151
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Vogt AD, Chakraborty P, Di Cera E. Kinetic dissection of the pre-existing conformational equilibrium in the trypsin fold. J Biol Chem 2015. [PMID: 26216877 DOI: 10.1074/jbc.m115.675538] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Structural biology has recently documented the conformational plasticity of the trypsin fold for both the protease and zymogen in terms of a pre-existing equilibrium between closed (E*) and open (E) forms of the active site region. How such plasticity is manifested in solution and affects ligand recognition by the protease and zymogen is poorly understood in quantitative terms. Here we dissect the E*-E equilibrium with stopped-flow kinetics in the presence of excess ligand or macromolecule. Using the clotting protease thrombin and its zymogen precursor prethrombin-2 as relevant models we resolve the relative distribution of the E* and E forms and the underlying kinetic rates for their interconversion. In the case of thrombin, the E* and E forms are distributed in a 1:4 ratio and interconvert on a time scale of 45 ms. In the case of prethrombin-2, the equilibrium is shifted strongly (10:1 ratio) in favor of the closed E* form and unfolds over a faster time scale of 4.5 ms. The distribution of E* and E forms observed for thrombin and prethrombin-2 indicates that zymogen activation is linked to a significant shift in the pre-existing equilibrium between closed and open conformations that facilitates ligand binding to the active site. These findings broaden our mechanistic understanding of how conformational transitions control ligand recognition by thrombin and its zymogen precursor prethrombin-2 and have direct relevance to other members of the trypsin fold.
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Affiliation(s)
- Austin D Vogt
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
| | - Pradipta Chakraborty
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
| | - Enrico Di Cera
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
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152
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Kim MS, Buisson LA, Heathcote DA, Hu H, Braddock DC, Barrett AGM, Ashton-Rickardt PG, Snyder JP. Approaches to design non-covalent inhibitors for human granzyme B (hGrB). Org Biomol Chem 2015; 12:8952-65. [PMID: 25277547 DOI: 10.1039/c4ob01874e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A structure-based design campaign for non-covalent small molecule inhibitors of human granzyme B was carried out by means of a virtual screening strategy employing three constraints and probe site-mapping with FTMAP to identify ligand "hot spots". In addition, new scaffolds of diverse structures were subsequently explored with ROCS shape-based superposition methods, following by Glide SP docking, induced fit docking and analysis of QikProp molecular properties. Novel classes of moderately active small molecule blockers (≥25 μM IC50 values) from commercially available libraries were identified, and three novel scaffolds have been synthesized by multi-step procedures. Furthermore, we provide an example of a comprehensive structure-based drug discovery approach to non-covalent inhibitors that relies on the X-ray structure of a covalently bound ligand and suggest that the design path may be compromised by alternative and unknown binding poses.
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Affiliation(s)
- Mi-Sun Kim
- Department of Chemistry, 1515 Dickey Drive. and Emory University, Atlanta, GA 30322, USA.
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153
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Juntunen K, Mäkinen S, Isoniemi S, Valtakari L, Pelzer A, Jänis J, Paloheimo M. A New Subtilase-Like Protease Deriving from Fusarium equiseti with High Potential for Industrial Applications. Appl Biochem Biotechnol 2015; 177:407-30. [DOI: 10.1007/s12010-015-1752-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/06/2015] [Indexed: 11/28/2022]
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154
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Cao X, He Y, Hu Y, Zhang X, Wang Y, Zou Z, Chen Y, Blissard GW, Kanost MR, Jiang H. Sequence conservation, phylogenetic relationships, and expression profiles of nondigestive serine proteases and serine protease homologs in Manduca sexta. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2015; 62:51-63. [PMID: 25530503 PMCID: PMC4474797 DOI: 10.1016/j.ibmb.2014.10.006] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 10/14/2014] [Accepted: 10/20/2014] [Indexed: 05/09/2023]
Abstract
Serine protease (SP) and serine protease homolog (SPH) genes in insects encode a large family of proteins involved in digestion, development, immunity, and other processes. While 68 digestive SPs and their close homologs are reported in a companion paper (Kuwar et al., in preparation), we have identified 125 other SPs/SPHs in Manduca sexta and studied their structure, evolution, and expression. Fifty-two of them contain cystine-stabilized structures for molecular recognition, including clip, LDLa, Sushi, Wonton, TSP, CUB, Frizzle, and SR domains. There are nineteen groups of genes evolved from relatively recent gene duplication and sequence divergence. Thirty-five SPs and seven SPHs contain 1, 2 or 5 clip domains. Multiple sequence alignment and molecular modeling of the 54 clip domains have revealed structural diversity of these regulatory modules. Sequence comparison with their homologs in Drosophila melanogaster, Anopheles gambiae and Tribolium castaneum allows us to classify them into five subfamilies: A are SPHs with 1 or 5 group-3 clip domains, B are SPs with 1 or 2 group-2 clip domains, C, D1 and D2 are SPs with a single clip domain in group-1a, 1b and 1c, respectively. We have classified into six categories the 125 expression profiles of SP-related proteins in fat body, brain, midgut, Malpighian tubule, testis, and ovary at different stages, suggesting that they participate in various physiological processes. Through RNA-Seq-based gene annotation and expression profiling, as well as intragenomic sequence comparisons, we have established a framework of information for future biochemical research of nondigestive SPs and SPHs in this model species.
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Affiliation(s)
- Xiaolong Cao
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Yan He
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Yingxia Hu
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Xiufeng Zhang
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Yang Wang
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Zhen Zou
- The State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Yunru Chen
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Gary W Blissard
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Michael R Kanost
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Haobo Jiang
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74078, USA.
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155
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Tsai YF, Hwang TL. Neutrophil elastase inhibitors: a patent review and potential applications for inflammatory lung diseases (2010 - 2014). Expert Opin Ther Pat 2015; 25:1145-58. [PMID: 26118988 DOI: 10.1517/13543776.2015.1061998] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
INTRODUCTION The proteolytic activity of neutrophil elastase (NE) not only destroys pathogens but also degrades host matrix tissues by generating a localized protease-antiprotease imbalance. In humans, NE is well known to be involved in various acute and chronic inflammatory diseases, such as chronic obstructive pulmonary disease, emphysema, asthma, acute lung injury, acute respiratory distress syndrome and cystic fibrosis. The regulation of NE activity is thought to represent a promising therapeutic approach, and NE is considered as an important target for the development of novel selective inhibitors to treat these diseases. AREAS COVERED This article summarizes and analyzes patents on NE inhibitors and their therapeutic potential based on a review of patent applications disclosed between 2010 and 2014. EXPERT OPINION According to this review of recent NE inhibitor patents, all of the disclosed inhibitors can be classified into peptide- and non-peptide-based groups. The non-peptide NE inhibitors include heterocyclics, uracil derivatives and deuterium oxide. Among the heterocyclic analogs, derivatives of pyrimidinones, tetrahydropyrrolopyrimidinediones, pyrazinones, benzoxazinones and hypersulfated disaccharides were introduced. The literature has increasingly implicated NE in the pathogenesis of various diseases, of which inflammatory destructive lung diseases remain a major concern. However, only a few agents have been validated for therapeutic use in clinical settings to date.
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Affiliation(s)
- Yung-Fong Tsai
- a 1 Chang Gung University, Graduate Institute of Natural Products, School of Traditional Chinese Medicine, College of Medicine , Taoyuan 33302, Taiwan.,b 2 Chang Gung Memorial Hospital, Department of Anesthesiology , Kweishan, Taoyuan, Taiwan
| | - Tsong-Long Hwang
- a 1 Chang Gung University, Graduate Institute of Natural Products, School of Traditional Chinese Medicine, College of Medicine , Taoyuan 33302, Taiwan.,c 3 Chang Gung University, Healthy Aging Research Center, Chinese Herbal Medicine Research Team , Taoyuan 33302, Taiwan.,d 4 Chang Gung University of Science and Technology, Department of Cosmetic Science and Research Center for Industry of Human Ecology , Taoyuan 33302, Taiwan.,e 5 Chang Gung University, Graduate Institute of Natural Products, School of Traditional Chinese Medicine, College of Medicine , Taoyuan 33302, Taiwan +88 6 3211 8506 ; +88 6 3211 8506 ;
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156
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Glaza P, Osipiuk J, Wenta T, Zurawa-Janicka D, Jarzab M, Lesner A, Banecki B, Skorko-Glonek J, Joachimiak A, Lipinska B. Structural and Functional Analysis of Human HtrA3 Protease and Its Subdomains. PLoS One 2015; 10:e0131142. [PMID: 26110759 PMCID: PMC4481513 DOI: 10.1371/journal.pone.0131142] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 05/27/2015] [Indexed: 11/18/2022] Open
Abstract
Human HtrA3 protease, which induces mitochondria-mediated apoptosis, can be a tumor suppressor and a potential therapeutic target in the treatment of cancer. However, there is little information about its structure and biochemical properties. HtrA3 is composed of an N-terminal domain not required for proteolytic activity, a central serine protease domain and a C-terminal PDZ domain. HtrA3S, its short natural isoform, lacks the PDZ domain which is substituted by a stretch of 7 C-terminal amino acid residues, unique for this isoform. This paper presents the crystal structure of the HtrA3 protease domain together with the PDZ domain (ΔN-HtrA3), showing that the protein forms a trimer whose protease domains are similar to those of human HtrA1 and HtrA2. The ΔN-HtrA3 PDZ domains are placed in a position intermediate between that in the flat saucer-like HtrA1 SAXS structure and the compact pyramidal HtrA2 X-ray structure. The PDZ domain interacts closely with the LB loop of the protease domain in a way not found in other human HtrAs. ΔN-HtrA3 with the PDZ removed (ΔN-HtrA3-ΔPDZ) and an N-terminally truncated HtrA3S (ΔN-HtrA3S) were fully active at a wide range of temperatures and their substrate affinity was not impaired. This indicates that the PDZ domain is dispensable for HtrA3 activity. As determined by size exclusion chromatography, ΔN-HtrA3 formed stable trimers while both ΔN-HtrA3-ΔPDZ and ΔN-HtrA3S were monomeric. This suggests that the presence of the PDZ domain, unlike in HtrA1 and HtrA2, influences HtrA3 trimer formation. The unique C-terminal sequence of ΔN-HtrA3S appeared to have little effect on activity and oligomerization. Additionally, we examined the cleavage specificity of ΔN-HtrA3. Results reported in this paper provide new insights into the structure and function of ΔN-HtrA3, which seems to have a unique combination of features among human HtrA proteases.
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Affiliation(s)
- Przemyslaw Glaza
- Department of Biochemistry, Faculty of Biology, University of Gdansk, 80–308 Gdansk, Poland
| | - Jerzy Osipiuk
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois, IL 60439, United States of America
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois, IL 60439, United States of America
| | - Tomasz Wenta
- Department of Biochemistry, Faculty of Biology, University of Gdansk, 80–308 Gdansk, Poland
| | - Dorota Zurawa-Janicka
- Department of Biochemistry, Faculty of Biology, University of Gdansk, 80–308 Gdansk, Poland
| | - Miroslaw Jarzab
- Department of Biochemistry, Faculty of Biology, University of Gdansk, 80–308 Gdansk, Poland
| | - Adam Lesner
- Department of Biochemistry, Faculty of Chemistry, University of Gdansk, 80–308 Gdansk, Poland
| | - Bogdan Banecki
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology of the University of Gdansk and the Medical University of Gdansk, 80–822 Gdansk, Poland
| | - Joanna Skorko-Glonek
- Department of Biochemistry, Faculty of Biology, University of Gdansk, 80–308 Gdansk, Poland
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois, IL 60439, United States of America
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois, IL 60439, United States of America
| | - Barbara Lipinska
- Department of Biochemistry, Faculty of Biology, University of Gdansk, 80–308 Gdansk, Poland
- * E-mail:
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157
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Characterization of digestive enzymes from de-oiled mackerel (Scomber japonicus) muscle obtained by supercritical carbon dioxide and n-hexane extraction as a comparative study. Journal of Food Science and Technology 2015; 52:3494-503. [PMID: 26028731 DOI: 10.1007/s13197-014-1408-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 04/16/2014] [Accepted: 05/05/2014] [Indexed: 10/25/2022]
Abstract
The oil in mackerel muscle was extracted using an environmental friendly solvent, supercritical carbon dioxide (SC-CO2) at a semi-batch flow extraction process and an n-hexane. The SC-CO2 was carried out at temperature 45 °C and pressures ranging from 15 to 25 MPa. The flow rate of CO2 (27 g/min) was constant at the entire extraction period of 2 h. The highest oil extracted residues after SC-CO2 extraction was used for activity measurement of digestive enzymes. Four digestive enzymes were found in water soluble extracts after n-hexane and SC-CO2 treated samples. Amylase, lipase and trypsin activities were higher in water soluble extracts after SC-CO2 treated samples except protease. Among the four digestive enzymes, the activity of amylase was highest and the value was 44.57 uM/min/mg of protein. The water soluble extracts of SC-CO2 and n-hexane treated mackerel samples showed same alkaline optimum pH and pH stability for each of the digestive enzymes. Optimum temperature of amylase, lipase, protease and trypsin was 40, 50, 60 and 30 °C, respectively of both extracts. More than 80 % temperature stability of amylase, lipase, protease and trypsin were retained at mentioned optimum temperature in water soluble extracts of both treated samples. Based on protein patterns, prominent protein band showed in water soluble extracts after SC-CO2 treated samples indicates no denaturation of protein than untreated and n-hexane.
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158
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Hardes K, Becker GL, Lu Y, Dahms SO, Köhler S, Beyer W, Sandvig K, Yamamoto H, Lindberg I, Walz L, von Messling V, Than ME, Garten W, Steinmetzer T. Novel Furin Inhibitors with Potent Anti-infectious Activity. ChemMedChem 2015; 10:1218-31. [PMID: 25974265 DOI: 10.1002/cmdc.201500103] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Indexed: 11/10/2022]
Abstract
New peptidomimetic furin inhibitors with unnatural amino acid residues in the P3 position were synthesized. The most potent compound 4-guanidinomethyl-phenylacteyl-Arg-Tle-Arg-4-amidinobenzylamide (MI-1148) inhibits furin with a Ki value of 5.5 pM. The derivatives also strongly inhibit PC1/3, whereas PC2 is less affected. Selected inhibitors were tested in cell culture for antibacterial and antiviral activity against infectious agents known to be dependent on furin activity. A significant protective effect against anthrax and diphtheria toxin was observed in the presence of the furin inhibitors. Furthermore, the spread of the highly pathogenic H5N1 and H7N1 avian influenza viruses and propagation of canine distemper virus was strongly inhibited. Inhibitor MI-1148 was crystallized in complex with human furin. Its N-terminal guanidinomethyl group in the para position of the P5 phenyl ring occupies the same position as that found previously for a structurally related inhibitor containing this substitution in the meta position, thereby maintaining all of the important P5 interactions. Our results confirm that the inhibition of furin is a promising strategy for a short-term treatment of acute infectious diseases.
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Affiliation(s)
- Kornelia Hardes
- Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 6, 35032 Marburg (Germany)
| | - Gero L Becker
- Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 6, 35032 Marburg (Germany)
| | - Yinghui Lu
- Institute of Virology, Philipps University, Hans-Meerwein-Strasse 2, Marburg (Germany)
| | - Sven O Dahms
- Protein Crystallography Group, Leibniz Institute for Age Research-Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena (Germany)
| | - Susanne Köhler
- Institute of Environmental and Animal Hygiene, University of Hohenheim, Garbenstrasse 30, 70599 Stuttgart (Germany)
| | - Wolfgang Beyer
- Institute of Environmental and Animal Hygiene, University of Hohenheim, Garbenstrasse 30, 70599 Stuttgart (Germany)
| | - Kirsten Sandvig
- Department of Biochemistry and Centre for Cancer Biomedicine, Institute for Cancer Research, The Norwegian Radium Hospital, Montebello, 0310 Oslo (Norway)
| | - Hiroyuki Yamamoto
- Department of Anatomy and Neurobiology, University of Maryland, Baltimore, Maryland 21201 (USA)
| | - Iris Lindberg
- Department of Anatomy and Neurobiology, University of Maryland, Baltimore, Maryland 21201 (USA)
| | - Lisa Walz
- Veterinary Medicine Division, Paul-Ehrlich-Institute, Federal Institute for Vaccines and Biomedicines, Paul-Ehrlich-Strasse 51-59, 63225 Langen (Germany)
| | - Veronika von Messling
- Veterinary Medicine Division, Paul-Ehrlich-Institute, Federal Institute for Vaccines and Biomedicines, Paul-Ehrlich-Strasse 51-59, 63225 Langen (Germany)
| | - Manuel E Than
- Protein Crystallography Group, Leibniz Institute for Age Research-Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena (Germany)
| | - Wolfgang Garten
- Institute of Virology, Philipps University, Hans-Meerwein-Strasse 2, Marburg (Germany)
| | - Torsten Steinmetzer
- Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 6, 35032 Marburg (Germany).
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159
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Abstract
The carbamate group is a key structural motif in many approved drugs and prodrugs. There is an increasing use of carbamates in medicinal chemistry and many derivatives are specifically designed to make drug-target interactions through their carbamate moiety. In this Perspective, we present properties and stabilities of carbamates, reagents and chemical methodologies for the synthesis of carbamates, and recent applications of carbamates in drug design and medicinal chemistry.
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Affiliation(s)
- Arun K. Ghosh
- Department of Chemistry and
Department of Medicinal Chemistry, Purdue
University, West Lafayette, Indiana 47907, United States
| | - Margherita Brindisi
- Department of Chemistry and
Department of Medicinal Chemistry, Purdue
University, West Lafayette, Indiana 47907, United States
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160
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Aguirre C, Condado-Morales I, Olguin LF, Costas M. Isothermal titration calorimetry determination of individual rate constants of trypsin catalytic activity. Anal Biochem 2015; 479:18-27. [PMID: 25823683 DOI: 10.1016/j.ab.2015.03.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 03/02/2015] [Accepted: 03/11/2015] [Indexed: 11/25/2022]
Abstract
Determination of individual rate constants for enzyme-catalyzed reactions is central to the understanding of their mechanism of action and is commonly obtained by stopped-flow kinetic experiments. However, most natural substrates either do not fluoresce/absorb or lack a significant change in their spectra while reacting and, therefore, are frequently chemically modified to render adequate molecules for their spectroscopic detection. Here, isothermal titration calorimetry (ITC) was used to obtain Michaelis-Menten plots for the trypsin-catalyzed hydrolysis of several substrates at different temperatures (278-318K): four spectrophotometrically blind lysine and arginine N-free esters, one N-substituted arginine ester, and one amide. A global fitting of these data provided the individual rate constants and activation energies for the acylation and deacylation reactions, and the ratio of the formation and dissociation rates of the enzyme-substrate complex, leading also to the corresponding free energies of activation. The results indicate that for lysine and arginine N-free esters deacylation is the rate-limiting step, but for the N-substituted ester and the amide acylation is the slowest step. It is shown that ITC is able to produce quality kinetic data and is particularly well suited for those enzymatic reactions that cannot be measured by absorption or fluorescence spectroscopy.
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Affiliation(s)
- César Aguirre
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, México, D.F. 04510, Mexico
| | - Itzel Condado-Morales
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, México, D.F. 04510, Mexico
| | - Luis F Olguin
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, México, D.F. 04510, Mexico.
| | - Miguel Costas
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, México, D.F. 04510, Mexico.
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161
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Dias RO, Via A, Brandão MM, Tramontano A, Silva-Filho MC. Digestive peptidase evolution in holometabolous insects led to a divergent group of enzymes in Lepidoptera. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2015; 58:1-11. [PMID: 25600115 DOI: 10.1016/j.ibmb.2014.12.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 12/13/2014] [Accepted: 12/29/2014] [Indexed: 06/04/2023]
Abstract
Trypsins and chymotrypsins are well-studied serine peptidases that cleave peptide bonds at the carboxyl side of basic and hydrophobic L-amino acids, respectively. These enzymes are largely responsible for the digestion of proteins. Three primary processes regulate the activity of these peptidases: secretion, precursor (zymogen) activation and substrate-binding site recognition. Here, we present a detailed phylogenetic analysis of trypsins and chymotrypsins in three orders of holometabolous insects and reveal divergent characteristics of Lepidoptera enzymes in comparison with those of Coleoptera and Diptera. In particular, trypsin subsite S1 was more hydrophilic in Lepidoptera than in Coleoptera and Diptera, whereas subsites S2-S4 were more hydrophobic, suggesting different substrate preferences. Furthermore, Lepidoptera displayed a lineage-specific trypsin group belonging only to the Noctuidae family. Evidence for facilitated trypsin auto-activation events were also observed in all the insect orders studied, with the characteristic zymogen activation motif complementary to the trypsin active site. In contrast, insect chymotrypsins did not seem to have a peculiar evolutionary history with respect to their mammal counterparts. Overall, our findings suggest that the need for fast digestion allowed holometabolous insects to evolve divergent groups of peptidases with high auto-activation rates, and highlight that the evolution of trypsins led to a most diverse group of enzymes in Lepidoptera.
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Affiliation(s)
- Renata O Dias
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Av. Pádua Dias, 11, 13418-900 Piracicaba, SP, Brazil
| | - Allegra Via
- Department of Physics and Istituto Pasteur, Fondazione Cenci Bolognetti, Sapienza University, P.le A. Moro, 5, 00185 Rome, Italy
| | - Marcelo M Brandão
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Cândido Rondon, 400, 13083-875 Campinas, SP, Brazil
| | - Anna Tramontano
- Department of Physics and Istituto Pasteur, Fondazione Cenci Bolognetti, Sapienza University, P.le A. Moro, 5, 00185 Rome, Italy
| | - Marcio C Silva-Filho
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Av. Pádua Dias, 11, 13418-900 Piracicaba, SP, Brazil.
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162
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de Assis Fonseca FC, Firmino AAP, de Macedo LLP, Coelho RR, de Sousa Júnior JDA, Silva-Junior OB, Togawa RC, Pappas GJ, de Góis LAB, da Silva MCM, Grossi-de-Sá MF. Sugarcane giant borer transcriptome analysis and identification of genes related to digestion. PLoS One 2015; 10:e0118231. [PMID: 25706301 PMCID: PMC4338194 DOI: 10.1371/journal.pone.0118231] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 01/11/2015] [Indexed: 11/25/2022] Open
Abstract
Sugarcane is a widely cultivated plant that serves primarily as a source of sugar and ethanol. Its annual yield can be significantly reduced by the action of several insect pests including the sugarcane giant borer (Telchin licus licus), a lepidopteran that presents a long life cycle and which efforts to control it using pesticides have been inefficient. Although its economical relevance, only a few DNA sequences are available for this species in the GenBank. Pyrosequencing technology was used to investigate the transcriptome of several developmental stages of the insect. To maximize transcript diversity, a pool of total RNA was extracted from whole body insects and used to construct a normalized cDNA database. Sequencing produced over 650,000 reads, which were de novo assembled to generate a reference library of 23,824 contigs. After quality score and annotation, 43% of the contigs had at least one BLAST hit against the NCBI non-redundant database, and 40% showed similarities with the lepidopteran Bombyx mori. In a further analysis, we conducted a comparison with Manduca sexta midgut sequences to identify transcripts of genes involved in digestion. Of these transcripts, many presented an expansion or depletion in gene number, compared to B. mori genome. From the sugarcane giant borer (SGB) transcriptome, a number of aminopeptidase N (APN) cDNAs were characterized based on homology to those reported as Cry toxin receptors. This is the first report that provides a large-scale EST database for the species. Transcriptome analysis will certainly be useful to identify novel developmental genes, to better understand the insect's biology and to guide the development of new strategies for insect-pest control.
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Affiliation(s)
- Fernando Campos de Assis Fonseca
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Alexandre Augusto Pereira Firmino
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Leonardo Lima Pepino de Macedo
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Roberta Ramos Coelho
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | | | - Orzenil Bonfim Silva-Junior
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | | | | | | | | | - Maria Fátima Grossi-de-Sá
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
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163
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Akparov VK, Timofeev VI, Khaliullin IG, Švedas V, Chestukhina GG, Kuranova IP. Structural insights into the broad substrate specificity of carboxypeptidase T fromThermoactinomyces vulgaris. FEBS J 2015; 282:1214-24. [DOI: 10.1111/febs.13210] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 12/19/2014] [Accepted: 01/20/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Valery Kh. Akparov
- State Research Institute for Genetics and Selection of Industrial Microorganisms; Moscow Russia
| | - Vladimir I. Timofeev
- Shubnikov Institute of Crystallography; Russian Academy of Sciences; Moscow Russia
| | - Ilyas G. Khaliullin
- Belozersky Institute of Physicochemical Biology; Lomonosov Moscow State University; Russia
- Moscow Institute of Physics and Technology (State University); Russia
| | - Vytas Švedas
- Belozersky Institute of Physicochemical Biology; Lomonosov Moscow State University; Russia
| | - Galina G. Chestukhina
- State Research Institute for Genetics and Selection of Industrial Microorganisms; Moscow Russia
| | - Inna P. Kuranova
- Shubnikov Institute of Crystallography; Russian Academy of Sciences; Moscow Russia
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164
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Pelc LA, Chen Z, Gohara DW, Vogt AD, Pozzi N, Di Cera E. Why Ser and not Thr brokers catalysis in the trypsin fold. Biochemistry 2015; 54:1457-64. [PMID: 25664608 DOI: 10.1021/acs.biochem.5b00014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Although Thr is equally represented as Ser in the human genome and as a nucleophile is as good as Ser, it is never found in the active site of the large family of trypsin-like proteases that utilize the Asp/His/Ser triad. The molecular basis of the preference of Ser over Thr in the trypsin fold was investigated with X-ray structures of the thrombin mutant S195T free and bound to an irreversible active site inhibitor. In the free form, the methyl group of T195 is oriented toward the incoming substrate in a conformation seemingly incompatible with productive binding. In the bound form, the side chain of T195 is reoriented for efficient substrate acylation without causing steric clash within the active site. Rapid kinetics prove that this change is due to selection of an active conformation from a preexisting ensemble of reactive and unreactive rotamers whose relative distribution determines the level of activity of the protease. Consistent with these observations, the S195T substitution is associated with a weak yet finite activity that allows identification of an unanticipated important role for S195 as the end point of allosteric transduction in the trypsin fold. The S195T mutation abrogates the Na(+)-dependent enhancement of catalytic activity in thrombin, activated protein C, and factor Xa and significantly weakens the physiologically important allosteric effects of thrombomodulin on thrombin and of cofactor Va on factor Xa. The evolutionary selection of Ser over Thr in trypsin-like proteases was therefore driven by the need for high catalytic activity and efficient allosteric regulation.
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Affiliation(s)
- Leslie A Pelc
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine , St. Louis, Missouri 63104, United States
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165
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Borgo B, Havranek JJ. Computer-aided design of a catalyst for Edman degradation utilizing substrate-assisted catalysis. Protein Sci 2015. [PMCID: PMC4380987 DOI: 10.1002/pro.2633] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Molecular biology has been revolutionized by the miniaturization and parallelization of DNA sequencing assays previously performed on bulk samples. Many of these technologies rely on biomolecular reagents to facilitate detection, synthesis, or labeling of samples. To aid in the construction of analogous experimental approaches for proteins and peptides, we have used computer-aided design to engineer an enzyme capable of catalyzing the cleavage step of the Edman degradation. We exploit the similarity between the sulfur nucleophile on the Edman reagent and the catalytic cysteine in a naturally occurring protease to adopt a substrate-assisted mechanism for achieving controlled, step-wise removal of N-terminal amino acids. The ability to expose amino acids iteratively at the N-terminus of peptides is a central requirement for protein sequencing techniques that utilize processive degradation of the peptide chain. While this can be easily accomplished using the chemical Edman degradation, achieving this activity enzymatically in aqueous solution removes the requirement for harsh acid catalysis, improving compatibility with low adsorption detection surfaces, such as those used in single molecule assays.
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Affiliation(s)
- Benjamin Borgo
- Program in Computational and Systems Biology; Washington University in St. Louis; St. Louis Missouri 63110
| | - James J. Havranek
- Department of Genetics; Washington University in St. Louis; St. Louis Missouri 63110
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166
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Plasmin regulation through allosteric, sulfated, small molecules. Molecules 2015; 20:608-24. [PMID: 25569517 PMCID: PMC6272155 DOI: 10.3390/molecules20010608] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 12/26/2014] [Indexed: 01/16/2023] Open
Abstract
Plasmin, a key serine protease, plays a major role in clot lysis and extracellular matrix remodeling. Heparin, a natural polydisperse sulfated glycosaminoglycan, is known to allosterically modulate plasmin activity. No small allosteric inhibitor of plasmin has been discovered to date. We screened an in-house library of 55 sulfated, small glycosaminoglycan mimetics based on nine distinct scaffolds and varying number and positions of sulfate groups to discover several promising hits. Of these, a pentasulfated flavonoid-quinazolinone dimer 32 was found to be the most potent sulfated small inhibitor of plasmin (IC50 = 45 μM, efficacy = 100%). Michaelis-Menten kinetic studies revealed an allosteric inhibition of plasmin by these inhibitors. Studies also indicated that the most potent inhibitors are selective for plasmin over thrombin and factor Xa, two serine proteases in coagulation cascade. Interestingly, different inhibitors exhibited different levels of efficacy (40%–100%), an observation alluding to the unique advantage offered by an allosteric process. Overall, our work presents the first small, synthetic allosteric plasmin inhibitors for further rational design.
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167
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The Secretion and Action of Brush Border Enzymes in the Mammalian Small Intestine. Rev Physiol Biochem Pharmacol 2015; 168:59-118. [PMID: 26345415 DOI: 10.1007/112_2015_24] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Microvilli are conventionally regarded as an extension of the small intestinal absorptive surface, but they are also, as latterly discovered, a launching pad for brush border digestive enzymes. Recent work has demonstrated that motor elements of the microvillus cytoskeleton operate to displace the apical membrane toward the apex of the microvillus, where it vesiculates and is shed into the periapical space. Catalytically active brush border digestive enzymes remain incorporated within the membranes of these vesicles, which shifts the site of BB digestion from the surface of the enterocyte to the periapical space. This process enables nutrient hydrolysis to occur adjacent to the membrane in a pre-absorptive step. The characterization of BB digestive enzymes is influenced by the way in which these enzymes are anchored to the apical membranes of microvilli, their subsequent shedding in membrane vesicles, and their differing susceptibilities to cleavage from the component membranes. In addition, the presence of active intracellular components of these enzymes complicates their quantitative assay and the elucidation of their dynamics. This review summarizes the ontogeny and regulation of BB digestive enzymes and what is known of their kinetics and their action in the peripheral and axial regions of the small intestinal lumen.
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168
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Doron L, Coppenhagen-Glazer S, Ibrahim Y, Eini A, Naor R, Rosen G, Bachrach G. Identification and characterization of fusolisin, the Fusobacterium nucleatum autotransporter serine protease. PLoS One 2014; 9:e111329. [PMID: 25357190 PMCID: PMC4214739 DOI: 10.1371/journal.pone.0111329] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 08/11/2014] [Indexed: 12/30/2022] Open
Abstract
Fusobacterium nucleatum is an oral anaerobe associated with periodontal disease, adverse pregnancy outcomes and colorectal carcinoma. A serine endopeptidase of 61–65 kDa capable of damaging host tissue and of inactivating immune effectors was detected previously in F. nucleatum. Here we describe the identification of this serine protease, named fusolisin, in three oral F. nucleatum sub-species. Gel zymogram revealed fusobacterial proteolytic activity with molecular masses ranging from 55–101 kDa. All of the detected proteases were inhibited by the serine protease inhibitor PMSF. analysis revealed that all of the detected proteases are encoded by genes encoding an open reading frame (ORF) with a calculated mass of approximately 115 kDa. Bioinformatics analysis of the identified ORFs demonstrated that they consist of three domains characteristic of autotransporters of the type Va secretion system. Our results suggest that the F. nucleatum fusolisins are derived from a precursor of approximately 115 kDa. After crossing the cytoplasmic membrane and cleavage of the leader sequence, the C-terminal autotransporter domain of the remaining 96–113 kDa protein is embedded in the outer membrane and delivers the N-terminal S8 serine protease passenger domain to the outer cell surface. In most strains the N-terminal catalytic 55–65 kDa domain self cleaves and liberates itself from the autotransporter domain after its transfer across the outer cell membrane. In F. nucleatum ATCC 25586 this autocatalytic activity is less efficient resulting in a full length membrane-anchored serine protease. The mature serine protease was found to cleave after Thr, Gly, Ala and Leu residues at the P1 position. Growth of F. nucleatum in complex medium was inhibited when serine protease inhibitors were used. Additional experiments are needed to determine whether fusolisin might be used as a target for controlling fusobacterial infections.
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Affiliation(s)
- Lior Doron
- Institute of Dental Sciences, Hebrew University-Hadassah School of Dental Medicine, Jerusalem, Israel
| | - Shunit Coppenhagen-Glazer
- Institute of Dental Sciences, Hebrew University-Hadassah School of Dental Medicine, Jerusalem, Israel
| | - Yara Ibrahim
- Institute of Dental Sciences, Hebrew University-Hadassah School of Dental Medicine, Jerusalem, Israel
| | - Amir Eini
- Institute of Dental Sciences, Hebrew University-Hadassah School of Dental Medicine, Jerusalem, Israel
| | - Ronit Naor
- Institute of Dental Sciences, Hebrew University-Hadassah School of Dental Medicine, Jerusalem, Israel
| | - Graciela Rosen
- Institute of Dental Sciences, Hebrew University-Hadassah School of Dental Medicine, Jerusalem, Israel
| | - Gilad Bachrach
- Institute of Dental Sciences, Hebrew University-Hadassah School of Dental Medicine, Jerusalem, Israel
- * E-mail:
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169
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Weaver J, Watts T, Li P, Rye HS. Structural basis of substrate selectivity of E. coli prolidase. PLoS One 2014; 9:e111531. [PMID: 25354344 PMCID: PMC4213023 DOI: 10.1371/journal.pone.0111531] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 10/03/2014] [Indexed: 11/19/2022] Open
Abstract
Prolidases, metalloproteases that catalyze the cleavage of Xaa-Pro dipeptides, are conserved enzymes found in prokaryotes and eukaryotes. In humans, prolidase is crucial for the recycling of collagen. To further characterize the essential elements of this enzyme, we utilized the Escherichia coli prolidase, PepQ, which shares striking similarity with eukaryotic prolidases. Through structural and bioinformatic insights, we have extended previous characterizations of the prolidase active site, uncovering a key component for substrate specificity. Here we report the structure of E. coli PepQ, solved at 2.0 Å resolution. The structure shows an antiparallel, dimeric protein, with each subunit containing N-terminal and C-terminal domains. The C-terminal domain is formed by the pita-bread fold typical for this family of metalloproteases, with two Mg(II) ions coordinated by five amino-acid ligands. Comparison of the E. coli PepQ structure and sequence with homologous structures and sequences from a diversity of organisms reveals distinctions between prolidases from Gram-positive eubacteria and archaea, and those from Gram-negative eubacteria, including the presence of loop regions in the E. coli protein that are conserved in eukaryotes. One such loop contains a completely conserved arginine near the catalytic site. This conserved arginine is predicted by docking simulations to interact with the C-terminus of the substrate dipeptide. Kinetic analysis using both a charge-neutralized substrate and a charge-reversed variant of PepQ support this conclusion, and allow for the designation of a new role for this key region of the enzyme active site.
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Affiliation(s)
- Jeremy Weaver
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Tylan Watts
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Pingwei Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Hays S. Rye
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
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170
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Trypsin isozymes in the lobster Panulirus argus (Latreille, 1804): from molecules to physiology. J Comp Physiol B 2014; 185:17-35. [PMID: 25192870 DOI: 10.1007/s00360-014-0851-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 06/10/2014] [Accepted: 07/30/2014] [Indexed: 10/24/2022]
Abstract
Trypsin enzymes have been studied in a wide variety of animal taxa due to their central role in protein digestion as well as in other important physiological and biotechnological processes. Crustacean trypsins exhibit a high number of isoforms. However, while differences in properties of isoenzymes are known to play important roles in regulating different physiological processes, there is little information on this aspect for decapod trypsins. The aim of this review is to integrate recent findings at the molecular level on trypsin enzymes of the spiny lobster Panulirus argus, into higher levels of organization (biochemical, organism) and to interpret those findings in relation to the feeding ecology of these crustaceans. Trypsin in lobster is a polymorphic enzyme, showing isoforms that differ in their biochemical features and catalytic efficiencies. Molecular studies suggest that polymorphism in lobster trypsins may be non-neutral. Trypsin isoenzymes are differentially regulated by dietary proteins, and it seems that some isoenzymes have undergone adaptive evolution coupled with a divergence in expression rate to increase fitness. This review highlights important but poorly studied issues in crustaceans in general, such as the relation among trypsin polymorphism, phenotypic (digestive) flexibility, digestion efficiency, and feeding ecology.
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171
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Striped murrel S1 family serine protease: immune characterization, antibacterial property and enzyme activities. Biologia (Bratisl) 2014. [DOI: 10.2478/s11756-014-0410-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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172
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Clemente A, Arques MDC. Bowman-Birk inhibitors from legumes as colorectal chemopreventive agents. World J Gastroenterol 2014; 20:10305-10315. [PMID: 25132747 PMCID: PMC4130838 DOI: 10.3748/wjg.v20.i30.10305] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 02/21/2014] [Accepted: 04/23/2014] [Indexed: 02/06/2023] Open
Abstract
Aberrant functioning of serine proteases in inflammatory and carcinogenic processes within the gastrointestinal tract (GIT) has prompted scientists to investigate the potential of serine protease inhibitors, both natural and synthetic, as modulators of their proteolytic activities. Protease inhibitors of the Bowman-Birk type, a major protease inhibitor family in legume seeds, which inhibit potently and specifically trypsin- and chymotrypsin-like proteases, are currently being investigated as colorectal chemopreventive agents. Physiologically relevant amounts of Bowman-Birk inhibitors (BBI) can reach the large intestine in active form due to their extraordinary resistance to extreme conditions within the GIT. Studies in animal models have proven that dietary BBI from several legume sources, including soybean, pea, lentil and chickpea, can prevent or suppress carcinogenic and inflammatory processes within the GIT. Although the therapeutic targets and the action mechanism of BBI have not yet been elucidated, the emerging evidence suggests that BBI exert their preventive properties via protease inhibition; in this sense, serine proteases should be considered as primary targets in early stages of carcinogenesis. The validation of candidate serine proteases as therapeutic targets together with the identification, within the wide array of natural BBI variants, of the most potent and specific protease inhibitors, are necessary to better understand the potential of this protein family as colorectal chemopreventive agents.
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173
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Gong J, Xie Y, Yu K, Yang Y, Huang H, Ye H. Characterization and expression analysis of chymotrypsin after bacterial challenge in the mud crab, Scylla paramamosain. Genet Mol Biol 2014; 37:381-8. [PMID: 25071403 PMCID: PMC4094611 DOI: 10.1590/s1415-47572014005000007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 11/13/2013] [Indexed: 11/25/2022] Open
Abstract
Chymotrypsin is one of the serine proteases families that have various biological functions. A chymotrypsin gene was isolated from hepatopancreas of the mud crab, Scylla paramamosain (designated SpCHY) in this study. The full-length cDNA of SpCHY contained 942 nucleotides with a polyadenylation sequence and encoded a peptide of 270 amino acids with a signal peptide of 17 amino acids. The SpCHY gene contains seven exons, six introns, a TATA box and several transcription factor binding sites that were found in 5’-promoter region which is 1221 bp in length. Real-time quantitative PCR analysis indicated that the expression level of SpCHY mRNA in hepatopancreas was significantly higher than that in other tissues. Immunocytochemistry and in situ hybridization exhibited the CHY-like reactivity presented in resorptive cells of the hepatopancreas. After bacterial challenge with Vibrio alginolyticus, the expression level of SpCHY mRNA was extremely up-regulated at 3 h in hepatopancreas. Our results suggest that SpCHY might play an important role in the mud crab’s immune response.
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Affiliation(s)
- Jie Gong
- College of Ocean and Earth Sciences , Xiamen University , Xiamen, Fujian , China
| | - Yinjie Xie
- College of Ocean and Earth Sciences , Xiamen University , Xiamen, Fujian , China
| | - Kun Yu
- College of Ocean and Earth Sciences , Xiamen University , Xiamen, Fujian , China
| | - Ya'nan Yang
- College of Ocean and Earth Sciences , Xiamen University , Xiamen, Fujian , China
| | - Huiyang Huang
- College of Ocean and Earth Sciences , Xiamen University , Xiamen, Fujian , China
| | - Haihui Ye
- College of Ocean and Earth Sciences , Xiamen University , Xiamen, Fujian , China . ; Center for Marine Biotechnology , Xiamen University , Xiamen, Fujian , China
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174
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Structure modeling and hybrid virtual screening study of Alzheimer’s associated protease kallikrein 8 for the identification of novel inhibitors. Med Chem Res 2014. [DOI: 10.1007/s00044-014-0932-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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175
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Taniguchi M, Atiwetin P, Hirai T, Itoh M, Harada S, Hara S, Kamei K. Interaction of Subtilisin BPN′ and Recombinant Fungal Protease Inhibitor F from Silkworm with Substituted P1Site Residues. Biosci Biotechnol Biochem 2014; 70:1262-4. [PMID: 16717433 DOI: 10.1271/bbb.70.1262] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Fungal protease inhibitor F (FPI-F) from silkworm inhibits subtilisin and fungal proteases. FPI-F mutants P(1) residues of which, Thr(29), were replaced with Glu, Phe, Gly, Leu, Met, and Arg, were prepared. The inhibitory activities of mutated FPI-F against subtilisin and other mammalian proteases indicated that FPI-F might be a specific inhibitor toward subtilisin-type protease.
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Affiliation(s)
- Mai Taniguchi
- Department of Applied Biology, Kyoto Institute of Technology, Japan
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176
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S46 peptidases are the first exopeptidases to be members of clan PA. Sci Rep 2014; 4:4977. [PMID: 24827749 PMCID: PMC4021333 DOI: 10.1038/srep04977] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 04/24/2014] [Indexed: 01/09/2023] Open
Abstract
The dipeptidyl aminopeptidase BII (DAP BII) belongs to a serine peptidase family, S46. The amino acid sequence of the catalytic unit of DAP BII exhibits significant similarity to those of clan PA endopeptidases, such as chymotrypsin. However, the molecular mechanism of the exopeptidase activity of family S46 peptidase is unknown. Here, we report crystal structures of DAP BII. DAP BII contains a peptidase domain including a typical double β-barrel fold and previously unreported α-helical domain. The structures of peptide complexes revealed that the α-helical domain covers the active-site cleft and the side chain of Asn330 in the domain forms hydrogen bonds with the N-terminus of the bound peptide. These observations indicate that the α-helical domain regulates the exopeptidase activity of DAP BII. Because S46 peptidases are not found in mammals, we expect that our study will be useful for the design of specific inhibitors of S46 peptidases from pathogens.
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177
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Mo CY, Birdwell LD, Kohli RM. Specificity determinants for autoproteolysis of LexA, a key regulator of bacterial SOS mutagenesis. Biochemistry 2014; 53:3158-68. [PMID: 24779472 PMCID: PMC4030785 DOI: 10.1021/bi500026e] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Bacteria utilize the tightly regulated
stress response (SOS) pathway
to respond to a variety of genotoxic agents, including antimicrobials.
Activation of the SOS response is regulated by a key repressor-protease,
LexA, which undergoes autoproteolysis in the setting of stress, resulting
in derepression of SOS genes. Remarkably, genetic inactivation of
LexA’s self-cleavage activity significantly decreases acquired
antibiotic resistance in infection models and renders bacteria hypersensitive
to traditional antibiotics, suggesting that a mechanistic study of
LexA could help inform its viability as a novel target for combating
acquired drug resistance. Despite structural insights into LexA, a
detailed knowledge of the enzyme’s protease specificity is
lacking. Here, we employ saturation and positional scanning mutagenesis
on LexA’s internal cleavage region to analyze >140 mutants
and generate a comprehensive specificity profile of LexA from the
human pathogen Pseudomonas aeruginosa (LexAPa). We find that the LexAPa active site possesses a unique mode of substrate recognition.
Positions P1–P3 prefer small hydrophobic residues that suggest
specific contacts with the active site, while positions P5 and P1′
show a preference for flexible glycine residues that may facilitate
the conformational change that permits autoproteolysis. We further
show that stabilizing the β-turn within the cleavage region
enhances LexA autoproteolytic activity. Finally, we identify permissive
positions flanking the scissile bond (P4 and P2′) that are
tolerant to extensive mutagenesis. Our studies shed light on the active
site architecture of the LexA autoprotease and provide insights that
may inform the design of probes of the SOS pathway.
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Affiliation(s)
- Charlie Y Mo
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania , 3610 Hamilton Walk, Philadelphia, Pennsylvania 19014, United States
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178
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Figaj D, Gieldon A, Polit A, Sobiecka-Szkatula A, Koper T, Denkiewicz M, Banecki B, Lesner A, Ciarkowski J, Lipinska B, Skorko-Glonek J. The LA loop as an important regulatory element of the HtrA (DegP) protease from Escherichia coli: structural and functional studies. J Biol Chem 2014; 289:15880-93. [PMID: 24737328 DOI: 10.1074/jbc.m113.532895] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Bacterial HtrAs are serine proteases engaged in extracytoplasmic protein quality control and are required for the virulence of several pathogenic species. The proteolytic activity of HtrA (DegP) from Escherichia coli, a model prokaryotic HtrA, is stimulated by stressful conditions; the regulation of this process is mediated by the LA, LD, L1, L2, and L3 loops. The precise mechanism of action of the LA loop is not known due to a lack of data concerning its three-dimensional structure as well as its mode of interaction with other regulatory elements. To address these issues we generated a theoretical model of the three-dimensional structure of the LA loop as per the resting state of HtrA and subsequently verified its correctness experimentally. We identified intra- and intersubunit contacts that formed with the LA loops; these played an important role in maintaining HtrA in its inactive conformation. The most significant proved to be the hydrophobic interactions connecting the LA loops of the hexamer and polar contacts between the LA' (the LA loop on an opposite subunit) and L1 loops on opposite subunits. Disturbance of these interactions caused the stimulation of HtrA proteolytic activity. We also demonstrated that LA loops contribute to the preservation of the integrity of the HtrA oligomer and to the stability of the monomer. The model presented in this work explains the regulatory role of the LA loop well; it should also be applicable to numerous Enterobacteriaceae pathogenic species as the amino acid sequences of the members of this bacterial family are highly conserved.
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Affiliation(s)
- Donata Figaj
- From the Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Artur Gieldon
- Department of Theoretical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-952 Gdansk
| | - Agnieszka Polit
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Anna Sobiecka-Szkatula
- From the Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Tomasz Koper
- From the Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Milena Denkiewicz
- From the Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Bogdan Banecki
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Kladki 24, 80-822 Gdansk, Poland, and
| | - Adam Lesner
- Department of Biochemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-952 Gdansk, Poland
| | - Jerzy Ciarkowski
- Department of Theoretical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-952 Gdansk
| | - Barbara Lipinska
- From the Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Joanna Skorko-Glonek
- From the Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland,
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179
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Sun Y, Yin S, Feng Y, Li J, Zhou J, Liu C, Zhu G, Guo Z. Molecular basis of the general base catalysis of an α/β-hydrolase catalytic triad. J Biol Chem 2014; 289:15867-79. [PMID: 24737327 DOI: 10.1074/jbc.m113.535641] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The serine-histidine-aspartate triad is well known for its covalent, nucleophilic catalysis in a diverse array of enzymatic transformations. Here we show that its nucleophilicity is shielded and its catalytic role is limited to being a specific general base by an open-closed conformational change in the catalysis of (1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (or MenH), a typical α/β-hydrolase fold enzyme in the vitamin K biosynthetic pathway. This enzyme is found to adopt an open conformation without a functional triad in its ligand-free form and a closed conformation with a fully functional catalytic triad in the presence of its reaction product. The open-to-closed conformational transition involves movement of half of the α-helical cap domain, which causes extensive structural changes in the α/β-domain and forces the side chain of the triad histidine to adopt an energetically disfavored gauche conformation to form the functional triad. NMR analysis shows that the inactive open conformation without a triad prevails in ligand-free solution and is converted to the closed conformation with a properly formed triad by the reaction product. Mutation of the residues crucial to this open-closed transition either greatly decreases or completely eliminates the enzyme activity, supporting an important catalytic role for the structural change. These findings suggest that the open-closed conformational change tightly couples formation of the catalytic triad to substrate binding to enhance the substrate specificities and simultaneously shield the nucleophilicity of the triad, thus allowing it to expand its catalytic power beyond the nucleophilic catalysis.
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Affiliation(s)
- Yueru Sun
- From the Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region (SAR), China and
| | - Shuhui Yin
- From the Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region (SAR), China and
| | - Yitao Feng
- From the Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region (SAR), China and
| | - Jie Li
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Jiahai Zhou
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Changdong Liu
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region (SAR), China and Division of Life Sciences, and
| | - Guang Zhu
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region (SAR), China and Division of Life Sciences, and
| | - Zhihong Guo
- From the Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region (SAR), China and
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180
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Blankenship E, Vukoti K, Miyagi M, Lodowski DT. Conformational flexibility in the catalytic triad revealed by the high-resolution crystal structure of Streptomyces erythraeus trypsin in an unliganded state. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:833-40. [PMID: 24598752 PMCID: PMC3949523 DOI: 10.1107/s1399004713033658] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 12/12/2013] [Indexed: 05/20/2024]
Abstract
With more than 500 crystal structures determined, serine proteases make up greater than one-third of all proteases structurally examined to date, making them among the best biochemically and structurally characterized enzymes. Despite the numerous crystallographic and biochemical studies of trypsin and related serine proteases, there are still considerable shortcomings in the understanding of their catalytic mechanism. Streptomyces erythraeus trypsin (SET) does not exhibit autolysis and crystallizes readily at physiological pH; hence, it is well suited for structural studies aimed at extending the understanding of the catalytic mechanism of serine proteases. While X-ray crystallographic structures of this enzyme have been reported, no coordinates have ever been made available in the Protein Data Bank. Based on this, and observations on the extreme stability and unique properties of this particular trypsin, it was decided to crystallize it and determine its structure. Here, the first sub-angstrom resolution structure of an unmodified, unliganded trypsin crystallized at physiological pH is reported. Detailed structural analysis reveals the geometry and structural rigidity of the catalytic triad in the unoccupied active site and comparison to related serine proteases provides a context for interpretation of biochemical studies of catalytic mechanism and activity.
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Affiliation(s)
- Elise Blankenship
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Krishna Vukoti
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Masaru Miyagi
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Opthalmology and Visual Sciences, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - David T. Lodowski
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
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181
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Hou MZ, Shen GM, Wei D, Li YL, Dou W, Wang JJ. Characterization of Bactrocera dorsalis serine proteases and evidence for their indirect role in insecticide tolerance. Int J Mol Sci 2014; 15:3272-86. [PMID: 24566149 PMCID: PMC3958911 DOI: 10.3390/ijms15023272] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 02/09/2014] [Accepted: 02/12/2014] [Indexed: 01/19/2023] Open
Abstract
The oriental fruit fly Bactrocera dorsalis (Hendel) causes devastating losses to agricultural crops world-wide and is considered to be an economically important pest. Little is known about the digestive enzymes such as serine proteases (SPs) in B. dorsalis, which are important both for energy supply and mitigation of fitness cost associated with insecticide tolerance. In this study, we identified five SP genes in the midgut of B. dorsalis, and the alignments of their deduced amino acid sequences revealed the presence of motifs conserved in the SP superfamily. Phylogenetic analyses with known SPs from other insect species suggested that three of them were trypsin-like proteases. Analyses of the expression profiles among the different developmental stages showed that all five genes were most abundant in larvae than in other stages. When larvae were continuously fed on diet containing 0.33 μg/g β-Cypermethrin, expression of all five genes were upregulated in the midgut but the larval development was delayed. Biochemical assays were consistent with the increased protease activity exhibited by SPs in the midgut after treatment with β-Cypermethrin. Taken together, these findings provide evidence for the hypothesis that enhanced SP activity may play an indirect role in relieving the toxicity stress of insecticide in B. dorsalis.
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Affiliation(s)
- Ming-Zhe Hou
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China.
| | - Guang-Mao Shen
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China.
| | - Dong Wei
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China.
| | - Ya-Li Li
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China.
| | - Wei Dou
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China.
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China.
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182
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Fukumori H, Teshiba S, Shigeoka Y, Yamamoto K, Banno Y, Aso Y. Purification and characterization of cocoonase from the silkworm Bombyx mori. Biosci Biotechnol Biochem 2014; 78:202-11. [DOI: 10.1080/09168451.2014.878215] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Abstract
Cocoonase (CCN) which facilitates the degradation of a cocoon is recognized as a trypsin-like serine protease. In this study, CCN from the silkworm Bombyx mori was purified and comprehensively characterized. Its activity was maximal at about pH 9.8. It was stable above pH 3.4 at 4 °C and below 50 °C at pH 7.5. CuSO4, FeSO4, and ZnSO4 showed inhibitory effects on CCN, but other salts improved activity. Typical trypsin inhibitors inhibited CCN, but the relative inhibitory activities were much lower than those against bovine trypsin. An extract of cocoon shells inhibited trypsin, but it was only slightly inhibitory against CCN. There were significant differences in catalytic efficiencies and substrate specificities as between CCN and bovine trypsin.
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Affiliation(s)
- Hisayoshi Fukumori
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Satoshi Teshiba
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Yuichi Shigeoka
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Kohji Yamamoto
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Yutaka Banno
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Yoichi Aso
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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183
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Ran LY, Su HN, Zhou MY, Wang L, Chen XL, Xie BB, Song XY, Shi M, Qin QL, Pang X, Zhou BC, Zhang YZ, Zhang XY. Characterization of a novel subtilisin-like protease myroicolsin from deep sea bacterium Myroides profundi D25 and molecular insight into its collagenolytic mechanism. J Biol Chem 2014; 289:6041-53. [PMID: 24429289 DOI: 10.1074/jbc.m113.513861] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Collagen is an insoluble protein that widely distributes in the extracellular matrix of marine animals. Collagen degradation is an important step in the marine nitrogen cycle. However, the mechanism of marine collagen degradation is still largely unknown. Here, a novel subtilisin-like collagenolytic protease, myroicolsin, which is secreted by the deep sea bacterium Myroides profundi D25, was purified and characterized, and its collagenolytic mechanism was studied. Myroicolsin displays low identity (<30%) to previously characterized subtilisin-like proteases, and it contains a novel domain structure. Protein truncation indicated that the Pro secretion system C-terminal sorting domain in the precursor protein is involved in the cleavage of the N-propeptide, and the linker is required for protein folding during myroicolsin maturation. The C-terminal β-jelly roll domain did not bind insoluble collagen fiber, suggesting that myroicolsin may degrade collagen without the assistance of a collagen-binding domain. Myroicolsin had broad specificity for various collagens, especially fish-insoluble collagen. The favored residue at the P1 site was basic arginine. Scanning electron microscopy and atomic force microscopy, together with biochemical analyses, confirmed that collagen fiber degradation by myroicolsin begins with the hydrolysis of proteoglycans and telopeptides in collagen fibers and fibrils. Myroicolsin showed strikingly different cleavage patterns between native and denatured collagens. A collagen degradation model of myroicolsin was proposed based on our results. Our study provides molecular insight into the collagen degradation mechanism and structural characterization of a subtilisin-like collagenolytic protease secreted by a deep sea bacterium, shedding light on the degradation mechanism of deep sea sedimentary organic nitrogen.
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Affiliation(s)
- Li-Yuan Ran
- From the State Key Laboratory of Microbial Technology
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184
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Fuchs JE, von Grafenstein S, Huber RG, Kramer C, Liedl KR. Substrate-driven mapping of the degradome by comparison of sequence logos. PLoS Comput Biol 2013; 9:e1003353. [PMID: 24244149 PMCID: PMC3828135 DOI: 10.1371/journal.pcbi.1003353] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 10/05/2013] [Indexed: 12/27/2022] Open
Abstract
Sequence logos are frequently used to illustrate substrate preferences and specificity of proteases. Here, we employed the compiled substrates of the MEROPS database to introduce a novel metric for comparison of protease substrate preferences. The constructed similarity matrix of 62 proteases can be used to intuitively visualize similarities in protease substrate readout via principal component analysis and construction of protease specificity trees. Since our new metric is solely based on substrate data, we can engraft the protease tree including proteolytic enzymes of different evolutionary origin. Thereby, our analyses confirm pronounced overlaps in substrate recognition not only between proteases closely related on sequence basis but also between proteolytic enzymes of different evolutionary origin and catalytic type. To illustrate the applicability of our approach we analyze the distribution of targets of small molecules from the ChEMBL database in our substrate-based protease specificity trees. We observe a striking clustering of annotated targets in tree branches even though these grouped targets do not necessarily share similarity on protein sequence level. This highlights the value and applicability of knowledge acquired from peptide substrates in drug design of small molecules, e.g., for the prediction of off-target effects or drug repurposing. Consequently, our similarity metric allows to map the degradome and its associated drug target network via comparison of known substrate peptides. The substrate-driven view of protein-protein interfaces is not limited to the field of proteases but can be applied to any target class where a sufficient amount of known substrate data is available.
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Affiliation(s)
- Julian E. Fuchs
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Susanne von Grafenstein
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Roland G. Huber
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Christian Kramer
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
- * E-mail:
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185
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Umar M, Upadhyay R, Kumar S, Ghoshal UC, Mittal B. Modification of risk, but not survival of esophageal cancer patients by esophageal cancer-related gene 1 Arg290Gln polymorphism: a case-control study and meta-analysis. J Gastroenterol Hepatol 2013; 28:1717-24. [PMID: 23869757 DOI: 10.1111/jgh.12335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/01/2013] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND AIM Esophageal cancer-related gene 1 (ECRG1) is a novel tumor suppressor gene known to affect matrix remodeling, cell growth, and differentiation. Previous studies in high incidence geographical regions of esophageal cancer (EC) have shown association of ECRG1 Arg290Gln polymorphism with risk of esophageal squamous cell carcinoma (ESCC); however, role of this variant in low incidence region is missing. So, we aimed to evaluate association of ECRG1 Arg290Gln with susceptibility and prognosis of EC patients in low-risk north Indian population. METHODS The genotyping of ECRG1 Arg290Gln polymorphism was done in 310 incident EC cases (including 179 follow up cases) and 310 healthy controls through polymerase chain reaction-restriction fragment length polymorphism. Statistical analysis applied were binary logistic regression for risk estimation and Kaplan-Meier/log-rank test for survival analysis. Meta-analysis of published studies, exploring role of ECRG1 polymorphism in ESCC risk, was carried out using MIX 2.0 software. RESULTS ECRG1 Arg290Gln polymorphism significantly conferred 1.8-fold increased risk of EC in dominant model (odds ratio = 1.78, 95% confidence interval = 1.27-2.49, P = 0.001). Stratification based on clinical phenotypes showed pronounced risk in cases with ESCC histopathology and middle/lower third tumor locations. No significant interaction with environmental risk factors was observed. Meta-analysis also showed significant association of ECRG1 Arg290Gln polymorphism with risk of ESCC. Kaplan-Meier and Cox regression tests suggested that ECRG1 polymorphism did not modulate survival outcome of ESCC patients. CONCLUSIONS ECRG1 Arg290Gln polymorphism significantly affects the susceptibility but not the prognosis of ESCC patients in low-risk north Indian population.
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Affiliation(s)
- Meenakshi Umar
- Department of Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
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186
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Zhu H, Xu BL, Liang X, Yang YR, Tang XF, Tang B. Molecular basis for auto- and hetero-catalytic maturation of a thermostable subtilase from thermophilic Bacillus sp. WF146. J Biol Chem 2013; 288:34826-38. [PMID: 24145031 DOI: 10.1074/jbc.m113.498774] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The proform of the WF146 protease, an extracellular subtilase produced by thermophilic Bacillus sp. WF146, matures efficiently at high temperatures. Here we report that the proform, which contains an N-terminal propeptide composed of a core domain (N*) and a linker peptide, is intrinsically able to mature via multiple pathways. One autocatalytic pathway is initiated by cis-processing of N* to generate an autoprocessed complex N*-I(WT), and this step is followed by truncation of the linker peptide and degradation of N*. Another autocatalytic pathway is initiated by trans-processing of the linker peptide followed by degradation of N*. Unlike most reported subtilases, the maturation of the WF146 protease occurs not only autocatalytically but also hetero-catalytically whereby heterogeneous proteases accelerate the maturation of the WF146 protease via trans-processing of the proform and N*-I(WT). Although N* acts as an intramolecular chaperone and an inhibitor of the mature enzyme, the linker peptide is susceptible to proteolysis, allowing the trans-processing reaction to occur auto- and hetero-catalytically. These studies also demonstrate that the WF146 protease undergoes subtle structural adjustments during the maturation process and that the binding of Ca(2+) is required for routing the proform to mature properly at high temperatures. Interestingly, under Ca(2+)-free conditions, the proform is cis-processed into a unique propeptide-intermediate complex (N*-I(E)) capable of re-synthesis of the proform. Based on the basic catalytic principle of serine proteases and these experimental results, a mechanism for the cis-processing/re-synthesis equilibrium of the proform and the role of the linker peptide in regulation of this equilibrium has been proposed.
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Affiliation(s)
- Hui Zhu
- From the State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
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187
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Fuchs JE, von Grafenstein S, Huber RG, Wallnoefer HG, Liedl KR. Specificity of a protein-protein interface: local dynamics direct substrate recognition of effector caspases. Proteins 2013; 82:546-55. [PMID: 24085488 PMCID: PMC4282588 DOI: 10.1002/prot.24417] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 09/03/2013] [Indexed: 12/29/2022]
Abstract
Proteases are prototypes of multispecific protein–protein interfaces. Proteases recognize and cleave protein and peptide substrates at a well-defined position in a substrate binding groove and a plethora of experimental techniques provide insights into their substrate recognition. We investigate the caspase family of cysteine proteases playing a key role in programmed cell death and inflammation, turning caspases into interesting drug targets. Specific ligand binding to one particular caspase is difficult to achieve, as substrate specificities of caspase isoforms are highly similar. In an effort to rationalize substrate specificity of two closely related caspases, we investigate the substrate promiscuity of the effector Caspases 3 and 7 by data mining (cleavage entropy) and by molecular dynamics simulations. We find a strong correlation between binding site rigidity and substrate readout for individual caspase subpockets explaining more stringent substrate readout of Caspase 7 via its narrower conformational space. Caspase 3 subpockets S3 and S4 show elevated local flexibility explaining the more unspecific substrate readout of that isoform in comparison to Caspase 7. We show by in silico exchange mutations in the S3 pocket of the proteases that a proline residue in Caspase 7 contributes to the narrowed conformational space of the binding site. These findings explain the substrate specificities of caspases via a mechanism of conformational selection and highlight the crucial importance of binding site local dynamics in substrate recognition of proteases. Proteins 2014; 82:546–555.
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Affiliation(s)
- Julian E Fuchs
- Institute of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, A-6020, Innsbruck, Austria
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188
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Ran LY, Su HN, Zhao GY, Gao X, Zhou MY, Wang P, Zhao HL, Xie BB, Zhang XY, Chen XL, Zhou BC, Zhang YZ. Structural and mechanistic insights into collagen degradation by a bacterial collagenolytic serine protease in the subtilisin family. Mol Microbiol 2013; 90:997-1010. [DOI: 10.1111/mmi.12412] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2013] [Indexed: 01/22/2023]
Affiliation(s)
- Li-Yuan Ran
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
| | - Hai-Nan Su
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
| | - Guo-Yan Zhao
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
| | - Xiang Gao
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
| | - Ming-Yang Zhou
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
| | - Peng Wang
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
| | - Hui-Lin Zhao
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
| | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
| | - Bai-Cheng Zhou
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
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189
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Zdzalik M, Kalinska M, Wysocka M, Stec-Niemczyk J, Cichon P, Stach N, Gruba N, Stennicke HR, Jabaiah A, Markiewicz M, Kedracka-Krok S, Wladyka B, Daugherty PS, Lesner A, Rolka K, Dubin A, Potempa J, Dubin G. Biochemical and structural characterization of SplD protease from Staphylococcus aureus. PLoS One 2013; 8:e76812. [PMID: 24130791 PMCID: PMC3793935 DOI: 10.1371/journal.pone.0076812] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 08/29/2013] [Indexed: 01/11/2023] Open
Abstract
Staphylococcus aureus is a dangerous human pathogen. A number of the proteins secreted by this bacterium are implicated in its virulence, but many of the components of its secretome are poorly characterized. Strains of S. aureus can produce up to six homologous extracellular serine proteases grouped in a single spl operon. Although the SplA, SplB, and SplC proteases have been thoroughly characterized, the properties of the other three enzymes have not yet been investigated. Here, we describe the biochemical and structural characteristics of the SplD protease. The active enzyme was produced in an Escherichia coli recombinant system and purified to homogeneity. P1 substrate specificity was determined using a combinatorial library of synthetic peptide substrates showing exclusive preference for threonine, serine, leucine, isoleucine, alanine, and valine. To further determine the specificity of SplD, we used high-throughput synthetic peptide and cell surface protein display methods. The results not only confirmed SplD preference for a P1 residue, but also provided insight into the specificity of individual primed- and non-primed substrate-binding subsites. The analyses revealed a surprisingly narrow specificity of the protease, which recognized five consecutive residues (P4-P3-P2-P1-P1’) with a consensus motif of R-(Y/W)-(P/L)-(T/L/I/V)↓S. To understand the molecular basis of the strict substrate specificity, we crystallized the enzyme in two different conditions, and refined the structures at resolutions of 1.56 Å and 2.1 Å. Molecular modeling and mutagenesis studies allowed us to define a consensus model of substrate binding, and illustrated the molecular mechanism of protease specificity.
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Affiliation(s)
- Michal Zdzalik
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Magdalena Kalinska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Justyna Stec-Niemczyk
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Przemyslaw Cichon
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Natalia Stach
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Natalia Gruba
- Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | | | - Abeer Jabaiah
- Department of Chemical Engineering, University of California at Santa Barbara, Santa Barbara, California, United States of America
| | - Michal Markiewicz
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Sylwia Kedracka-Krok
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- Malopolska Centre of Biotechnology, Krakow, Poland
| | - Benedykt Wladyka
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- Malopolska Centre of Biotechnology, Krakow, Poland
| | - Patrick S. Daugherty
- Department of Chemical Engineering, University of California at Santa Barbara, Santa Barbara, California, United States of America
| | - Adam Lesner
- Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | | | - Adam Dubin
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Jan Potempa
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- Center of Oral Health and Systemic Disease, School of Dentistry, University of Louisville, Louisville, Kentucky, United States of America
| | - Grzegorz Dubin
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- Malopolska Centre of Biotechnology, Krakow, Poland
- * E-mail:
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190
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Kromann-Hansen T, Lund IK, Liu Z, Andreasen PA, Høyer-Hansen G, Sørensen HP. Allosteric inactivation of a trypsin-like serine protease by an antibody binding to the 37- and 70-loops. Biochemistry 2013; 52:7114-26. [PMID: 24079451 DOI: 10.1021/bi400491k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Serine protease catalytic activity is in many cases regulated by conformational changes initiated by binding of physiological modulators to exosites located distantly from the active site. Inhibitory monoclonal antibodies binding to such exosites are potential therapeutics and offer opportunities for elucidating fundamental allosteric mechanisms. The monoclonal antibody mU1 has previously been shown to be able to inhibit the function of murine urokinase-type plasminogen activator in vivo. We have now mapped the epitope of mU1 to the catalytic domain's 37- and 70-loops, situated about 20 Å from the S1 specificity pocket of the active site. Our data suggest that binding of mU1 destabilizes the catalytic domain and results in conformational transition into a state, in which the N-terminal amino group of Ile16 is less efficiently stabilizing the oxyanion hole and in which the active site has a reduced affinity for substrates and inhibitors. Furthermore, we found evidence for functional interactions between residues in uPA's C-terminal catalytic domain and its N-terminal A-chain, as deletion of the A-chain facilitates the mU1-induced conformational distortion. The inactive, distorted state is by several criteria similar to the E* conformation described for other serine proteases. Hence, agents targeting serine protease conformation through binding to exosites in the 37- and 70-loops represent a new class of potential therapeutics.
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Affiliation(s)
- Tobias Kromann-Hansen
- Danish-Chinese Centre for Proteases and Cancer and ‡Department of Molecular Biology and Genetics, Aarhus University , DK-8000 Aarhus C, Denmark
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191
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Molnár T, Vörös J, Szeder B, Takáts K, Kardos J, Katona G, Gráf L. Comparison of complexes formed by a crustacean and a vertebrate trypsin with bovine pancreatic trypsin inhibitor - the key to achieving extreme stability? FEBS J 2013; 280:5750-63. [DOI: 10.1111/febs.12491] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 07/31/2013] [Accepted: 08/15/2013] [Indexed: 01/23/2023]
Affiliation(s)
- Tamás Molnár
- Department of Biochemistry; Eötvös Loránd University; Budapest Hungary
- Department of Functional Pharmacology; Institute of Molecular Pharmacology; Research Centre of Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
| | - Judit Vörös
- Department of Biochemistry; Eötvös Loránd University; Budapest Hungary
| | - Bálint Szeder
- Department of Biochemistry; Eötvös Loránd University; Budapest Hungary
| | - Kornél Takáts
- Molecular Biophysics Research Group; Hungarian Academy of Sciences; Budapest Hungary
| | - József Kardos
- Department of Biochemistry; Eötvös Loránd University; Budapest Hungary
| | - Gergely Katona
- Department of Chemistry and Molecular Biology; University of Gothenburg; Gothenburg Sweden
| | - László Gráf
- Department of Biochemistry; Eötvös Loránd University; Budapest Hungary
- Molecular Biophysics Research Group; Hungarian Academy of Sciences; Budapest Hungary
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192
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Chen C, Krishnan V, Macon K, Manne K, Narayana SVL, Schneewind O. Secreted proteases control autolysin-mediated biofilm growth of Staphylococcus aureus. J Biol Chem 2013; 288:29440-52. [PMID: 23970550 PMCID: PMC3795244 DOI: 10.1074/jbc.m113.502039] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Staphylococcus epidermidis, a commensal of humans, secretes Esp protease to prevent Staphylococcus aureus biofilm formation and colonization. Blocking S. aureus colonization may reduce the incidence of invasive infectious diseases; however, the mechanism whereby Esp disrupts biofilms is unknown. We show here that Esp cleaves autolysin (Atl)-derived murein hydrolases and prevents staphylococcal release of DNA, which serves as extracellular matrix in biofilms. The three-dimensional structure of Esp was revealed by x-ray crystallography and shown to be highly similar to that of S. aureus V8 (SspA). Both atl and sspA are necessary for biofilm formation, and purified SspA cleaves Atl-derived murein hydrolases. Thus, S. aureus biofilms are formed via the controlled secretion and proteolysis of autolysin, and this developmental program appears to be perturbed by the Esp protease of S. epidermidis.
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Affiliation(s)
- Chen Chen
- From the Department of Microbiology, University of Chicago, Chicago, Illinois 60637
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193
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Luo Y, Sun L, Zhu Z, Ran W, Shen Q. Identification and characterization of an anti-fungi Fusarium oxysporum f. sp. cucumerium protease from the Bacillus subtilis strain N7. J Microbiol 2013; 51:359-66. [PMID: 23812816 DOI: 10.1007/s12275-013-2627-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 02/04/2013] [Indexed: 11/29/2022]
Abstract
A newly discovered alkaline antifungal protease named P6 from Bacillus subtilis N7 was purified and partially characterized. B. subtilis N7 culture filtrates were purified by 30-60% (NH4)2SO4 precipitation, anion-exchange chromatography and gel filtration chromatography. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) revealed a single band of 41.38 kDa. Peptide sequence of protease P6 was determined using a 4800 Plus MALDI TOF/TOF™ Analyzer System. Self-Formed Adaptor PCR (SEFA-PCR) was used to amplify the 1,149 bp open read frame of P6. Dimensional structure prediction using Automatic Modeling Mode software showed that the protease P6 consisted of two β-barrel domains. Purified P6 strongly inhibited spore and mycelium growth of Fusarium oxysporum f. sp. cucumerium (FOC) by causing hypha lysis when the concentration was 25 μg/ml. Characterization of the purified protease indicated that it had substrate specificity for gelatin and was highly active at pH 8.0-10.6 and 70°C. The P6 protease was inhibited by EDTA (2 mmol/L), phenyl methyl sulfonyl fluoride (PMSF, 1 mmol/L), Na(+), Fe(3+), Cu(2+), Mg(2+) (5 mmol/L each) and H2O2 (2%, v/v). However, protease activity was activated by Ca(2+), K(+), Mn(2+) (5 mmol/L each), mercaptoethanol (2%, v/v) and Tween 80 (1%, v/v). In addition, activity was also affected by organic solvents such as acetone, normal butanol and ethanol, but not hexane (25%, v/v each).
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Affiliation(s)
- Yi Luo
- Jiangsu Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing 210095, PR China
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194
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Fang DA, Huang XM, Zhang ZQ, Xu DP, Zhou YF, Zhang MY, Liu K, Duan JR, Shi WG. Molecular cloning and expression analysis of chymotrypsin-like serine protease from the redclaw crayfish (Cherax quadricarinatus): a possible role in the junior and adult innate immune systems. FISH & SHELLFISH IMMUNOLOGY 2013; 34:1546-1552. [PMID: 23541770 DOI: 10.1016/j.fsi.2013.03.360] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 03/12/2013] [Accepted: 03/15/2013] [Indexed: 06/02/2023]
Abstract
A novel chymotrypsin-like serine protease (CLSP) was isolated from the hepatopancreas of the redclaw crayfish Cherax quadricarinatus (Cq-chy). The full-length cDNA of Cq-chy contains 951 nucleotides encodes a peptide of 270 amino acids. The mature peptide comprising 223 amino acids contains the conserved catalytic triad (H, D, and S). Similarity analysis showed that Cq-chy shares high identity with chymotrypsins from the fiddler crab; Uca pugilator. Cq-chy mRNA expression in C. quadricarinatus was shown to be: (a) tissue-related with the highest expression in the hepatotpancreas and widely distributed, (b) highly responsive in the hepatopancreas to White Spot Syndrome Virus (WSSV) challenge, and (c) differently regulated in immature and adult crayfish. In this study we successfully isolated Cq-chy. Our observations indicate that Cq-chy is differently involved in the immature and adult innate immune reactions, thus suggesting a role for CLSPs in the invertebrate innate immune system.
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Affiliation(s)
- Di-An Fang
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Changjiang River, Freshwater Fisheries Research Center, Wuxi 214081, China.
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195
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Fuchs JE, von Grafenstein S, Huber RG, Margreiter MA, Spitzer GM, Wallnoefer HG, Liedl KR. Cleavage entropy as quantitative measure of protease specificity. PLoS Comput Biol 2013; 9:e1003007. [PMID: 23637583 PMCID: PMC3630115 DOI: 10.1371/journal.pcbi.1003007] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 02/07/2013] [Indexed: 01/05/2023] Open
Abstract
A purely information theory-guided approach to quantitatively characterize protease specificity is established. We calculate an entropy value for each protease subpocket based on sequences of cleaved substrates extracted from the MEROPS database. We compare our results with known subpocket specificity profiles for individual proteases and protease groups (e.g. serine proteases, metallo proteases) and reflect them quantitatively. Summation of subpocket-wise cleavage entropy contributions yields a measure for overall protease substrate specificity. This total cleavage entropy allows ranking of different proteases with respect to their specificity, separating unspecific digestive enzymes showing high total cleavage entropy from specific proteases involved in signaling cascades. The development of a quantitative cleavage entropy score allows an unbiased comparison of subpocket-wise and overall protease specificity. Thus, it enables assessment of relative importance of physicochemical and structural descriptors in protease recognition. We present an exemplary application of cleavage entropy in tracing substrate specificity in protease evolution. This highlights the wide range of substrate promiscuity within homologue proteases and hence the heavy impact of a limited number of mutations on individual substrate specificity. Proteases show a broad range of cleavage specificities. Promiscuous proteases as digestive enzymes unspecifically degrade peptides, whereas highly specific proteases are involved in signaling cascades. As a quantitative index of substrate specificity was lacking, we introduce cleavage entropy as a measure of substrate specificity of proteases. This quantitative score allows for straight-forward rationalization of substrate recognition by a subpocket-wise assessment of substrate readout leading to specificity profiles of individual proteases as well as an estimate of overall substrate promiscuity. We present an exemplary application of the descriptor ‘cleavage entropy’ to trace substrate specificity through the evolution of different protease folds. Our score highlights the diversity of substrate specificity within evolutionary related proteases and hence the complex relationship between sequence, structure and substrate recognition. By taking into account the whole distribution of known substrates rather than simple substrate counting, cleavage entropy provides the unique opportunity to dissect the molecular origins of protease substrate specificity.
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Affiliation(s)
- Julian E. Fuchs
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Susanne von Grafenstein
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Roland G. Huber
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Michael A. Margreiter
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Gudrun M. Spitzer
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Hannes G. Wallnoefer
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
- * E-mail:
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196
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Strisovsky K. Structural and mechanistic principles of intramembrane proteolysis--lessons from rhomboids. FEBS J 2013; 280:1579-603. [PMID: 23432912 DOI: 10.1111/febs.12199] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 02/11/2013] [Accepted: 02/18/2013] [Indexed: 02/03/2023]
Abstract
Intramembrane proteases cleave membrane proteins in their transmembrane helices to regulate a wide range of biological processes. They catalyse hydrolytic reactions within the hydrophobic environment of lipid membranes where water is normally excluded. How? Do the different classes of intramembrane proteases share any mechanistic principles? In this review these questions will be discussed in view of the crystal structures of prokaryotic members of the three known catalytic types of intramembrane proteases published over the past 7 years. Rhomboids, the intramembrane serine proteases that are the best understood family, will be the initial area of focus, and the principles that have arisen from a number of structural and biochemical studies will be considered. The site-2 metalloprotease and GXGD-type aspartyl protease structures will then be discussed, with parallels drawn and differences highlighted between these enzymes and the rhomboids. Despite the significant advances achieved so far, to obtain a detailed understanding of the mechanism of any intramembrane protease, high-resolution structural information on the substrate-enzyme complex is required. This remains a major challenge for the field.
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Affiliation(s)
- Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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197
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Brabcová J, Kindl J, Valterová I, Pichová I, Zarevúcka M, Brabcová J, Jágr M, Mikšík I. Serine protease from midgut of Bombus terrestris males. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2013; 82:117-128. [PMID: 23303700 DOI: 10.1002/arch.21075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A serine protease was isolated from midguts of the bumblebee male Bombus terrestris by a combination of precipitation procedures with column chromatography. The purified enzyme exhibited two bands with molecular masses of 25 and 26 kDa as determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis. These bands showed a proteolytic activity in zymography assay. Midgut enzymes showed optimum proteolytic activity at pH 9 and 35°C using N-succinyl-L-alanyl-L-alanyl-L-prolyl-L-phenyl-alanine 4-nitroanilide as a substrate. The Michaelis constant (Km) and maximum reaction rate (Vmax) were 0.55±0.042 mM and 0.714±0.056 μmol p-nitroalanine produced min(-1) mg protein(-1) , respectively. Inhibition was affected by trypsin inhibitor, but not by phenylmethylsulfonyl fluoride and N-tosyl-L-phenylalanine chloromethyl ketone, which indicated the trypsin-like but not chymotrypsin-like specificity. The identity of the serine protease was confirmed by nanoliquid-tandem mass spectrometry. Eleven unique peptides of the B. terrestris serine protease were found. It shows high homology to a previously reported B. ignitus serine protease covering more than 65% of the protein amino acid sequence.
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Affiliation(s)
- Jana Brabcová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
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198
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Batra J, Szabó A, Caulfield TR, Soares AS, Sahin-Tóth M, Radisky ES. Long-range electrostatic complementarity governs substrate recognition by human chymotrypsin C, a key regulator of digestive enzyme activation. J Biol Chem 2013; 288:9848-9859. [PMID: 23430245 DOI: 10.1074/jbc.m113.457382] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Human chymotrypsin C (CTRC) is a pancreatic serine protease that regulates activation and degradation of trypsinogens and procarboxypeptidases by targeting specific cleavage sites within their zymogen precursors. In cleaving these regulatory sites, which are characterized by multiple flanking acidic residues, CTRC shows substrate specificity that is distinct from that of other isoforms of chymotrypsin and elastase. Here, we report the first crystal structure of active CTRC, determined at 1.9-Å resolution, revealing the structural basis for binding specificity. The structure shows human CTRC bound to the small protein protease inhibitor eglin c, which binds in a substrate-like manner filling the S6-S5' subsites of the substrate binding cleft. Significant binding affinity derives from burial of preferred hydrophobic residues at the P1, P4, and P2' positions of CTRC, although acidic P2' residues can also be accommodated by formation of an interfacial salt bridge. Acidic residues may also be specifically accommodated in the P6 position. The most unique structural feature of CTRC is a ring of intense positive electrostatic surface potential surrounding the primarily hydrophobic substrate binding site. Our results indicate that long-range electrostatic attraction toward substrates of concentrated negative charge governs substrate discrimination, which explains CTRC selectivity in regulating active digestive enzyme levels.
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Affiliation(s)
- Jyotica Batra
- Department of Cancer Biology, Mayo Clinic Cancer Center, Jacksonville, Florida 32224
| | - András Szabó
- Department of Molecular and Cell Biology, Boston University Henry M. Goldman School of Dental Medicine, Boston, Massachusetts 02118
| | - Thomas R Caulfield
- Department of Cancer Biology, Mayo Clinic Cancer Center, Jacksonville, Florida 32224; Department of Neuroscience, Mayo Clinic Cancer Center, Jacksonville, Florida 32224
| | - Alexei S Soares
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973
| | - Miklós Sahin-Tóth
- Department of Molecular and Cell Biology, Boston University Henry M. Goldman School of Dental Medicine, Boston, Massachusetts 02118.
| | - Evette S Radisky
- Department of Cancer Biology, Mayo Clinic Cancer Center, Jacksonville, Florida 32224.
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199
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Perera NC, Jenne DE. Perspectives and potential roles for the newly discovered NSP4 in the immune system. Expert Rev Clin Immunol 2013; 8:501-3. [PMID: 22992141 DOI: 10.1586/eci.12.39] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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200
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Nazari-Robati M, Khajeh K, Aminian M, Mollania N, Golestani A. Enhancement of thermal stability of chondroitinase ABC I by site-directed mutagenesis: An insight from Ramachandran plot. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:479-86. [DOI: 10.1016/j.bbapap.2012.11.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Revised: 11/05/2012] [Accepted: 11/09/2012] [Indexed: 10/27/2022]
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