chemo-enzymatically synthesized cationic peptides are evaluated for their novel use as gene delivery agents. Synthesized peptides exhibit transfection efficiencies comparable to previously reported monodisperse peptides. Chemo-enzymatic synthesis opens the door for efficient production of cationic peptides for their use as gene delivery carriers.
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Affiliation(s)
- Jose Manuel Ageitos
- Enzyme Research Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Jo-Ann Chuah
- Enzyme Research Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Keiji Numata
- Enzyme Research Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.
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Zhang H, Wu R. Proteomic profiling of protein corona formed on the surface of nanomaterial. Sci China Chem 2015. [DOI: 10.1007/s11426-015-5395-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Goswami A, Van Lanen SG. Enzymatic strategies and biocatalysts for amide bond formation: tricks of the trade outside of the ribosome. MOLECULAR BIOSYSTEMS 2015; 11:338-53. [PMID: 25418915 PMCID: PMC4304603 DOI: 10.1039/c4mb00627e] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Amide bond-containing (ABC) biomolecules are some of the most intriguing and functionally significant natural products with unmatched utility in medicine, agriculture and biotechnology. The enzymatic formation of an amide bond is therefore a particularly interesting platform for engineering the synthesis of structurally diverse natural and unnatural ABC molecules for applications in drug discovery and molecular design. As such, efforts to unravel the mechanisms involved in carboxylate activation and substrate selection has led to the characterization of a number of structurally and functionally distinct protein families involved in amide bond synthesis. Unlike ribosomal synthesis and thio-templated synthesis using nonribosomal peptide synthetases, which couple the hydrolysis of phosphoanhydride bond(s) of ATP and proceed via an acyl-adenylate intermediate, here we discuss two mechanistically alternative strategies: ATP-dependent enzymes that generate acylphosphate intermediates and ATP-independent transacylation strategies. Several examples highlighting the function and synthetic utility of these amide bond-forming strategies are provided.
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Affiliation(s)
- Anwesha Goswami
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 S. Limestone, Lexington, KY 40536, USA.
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Patra AK, Kundu SK, Kim D, Bhaumik A. Controlled Synthesis of a Hexagonal-Shaped NiO Nanocatalyst with Highly Reactive Facets {1 1 0} and Its Catalytic Activity. ChemCatChem 2015. [DOI: 10.1002/cctc.201402871] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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