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Structural Analysis and Construction of a Thermostable Antifungal Chitinase. Appl Environ Microbiol 2022; 88:e0065222. [PMID: 35652665 DOI: 10.1128/aem.00652-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chitin is a biopolymer of N-acetyl-d-glucosamine with β-1,4-bond and is the main component of arthropod exoskeletons and the cell walls of many fungi. Chitinase (EC 3.2.1.14) is an enzyme that hydrolyzes the β-1,4-bond in chitin and degrades chitin into oligomers. It has been found in a wide range of organisms. Chitinase from Gazyumaru (Ficus microcarpa) latex exhibits antifungal activity by degrading chitin in the cell wall of fungi and is expected to be used in medical and agricultural fields. However, the enzyme's thermostability is an important factor; chitinase is not thermostable enough to maintain its activity under the actual application conditions. In addition to the fact that thermostable chitinases exhibiting antifungal activity can be used under various conditions, they have some advantages for the production process and long-term preservation, which are highly demanded in industrial use. We solved the crystal structure of chitinase to explore the target sites to improve its thermostability. We rationally introduced proline residues, a disulfide bond, and salt bridges in the chitinase using protein-engineering methods based on the crystal structure and sequence alignment among other chitinases. As a result, we successfully constructed the thermostable mutant chitinases rationally with high antifungal and specific activities. The results provide a useful strategy to enhance the thermostability of this enzyme family. IMPORTANCE We solved the crystal structure of the chitinase from Gazyumaru (Ficus microcarpa) latex exhibiting antifungal activity. Furthermore, we demonstrated that the thermostable mutant enzyme with a melting temperature (Tm) 6.9°C higher than wild type (WT) and a half-life at 60°C that is 15 times longer than WT was constructed through 10 amino acid substitutions, including 5 proline residues substitutions, making disulfide bonding, and building a salt bridge network in the enzyme. These mutations do not affect its high antifungal activity and chitinase activity, and the principle for the construction of the thermostable chitinase was well explained by its crystal structure. Our results provide a useful strategy to enhance the thermostability of this enzyme family and to use the thermostable mutant as a seed for antifungal agents for practical use.
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Relationship between the Stability of Hen Egg-White Lysozymes Mutated at Sites Designed to Interact with α-Helix Dipoles and Their Secretion Amounts in Yeast. Biosci Biotechnol Biochem 2014; 71:2952-61. [DOI: 10.1271/bbb.70354] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Allaire M, Moiseeva N, Botez CE, Engel MA, Stephens PW. On the possibility of using polycrystalline material in the development of structure-based generic assays. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:379-82. [PMID: 19307720 PMCID: PMC2659885 DOI: 10.1107/s090744490900256x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Accepted: 01/20/2009] [Indexed: 12/04/2022]
Abstract
The correlation coefficients calculated between raw powder diffraction profiles can be used to identify ligand-bound/unbound states of lysozyme. The discovery of ligands that bind specifically to a targeted protein benefits from the development of generic assays for high-throughput screening of a library of chemicals. Protein powder diffraction (PPD) has been proposed as a potential method for use as a structure-based assay for high-throughput screening applications. Building on this effort, powder samples of bound/unbound states of soluble hen-egg white lysozyme precipitated with sodium chloride were compared. The correlation coefficients calculated between the raw diffraction profiles were consistent with the known binding properties of the ligands and suggested that the PPD approach can be used even prior to a full description using stereochemically restrained Rietveld refinement.
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Affiliation(s)
- Marc Allaire
- National Synchrotron Light Source, Brookhaven National Laboratory, Upton, NY 11973-5000, USA.
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Oda M, Uchiyama S, Robinson CV, Fukui K, Kobayashi Y, Azuma T. Regional and segmental flexibility of antibodies in interaction with antigens of different size. FEBS J 2006; 273:1476-87. [PMID: 16689933 DOI: 10.1111/j.1742-4658.2006.05168.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The interaction of antibodies (Abs) with protein antigens (Ags) of different size, such as hen egg white lysozyme, ovalbumin, and bovine serum albumin, was examined using analytical ultracentrifugation, electrospray ionization time-of-flight mass spectrometry, and surface plasmon resonance in order to estimate regional and segmental Ab flexibility. When both Abs and Ags were free in solution, sedimentation equilibrium and surface plasmon resonance analyses showed the formation of an Ag(2)Ab(1) complexes regardless of Ag size, suggesting that the Fab arms were able to move to avoid interference between Ags bound to Ab combining sites. The Ag(2)Ab(1) complex, as well as the Ag(1)Ab(1) complex, was observed by MS. However, when Abs were immobilized on the surface of a sensor chip through the Fc region, the stoichiometry of the Ag-Ab complex was dependent on the Ag size; Ag(2)Ab(1) forming with hen egg white lysozyme and Ag(1)Ab(1) with ovalbumin and bovine serum albumin. These results indicated that immobilization of the Fc region reduces the dynamic range of the Fab arms and results in interference from the first Ag bound to either combining site, which in turn prevents the binding of the second Ag to the other combining site. Our results allow us to propose that the Fab arms of B-cell receptors whose Fc regions are immobilized on cell surface have a reduced dynamic range.
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Affiliation(s)
- Masayuki Oda
- Graduate School of Agriculture, Kyoto Prefectural University, Japan
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Higman VA, Boyd J, Smith LJ, Redfield C. Asparagine and glutamine side-chain conformation in solution and crystal: a comparison for hen egg-white lysozyme using residual dipolar couplings. JOURNAL OF BIOMOLECULAR NMR 2004; 30:327-346. [PMID: 15754058 DOI: 10.1007/s10858-004-3218-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2004] [Accepted: 08/11/2004] [Indexed: 05/24/2023]
Abstract
Experimental (15)N-(1)H and (1)H-(1)H residual dipolar couplings (RDCs) for the asparagine (Asn) and glutamine (Gln) side chains of hen egg-white lysozyme are measured and analysed in conjunction with (1)N relaxation data, information about chi(1) torsion angles in solution and molecular dynamics simulations. The RDCs are compared to values predicted from 16 high-resolution crystal structures. Two distinct groups of Asn and Gln side chains are identified. The first contains residues whose side chains show a fixed, relatively rigid, conformation in solution. For these residues there is good agreement between the experimental and predicted RDCs. This agreement improves when the experimental order parameter, S, is included in the calculation of the RDCs from the crystal structures. The comparison of the experimental RDCs with values calculated from the X-ray structures shows that the similarity between the oxygen and nitrogen electron densities is a limitation to the correct assignment of the Asn and Gln side-chain orientation in X-ray structures. In the majority of X-ray structures a 180 degrees rotation about chi(2) or chi(3), leading to the swapping of N(delta/epsilon 2) and O(delta/epsilon 1), is necessary for at least one Asn or Gln residue in order to achieve good agreement between experimental and predicted RDCs. The second group contains residues whose side chains do not adopt a single, well-defined, conformation in solution. These residues do not show a correlation between the experimental and predicted RDCs. In many cases the family of crystal structures shows a range of orientations for these side chains, but in others the crystal structures show a well-defined side-chain position. In the latter case, this is found to arise from crystallographic contacts and does not represent the behaviour of the side chain in solution.
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Anderson TA, Sauer RT. Role of an N(cap) residue in determining the stability and operator-binding affinity of Arc repressor. Biophys Chem 2003; 100:341-50. [PMID: 12646376 DOI: 10.1016/s0301-4622(02)00291-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Arc repressor of bacteriophage P22 is a member of the ribbon-helix-helix family of transcription factors. Ser32 is a solvent-exposed position that serves a structural role as the N(cap) residue of alpha-helix B of Arc, but also serves a functional role because its side chain is packed close to the sugar-phosphate DNA backbone in the repressor-operator complex. The tolerance of this N(cap) position to amino-acid substitutions was probed by determining the repressor activity in vivo, the thermal stability and the operator-binding activity in vitro of a set of 13 mutant proteins. The stability of position-32 Arc variants, except for Cys32, correlated well with the frequencies observed for the corresponding residues at N(cap) positions in alpha-helices of other proteins. Cysteine was quite stabilizing at the helix-B N(cap) position in Arc, but surprisingly was the least frequent N(cap) residue in the protein database. This latter finding may reflect a hyper-reactivity of N(cap) cysteines, which makes them prone to chemical modification. In general, only Arc variants with small, uncharged residues at position 32 were active in vivo or showed strong operator binding in vitro. Based upon the results presented here, revised sequence alignments of the MetJ and NikR subfamilies with Arc and other ribbon-helix-helix proteins are proposed.
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Affiliation(s)
- Thomas A Anderson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Muraki M, Harata K. X-ray structural analysis of the ligand-recognition mechanism in the dual-affinity labeling of c-type lysozyme with 2',3'-epoxypropyl beta-glycoside of N-acetyllactosamine. J Mol Recognit 2003; 16:72-82. [PMID: 12720276 DOI: 10.1002/jmr.611] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In spite of the belonging to the same c-type lysozyme family, hen egg-white lysozyme (HEWL) was much less susceptible to the dual-affinity labeling with 2',3'-epoxypropyl beta-glycoside of N-acetyllactosamine (Galbeta1,4GlcNAc-Epo) than human lysozyme (HL). The three-dimensional structures of the HEWL labeled with single Galbeta1,4GlcNAc-Epo and the Glu102-mutant HL labeled with double Galbeta1,4GlcNAc-Epo were determined by X-ray crystallography at resolutions of 1.85 and 2.0 A, respectively. The overall conformation and the interaction mode of the carbohydrate ligand part in the singly labeled HEWL and the doubly labeled Glu102-mutant HL were basically identical to those of the correspondingly labeled wild-type HL with minor alterations in some stereochemical parameters. A detailed comparison of the structures revealed the key protein-carbohydrate and carbohydrate-carbohydrate interactions essential for the dual labeling. It was suggested that the difference in the efficiency of the dual labeling was caused by the structural difference between Gln104 in HL and Asn103 in HEWL. The relevance to our previous study and the carbohydrate-carbohydrate interaction on cell-surface membranes were discussed.
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Affiliation(s)
- Michiro Muraki
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan.
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Bergasa-Caceres F, Rabitz HA. Role of Topology in the Cooperative Collapse of the Protein Core in the Sequential Collapse Model. Folding Pathway of α-Lactalbumin and Hen Lysozyme. J Phys Chem B 2001. [DOI: 10.1021/jp004421e] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Herschel A. Rabitz
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544
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Oda M, Azuma T. Reevaluation of stoichiometry and affinity/avidity in interactions between anti-hapten antibodies and mono- or multi-valent antigens. Mol Immunol 2000; 37:1111-22. [PMID: 11451416 DOI: 10.1016/s0161-5890(01)00028-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
In order to obtain further information on the interaction between antigens (Ags) and B cell Ag receptors (BCR) for a better understanding of the relationship between signals resulting from Ag binding and B cell activation, effects of Ag valence and size on the apparent association constant, i.e. the avidity as well as the molecular stoichiometry of immune complexes in Ag-antibody (Ab) interactions were studied. Hapten conjugates using proteins of various molecular weights, such as hen egg lysozyme (HEL), ovalbumin (OVA), bovine serum albumin (BSA), and chicken gammaglobulin (CGG), were prepared for this purpose. Different ratios of the hapten, (4-hydroxy-3-nitrophenyl)acetyl (NP), to the protein were used for conjugation, and interactions between anti-NP monoclonal Abs (mAbs) and the NP conjugates were evaluated by surface plasmon resonance. It was founded that the two binding sites of an Ab were able to simultaneously accommodate two NP(1)-HEL, resulting in a tri-molecular complex, Ag(2)Ab(1). However, NP conjugates of the higher-molecular-weight proteins, OVA and BSA, formed only Ag(1)Ab(1), irrespective of hapten valence. This was thought to be due to steric hindrance caused by the binding of the first Ag. These results suggested that the stoichiometry depended largely on the size of the Ag involved and that mAbs with a low affinity are more efficient at raising the binding strength through divalent interaction since the avidity of two mAbs in interactions with highly haptenated BSA was not significantly different in spite of a 10-fold difference in affinity to the monovalent NP(1)-HEL.
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Affiliation(s)
- M Oda
- Research Institute for Biological Sciences (RIBS), Science University of Tokyo, 2669 Noda, Chiba 278-0022, Japan
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Tsujihata Y, So T, Chijiiwa Y, Hashimoto Y, Hirata M, Ueda T, Imoto T. Mutant mouse lysozyme carrying a minimal T cell epitope of hen egg lysozyme evokes high autoantibody response. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2000; 165:3606-11. [PMID: 11034362 DOI: 10.4049/jimmunol.165.7.3606] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Self proteins including foreign T cell epitope induce autoantibodies. We evaluated the relationship between the size of foreign Ag introduced into self protein and the magnitude of autoantibody production. Mouse lysozyme (ML) was used as a model self protein, and we prepared three different ML derivatives carrying T cell epitope of hen egg white lysozyme (HEL) 107-116, i.e, heterodimer of ML and HEL (ML-HEL), chimeric lysozyme that has residue 1-82 of ML and residue 83-130 of HEL in its sequence (chiMH), and mutant ML that has triple mutations rendering the most potent T cell epitope of HEL (sequence 107-116). Immunization of BALB/c mice with these three ML derivatives induced anti-ML autoantibody responses, whereas native ML induced no detectable response. In particular, mutML generated a 10(4) times higher autoantibody titer than did ML-HEL. Anti-HEL107-116 T cell-priming activities were almost similar among the ML derivatives. The heterodimerization of mutant ML and HEL led to significant reduction of the autoantibody response, whereas the mixture did not. These results show that size of the nonself region in modified self Ag has an important role in determining the magnitude of the autoantibody response, and that decrease in the foreign region in a modified self protein may cause high-titered autoantibody response.
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MESH Headings
- Animals
- Autoantibodies/biosynthesis
- Autoantibodies/metabolism
- Binding Sites, Antibody
- Chickens
- Dose-Response Relationship, Immunologic
- Enzyme-Linked Immunosorbent Assay
- Epitopes, T-Lymphocyte/administration & dosage
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/metabolism
- Female
- Immunoglobulin G/biosynthesis
- Immunoglobulin G/metabolism
- Injections, Subcutaneous
- Lymphocyte Activation/genetics
- Male
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C3H
- Mice, Inbred C57BL
- Muramidase/administration & dosage
- Muramidase/genetics
- Muramidase/immunology
- Ovum/immunology
- Peptide Fragments/administration & dosage
- Peptide Fragments/genetics
- Peptide Fragments/immunology
- Recombinant Fusion Proteins/administration & dosage
- Recombinant Fusion Proteins/immunology
- Recombinant Proteins/administration & dosage
- Recombinant Proteins/immunology
- T-Lymphocytes/immunology
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Affiliation(s)
- Y Tsujihata
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
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Masumoto K, Ueda T, Motoshima H, Imoto T. Relationship between local structure and stability in hen egg white lysozyme mutant with alanine substituted for glycine. PROTEIN ENGINEERING 2000; 13:691-5. [PMID: 11112507 DOI: 10.1093/protein/13.10.691] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We prepared five mutant lysozymes in which glycines whose dihedral angles are located in the region of the left-handed helix, Gly49, Gly67, Gly71, Gly102 and Gly117, were mutated to an alanine residue. From analyses of their thermal stabilities using differential scanning calorimetry, most of them were more destabilized than the native lysozyme, except for the G102A mutant, which has a stability similar to that of the native lysozyme at pH 2.7. As for the destabilized mutant lysozymes, their X-ray crystallographic analyses showed that their global structures did not change but that the local structures changed slightly. By examining the dihedral angles at the mutation sites based on X-ray crystallographic results, it was found that the dihedral angles at these mutation sites tended to adopt favorable values in a Ramachandran plot and that the extent and direction of their shifts from the original value had similar tendencies. Therefore, the change in dihedral angles may be the cause of the slight local structural changes around the mutation site. On the other hand, regarding the mutation of G102A, the global structure was almost identical with that of the native structure but the local structure was drastically changed. Therefore, it was suggested that the drastic local conformational change might be effective in releasing the unfavorable interaction of the native state at the mutation site.
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Affiliation(s)
- K Masumoto
- Graduate School of Pharmaceutical Sciences, Kyushu University, 62 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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Satoh T, Takahashi Y, Oshida N, Shimizu A, Shinoda H, Watanabe M, Samejima T. A chimeric inorganic pyrophosphatase derived from Escherichia coli and Thermus thermophilus has an increased thermostability. Biochemistry 1999; 38:1531-6. [PMID: 9931019 DOI: 10.1021/bi981445r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Factors contributing to the thermostability of inorganic pyrophosphatase (PPase) were investigated by examining chimeric PPases from Escherichia coli and Thermus thermophilus (Tth). Two chimeric PPase genes, T1-135E (residues 1-135 from the N terminus are comprised of Tth PPase and residues 136-173 are derived from the C terminus of E. coli PPase) and T1-149E [residues 1-149 from the N terminus are from Tth PPase and the rest (150-175) are from E. coli PPase], were constructed by random chimeragenesis. After the genes were overexpressed in the E. coli BL21(DE3) strain and the expression products were purified, we compared the characteristics of these chimeric PPases with those of the parental PPases. We found that the two chimeras had higher activity than either parent PPase at the optimum temperature. We also examined thermal stability in terms of CD spectra, fluorescence spectra, and thermal changes in enzyme activity. The results revealed that the thermal stability of T1-149E is similar to that of Tth PPase, but T1-135E is much more stable. This suggests that the four residues that are different between T1-135E and T1-149E may be critical for thermostability between the two chimeras. By comparing the three-dimensional structures of Tth and E. coli PPases, we deduced that the following two factors may contribute to differences in thermostability. (1) Two residues (Thr138 and Ala141 in the Tth PPase and His140 and Asp143 in the E. coli PPase) in the vicinity of the trimer-trimer interface were different. (2) The Ala144-Lys145 loop in the Tth PPase was deleted in the E. coli PPase and also in the T1-135E chimera. Therefore, we conclude that T1-135E was thermostabilized by these two factors, and also, the Tth PPase moiety may contribute to the structural integrity of the chimeric enzymes.
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Affiliation(s)
- T Satoh
- Department of Chemistry, College of Science and Engineering, Aoyama Gakuin University, Tokyo, Japan
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