1
|
Ryder S, Pedigo J, Ojennus DD. Elucidating the Role of a Calcium-Binding Loop in an x-Prolyl Aminodipeptidase from Lb. helveticus. ACS OMEGA 2023; 8:35410-35416. [PMID: 37779945 PMCID: PMC10536834 DOI: 10.1021/acsomega.3c05639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/31/2023] [Indexed: 10/03/2023]
Abstract
Prolyl aminodipeptidase (PepX) is an α/β hydrolase that cleaves at penultimate N-terminal prolyl peptide bonds. The crystal structure of PepX from Lactobacillus helveticus exhibits a calcium-binding loop within the catalytic domain. The calcium-binding sequence of xDxDxDGxxD within this loop is highly conserved in PepX proteins among lactic acid bacteria, but its purpose remains unknown. Enzyme activity is not significantly affected in the presence of the metal chelator ethylenediaminetetraacetic acid (EDTA), nor in the presence of excess calcium ions. To eliminate calcium binding, D196A and D194A/D196A mutations were constructed within the conserved calcium-binding sequence motif. Enzyme activity and stability of the D196A mutant were comparable to the wild-type enzyme by colorimetric kinetic assays and protein thermal shift assays. However, the D194A/D196A mutant was inactive though it retained native-like structure and thermal stability, contradicting the EDTA and calcium titration results. This suggests calcium binding to PepX may be essential for activity.
Collapse
Affiliation(s)
- Stephanie Ryder
- Department of Chemistry, Whitworth
University, 300 W. Hawthorne Rd., Spokane, Washington 99251, United States
| | | | - Deanna Dahlke Ojennus
- Department of Chemistry, Whitworth
University, 300 W. Hawthorne Rd., Spokane, Washington 99251, United States
| |
Collapse
|
2
|
Elhamdi M, Ghorbel S, Hmidet N. Bacillus Swezeyi B2 Strain: A Novel Alkaliphilic Bacterium Producer of Alkaline-, Thermal, Oxidant-, and Surfactant-Stable Protease, Extremely Efficient in Detergency. Curr Microbiol 2023; 80:95. [PMID: 36737528 DOI: 10.1007/s00284-022-03156-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 12/13/2022] [Indexed: 02/05/2023]
Abstract
Proteolytic enzymes that are currently used to meet industrial demand are usually derived from Bacillus species. They find multiple technical applications, particularly they have been increasingly used as a key bio-additive in detergents. In this study, a novel alkalophilic bacterium was isolated from contaminated soil, exhibiting 1400 U/ml proteolytic activity, and identified as Bacillus swezeyi B2. The crude enzyme likely contained a single extracellular protease. This enzyme revealed optimum activity at pH 10 and 70 °C and was highly alkaline thermostable (7-12.5) and up to 70 °C. The protease activity was completely inhibited by Phenylmethylsulfonyl fluoride (PMSF) suggesting that it belongs to the serine protease group. It was highly stable in the presence of the strong anionic surfactant (SDS) and oxidizing agents (H2O2). The supernatant was lyophilized and showed high storage stability retaining 100% of its original activity after one year of conservation at 4 °C. The lyophilized product was evaluated for its detergent efficacy, it revealed excellent compatibility with various laundry detergents keeping its full original activity after incubation for 1 h with seven solid and liquid commercial detergents and it effectively removed chocolate stains at low washing temperature (40 °C) and low supplementation level (125 U/ml). The features of this single alkaline and thermotolerant protease, stable toward surfactants, oxidizing agents, and commercial detergents with stain removal efficacy support its ideal choice for supplementation in detergent formulations.
Collapse
Affiliation(s)
- Marwa Elhamdi
- Enzyme Engineering and Microbiology Laboratory, National Engineering School of Sfax-University of Sfax, Sfax, Tunisia
| | - Sofiane Ghorbel
- Biology Department, College of Science and Arts at Khulis, University of Jeddah, Jeddah, Saudi Arabia
| | - Noomen Hmidet
- Enzyme Engineering and Microbiology Laboratory, National Engineering School of Sfax-University of Sfax, Sfax, Tunisia.
| |
Collapse
|
3
|
A survey of elastase-producing bacteria and characteristics of the most potent producer, Priestia megaterium gasm32. PLoS One 2023; 18:e0282963. [PMID: 36913358 PMCID: PMC10010523 DOI: 10.1371/journal.pone.0282963] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/27/2023] [Indexed: 03/14/2023] Open
Abstract
Ninety-one elastase-producing bacterial isolates were recovered from different localities of the Eastern Province of Saudi Arabia. Elastase from the best isolate Priestia megaterium gasm32, from luncheon samples was purified to electrophoretic homogeneity using DEAE-Sepharose CL-6B and Sephadex G-100 chromatographic techniques. The recovery was 17.7%, the purification fold was 11.7x, and the molecular mass was 30 kDa. Enzymatic activity was highly repressed by Ba2+ and almost completely lost by EDTA, but it was greatly stimulated by Cu2+ ions, suggesting a metalloprotease type. The enzyme was stable at 45°C and pH 6.0-10.0 for 2 hours. Ca2+ ions considerably enhanced the stability of the heat-treated enzyme. The Vmax and Km against the synthetic substrate elastin-Congo red were 6.03 mg/mL, and 8.82 U/mg, respectively. Interestingly, the enzyme showed potent antibacterial activity against many bacterial pathogens. Under SEM, most bacterial cells showed loss of integrity, damage, and perforation. SEM micrographs also showed a time-dependent gradual breakdown of elastin fibers exposed to elastase. After 3 hours, intact elastin fibers disappeared, leaving irregular pieces. Given these good features, this elastase may be a promising candidate for treating damaged skin fibers with the inhibition of contaminating bacteria.
Collapse
|
4
|
Azrin NAM, Ali MSM, Rahman RNZRA, Oslan SN, Noor NDM. Versatility of subtilisin: A review on structure, characteristics, and applications. Biotechnol Appl Biochem 2022; 69:2599-2616. [PMID: 35019178 DOI: 10.1002/bab.2309] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 12/27/2021] [Indexed: 12/27/2022]
Abstract
Due to its thermostability and high pH compatibility, subtilisin is most known for its role as an additive for detergents in which it is categorized as a serine protease according to MEROPS database. Subtilisin is typically isolated from various bacterial species of the Bacillus genus such as Bacillus subtilis, B. amyloliquefaciens, B. licheniformis, and various other organisms. It is composed of 268-275 amino acid residues and is initially secreted in the precursor form, preprosubtilisin, which is composed of 29-residues signal peptide, 77-residues propeptide, and 275-residues active subtilisin. Subtilisin is known for the presence of high and low affinity calcium binding sites in its structure. Native subtilisin has general properties of thermostability, tolerance to neutral to high pH, broad specificity, and calcium-dependent stability, which contribute to the versatility of subtilisin applicability. Through protein engineering and immobilization technologies, many variants of subtilisin have been generated, which increase the applicability of subtilisin in various industries including detergent, food processing and packaging, synthesis of inhibitory peptides, therapeutic, and waste management applications.
Collapse
Affiliation(s)
- Nur Aliyah Mohd Azrin
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, Malaysia.,Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, Malaysia.,Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Siti Nurbaya Oslan
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, Malaysia.,Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, Malaysia.,Institute of Bioscience, Universiti Putra Malaysia, Selangor, Malaysia
| | - Noor Dina Muhd Noor
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, Malaysia.,Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| |
Collapse
|
5
|
Abstract
Trypsin is a long-known serine protease widely used in biochemical, analytical, biotechnological, or biocatalytic applications. The high biotechnological potential is based on its high catalytic activity, substrate specificity, and catalytic robustness in non-physiological reaction conditions. The latter is mainly due to its stable protein fold, to which six intramolecular disulfide bridges make a significant contribution. Although trypsin does not depend on cofactors, it essentially requires the binding of calcium ions to its calcium-binding site to obtain complete enzymatic activity and stability. This behavior is inevitably associated with a limitation of the enzyme’s applicability. To make trypsin intrinsically calcium-independent, we removed the native calcium-binding site and replaced it with another disulfide bridge. The resulting stabilized apo-trypsin (aTn) retains full catalytic activity as proven by enzyme kinetics. Studies using Ellmann’s reagent further prove that the two inserted cysteines at positions Glu70 and Glu80 are in their oxidized state, creating the desired functional disulfide bond. Furthermore, aTn is independent of calcium ions, possesses increased thermal and functional stability, and significantly reduced autolysis compared to wildtype trypsin. Finally, we confirmed our experimental data by solving the X-ray crystal structure of aTn.
Collapse
|
6
|
Li X, Zhang S, Zhang Q, Gan L, Jiang G, Tian Y, Shi B. Characterization and application of a novel halotolerant protease with no collagenase activity for cleaner dehairing of goatskin. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.01.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
7
|
Wang H, Cai C, Gan L, Tian Y. New application of SptA protease: A cleaner and potential water-conserving approach to dehairing of skin. BIOCATAL BIOTRANSFOR 2021. [DOI: 10.1080/10242422.2021.2003788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Hongbin Wang
- College of Biomass Science and Engineering, Sichuan University, Chengdu, PR China
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu, PR China
| | - Chufan Cai
- College of Biomass Science and Engineering, Sichuan University, Chengdu, PR China
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu, PR China
| | - Longzhan Gan
- College of Biomass Science and Engineering, Sichuan University, Chengdu, PR China
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu, PR China
| | - Yongqiang Tian
- College of Biomass Science and Engineering, Sichuan University, Chengdu, PR China
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu, PR China
| |
Collapse
|
8
|
Wang H, Cai C, Gan L, Wang S, Tian Y. Expression and Characterization of Surfactnt-Stable Calcium-Dependent Protease: a Potential Additive for Laundry Detergents. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821040165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
9
|
Sharma C, Nigam A, Singh R. Computational-approach understanding the structure-function prophecy of Fibrinolytic Protease RFEA1 from Bacillus cereus RSA1. PeerJ 2021; 9:e11570. [PMID: 34141495 PMCID: PMC8183432 DOI: 10.7717/peerj.11570] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/17/2021] [Indexed: 12/02/2022] Open
Abstract
Microbial fibrinolytic proteases are therapeutic enzymes responsible to ameliorate thrombosis, a fatal cardiac-disorder which effectuates due to excessive fibrin accumulation in blood vessels. Inadequacies such as low fibrin specificity, lethal after-effects and short life-span of available fibrinolytic enzymes stimulates an intensive hunt for novel, efficient and safe substitutes. Therefore, we herewith suggest a novel and potent fibrinolytic enzyme RFEA1 from Bacillus cereus RSA1 (MK288105). Although, attributes such as in-vitro purification, characterization and thrombolytic potential of RFEA1 were successfully accomplished in our previous study. However, it is known that structure-function traits and mode of action significantly aid to commercialization of an enzyme. Also, predicting structural model of a protein from its amino acid sequence is challenging in computational biology owing to intricacy of energy functions and inspection of vast conformational space. Our present study thus reports In-silico structural-functional analysis of RFEA1. Sequence based modelling approaches such as-Iterative threading ASSEmbly Refinement (I-TASSER), SWISS-MODEL, RaptorX and Protein Homology/analogY Recognition Engine V 2.0 (Phyre2) were employed to model three-dimensional structure of RFEA1 and the modelled RFEA1 was validated by structural analysis and verification server (SAVES v6.0). The modelled crystal structure revealed the presence of high affinity Ca1 binding site, associated with hydrogen bonds at Asp147, Leu181, Ile185 and Val187residues. RFEA1 is structurally analogous to Subtilisin E from Bacillus subtilis 168. Molecular docking analysis using PATCH DOCK and FIRE DOCK servers was performed to understand the interaction of RFEA1 with substrate fibrin. Strong RFEA1-fibrin interaction was observed with high binding affinity (-21.36 kcal/mol), indicating significant fibrinolytic activity and specificity of enzyme RFEA1. Overall, the computational research suggests that RFEA1 is a subtilisin-like serine endopeptidase with proteolytic potential, involved in thrombus hydrolysis.
Collapse
Affiliation(s)
- Chhavi Sharma
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida, India
| | - Arti Nigam
- Department of Microbiology, Institute of Home Economics, Delhi University South Campus, Delhi, India
| | - Rajni Singh
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida, India
| |
Collapse
|
10
|
Yang S, Zhai L, Huang L, Meng D, Li J, Hao Z, Guan Z, Cai Y, Liao X. Mining of alkaline proteases from Bacillus altitudinis W3 for desensitization of milk proteins: Their heterologous expression, purification, and characterization. Int J Biol Macromol 2020; 153:1220-1230. [DOI: 10.1016/j.ijbiomac.2019.10.252] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/26/2019] [Accepted: 10/27/2019] [Indexed: 02/06/2023]
|
11
|
Zn2+ stapling of N and C-terminal maintains stability and substrate affinity in GH26 endo-mannanase. Enzyme Microb Technol 2020; 135:109497. [DOI: 10.1016/j.enzmictec.2019.109497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/13/2019] [Accepted: 12/20/2019] [Indexed: 01/09/2023]
|
12
|
Liu K, Ma C, Wang W, Zang S, Cai Y, Chen W, Liu Z, Huang J, Yan Y. A metalloprotein-inspired thermo-gene for thermogels. Inorg Chem Front 2020. [DOI: 10.1039/d0qi00788a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Coordinating hydrogels may act as a thermo-gene to endow heat-melting conventional hydrogels with superior thermal stability at temperatures over 80 °C.
Collapse
Affiliation(s)
- Kaerdun Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing
- P. R. China
| | - Cheng Ma
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing
- P. R. China
| | - Wenkai Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing
- P. R. China
| | - Shihao Zang
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing
- P. R. China
| | - Yiteng Cai
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing
- P. R. China
| | - Wei Chen
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing
- P. R. China
| | - Zeyu Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing
- P. R. China
| | - Jianbin Huang
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing
- P. R. China
| | - Yun Yan
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing
- P. R. China
| |
Collapse
|
13
|
Cloning, expression, purification and characterization of a thermo- and surfactant-stable protease from Thermomonospora curvata. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
14
|
Kovalenko AO, Chernyshov SV, Kutyshenko VP, Molochkov NV, Prokhorov DA, Odinokova IV, Mikoulinskaia GV. Investigation of the calcium-induced activation of the bacteriophage T5 peptidoglycan hydrolase promoting host cell lysis. Metallomics 2019; 11:799-809. [DOI: 10.1039/c9mt00020h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bacteriophage T5 endolysin could be activated by Ca2+ in the periplasm of the host cell, thereby promoting bacterial lysis.
Collapse
Affiliation(s)
- Angelina O. Kovalenko
- Branch of Shemyakin & Ovchinnikov's Institute of Bioorganic Chemistry RAS
- Moscow region 142290
- Russia
| | - Sergei V. Chernyshov
- Branch of Shemyakin & Ovchinnikov's Institute of Bioorganic Chemistry RAS
- Moscow region 142290
- Russia
| | - Victor P. Kutyshenko
- Institute of Theoretical and Experimental Biophysics RAS
- Moscow region 142290
- Russia
| | - Nikolai V. Molochkov
- Institute of Theoretical and Experimental Biophysics RAS
- Moscow region 142290
- Russia
| | - Dmitry A. Prokhorov
- Institute of Theoretical and Experimental Biophysics RAS
- Moscow region 142290
- Russia
| | - Irina V. Odinokova
- Institute of Theoretical and Experimental Biophysics RAS
- Moscow region 142290
- Russia
| | - Galina V. Mikoulinskaia
- Branch of Shemyakin & Ovchinnikov's Institute of Bioorganic Chemistry RAS
- Moscow region 142290
- Russia
| |
Collapse
|
15
|
Óskarsson KR, Kristjánsson MM. Improved expression, purification and characterization of VPR, a cold active subtilisin-like serine proteinase and the effects of calcium on expression and stability. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:152-162. [PMID: 30502512 DOI: 10.1016/j.bbapap.2018.11.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 11/22/2018] [Accepted: 11/26/2018] [Indexed: 01/21/2023]
Abstract
Cloning into a pET 11a vector, followed by high-level expression of the cold adapted subtilase, VPR, utilizing the rhamnose titratable T7 system of Lemo21, resulted in a dramatic increase of soluble protein compared to the older system used. Expression optimization clearly shows the importance of calcium in the medium after induction, both for stability of the proteinase and cell health. Characterization of the purified enzyme obtained in a redesigned purification protocol which removed apparent RNA contaminants, resulted in a significantly higher value for kcat than previously reported. The new recombinant protein exhibited slightly lower stability against thermal denaturation and thermal inactivation. Our results also indicate that two of the calcium binding sites have apparent binding constants in the mM range. Binding of calcium to the weaker of those two sites only affects resistance of the enzyme against irreversible thermal inactivation. Differential scanning calorimetry revealed a non-two-state denaturation process, with indication of presence of intermediates caused by unfolding of calcium binding motifs.
Collapse
Affiliation(s)
- Kristinn R Óskarsson
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavík, Iceland
| | - Magnús M Kristjánsson
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavík, Iceland.
| |
Collapse
|
16
|
Ding X, Dong CL, Guan Z, He YH. Concurrent Asymmetric Reactions Combining Photocatalysis and Enzyme Catalysis: Direct Enantioselective Synthesis of 2,2-Disubstituted Indol-3-ones from 2-Arylindoles. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201811085] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Xuan Ding
- Key Laboratory of Applied Chemistry of Chongqing Municipality; School of Chemistry and Chemical Engineering; Southwest University; Chongqing 400715 China
| | - Chun-Lin Dong
- Key Laboratory of Applied Chemistry of Chongqing Municipality; School of Chemistry and Chemical Engineering; Southwest University; Chongqing 400715 China
| | - Zhi Guan
- Key Laboratory of Applied Chemistry of Chongqing Municipality; School of Chemistry and Chemical Engineering; Southwest University; Chongqing 400715 China
| | - Yan-Hong He
- Key Laboratory of Applied Chemistry of Chongqing Municipality; School of Chemistry and Chemical Engineering; Southwest University; Chongqing 400715 China
| |
Collapse
|
17
|
Ding X, Dong CL, Guan Z, He YH. Concurrent Asymmetric Reactions Combining Photocatalysis and Enzyme Catalysis: Direct Enantioselective Synthesis of 2,2-Disubstituted Indol-3-ones from 2-Arylindoles. Angew Chem Int Ed Engl 2018; 58:118-124. [PMID: 30421485 DOI: 10.1002/anie.201811085] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/30/2018] [Indexed: 11/12/2022]
Abstract
The combination of photoredox and enzymatic catalysis for the direct asymmetric one-pot synthesis of 2,2-disubstituted indol-3-ones from 2-arylindoles through concurrent oxidization and alkylation reactions is described. 2-Arylindoles can be photocatalytically oxidized to 2-arylindol-3-one with subsequent enantioselective alkylation with ketones catalyzed by wheat germ lipase (WGL). The chiral quaternary carbon center at C2 of the indoles was directly constructed. This mode of concurrent photobiocatalysis provides a mild and powerful strategy for one-pot enantioselective synthesis of complex compounds. The experiments proved that other lipases containing structurally analogous catalytic triad in the active site also can catalyze the reaction in the same way. This reaction is the first example of combining the non-natural catalytic activity of hydrolases with visible-light catalysis for enantioselective organic synthesis and it does not require any cofactors.
Collapse
Affiliation(s)
- Xuan Ding
- Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Chun-Lin Dong
- Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Zhi Guan
- Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Yan-Hong He
- Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| |
Collapse
|
18
|
Oda M, Yamagami Y, Inaba S, Oida T, Yamamoto M, Kitajima S, Kawai F. Enzymatic hydrolysis of PET: functional roles of three Ca2+ ions bound to a cutinase-like enzyme, Cut190*, and its engineering for improved activity. Appl Microbiol Biotechnol 2018; 102:10067-10077. [DOI: 10.1007/s00253-018-9374-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 08/21/2018] [Accepted: 09/05/2018] [Indexed: 10/28/2022]
|
19
|
Abstract
Germination of Clostridium difficile spores is a crucial early requirement for colonization of the gastrointestinal tract. Likewise, C. difficile cannot cause disease pathologies unless its spores germinate into metabolically active, toxin-producing cells. Recent advances in our understanding of C. difficile spore germination mechanisms indicate that this process is both complex and unique. This review defines unique aspects of the germination pathways of C. difficile and compares them to those of two other well-studied organisms, Bacillus anthracis and Clostridium perfringensC. difficile germination is unique, as C. difficile does not contain any orthologs of the traditional GerA-type germinant receptor complexes and is the only known sporeformer to require bile salts in order to germinate. While recent advances describing C. difficile germination mechanisms have been made on several fronts, major gaps in our understanding of C. difficile germination signaling remain. This review provides an updated, in-depth summary of advances in understanding of C. difficile germination and potential avenues for the development of therapeutics, and discusses the major discrepancies between current models of germination and areas of ongoing investigation.
Collapse
|
20
|
Purification and Characterization of Microbial Protease Produced Extracellularly from Bacillus subtilis FBL-1. BIOTECHNOL BIOPROC E 2018. [DOI: 10.1007/s12257-017-0495-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
|
21
|
Figueiredo J, Sousa Silva M, Figueiredo A. Subtilisin-like proteases in plant defence: the past, the present and beyond. MOLECULAR PLANT PATHOLOGY 2018; 19:1017-1028. [PMID: 28524452 PMCID: PMC6638164 DOI: 10.1111/mpp.12567] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 04/19/2017] [Accepted: 05/13/2017] [Indexed: 05/13/2023]
Abstract
Subtilisin-like proteases (or subtilases) are a very diverse family of serine peptidases present in many organisms, but mostly in plants. With a broad spectrum of biological functions, ranging from protein turnover and plant development to interactions with the environment, subtilases have been gaining increasing attention with regard to their involvement in plant defence responses against the most diverse pathogens. Over the last 5 years, the number of published studies associating plant subtilases with pathogen resistance and plant immunity has increased tremendously. In addition, the observation of subtilases and serine protease inhibitors secreted by pathogens has also gained prominence. In this review, we focus on the active participation of subtilases in the interactions established by plants with the environment, highlighting their role in plant-pathogen communication.
Collapse
Affiliation(s)
- Joana Figueiredo
- Biosystems & Integrative Sciences Institute (BioISI)Faculdade de Ciências da Universidade de LisboaLisbon 1749‐016Portugal
- Laboratório de FTICR e Espectrometria de Massa EstruturalFaculdade de Ciências da Universidade de LisboaLisbon 1749‐016Portugal
- Centro de Química e BioquímicaFaculdade de Ciências da Universidade de LisboaLisbon 1749‐016Portugal
| | - Marta Sousa Silva
- Laboratório de FTICR e Espectrometria de Massa EstruturalFaculdade de Ciências da Universidade de LisboaLisbon 1749‐016Portugal
- Centro de Química e BioquímicaFaculdade de Ciências da Universidade de LisboaLisbon 1749‐016Portugal
| | - Andreia Figueiredo
- Biosystems & Integrative Sciences Institute (BioISI)Faculdade de Ciências da Universidade de LisboaLisbon 1749‐016Portugal
| |
Collapse
|
22
|
Zheng Q, Lazo ND. Mechanistic Studies of the Inhibition of Insulin Fibril Formation by Rosmarinic Acid. J Phys Chem B 2018; 122:2323-2331. [PMID: 29401384 DOI: 10.1021/acs.jpcb.8b00689] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The self-assembly of insulin to form amyloid fibrils has been widely studied because it is a significant problem in the medical management of diabetes and is an important model system for the investigation of amyloid formation and its inhibition. A few inhibitors of insulin fibrillation have been identified with potencies that could be higher. Knowledge of how these work at the molecular level is not known but important for the development of more potent inhibitors. Here we show that rosmarinic acid completely inhibits amyloid formation by dimeric insulin at pH 2 and 60 °C. In contrast to other polyphenols, rosmarinic acid is soluble in water and does not degrade at elevated temperatures, and thus we were able to decipher the mechanism of inhibition by a combination of solution-state 1H NMR spectroscopy and molecular docking. On the basis of 1H chemical shift perturbations, intermolecular nuclear Overhauser effect enhancements between rosmarinic acid and specific residues of insulin, and slowed dynamics of rosmarinic acid in the presence of insulin, we show that rosmarinic acid binds to a pocket found on the surface of each insulin monomer. This results in the formation of a mixed tetramolecular aromatic network on the surface of insulin dimer, resulting in increased resistance of the amyloidogenic protein to thermal unfolding. This finding opens new avenues for the design of potent inhibitors of amyloid formation and provides strong experimental evidence for the role of surface aromatic clusters in increasing the thermal stability of proteins.
Collapse
Affiliation(s)
- Qiuchen Zheng
- Carlson School of Chemistry and Biochemistry, Clark University , 950 Main Street, Worcester, Massachusetts 01610, United States
| | - Noel D Lazo
- Carlson School of Chemistry and Biochemistry, Clark University , 950 Main Street, Worcester, Massachusetts 01610, United States
| |
Collapse
|
23
|
Jeong YJ, Baek SC, Kim H. Cloning and characterization of a novel intracellular serine protease (IspK) from Bacillus megaterium with a potential additive for detergents. Int J Biol Macromol 2018; 108:808-816. [DOI: 10.1016/j.ijbiomac.2017.10.173] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 10/21/2017] [Accepted: 10/27/2017] [Indexed: 11/15/2022]
|
24
|
Crystal structure of a cold-active protease (Pro21717) from the psychrophilic bacterium, Pseudoalteromonas arctica PAMC 21717, at 1.4 Å resolution: Structural adaptations to cold and functional analysis of a laundry detergent enzyme. PLoS One 2018; 13:e0191740. [PMID: 29466378 PMCID: PMC5821440 DOI: 10.1371/journal.pone.0191740] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 01/10/2018] [Indexed: 02/04/2023] Open
Abstract
Enzymes isolated from organisms found in cold habitats generally exhibit higher catalytic activity at low temperatures than their mesophilic homologs and are therefore known as cold-active enzymes. Cold-active proteases are very useful in a variety of biotechnological applications, particularly as active ingredients in laundry and dishwashing detergents, where they provide strong protein-degrading activity in cold water. We identified a cold-active protease (Pro21717) from a psychrophilic bacterium, Pseudoalteromonas arctica PAMC 21717, and determined the crystal structure of its catalytic domain (CD) at a resolution of 1.4 Å. The Pro21717-CD structure shows a conserved subtilisin-like fold with a typical catalytic triad (Asp185, His244, and Ser425) and contains four calcium ions and three disulfide bonds. Interestingly, we observed an unexpected electron density at the substrate-binding site from a co-purified peptide. Although the sequence of this peptide is unknown, analysis of the peptide-complexed structure nonetheless provides some indication of the substrate recognition and binding mode of Pro21717. Moreover, various parameters, including a wide substrate pocket size, an abundant active-site loop content, and a flexible structure provide potential explanations for the cold-adapted properties of Pro21717. In conclusion, this is first structural characterization of a cold-adapted subtilisin-like protease, and these findings provide a structural and functional basis for industrial applications of Pro21717 as a cold-active laundry or dishwashing detergent enzyme.
Collapse
|
25
|
Shahaboddin ME, Khajeh K, Maleki M, Golestani A. Improvement of activity and stability of Chondroitinase ABC I by introducing an aromatic cluster at the surface of protein. Enzyme Microb Technol 2017; 105:38-44. [DOI: 10.1016/j.enzmictec.2017.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 05/22/2017] [Accepted: 06/03/2017] [Indexed: 11/16/2022]
|
26
|
Zarafeta D, Moschidi D, Ladoukakis E, Gavrilov S, Chrysina ED, Chatziioannou A, Kublanov I, Skretas G, Kolisis FN. Metagenomic mining for thermostable esterolytic enzymes uncovers a new family of bacterial esterases. Sci Rep 2016; 6:38886. [PMID: 27991516 PMCID: PMC5171882 DOI: 10.1038/srep38886] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 11/14/2016] [Indexed: 11/09/2022] Open
Abstract
Biocatalysts exerting activity against ester bonds have a broad range of applications in modern biotechnology. Here, we have identified a new esterolytic enzyme by screening a metagenomic sample collected from a hot spring in Kamchatka, Russia. Biochemical characterization of the new esterase, termed EstDZ2, revealed that it is highly active against medium chain fatty acid esters at temperatures between 25 and 60 °C and at pH values 7-8. The new enzyme is moderately thermostable with a half-life of more than six hours at 60 °C, but exhibits exquisite stability against high concentrations of organic solvents. Phylogenetic analysis indicated that EstDZ2 is likely an Acetothermia enzyme that belongs to a new family of bacterial esterases, for which we propose the index XV. One distinctive feature of this new family, is the presence of a conserved GHSAG catalytic motif. Multiple sequence alignment, coupled with computational modelling of the three-dimensional structure of EstDZ2, revealed that the enzyme lacks the largest part of the "cap" domain, whose extended structure is characteristic for the closely related Family IV esterases. Thus, EstDZ2 appears to be distinct from known related esterolytic enzymes, both in terms of sequence characteristics, as well as in terms of three-dimensional structure.
Collapse
Affiliation(s)
- Dimitra Zarafeta
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Danai Moschidi
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Efthymios Ladoukakis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Sergey Gavrilov
- Winogradsky Institute of Microbiology, Research Center for Biotechnology Russian Academy of Sciences, Moscow, Russian Federation
| | - Evangelia D. Chrysina
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Aristotelis Chatziioannou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Ilya Kublanov
- Winogradsky Institute of Microbiology, Research Center for Biotechnology Russian Academy of Sciences, Moscow, Russian Federation
| | - Georgios Skretas
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Fragiskos N. Kolisis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| |
Collapse
|
27
|
Zarafeta D, Szabo Z, Moschidi D, Phan H, Chrysina ED, Peng X, Ingham CJ, Kolisis FN, Skretas G. EstDZ3: A New Esterolytic Enzyme Exhibiting Remarkable Thermostability. Front Microbiol 2016; 7:1779. [PMID: 27899916 PMCID: PMC5110521 DOI: 10.3389/fmicb.2016.01779] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/24/2016] [Indexed: 11/25/2022] Open
Abstract
Lipolytic enzymes that retain high levels of catalytic activity when exposed to a variety of denaturing conditions are of high importance for a number of biotechnological applications. In this study, we aimed to identify new lipolytic enzymes, which are highly resistant to prolonged exposure to elevated temperatures. To achieve this, we searched for genes encoding for such proteins in the genomes of a microbial consortium residing in a hot spring located in China. After performing functional genomic screening on a bacterium of the genus Dictyoglomus, which was isolated from this hot spring following in situ enrichment, we identified a new esterolytic enzyme, termed EstDZ3. Detailed biochemical characterization of the recombinant enzyme, revealed that it constitutes a slightly alkalophilic and highly active esterase against esters of fatty acids with short to medium chain lengths. Importantly, EstDZ3 exhibits remarkable thermostability, as it retains high levels of catalytic activity after exposure to temperatures as high as 95°C for several hours. Furthermore, it exhibits very good stability against exposure to high concentrations of a variety of organic solvents. Interestingly, EstDZ3 was found to have very little similarity to previously characterized esterolytic enzymes. Computational modeling of the three-dimensional structure of this new enzyme predicted that it exhibits a typical α/β hydrolase fold that seems to include a “subdomain insertion”, which is similar to the one present in its closest homolog of known function and structure, the cinnamoyl esterase Lj0536 from Lactobacillus johnsonii. As it was found in the case of Lj0536, this structural feature is expected to be an important determinant of the catalytic properties of EstDZ3. The high levels of esterolytic activity of EstDZ3, combined with its remarkable thermostability and good stability against a range of organic solvents and other denaturing agents, render this new enzyme a candidate biocatalyst for high-temperature biotechnological applications.
Collapse
Affiliation(s)
- Dimitra Zarafeta
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research FoundationAthens, Greece; Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of AthensAthens, Greece
| | | | - Danai Moschidi
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens Athens, Greece
| | - Hien Phan
- Danish Archaea Centre, Department of Biology, Copenhagen University Copenhagen, Denmark
| | - Evangelia D Chrysina
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation Athens, Greece
| | - Xu Peng
- Danish Archaea Centre, Department of Biology, Copenhagen University Copenhagen, Denmark
| | | | - Fragiskos N Kolisis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens Athens, Greece
| | - Georgios Skretas
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation Athens, Greece
| |
Collapse
|
28
|
A single mutation Gln142Lys doubles the catalytic activity of VPR, a cold adapted subtilisin-like serine proteinase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1436-43. [PMID: 27456266 DOI: 10.1016/j.bbapap.2016.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 07/11/2016] [Accepted: 07/15/2016] [Indexed: 11/20/2022]
Abstract
Structural comparisons of the cold adapted subtilase VPR and its thermophilic homologue, aqualysin I (AQUI) indicated the presence of additional salt bridges in the latter. Few of those appear to contribute significantly to thermal stability of AQUI. This includes a putative salt bridge between residues Lys142 and Glu172 as its deletion did not have any significant effect on its stability or activity (Jónsdóttir et al. (2014)). Insertion of this putative salt bridge into the structure of VPR, in a double mutant (VPRΔC_Q142K/S172E), however was detrimental to the stability of the enzyme. Incorporation of either the Q142K or S172E mutations into VPR, were found to significantly affect the catalytic properties of the enzyme. The single mutation Q142K was highly effective, as it increased the kcat and kcat/Km more than twofold. When the Q142K mutation was inserted into a thermostabilized, but a low activity mutant of VPR (VPRΔC_N3P/I5P), the activity increased about tenfold in terms of kcat and kcat/Km, while retaining the stability of the mutant. Molecular dynamics simulations of the single mutants were carried out to provide structural rationale for these experimental observations. Based on root mean square fluctuation (RMSF) profiles, the two mutants were more flexible in certain regions of the structure and the Q142K mutant had the highest overall flexibility of the three enzymes. The results suggest that weakening of specific H-bonds resulting from the mutations may be propagated over some distance giving rise to higher flexibility in the active site regions of the enzyme, causing higher catalytic activity in the mutants.
Collapse
|
29
|
Devi SG, Fathima AA, Sanitha M, Iyappan S, Curtis WR, Ramya M. Expression and characterization of alkaline protease from the metagenomic library of tannery activated sludge. J Biosci Bioeng 2016; 122:694-700. [PMID: 27323930 DOI: 10.1016/j.jbiosc.2016.05.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 05/24/2016] [Accepted: 05/30/2016] [Indexed: 11/17/2022]
Abstract
Metagenomics has the potential to facilitate the discovery of novel enzymes; however, to date, only a few alkaline proteases have been characterized from environmentally-sourced DNA. We report the identification and characterization of an alkaline serine protease designated as Prt1A from the metagenomic library of tannery activated sludge. Sequence analysis revealed that Prt1A is closely related to S8A family subtilisins with a catalytic triad of Asp143, His173, and Ser326. The putative protease gene (prt-1A) was subcloned in pET 28a (+) vector and overexpressed in Escherichia coli BL21(DE3)pLysS cells. This 38.8 KDa recombinant protease was purified to homogeneity by nickel affinity chromatography and exhibited optimal enzyme activity at elevated pH (11.0) and temperature (55°C). The enzyme activity was enhanced by the addition of 5 mM Ca2+ ions, and was stable in the presence of anionic detergent, oxidizing agent and various organic solvents. The enzyme displayed high affinity and catalytic efficiency for casein under standard assay conditions (Vmax = 279 U/mg/min, Km = 1.70 mg/mL) and was also compatible with commercial detergents. These results suggest that Prt1A protease could act as an efficient enzyme in various industrial applications.
Collapse
Affiliation(s)
| | | | - Mary Sanitha
- Department of Genetic Engineering, SRM University, Tamilnadu 603203, India
| | - Sellamuthu Iyappan
- Department of Genetic Engineering, SRM University, Tamilnadu 603203, India
| | - Wayne R Curtis
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Mohandass Ramya
- Department of Genetic Engineering, SRM University, Tamilnadu 603203, India.
| |
Collapse
|
30
|
Improved catalytic efficiency, thermophilicity, anti-salt and detergent tolerance of keratinase KerSMD by partially truncation of PPC domain. Sci Rep 2016; 6:27953. [PMID: 27298079 PMCID: PMC4906391 DOI: 10.1038/srep27953] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 05/27/2016] [Indexed: 11/25/2022] Open
Abstract
The keratinase from Stenotrophomonas maltophilia (KerSMD) is known for its high activity and pH stability in keratin degradation. However, catalytic efficiency and detergent tolerability need to be improved in order to be used for industrial application. In this work, we obtained several keratinase variants with enhanced catalytic efficiency, thermophilicity, and anti-salt and detergent tolerability by partially truncating the PPC domain of KerSMD. The variants all showed improved catalytic efficiency to synthetic substrate AAPF, with the V355 variant having the highest kcat /Km value of 143.6 s−1 mM−1. The truncation of keratinase had little effect on alkaline stability but obviously decreased collagenase activity, developing its potential application in leather treatment. The variants V380, V370, and V355 were thermophilic, with a 1.7-fold enhancement of keratinlytic activity at 60 °C when compared to the wild type. The entire truncation of PPC domain obtained the variant V355 with improved tolerance to alkalinity, salt, chaotropic agents, and detergents. The V355 variant showed more than a 40% improvement in activity under 15% (w/v) NaCl or 4% (w/v) SDS solution, showing excellent stability under harsh washing and unhairing conditions. Our work investigated how protein engineering affects the function of PPC domain of KerSMD.
Collapse
|
31
|
Jankiewicz U, Larkowska E, Swiontek Brzezinska M. Production, characterization, gene cloning, and nematocidal activity of the extracellular protease from Stenotrophomonas maltophilia N4. J Biosci Bioeng 2016; 121:614-618. [PMID: 26896861 DOI: 10.1016/j.jbiosc.2015.11.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 09/15/2015] [Accepted: 11/12/2015] [Indexed: 02/01/2023]
Abstract
A rhizosphere strain of the bacterium Stenotrophomonas maltophilia N4 secretes the serine protease PN4, whose molecular mass is approximately 42 kDa. The optimal temperature for the enzyme activity of the 11-fold purified protein was 50°C and the optimal pH was 10.5. The activity of the enzyme was strongly inhibited by specific serine protease inhibitors, which allowed for its classification as an alkaline serine protease family. Ca(2+) ions stimulated the activity of the protease PN4, while Mg(2+) ions stabilized its activity, and Zn(2+) and Cd(2+) ions strongly inhibited its activity. The enzyme has broad substrate specificity. For example, it is able to hydrolyse casein, keratin, albumin, haemoglobin, and gelatin, as well as the insoluble modified substrates azure keratin and azocoll. The gene that encodes the 1740 bp precursor form of the enzyme (accession number: LC031815) was cloned. We then deduced that its amino acid sequence includes the region of the conserved domain of the S8 family of peptidases as well as the catalytic triad Asp/His/Ser. The bacterial culture fluid as well as the purified protease PN4 demonstrated biocidal activity with regard to the nematodes Caenorhabditis elegans and Panagrellus spp.
Collapse
Affiliation(s)
- Urszula Jankiewicz
- Department of Biochemistry, Warsaw University of Life Sciences, SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Ewa Larkowska
- Department of Biochemistry, Warsaw University of Life Sciences, SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Maria Swiontek Brzezinska
- Department of Environmental Microbiology and Biotechnology, Nicolaus Copernicus University, Lwowska 1, 87-100 Torun, Poland
| |
Collapse
|
32
|
Polarity Alteration of a Calcium Site Induces a Hydrophobic Interaction Network and Enhances Cel9A Endoglucanase Thermostability. Appl Environ Microbiol 2016; 82:1662-1674. [PMID: 26729722 DOI: 10.1128/aem.03326-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 12/16/2015] [Indexed: 01/07/2023] Open
Abstract
Structural calcium sites control protein thermostability and activity by stabilizing native folds and changing local conformations. Alicyclobacillus acidocaldarius survives in thermal-acidic conditions and produces an endoglucanase Cel9A (AaCel9A) which contains a calcium-binding site (Ser465 to Val470) near the catalytic cleft. By superimposing the Ca(2+)-free and Ca(2+)-bounded conformations of the calcium site, we found that Ca(2+) induces hydrophobic interactions between the calcium site and its nearby region by driving a conformational change. The hydrophobic interactions at the high-B-factor region could be enhanced further by replacing the surrounding polar residues with hydrophobic residues to affect enzyme thermostability and activity. Therefore, the calcium-binding residue Asp468 (whose side chain directly ligates Ca(2+)), Asp469, and Asp471 of AaCel9A were separately replaced by alanine and valine. Mutants D468A and D468V showed increased activity compared with those of the wild type with 0 mM or 10 mM Ca(2+) added, whereas the Asp469 or Asp471 substitution resulted in decreased activity. The D468A crystal structure revealed that mutation D468A triggered a conformational change similar to that induced by Ca(2+) in the wild type and developed a hydrophobic interaction network between the calcium site and the neighboring hydrophobic region (Ala113 to Ala117). Mutations D468V and D468A increased 4.5°C and 5.9°C, respectively, in melting temperature, and enzyme half-life at 75°C increased approximately 13 times. Structural comparisons between AaCel9A and other endoglucanases of the GH9 family suggested that the stability of the regions corresponding to the AaCel9A calcium site plays an important role in GH9 endoglucanase catalysis at high temperature.
Collapse
|
33
|
Panigrahi P, Sule M, Ghanate A, Ramasamy S, Suresh CG. Engineering Proteins for Thermostability with iRDP Web Server. PLoS One 2015; 10:e0139486. [PMID: 26436543 PMCID: PMC4593602 DOI: 10.1371/journal.pone.0139486] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 09/13/2015] [Indexed: 11/18/2022] Open
Abstract
Engineering protein molecules with desired structure and biological functions has been an elusive goal. Development of industrially viable proteins with improved properties such as stability, catalytic activity and altered specificity by modifying the structure of an existing protein has widely been targeted through rational protein engineering. Although a range of factors contributing to thermal stability have been identified and widely researched, the in silico implementation of these as strategies directed towards enhancement of protein stability has not yet been explored extensively. A wide range of structural analysis tools is currently available for in silico protein engineering. However these tools concentrate on only a limited number of factors or individual protein structures, resulting in cumbersome and time-consuming analysis. The iRDP web server presented here provides a unified platform comprising of iCAPS, iStability and iMutants modules. Each module addresses different facets of effective rational engineering of proteins aiming towards enhanced stability. While iCAPS aids in selection of target protein based on factors contributing to structural stability, iStability uniquely offers in silico implementation of known thermostabilization strategies in proteins for identification and stability prediction of potential stabilizing mutation sites. iMutants aims to assess mutants based on changes in local interaction network and degree of residue conservation at the mutation sites. Each module was validated using an extensively diverse dataset. The server is freely accessible at http://irdp.ncl.res.in and has no login requirements.
Collapse
Affiliation(s)
- Priyabrata Panigrahi
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, Maharashtra, 411008, India
| | - Manas Sule
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, Maharashtra, 411008, India
| | - Avinash Ghanate
- Division of Chemical Engineering and Process Development, CSIR-National Chemical Laboratory, Pune, Maharashtra, 411008, India
| | - Sureshkumar Ramasamy
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, Maharashtra, 411008, India
| | - C. G. Suresh
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, Maharashtra, 411008, India
| |
Collapse
|
34
|
Tang W, Dong SH, Repka LM, He C, Nair SK, van der Donk WA. Applications of the class II lanthipeptide protease LicP for sequence-specific, traceless peptide bond cleavage. Chem Sci 2015; 6:6270-6279. [PMID: 30090246 PMCID: PMC6054071 DOI: 10.1039/c5sc02329g] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Accepted: 08/30/2015] [Indexed: 12/21/2022] Open
Abstract
The class II lanthipeptide protease LicP maturates through self-cleavage and enables sequence-specific, traceless peptide bond cleavage.
The final step of lanthipeptide biosynthesis involves the removal of leader peptides by dedicated proteases. In vitro characterization of LicP, a class II LanP protease involved in the biosynthesis of the lantibiotic lichenicidin, revealed a self-cleavage step that removes 100 amino acids from the N-terminus. The 2.35 Å resolution crystal structure provides insights into the active site geometry and substrate specificity, and unveiled an unusual calcium-independent maturation mechanism of a subtilisin family member. LicP processes LicA2 peptides with or without post-translational modifications, but dehydrated and cyclized LicA2 is favored. Investigation of its substrate specificity demonstrated that LicP can serve as an efficient sequence-specific traceless protease and may have great utility in basic research and biotechnology. Encouraged by these findings for LicP, we identified 13 other class II LanPs, ten of which were previously unknown, and suggest that these proteins may serve as a pool of proteases with diverse recognition sequences for general traceless tag removal applications, expanding the current toolbox of proteases.
Collapse
Affiliation(s)
- Weixin Tang
- Department of Chemistry and Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , 600 S. Mathews Ave. , Urbana , IL 61801 , USA . ; ; Tel: +1 217 244 5360
| | - Shi-Hui Dong
- Department of Biochemistry , University of Illinois at Urbana-Champaign , 600 S. Mathews Ave. , Urbana , IL 61801 , USA
| | - Lindsay M Repka
- Department of Chemistry and Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , 600 S. Mathews Ave. , Urbana , IL 61801 , USA . ; ; Tel: +1 217 244 5360
| | - Chang He
- Department of Chemistry and Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , 600 S. Mathews Ave. , Urbana , IL 61801 , USA . ; ; Tel: +1 217 244 5360
| | - Satish K Nair
- Department of Biochemistry , University of Illinois at Urbana-Champaign , 600 S. Mathews Ave. , Urbana , IL 61801 , USA.,Center for Biophysics and Computational Biology , University of Illinois at Urbana-Champaign , 600 S. Mathews Ave. , Urbana , IL 61801 , USA . ; ; Tel: +1 217 333 0641
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , 600 S. Mathews Ave. , Urbana , IL 61801 , USA . ; ; Tel: +1 217 244 5360.,Department of Biochemistry , University of Illinois at Urbana-Champaign , 600 S. Mathews Ave. , Urbana , IL 61801 , USA
| |
Collapse
|
35
|
Šnajder M, Mihelič M, Turk D, Ulrih NP. Codon optimisation is key for pernisine expression in Escherichia coli. PLoS One 2015; 10:e0123288. [PMID: 25856104 PMCID: PMC4391949 DOI: 10.1371/journal.pone.0123288] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 02/17/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Pernisine is an extracellular serine protease from the hyperthermophilic Archaeon Aeropyrum pernix K1. Low yields from the natural host and expression problems in heterologous hosts have limited the potential applications of pernisine in industry. METHODOLOGY/ PRINCIPAL FINDINGS The challenges of pernisine overexpression in Escherichia coli were overcome by codon preference optimisation and de-novo DNA synthesis. The following forms of the pernisine gene were cloned into the pMCSGx series of vectors and expressed in E. coli cells: wild-type (pernisinewt), codon-optimised (pernisineco), and codon-optimised with a S355A mutation of a predicted active site (pernisineS355Aco). The fusion-tagged pernisines were purified using fast protein liquid chromatography equipped with Ni2+ chelate and gel filtration chromatography columns. The identities of the resultant proteins were confirmed with N-terminal sequencing, tandem mass spectrometry analysis, and immunodetection. Pernisinewt was not expressed in E. coli at detectable levels, while pernisineco and pernisineS355Aco were expressed and purified as 55-kDa proforms with yields of around 10 mg per litre E. coli culture. After heat activation of purified pernisine, the proteolytic activity of the mature pernisineco was confirmed using zymography, at a molecular weight of 36 kDa, while the mutant pernisineS355Aco remained inactive. Enzymatic performances of pernisine evaluated under different temperatures and pHs demonstrate that the optimal enzymatic activity of the recombinant pernisine is ca. 100°C and pH 7.0, respectively. CONCLUSIONS/ SIGNIFICANCE These data demonstrate that codon optimisation is crucial for pernisine overexpression in E. coli, and that the proposed catalytic Ser355 has an important role in pernisine activity, but not in its activation process. Pernisine is activated by autoproteolytical cleavage of its N-terminal proregion. We have also confirmed that the recombinant pernisine retains the characteristics of native pernisine, as a calcium modulated thermostable serine protease.
Collapse
Affiliation(s)
- Marko Šnajder
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Marko Mihelič
- Centre of Excellence for Integrated Approaches in Chemistry and Biology (CipKeBiP), Ljubljana, Slovenia
- Institute Jozef Stefan, Ljubljana, Slovenia
| | - Dušan Turk
- Centre of Excellence for Integrated Approaches in Chemistry and Biology (CipKeBiP), Ljubljana, Slovenia
- Institute Jozef Stefan, Ljubljana, Slovenia
| | - Nataša Poklar Ulrih
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology (CipKeBiP), Ljubljana, Slovenia
- * E-mail:
| |
Collapse
|
36
|
The malaria parasite egress protease SUB1 is a calcium-dependent redox switch subtilisin. Nat Commun 2014; 5:3726. [PMID: 24785947 PMCID: PMC4024747 DOI: 10.1038/ncomms4726] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 03/25/2014] [Indexed: 11/08/2022] Open
Abstract
Malaria is caused by a protozoan parasite that replicates within an intraerythrocytic parasitophorous vacuole. Release (egress) of malaria merozoites from the host erythrocyte is a highly regulated and calcium-dependent event that is critical for disease progression. Minutes before egress, an essential parasite serine protease called SUB1 is discharged into the parasitophorous vacuole, where it proteolytically processes a subset of parasite proteins that play indispensable roles in egress and invasion. Here we report the first crystallographic structure of Plasmodium falciparum SUB1 at 2.25 Å, in complex with its cognate prodomain. The structure highlights the basis of the calcium dependence of SUB1, as well as its unusual requirement for interactions with substrate residues on both prime and non-prime sides of the scissile bond. Importantly, the structure also reveals the presence of a solvent-exposed redox-sensitive disulphide bridge, unique among the subtilisin family, that likely acts as a regulator of protease activity in the parasite.
Collapse
|
37
|
The putative propeptide of MycP1 in mycobacterial type VII secretion system does not inhibit protease activity but improves protein stability. Protein Cell 2013; 4:921-31. [PMID: 24248472 DOI: 10.1007/s13238-013-3089-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 10/21/2013] [Indexed: 10/26/2022] Open
Abstract
Mycosin-1 protease (MycP1) is a serine protease anchored to the inner membrane of Mycobacterium tuberculosis, and is essential in virulence factor secretion through the ESX-1 type VII secretion system (T7SS). Bacterial physiology studies demonstrated that MycP1 plays a dual role in the regulation of ESX-1 secretion and virulence, primarily through cleavage of its secretion substrate EspB. MycP1 contains a putative N-terminal inhibitory propeptide and a catalytic triad of Asp-His-Ser, classic hallmarks of a subtilase family serine protease. The MycP1 propeptide was previously reported to be initially inactive and activated after prolonged incubation. In this study, we have determined crystal structures of MycP1 with (MycP1²⁴⁻⁴²²) and without (MycP1⁶³⁻⁴²²) the propeptide, and conducted EspB cleavage assays using the two proteins. Very high structural similarity was observed in the two crystal structures. Interestingly, protease assays demonstrated positive EspB cleavage for both proteins, indicating that the putative propeptide does not inhibit protease activity. Molecular dynamic simulations showed higher rigidity in regions guarding the entrance to the catalytic site in MycP1²⁴⁻⁴²² than in MycP1⁶³⁻⁴²², suggesting that the putative propeptide might contribute to the conformational stability of the active site cleft and surrounding regions.
Collapse
|
38
|
Biver S, Portetelle D, Vandenbol M. Characterization of a new oxidant-stable serine protease isolated by functional metagenomics. SPRINGERPLUS 2013; 2:410. [PMID: 24024096 PMCID: PMC3765597 DOI: 10.1186/2193-1801-2-410] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 08/26/2013] [Indexed: 11/10/2022]
Abstract
A novel serine protease gene, SBcas3.3, was identified by functional screening of a forest-soil metagenomic library on agar plates supplemented with AZCL-casein. Overproduction in Escherichia coli revealed that the enzyme is produced as a 770-amino-acid precursor which is processed to a mature protease of ~55 kDa. The latter was purified by affinity chromatography for characterization with the azocasein substrate. The enzyme proved to be an alkaline protease showing maximal activity between pH 9 and 10 and at 50°C. Treatment with the chelating agent ethylenediaminetetraacetic acid irreversibly denatured the protease, whose stability was found to depend strictly on calcium ions. The enzyme appeared relatively resistant to denaturing and reducing agents, and its activity was enhanced in the presence of 10 ml/l nonionic detergent (Tween 20, Tween 80, or Triton X-100). Moreover, SBcas3.3 displayed oxidant stability, a feature particularly sought in the detergent and bleaching industries. SBcas3.3 was activated by hydrogen peroxide at concentrations up to 10 g/l and it still retained 30% of activity in 50 g/l H2O2.
Collapse
Affiliation(s)
- Sophie Biver
- Unité de Microbiologie et Génomique, Gembloux Agro-Bio Tech, Université de Liège, Avenue Maréchal Juin 6, B-5030 Gembloux, Belgium
| | | | | |
Collapse
|
39
|
Gruene T. mrtailor: a tool for PDB-file preparation for the generation of external restraints. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1861-3. [PMID: 23999309 DOI: 10.1107/s090744491301648x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Accepted: 06/13/2013] [Indexed: 11/11/2022]
Abstract
Model building starting from, for example, a molecular-replacement solution with low sequence similarity introduces model bias, which can be difficult to detect, especially at low resolution. The program mrtailor removes low-similarity regions from a template PDB file according to sequence similarity between the target sequence and the template sequence and maps the target sequence onto the PDB file. The modified PDB file can be used to generate external restraints for low-resolution refinement with reduced model bias and can be used as a starting point for model building and refinement. The program can call ProSMART [Nicholls et al. (2012), Acta Cryst. D68, 404-417] directly in order to create external restraints suitable for REFMAC5 [Murshudov et al. (2011), Acta Cryst. D67, 355-367]. Both a command-line version and a GUI exist.
Collapse
Affiliation(s)
- Tim Gruene
- Department of Structural Chemistry, Georg-August-University Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany
| |
Collapse
|
40
|
Bose A, Chawdhary V, Keharia H, Subramanian RB. Production and characterization of a solvent-tolerant protease from a novel marine isolate Bacillus tequilensis P15. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0669-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
|
41
|
Cerff M, Scholz A, Käppler T, Ottow KE, Hobley TJ, Posten C. Semi-continuous in situ magnetic separation for enhanced extracellular protease production-modeling and experimental validation. Biotechnol Bioeng 2013; 110:2161-72. [PMID: 23475553 DOI: 10.1002/bit.24893] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 01/17/2013] [Accepted: 02/25/2013] [Indexed: 11/09/2022]
Abstract
In modern biotechnology proteases play a major role as detergent ingredients. Especially the production of extracellular protease by Bacillus species facilitates downstream processing because the protease can be directly harvested from the biosuspension. In situ magnetic separation (ISMS) constitutes an excellent adsorptive method for efficient extracellular protease removal during cultivation. In this work, the impact of semi-continuous ISMS on the overall protease yield has been investigated. Results reveal significant removal of the protease from Bacillus licheniformis cultivations. Bacitracin-functionalized magnetic particles were successfully applied, regenerated and reused up to 30 times. Immediate reproduction of the protease after ISMS proved the biocompatibility of this integrated approach. Six subsequent ISMS steps significantly increased the overall protease yield up to 98% because proteolytic degradation and potential inhibition of the protease in the medium could be minimized. Furthermore, integration of semi-continuous ISMS increased the overall process efficiency due to reduction of the medium consumption. Process simulation revealed a deeper insight into protease production, and was used to optimize ISMS steps to obtain the maximum overall protease yield.
Collapse
Affiliation(s)
- Martin Cerff
- Institute of Process Engineering in Life Sciences, Division of Bioprocess Engineering, Karlsruhe Institute of Technology (KIT), Fritz-Haber Weg 2, Karlsruhe 76131, Germany
| | | | | | | | | | | |
Collapse
|
42
|
Wang T, Zhang J, Zhang X, Xu C, Tu X. Solution structure of the Big domain from Streptococcus pneumoniae reveals a novel Ca2+-binding module. Sci Rep 2013; 3:1079. [PMID: 23326635 PMCID: PMC3546320 DOI: 10.1038/srep01079] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 12/03/2012] [Indexed: 01/22/2023] Open
Abstract
Streptococcus pneumoniae is a pathogen causing acute respiratory infection, otitis media and some other severe diseases in human. In this study, the solution structure of a bacterial immunoglobulin-like (Big) domain from a putative S. pneumoniae surface protein SP0498 was determined by NMR spectroscopy. SP0498 Big domain adopts an eight-β-strand barrel-like fold, which is different in some aspects from the two-sheet sandwich-like fold of the canonical Ig-like domains. Intriguingly, we identified that the SP0498 Big domain was a Ca(2+) binding domain. The structure of the Big domain is different from those of the well known Ca(2+) binding domains, therefore revealing a novel Ca(2+)-binding module. Furthermore, we identified the critical residues responsible for the binding to Ca(2+). We are the first to report the interactions between the Big domain and Ca(2+) in terms of structure, suggesting an important role of the Big domain in many essential calcium-dependent cellular processes such as pathogenesis.
Collapse
Affiliation(s)
- Tao Wang
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, PR China
| | | | | | | | | |
Collapse
|
43
|
Li Q, Yi L, Marek P, Iverson BL. Commercial proteases: present and future. FEBS Lett 2013; 587:1155-63. [PMID: 23318711 DOI: 10.1016/j.febslet.2012.12.019] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 12/19/2012] [Accepted: 12/20/2012] [Indexed: 12/23/2022]
Abstract
This review presents a brief overview of the general categories of commercially used proteases, and critically surveys the successful strategies currently being used to improve the properties of proteases for various commercial purposes. We describe the broad application of proteases in laundry detergents, food processing, and the leather industry. The review also introduces the expanding development of proteases as a class of therapeutic agents, as well as highlighting recent progress in the field of protease engineering. The potential commercial applications of proteases are rapidly growing as recent technological advances are producing proteases with novel properties and substrate specificities.
Collapse
Affiliation(s)
- Qing Li
- Department of Chemistry, University of Texas, Austin, TX 78712, USA
| | | | | | | |
Collapse
|
44
|
Involvement of minerals in adherence of Legionella pneumophila to surfaces. Curr Microbiol 2013; 66:437-42. [PMID: 23292133 DOI: 10.1007/s00284-012-0295-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 12/07/2012] [Indexed: 02/05/2023]
Abstract
Legionella pneumophila is the causative agent of 90 % of Legionnaires' disease cases. This bacterium lives naturally in fresh water and can colonize biofilms, which play an important role in the protection of Legionella against environmental stress factors. Relationship between the presence of minerals in water and Legionella adherence to surfaces is not well-known. In this study, we studied influence of minerals on bacterial adherence. For the first time, to our knowledge, this report shows that calcium and magnesium in a less extent, enhances the adherence of Legionella to surfaces compared to the bacteria behavior in distilled water. Treatment with proteinase K of live cells showed that surface proteins do not seem to play a crucial role in bacteria adherence to surfaces. Our results represent a first step in understanding effect of ions on Legionella adherence to surfaces. Such field of research could be helpful to better understand biofilm colonization by this bacterium to improve Legionella risk management in water networks.
Collapse
|
45
|
Murayama K, Kato-Murayama M, Hosaka T, Sotokawauchi A, Yokoyama S, Arima K, Shirouzu M. Crystal Structure of Cucumisin, a Subtilisin-Like Endoprotease from Cucumis melo L. J Mol Biol 2012; 423:386-96. [DOI: 10.1016/j.jmb.2012.07.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/13/2012] [Accepted: 07/17/2012] [Indexed: 10/28/2022]
|
46
|
Uehara R, Takeuchi Y, Tanaka SI, Takano K, Koga Y, Kanaya S. Requirement of Ca2+ Ions for the Hyperthermostability of Tk-Subtilisin from Thermococcus kodakarensis. Biochemistry 2012; 51:5369-78. [DOI: 10.1021/bi300427u] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Ryo Uehara
- Department of Material and Life Science, Graduate School
of Engineering, Osaka University, 2-1 Yamadaoka,
Suita, Osaka 565-0871, Japan
| | - Yuki Takeuchi
- Department of Material and Life Science, Graduate School
of Engineering, Osaka University, 2-1 Yamadaoka,
Suita, Osaka 565-0871, Japan
| | - Shun-ichi Tanaka
- Department of Material and Life Science, Graduate School
of Engineering, Osaka University, 2-1 Yamadaoka,
Suita, Osaka 565-0871, Japan
| | - Kazufumi Takano
- Department of Material and Life Science, Graduate School
of Engineering, Osaka University, 2-1 Yamadaoka,
Suita, Osaka 565-0871, Japan
| | - Yuichi Koga
- Department of Material and Life Science, Graduate School
of Engineering, Osaka University, 2-1 Yamadaoka,
Suita, Osaka 565-0871, Japan
| | - Shigenori Kanaya
- Department of Material and Life Science, Graduate School
of Engineering, Osaka University, 2-1 Yamadaoka,
Suita, Osaka 565-0871, Japan
| |
Collapse
|
47
|
Souza TACB, Okamoto DN, Ruiz DM, Oliveira LCG, Kondo MY, Tersario ILS, Juliano L, De Castro RE, Gouvea IE, Murakami MT. Correlation between catalysis and tertiary structure arrangement in an archaeal halophilic subtilase. Biochimie 2011; 94:798-805. [PMID: 22177966 DOI: 10.1016/j.biochi.2011.11.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 11/21/2011] [Indexed: 10/14/2022]
Abstract
Nep (Natrialba magadii extracellular protease) is a halolysin-like peptidase secreted by the haloalkaliphilic archaeon N. magadii that exhibits optimal activity and stability in salt-saturated solutions. In this work, the effect of salt on the function and structure of Nep was investigated. In absence of salt, Nep became unfolded and aggregated, leading to the loss of activity. The enzyme did not recover its structural and functional properties even after restoring the ideal conditions for catalysis. At salt concentrations higher than 1 M (NaCl), Nep behaved as monomers in solution and its enzymatic activity displayed a nonlinear concave-up dependence with salt concentration resulting in a 20-fold activation at 4 M NaCl. Although transition from a high to a low-saline environment (3-1 M NaCl) did not affect its secondary structure contents, it diminished the enzyme stability and provoked large structural rearrangements, changing from an elongated shape at 3 M NaCl to a compact conformational state at 1 M NaCl. The thermodynamic analysis of peptide hydrolysis by Nep suggests a significant enzyme reorganization depending on the environmental salinity, which supports in solution SAXS and DLS studies. Moreover, solvent kinetic isotopic effect (SKIE) data indicates the general acid-base mechanism as the rate-limiting step for Nep catalysis, like classical serine-peptidases. All these data correlate the Nep conformational states with the enzymatic behavior providing a further understanding on the stability and structural determinants for the functioning of halolysins under different salinities.
Collapse
Affiliation(s)
- Tatiana A C B Souza
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisas em Energia e Materiais, Giuseppe Maximo Scolfaro, 10000, Campinas 13083-970, Brazil
| | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Comparison of the structural basis for thermal stability between archaeal and bacterial proteins. Extremophiles 2011; 16:67-78. [PMID: 22015540 DOI: 10.1007/s00792-011-0406-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Accepted: 10/07/2011] [Indexed: 10/16/2022]
Abstract
In this study, the structural basis for thermal stability in archaeal and bacterial proteins was investigated. There were many common factors that confer resistance to high temperature in both archaeal and bacterial proteins. These factors include increases in the Lys content, the bends and blanks of secondary structure, the Glu content of salt bridge; decreases in the number of main-side chain hydrogen bond and exposed surface area, and changes in the bends and blanks of amino acids. Certainly, the utilization of charged amino acids to form salt bridges is a primary factor. In both heat-resistant archaeal and bacterial proteins, most Glu and Asp participate in the formation of salt bridges. Other factors may influence either archaeal or bacterial protein thermostability, which includes the more frequent occurrence of shorter 3(10)-helices and increased hydrophobicity in heat-resistant archaeal proteins. However, there were increases in average helix length, the Glu content in salt bridges, temperature factors and decreases in the number of main-side chain hydrogen bonds, uncharged-uncharged hydrogen bonds, hydrophobicity, and buried and exposed polar surface area in heat-resistant bacterial proteins. Evidently, there are few similarities and many disparities between the heat-resistant mechanisms of archaeal and bacterial proteins.
Collapse
|
49
|
Wiriyaphan C, Chitsomboon B, Yongsawadigul J. Antioxidant activity of protein hydrolysates derived from threadfin bream surimi byproducts. Food Chem 2011; 132:104-11. [PMID: 26434269 DOI: 10.1016/j.foodchem.2011.10.040] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2011] [Revised: 09/03/2011] [Accepted: 10/11/2011] [Indexed: 11/25/2022]
Abstract
Antioxidant activities of protein hydrolysates from threadfin bream surimi wastes, including frame, bone and skin (FBS) and refiner discharge (RD), were investigated. FBS and RD were rich in Lys, Glu, Gly, Pro, Asp, Leu, His, Tyr and Phe. FBS was hydrolysed to a greater extent than RD regardless of proteinases tested (Virgibacillus sp. SK33 proteinase, Alcalase, pepsin and trypsin). Pepsin-hydrolysed FBS, at a 5% degree of hydrolysis (DH), showed the highest antioxidant activity based on 2,2'-azinobis (3-ethyl-benzothiazoline-6-sulphonate) (ABTS) radical (0.455±0.054mg Trolox equivalents/mg leucine equivalents), ferric reducing antioxidant power (FRAP) (0.221±0.005mM Trolox equivalents) and inhibition of β-carotene bleaching assays. FBS hydrolysates showed higher antioxidant activity based on chemical assays than their RD counterparts. However, FBS and RD hydrolysates protected HepG2 cells against tert-butyl hydroperoxide-induced oxidative damage to a similar extent. Therefore, FBS and RD hydrolysates have a potential as antioxidative neutraceutical ingredients.
Collapse
Affiliation(s)
- Chompoonuch Wiriyaphan
- Food Protein Research Unit, School of Food Technology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Benjamart Chitsomboon
- School of Biology, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Jirawat Yongsawadigul
- Food Protein Research Unit, School of Food Technology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand.
| |
Collapse
|
50
|
Kinetic Stability Modelling of Keratinolytic Protease P45: Influence of Temperature and Metal Ions. Appl Biochem Biotechnol 2011; 165:1740-53. [DOI: 10.1007/s12010-011-9391-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 09/12/2011] [Indexed: 10/17/2022]
|