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Oda K, Dunn BM, Wlodawer A. Serine-Carboxyl Peptidases, Sedolisins: From Discovery to Evolution. Biochemistry 2022; 61:1643-1664. [PMID: 35862020 DOI: 10.1021/acs.biochem.2c00239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sedolisin is a proteolytic enzyme, listed in the peptidase database MEROPS as a founding member of clan SB, family S53. This enzyme, although active at low pH, was originally shown not to be inhibited by an aspartic peptidase specific inhibitor, S-PI (pepstatin Ac). In this Perspective, the S53 family is described from the moment of original identification to evolution. The representative enzymes of the family are sedolisin, kumamolisin, and TPP-1. They exhibit the following unique features. (1) The fold of the molecule is similar to that of subtilisin, but the catalytic residues consist of a triad, Ser/Glu/Asp, that is unlike the Ser/His/Asp triad of subtilisin. (2) The molecule is expressed as a pro-form composed of the amino-terminal prosegment and the active domain. Additionally, some members of this family have an additional, carboxy-terminal prosegment. (3) Their optimum pH for activity is in the acidic region, not in the neutral to alkaline region where subtilisin is active. (4) Their distribution in nature is very broad across the three kingdoms of life. (5) Some of these enzymes from fungi and bacteria are pathogens to plants. (6) Some of them have significant potential applications for industry. (7) The lack of a TPP-1 gene in human brain is the cause of incurable juvenile neuronal ceroid lipofuscinosis (Batten's disease).
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Affiliation(s)
- Kohei Oda
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Ben M Dunn
- Department of Biochemistry & Molecular Biology, University of Florida College of Medicine, Gainesville, Florida 32610-0245, United States
| | - Alexander Wlodawer
- Center for Structural Biology, National Cancer Institute, Frederick, Maryland 21702, United States
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Elsässer B, Goettig P. Mechanisms of Proteolytic Enzymes and Their Inhibition in QM/MM Studies. Int J Mol Sci 2021; 22:3232. [PMID: 33810118 PMCID: PMC8004986 DOI: 10.3390/ijms22063232] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/11/2022] Open
Abstract
Experimental evidence for enzymatic mechanisms is often scarce, and in many cases inadvertently biased by the employed methods. Thus, apparently contradictory model mechanisms can result in decade long discussions about the correct interpretation of data and the true theory behind it. However, often such opposing views turn out to be special cases of a more comprehensive and superior concept. Molecular dynamics (MD) and the more advanced molecular mechanical and quantum mechanical approach (QM/MM) provide a relatively consistent framework to treat enzymatic mechanisms, in particular, the activity of proteolytic enzymes. In line with this, computational chemistry based on experimental structures came up with studies on all major protease classes in recent years; examples of aspartic, metallo-, cysteine, serine, and threonine protease mechanisms are well founded on corresponding standards. In addition, experimental evidence from enzyme kinetics, structural research, and various other methods supports the described calculated mechanisms. One step beyond is the application of this information to the design of new and powerful inhibitors of disease-related enzymes, such as the HIV protease. In this overview, a few examples demonstrate the high potential of the QM/MM approach for sophisticated pharmaceutical compound design and supporting functions in the analysis of biomolecular structures.
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Affiliation(s)
| | - Peter Goettig
- Structural Biology Group, Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria;
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Liu H, Fan X, Song H, Hu X, Zhang G, Yu C, Yi L. Efficient production of gluten hydrolase Kuma030 in E. coli by hot acid treatment without chromatography. Enzyme Microb Technol 2019; 129:109356. [PMID: 31307580 DOI: 10.1016/j.enzmictec.2019.05.013] [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: 01/29/2019] [Revised: 04/12/2019] [Accepted: 05/26/2019] [Indexed: 01/28/2023]
Abstract
Kumamolisin from Alicyclobacillus sendaiensis strain NTAP-1 is a serine protease with collagenase activity. After molecular engineering, a kumamolisin mutant, named Kuma030, was obtained with high proteolytic activity against gluten, which might cause celiac disease. Kuma030 exhibited its potential application in industrial and medicine, while challenges remained of its large-scale purification and production. In the studies here, we successfully overexpressed the Kuma030 in E. coli BL21 (DE3) by anchoring a SUMO (Small Ubiquitin-like Modifier) fusion protein at its N-terminal end. In addition, a fast protein purification procedure was developed according to the acidophilic and thermophilic properties of Alicyclobacillus sendaiensis. After a simple acid treatment followed by a heat treatment, a total of 9.9 mg functional Kuma030 was quickly obtained form 1 L LB media culture. This purified Kuma030 was confirmed to be functional to cleave the PQ sequences in a designed protein substrate, and the gluten in actual food samples, such as whole wheat bread and beer, in a fast manner. Our studies provided an efficient strategy for the overexpression and purification of functional Kuma030 in E. coli, which might expand its broad practical applications.
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Affiliation(s)
- Houquan Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-Enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, College of Life Sciences, Hubei University, No. 368 Youyi Road, Wuchang District, Wuhan, 430062, China
| | - Xian Fan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-Enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, College of Life Sciences, Hubei University, No. 368 Youyi Road, Wuchang District, Wuhan, 430062, China
| | - Haoyue Song
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-Enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, College of Life Sciences, Hubei University, No. 368 Youyi Road, Wuchang District, Wuhan, 430062, China
| | - Xiaoyun Hu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-Enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, College of Life Sciences, Hubei University, No. 368 Youyi Road, Wuchang District, Wuhan, 430062, China
| | - Guimin Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-Enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, College of Life Sciences, Hubei University, No. 368 Youyi Road, Wuchang District, Wuhan, 430062, China
| | - Chan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-Enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, College of Life Sciences, Hubei University, No. 368 Youyi Road, Wuchang District, Wuhan, 430062, China.
| | - Li Yi
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-Enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, College of Life Sciences, Hubei University, No. 368 Youyi Road, Wuchang District, Wuhan, 430062, China.
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QM/MM free energy Simulations of an efficient Gluten Hydrolase (Kuma030) Implicate for a Reactant-State Based Protein-Design Strategy for General Acid/Base Catalysis. Sci Rep 2018; 8:7042. [PMID: 29728674 PMCID: PMC5935664 DOI: 10.1038/s41598-018-25471-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/23/2018] [Indexed: 01/16/2023] Open
Abstract
It is a grand attraction for contemporary biochemists to computationally design enzymes for novel chemical transformation or improved catalytic efficiency. Rosetta by Baker et al. is no doubt the leading software in the protein design society. Generally, optimization of the transition state (TS) is part of the Rosetta’s protocol to enhance the catalytic efficiency of target enzymes, since TS stabilization is the determining factor for catalytic efficiency based on the TS theory (TST). However, it is confusing that optimization of the reactant state (RS) also results in significant improvement of catalytic efficiency in some cases, such as design of gluten hydrolase (Kuma030). Therefore, it is interesting to uncover underlying reason why a better binding in the RS leading to an increased kcat. In this study, the combined quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) and free energy (PMF) simulations, pKa calculation, and the statistical analysis such as the ANOVA test were carried out to shed light on the interesting but elusive question. By integration of our computational results and general acid/base theory, we answered the question why optimization of RS stabilization leads to a better TS stabilization in the general acid/base catalysis. In addition, a new and simplified protein-design strategy is proposed for the general acid/base catalysis. The idea, that application of traditional well-defined enzyme mechanism to protein design strategy, would be a great help for methodology development of protein design.
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Yao J, Luo H, Wang X. Understanding the Catalytic Mechanism and the Substrate Specificity of an Engineered Gluten Hydrolase by QM/MM Molecular Dynamics and Free Energy Simulations. J Chem Inf Model 2017; 57:1179-1186. [DOI: 10.1021/acs.jcim.7b00167] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Jianzhuang Yao
- School
of Biological Science and Technology, University of Jinan, Jinan 250022, P. R. China
| | - Haixia Luo
- Key
Laboratory of Ministry of Education for Conservation and Utilization
of Special Biological Resources in the Western China, Life Science
School, Ningxia University, Yinchuan 750021, P. R. China
| | - Xia Wang
- School
of Biological Science and Technology, University of Jinan, Jinan 250022, P. R. China
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