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Barts N, Bhatt RH, Toner C, Meyer WK, Durrant JD, Kohl KD. Functional convergence in gastric lysozymes of foregut-fermenting rodents, ruminants, and primates is not attributed to convergent molecular evolution. Comp Biochem Physiol B Biochem Mol Biol 2024; 271:110949. [PMID: 38341948 DOI: 10.1016/j.cbpb.2024.110949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/28/2024] [Accepted: 01/28/2024] [Indexed: 02/13/2024]
Abstract
Convergent evolution is a widespread phenomenon. While there are many examples of convergent evolution at the phenotypic scale, convergence at the molecular level has been more difficult to identify. A classic example of convergent evolution across scales is that of the digestive lysozyme found in ruminants and Colobine monkeys. These herbivorous species rely on foregut fermentation, which has evolved to function more optimally under acidic conditions. Here, we explored if rodents with similar dietary strategies and digestive morphologies have convergently evolved a lysozyme with digestive functions. At the phenotypic level, we find that rodents with bilocular stomach morphologies exhibited a lysozyme that maintained higher relative activities at low pH values, similar to the lysozymes of ruminants and Colobine monkeys. Additionally, the lysozyme of Peromyscus leucopus shared a similar predicted protonation state as that observed in previously identified digestive lysozymes. However, we found limited evidence of positive selection acting on the lysozyme gene in foregut-fermenting species and did not identify patterns of convergent molecular evolution in this gene. This study emphasizes that phenotypic convergence need not be the result of convergent genetic modifications, and we encourage further exploration into the mechanisms regulating convergence across biological scales.
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Affiliation(s)
- Nick Barts
- Department of Biological and Clinical Sciences, University of Central Missouri, Warrensburg, MO, USA; Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Roshni H Bhatt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA. https://twitter.com/RoshniBhatt3
| | - Chelsea Toner
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wynn K Meyer
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA. https://twitter.com/sorrywm
| | - Jacob D Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA. https://twitter.com/KevinDKohl
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2
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Boorman J, Zeng X, Lin J, van den Akker F. Structural insights into peptidoglycan glycosidase EtgA binding to the inner rod protein EscI of the type III secretion system via a designed EscI-EtgA fusion protein. Protein Sci 2024; 33:e4930. [PMID: 38380768 PMCID: PMC10880428 DOI: 10.1002/pro.4930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/23/2024] [Accepted: 02/01/2024] [Indexed: 02/22/2024]
Abstract
Bacteria express lytic enzymes such as glycosidases, which have potentially self-destructive peptidoglycan (PG)-degrading activity and, therefore, require careful regulation in bacteria. The PG glycosidase EtgA is regulated by localization to the assembling type III secretion system (T3SS), generating a hole in the PG layer for the T3SS to reach the outer membrane. The EtgA localization was found to be mediated via EtgA interacting with the T3SS inner rod protein EscI. To gain structural insights into the EtgA recognition of EscI, we determined the 2.01 Å resolution structure of an EscI (51-87)-linker-EtgA fusion protein designed based on AlphaFold2 predictions. The structure revealed EscI residues 72-87 forming an α-helix interacting with the backside of EtgA, distant from the active site. EscI residues 56-71 also were found to interact with EtgA, with these residues stretching across the EtgA surface. The ability of the EscI to interact with EtgA was also probed using an EscI peptide. The EscI peptide comprising residues 66-87, slightly larger than the observed EscI α-helix, was shown to bind to EtgA using microscale thermophoresis and thermal shift differential scanning fluorimetry. The EscI peptide also had a two-fold activity-enhancing effect on EtgA, whereas the EscI-EtgA fusion protein enhanced activity over four-fold compared to EtgA. Our studies suggest that EtgA regulation by EscI could be trifold involving protein localization, protein activation, and protein stabilization components. Analysis of the sequence conservation of the EscI EtgA interface residues suggested a possible conservation of such regulation for related proteins from different bacteria.
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Affiliation(s)
- J. Boorman
- Department of BiochemistryCase Western Reserve UniversityClevelandOhioUSA
| | - X. Zeng
- Department of Animal ScienceUniversity of TennesseeKnoxvilleTennesseeUSA
| | - J. Lin
- Department of Animal ScienceUniversity of TennesseeKnoxvilleTennesseeUSA
| | - F. van den Akker
- Department of BiochemistryCase Western Reserve UniversityClevelandOhioUSA
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3
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Kalhor HR, Piraman Z, Fathali Y. Hen egg white lysozyme encapsulated in ZIF-8 for performing promiscuous enzymatic Mannich reaction. iScience 2023; 26:107807. [PMID: 37744039 PMCID: PMC10514465 DOI: 10.1016/j.isci.2023.107807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/05/2023] [Accepted: 08/30/2023] [Indexed: 09/26/2023] Open
Abstract
Hen egg white lysozyme (HEWL) was exploited for the synthesis of β-amino carbonyl compounds through a direct and three-component Mannich reaction in aqueous, confirming high chemoselectivity toward imine. In order to further extend the applications of the enzyme, HEWL was encapsulated using a metal-organic framework (MOF). The reactivity, stereoselectivity, and reusability of the encapsulated enzyme were investigated. The reaction was significantly enhanced as compared to the non-encapsulated enzyme. A mutated version of the enzyme, containing Asp52Ala (D52A), lacking important catalytical residue, has lost the bacterial site activity against Micrococcus luteus (M. luteus) while the D52A variant displayed an increased rate of the Mannich reaction, indicating a different catalytical residue involved in the promiscuous reaction. Based on site-directed mutagenesis, molecular docking, and molecular dynamic studies, it was proposed that π-stacking, H-bond interactions, and the presence of water in the active site may play crucial roles in the mechanism of the reaction.
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Affiliation(s)
- Hamid R. Kalhor
- Biochemistry and Chemical Biology Research Laboratory, Department of Chemistry, Sharif University of Technology, Tehran, Iran
| | - Zeinab Piraman
- Biochemistry and Chemical Biology Research Laboratory, Department of Chemistry, Sharif University of Technology, Tehran, Iran
| | - Yasaman Fathali
- Biochemistry and Chemical Biology Research Laboratory, Department of Chemistry, Sharif University of Technology, Tehran, Iran
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4
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Petri YD, Gutierrez CS, Raines RT. Chemoselective Caging of Carboxyl Groups for On-Demand Protein Activation with Small Molecules. Angew Chem Int Ed Engl 2023; 62:e202215614. [PMID: 36964973 PMCID: PMC10243506 DOI: 10.1002/anie.202215614] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 03/02/2023] [Accepted: 03/24/2023] [Indexed: 03/27/2023]
Abstract
Tools for on-demand protein activation enable impactful gain-of-function studies in biological settings. Thus far, however, proteins have been chemically caged at primarily Lys, Tyr, and Sec, typically through the genetic encoding of unnatural amino acids. Herein, we report that the preferential reactivity of diazo compounds with protonated acids can be used to expand this toolbox to solvent-accessible carboxyl groups with an elevated pKa value. As a model protein, we employed lysozyme (Lyz), which has an active-site Glu35 residue with a pKa value of 6.2. A diazo compound with a bioorthogonal self-immolative handle esterified Glu35 selectively, inactivating Lyz. The hydrolytic activity of the caged Lyz on bacterial cell walls was restored with two small-molecule triggers. The decaging was more efficient by small molecules than by esterases. This simple chemical strategy was also applied to a hemeprotein and an aspartyl protease, setting the stage for broad applicability.
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Affiliation(s)
- Yana D. Petri
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
| | - Clair S. Gutierrez
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
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5
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Dey D, Nishijima M, Tanaka R, Kurisu G, Tanaka H, Ito H. Crystal structure and reaction mechanism of a bacterial Mg-dechelatase homolog from the Chloroflexi Anaerolineae. Protein Sci 2022; 31:e4430. [PMID: 36173179 PMCID: PMC9514216 DOI: 10.1002/pro.4430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/05/2022]
Abstract
Chlorophyll degradation plays a myriad of physiological roles in photosynthetic organisms, including acclimation to light environment and nutrient remobilization during senescence. Mg extraction from chlorophyll a is the first and committed step of the chlorophyll degradation pathway. This reaction is catalyzed by the Mg-dechelatase enzyme encoded by Stay-Green (SGR). The reaction mechanism of SGR protein remains elusive since metal ion extraction from organic molecules is not a common enzymatic reaction. Additionally, experimentally derived structural information about SGR or its homologs has not yet been reported. In this study, the crystal structure of the SGR homolog from Anaerolineae bacterium was determined using the molecular replacement method at 1.85 Å resolution. Our previous study showed that three residues-H32, D34, and D62 are essential for the catalytic activity of the enzyme. Biochemical analysis involving mutants of D34 residue further strengthened its importance in the functioning of the dechelatase. Docking simulation also revealed the interaction between the D34 side chain and central Mg ion of chlorophyll a. Structural analysis showed the arrangement of D34/H32/D62 in the form of a catalytic triad that is generally found in hydrolases. The probable reaction mechanism suggests that deprotonated D34 side chain coordinates and destabilizes Mg, resulting in Mg extraction. Besides, H32 possibly acts as a general base catalyst and D62 facilitates H32 to be a better proton acceptor. Taken together, the reaction mechanism of SGR partially mirrors the one observed in hydrolases.
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Affiliation(s)
- Debayan Dey
- Graduate School of Life ScienceHokkaido UniversitySapporoJapan
- Institute of Low Temperature ScienceHokkaido UniversitySapporoJapan
| | | | - Ryouichi Tanaka
- Institute of Low Temperature ScienceHokkaido UniversitySapporoJapan
| | - Genji Kurisu
- Institute for Protein ResearchOsaka UniversitySuitaJapan
| | - Hideaki Tanaka
- Institute for Protein ResearchOsaka UniversitySuitaJapan
| | - Hisashi Ito
- Institute of Low Temperature ScienceHokkaido UniversitySapporoJapan
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6
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Kalra S, Dhamannapatil P, Panda S, Singh S, Sarwalia P, Mohanty AK, Datta TK, Kaushik JK. Recombinant expression and molecular characterization of buffalo sperm lysozyme-like protein 1. Protein Expr Purif 2021; 190:105993. [PMID: 34656738 DOI: 10.1016/j.pep.2021.105993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 10/20/2022]
Abstract
Several sperm lysozyme-like genes evolved from lysozyme by successive duplications and mutations; however their functional role in the reproduction of farm animals is not well understood. To understand the function and molecular properties of buffalo sperm lysozyme-like protein 1 (buSLLP1), it was expressed in E. coli; however, it partitioned to inclusion bodies. Lowering of temperature and inducer concentration did not help in the recovery of the expressed protein in the biologically active form. Therefore, buSLLP1 was cloned and expressed in Pichiapink system based on auxotrophic Pichia pastoris in a labscale fermenter. The expressed protein was obtained in flow-through by using a 30 kDa ultrafiltration membrane followed by MonoQ anion exchange chromatography, resulting in a homogenous preparation of 40 mg recombinant buSLLP1 per liter of initial spent culture-supernatant. Circular dichroism spectroscopy showed that recombinant buSLLP1 possessed a native-like secondary structure. The recombinant buSLLP1 also showed thermal denaturation profile typical of folded globular proteins; however, the thermal stability was lower than the hen egg white lysozyme. Binding of buSLLP1 to chitin and zona pellucida of buffalo oocytes showed that the recombinant buSLLP1 possessed a competent binding pocket, therefore, the produced protein could be used to study its functional role in the reproduction of farm animals.
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Affiliation(s)
- Shalini Kalra
- Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, 132001, India
| | - Prakash Dhamannapatil
- Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, 132001, India
| | - Santanu Panda
- Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, 132001, India
| | - Surender Singh
- Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, 132001, India
| | - Parul Sarwalia
- Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, 132001, India
| | - Ashok Kumar Mohanty
- Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, 132001, India
| | - Tirtha Kumar Datta
- Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, 132001, India
| | - Jai Kumar Kaushik
- Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, 132001, India.
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7
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Ogata M, Fukamizo T, Ohnuma T. Thermodynamic Analysis for Binding of 4- O-β-tri- N-acetylchitotriosyl Moranoline, a Transition State Analogue Inhibitor for Hen Egg White Lysozyme. Front Mol Biosci 2021; 8:654706. [PMID: 34179076 PMCID: PMC8222817 DOI: 10.3389/fmolb.2021.654706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 05/24/2021] [Indexed: 11/13/2022] Open
Abstract
4-O-β-tri-N-acetylchitotriosyl moranoline (GN3M) is a transition-state analogue for hen egg white lysozyme (HEWL) and identified as the most potent inhibitor till date. Isothermal titration calorimetry experiments provided the thermodynamic parameters for binding of GN3M to HEWL and revealed that the binding is driven by a favorable enthalpy change (ΔH° = -11.0 kcal/mol) with an entropic penalty (-TΔS° = 2.6 kcal/mol), resulting in a free energy change (ΔG°) of -8.4 kcal/mol [Ogata et al. (2013) 288, 6,072-6,082]. Dissection of the entropic term showed that a favorable solvation entropy change (-TΔS solv° = -9.2 kcal/mol) is its sole contributor. The change in heat capacity (ΔC p°) for the binding of GN3M was determined to be -120.2 cal/K·mol. These results indicate that the bound water molecules play a crucial role in the tight interaction between GN3M and HEWL.
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Affiliation(s)
- Makoto Ogata
- Faculty of Food and Agricultural Sciences, Fukushima University, Fukushima, Japan
| | - Tamo Fukamizo
- Department of Advanced Bioscience, Kindai University, Nara, Japan
| | - Takayuki Ohnuma
- Department of Advanced Bioscience, Kindai University, Nara, Japan
- Agricultural Technology and Innovation Research Institute(ATIRI), Kindai University, Nara, Japan
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8
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Identification and Functional Analysis of a Lysozyme Gene from Coridius chinensis (Hemiptera: Dinidoridae). BIOLOGY 2021; 10:biology10040330. [PMID: 33920041 PMCID: PMC8071013 DOI: 10.3390/biology10040330] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/02/2021] [Accepted: 04/09/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary As a medicinal insect, Coridius chinensis contains many active polypeptides. Extracts from C. chinensis are usually complex and it is not clear which polypeptides are effective medicinal ingredients. In addition, we also need to figure out the functions of various immune effectors in the innate immunity of C. chinensis. To explore the function of lysozyme in C. chinensis, a lysozyme gene CcLys2 was screened and identified from the transcriptome data of C. chinensis. The results showed that CcLys2 had a typical domain of the c-type lysozyme, belonging to the H-branch of the c-type lysozyme. The lysozyme Cclys2 is an effective immune effector in the immune response of C. chinensis and can be stimulated by bacterial infection. Like typical c-type lysozyme, Cclys2 has lytic activity against Gram-positive bacteria. The research holds promise for functional annotation of similar proteins from other dinidoridae insects and provides the theoretical feasibility for the development of medicinal components in C. chinensis. Our results also provide data for further investigating the origin and evolution of insect lysozymes. Abstract Coridius chinensis is a valuable medicinal insect resource in China. Previous studies have indicated that the antibacterial and anticancer effects of the C. chinensis extract mainly come from the active polypeptides. Lysozyme is an effective immune effector in insect innate immunity and usually has excellent bactericidal effects. There are two kinds of lysozymes in insects, c-type and i-type, which play an important role in innate immunity and intestinal digestion. Studying lysozyme in C. chinensis will be helpful to further explore the evolutionary relationship and functional differences among lysozymes of various species and to determine whether they have biological activity and medicinal value. In this study, a lysozyme CcLys2 was identified from C. chinensis. CcLys2 contains 223 amino acid residues, and possesses a typical domain of the c-type lysozyme and a putative catalytic site formed by two conserved residues Glu32 and Asp50. Phylogenetic analysis showed that CcLys2 belongs to the H-branch of the c-type lysozyme. The analysis of spatiotemporal expression patterns indicated that CcLys2 was mainly expressed in the fat body of C. chinensis adults and was highly expressed in the second- and fifth-instar nymphs. In addition, CcLys2 was significantly up-regulated after injecting and feeding bacteria. In the bacterial inhibition assay, it was found that CcLys2 had antibacterial activity against Gram-positive bacteria at a low pH. These results indicate that CcLys2 has muramidase activity, involves in the innate immunity of C. chinensis, and is also closely related to the bacterial immune defense or digestive function of the intestine.
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9
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Atkins DL, Magana JR, Sproncken CCM, van Hest JCM, Voets IK. Single Enzyme Nanoparticles with Improved Biocatalytic Activity through Protein Entrapment in a Surfactant Shell. Biomacromolecules 2021; 22:1159-1166. [PMID: 33630590 PMCID: PMC7944482 DOI: 10.1021/acs.biomac.0c01663] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
A polymeric corona
consisting of an alkyl-glycolic acid ethoxylate
(CXEOY) surfactant
offers a promising approach toward endowing proteins with thermotropic
phase behavior and hyperthermal activity. Typically, preparation of
protein–surfactant biohybrids is performed via chemical modification of acidic residues followed by electrostatic
conjugation of an anionic surfactant to encapsulate single proteins.
While this procedure has been applied to a broad range of proteins,
modification of acidic residues may be detrimental to function for
specific enzymes. Herein, we report on the one-pot preparation of
biohybrids via covalent conjugation of surfactants
to accessible lysine residues. We entrap the model enzyme hen egg-white
lysozyme (HEWL) in a shell of carboxyl-functionalized C12EO10 or C12EO22 surfactants. With
fewer surfactants, our covalent biohybrids display similar thermotropic
phase behavior to their electrostatically conjugated analogues. Through
a combination of small-angle X-ray scattering and circular dichroism
spectroscopy, we find that both classes of biohybrids consist of a
folded single-protein core decorated by surfactants. Whilst traditional
biohybrids retain densely packed surfactant coronas, our biohybrids
display a less dense and heterogeneously distributed surfactant coverage
located opposite to the catalytic cleft of HEWL. In solution, this
surfactant coating permits 7- or 3.5-fold improvements in activity
retention for biohybrids containing C12EO10 or
C12EO22, respectively. The reported alternative
pathway for biohybrid preparation offers a new horizon to expand upon
the library of proteins for which functional biohybrid materials can
be prepared. We also expect that an improved understanding of the
distribution of tethered surfactants in the corona will be crucial
for future structure–function investigations.
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Affiliation(s)
- Dylan L Atkins
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - J Rodrigo Magana
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Christian C M Sproncken
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Jan C M van Hest
- Institute for Complex Molecular Systems, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands.,Laboratory of Bio-Organic Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Ilja K Voets
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
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10
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Kumari P, Kumari M, Kashyap HK. How Pure and Hydrated Reline Deep Eutectic Solvents Affect the Conformation and Stability of Lysozyme: Insights from Atomistic Molecular Dynamics Simulations. J Phys Chem B 2020; 124:11919-11927. [DOI: 10.1021/acs.jpcb.0c09873] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Pratibha Kumari
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Monika Kumari
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Hemant K. Kashyap
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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11
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Ogata M. Chemoenzymatic Synthesis and Function of Chitin Derivatives. Curr Pharm Des 2020; 26:3522-3529. [DOI: 10.2174/1381612826666200515132623] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 04/15/2020] [Indexed: 11/22/2022]
Abstract
Chitin, abundant biomass found in crab shells and other marine life, has wide applications in the production of food, pharmaceuticals, and cosmetics. Our recent studies have focused on the development of new functional materials by derivatizing chitin oligosaccharides and monosaccharides. For example, we have prepared various derivatives by chemoenzymatic synthesis using N-acetylglucosamine (GlcNAc) or chitin oligosaccharide prepared from chitin as starting materials. First, we have achieved the total synthesis of two secondary metabolites (furanodictine A and B) with neuronal differentiation-inducing activity on PC12 cells by using a simple heatinduced structural transformation of GlcNAc and esterification reaction. Second, we synthesized both a novel inhibitor that has facilitated a re-examination of the reaction mechanism of hen egg-white lysozyme, and a new substrate for assaying lysozyme activity by using chitin oligosaccharides as raw materials. Thus, the development of new materials by simple derivatization of chitin mono- or oligo-saccharides is paving the way for effective use of chitin.
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Affiliation(s)
- Makoto Ogata
- Department of Applied Chemistry and Biochemistry, National Institute of Technology, Fukushima College, 30 Nagao, Iwaki, Fukushima 970-8034, Japan
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12
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Liu M, Liu T, Shi Y, Zhao Y, Yan H, Sun B, Wang Q, Wang Z, Han J. Comparative study on the interaction of oxyresveratrol and piceatannol with trypsin and lysozyme: binding ability, activity and stability. Food Funct 2020; 10:8182-8194. [PMID: 31696185 DOI: 10.1039/c9fo01888c] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Natural polyphenols showing a variety of beneficial effects will interact with multiple proteases after administration. The interactions of oxyresveratrol and piceatannol with trypsin and lysozyme were investigated using fluorescence spectroscopy, UV-vis absorption spectroscopy, circular dichroism spectroscopy, differential scanning calorimetry and molecular docking. Fluorescence quenching results and UV-vis absorption difference spectra revealed that the quenching process was a static mode initiated by ground-state complex formation. The different binding ability of oxyresveratrol and piceatannol with trypsin and lysozyme was discussed based on their different molecular structures. Moreover, the major driving force for the binding process was elucidated as hydrogen bonding and van der Waals forces by the negative enthalpy and entropy changes. Synchronous fluorescence, three-dimensional fluorescence and circular dichroism spectral analysis suggested that the binding of oxyresveratrol and piceatannol to trypsin and lysozyme induced some microenvironmental and conformational changes of the two enzymes. The thermal stability of the enzymes in the presence of polyphenols was studied based on the change in melting temperature by differential scanning calorimetry. The above experimental results were validated by the protein-ligand docking studies which showed the location of the two ligands in the enzymes and the surrounding amino acid residues. Furthermore, enzyme activity assays indicated that the enzymatic activity of trypsin and lysozyme was inhibited by oxyresveratrol and piceatannol. The effect of trypsin and lysozyme on the antioxidant activity and stability of oxyresveratrol and piceatannol was also investigated. In conclusion, the comparative study on the interaction of oxyresveratrol and piceatannol with trypsin and lysozyme showed that the positions of hydroxyl groups of the polyphenols had an important influence on their interaction with enzymes and their antioxidant activity and stability as well as the enzyme activities. The obtained results are expected to provide a theoretical basis for the application of polyphenols in functional foods and pharmaceuticals.
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Affiliation(s)
- Min Liu
- Institute of BioPharmceutical Research, Liaocheng University, Liaocheng 252059, China.
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13
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Molecular level insight into the counteraction of trehalose on the activity as well as denaturation of lysozyme induced by guanidinium chloride. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2019.110489] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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14
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Biswas B, Muttathukattil AN, Reddy G, Singh PC. Contrasting Effects of Guanidinium Chloride and Urea on the Activity and Unfolding of Lysozyme. ACS OMEGA 2018; 3:14119-14126. [PMID: 31458105 PMCID: PMC6644995 DOI: 10.1021/acsomega.8b01911] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/12/2018] [Indexed: 05/03/2023]
Abstract
Cosolvents play an important role in regulating the stability and function of proteins present in the cell. We studied the role of cosolvents, urea and guanidinium chloride (GdmCl), which act as protein denaturants, in the catalytic activity and structural stability of the protein lysozyme using activity measurements, spectroscopy, and molecular dynamics simulations. We find that the activity of lysozyme increases on the addition of urea, whereas it decreases sharply on the addition of GdmCl. At low GdmCl concentrations ([GdmCl] < 4 M), the activity of lysozyme decreases, even though there is no significant perturbation in the structure of the lysozyme folded state. We find that this is due to the strong interaction of the Gdm+ ion with the residues Asp52 and Glu35, which are present in the lysozyme catalytic site. In contrast, urea interacts with Trp63 present in the loop region present near the active site of lysozyme, inducing minor conformational changes in lysozyme, which can increase the activity of lysozyme. At higher denaturant concentrations, experiments show that GdmCl completely denatures the protein, whereas the folded state is stable in the presence of urea. We further show that GdmCl denatures lysozyme with the disulfide bonds intact in the protein, whereas urea denatures the protein only when the disulfide bonds are broken using reducing agents.
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Affiliation(s)
- Biswajit Biswas
- Department
of Spectroscopy, Indian Association for
the Cultivation of Science, 2A & 2B Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Aswathy N. Muttathukattil
- Solid
State and Structural Chemistry Unit, Indian
Institute of Science, Bengaluru 560012, Karnataka, India
| | - Govardhan Reddy
- Solid
State and Structural Chemistry Unit, Indian
Institute of Science, Bengaluru 560012, Karnataka, India
- E-mail: (G.R.)
| | - Prashant Chandra Singh
- Department
of Spectroscopy, Indian Association for
the Cultivation of Science, 2A & 2B Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
- E-mail: (P.C.S.)
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15
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Matsui M, Kono H, Ogata M. Molecular Design and Synthesis of a Novel Substrate for Assaying Lysozyme Activity. J Appl Glycosci (1999) 2018; 65:31-36. [PMID: 34354510 PMCID: PMC8056892 DOI: 10.5458/jag.jag.jag-2018_003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 05/23/2018] [Indexed: 11/26/2022] Open
Abstract
A novel substrate {Galβ1,4GlcNAcβ1,4GlcNAc-β-pNP [Gal(GlcNAc)2-β-pNP]} for assaying lysozyme activity has been designed using docking simulations and enzymatic synthesis via β-1,4-galactosyltransferase-mediated transglycosylation from UDP-Gal as the donor to (GlcNAc)2-β-pNP as the acceptor. Hydrolysis of the synthesized Gal(GlcNAc)2-β-pNP and related compounds using hen egg-white lysozyme (HEWL) demonstrated that the substrate was specifically cleaved to Gal(GlcNAc)2 and p-nitrophenol (pNP). A combination of kinetic studies and docking simulation was further conducted to elucidate the mode of substrate binding. The results demonstrate that Gal(GlcNAc)2-β-pNP selectively binds to a subsite of lysozyme to liberate the Gal(GlcNAc)2 and pNP products. The work therefore describes a new colorimetric method for quantifying lysozyme on the basis of the determination of pNP liberated from the substrate.
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Affiliation(s)
- Megumi Matsui
- Department of Applied Chemistry and Biochemistry, National Institute of Technology, Fukushima College
| | - Haruka Kono
- Department of Applied Chemistry and Biochemistry, National Institute of Technology, Fukushima College
| | - Makoto Ogata
- Department of Applied Chemistry and Biochemistry, National Institute of Technology, Fukushima College
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16
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A novel analytical procedure for assaying lysozyme activity using an end-blocked chitotetraose derivative as substrate. Anal Biochem 2017; 538:64-70. [PMID: 28951249 DOI: 10.1016/j.ab.2017.09.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 09/22/2017] [Indexed: 11/22/2022]
Abstract
An end-modified β-d-galactosyl chitotetraose derivative [44-O-β-d-galactosyl-β-tri-N-acetylchitotriosyl 2-acetamide-2,3-dideoxy-glucopyranose; Gal(GlcN)3D] was designed and synthesized from chitin tetrasaccharide. The derivative was chemically modified by dehydration of the reducing end GlcN and enzymatic addition of a Gal group to the non-reducing end GlcN. Hydrolysis of Gal(GlcN)3D and related compounds using hen egg-white lysozyme was then examined. Gal(GlcN)3D was specifically cleaved to Gal(GlcN)2 and GlcND. Kinetic studies and docking simulations were further conducted to elucidate its mode of binding to lysozyme. These analyses revealed the binding of Gal(GlcN)3D to lysozyme is more favorable than that of (GlcN)4D. We conclude the 4-O-substituted Gal group at the non-reducing end of Gal(GlcN)3D does not prohibit the action of lysozyme, but gives some affinity to the subsite (i.e. equivalent to GlcN). From these results, a new assay method for quantifying lysozyme was established by utilizing the Morgan-Elson reaction based on the generation of product D (2-acetamide-2,3-dideoxy-glucopyranose), which serves as a chromophore, formed from Gal(GlcN)3D by lysozyme through a conjugated reaction involving β-N-acetylhexosaminidase. The assay system gave a linear dose-response curve in the range of 2-31 μg of lysozyme during a 15 min incubation. This novel assay method for the quantification of lysozyme is highly specific, sensitive, accurate and reproducible.
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17
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Hirotsu T, Higashi T, Abu Hashim II, Misumi S, Wada K, Motoyama K, Arima H. Self-Assembly PEGylation Retaining Activity (SPRA) Technology via a Host-Guest Interaction Surpassing Conventional PEGylation Methods of Proteins. Mol Pharm 2017; 14:368-376. [PMID: 28032772 DOI: 10.1021/acs.molpharmaceut.6b00678] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Polyethylene glycol (PEG) modification (PEGylation) is one of the best approaches to improve the stabilities and blood half-lives of protein drugs; however, PEGylation dramatically reduces the bioactivities of protein drugs. Here, we present "self-assembly PEGylation retaining activity" (SPRA) technology via a host-guest interaction between PEGylated β-cyclodextrin (PEG-β-CyD) and adamantane-appended (Ad) proteins. PEG-β-CyD formed stable complexes with Ad-insulin and Ad-lysozyme to yield SPRA-insulin and SPRA-lysozyme, respectively. Both SPRA-proteins showed high stability against heat and trypsin digest, comparable with that of covalently PEGylated protein equivalents. Importantly, the SPRA-lysozyme possessed ca. 100% lytic activity, whereas the activity of the covalently PEGylated lysozyme was ca. 23%. Additionally, SPRA-insulin provided a prolonged and peakless blood glucose profile when compared with insulin glargine. It also showed no loss of activity. In contrast, the covalently PEGylated insulin showed a negligible hypoglycemic effect. These findings indicate that SPRA technology has potential as a generic method, surpassing conventional PEGylation methods for proteins.
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Affiliation(s)
- Tatsunori Hirotsu
- Graduate School of Pharmaceutical Sciences, Kumamoto University , 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan.,Program for Leading Graduate Schools "HIGO (Health life science: Interdisciplinary and Glocal Oriented) Program", Kumamoto University , 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Taishi Higashi
- Graduate School of Pharmaceutical Sciences, Kumamoto University , 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Irhan Ibrahim Abu Hashim
- Graduate School of Pharmaceutical Sciences, Kumamoto University , 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan.,Faculty of Pharmacy, Mansoura University , Mansoura 35516, Egypt
| | - Shogo Misumi
- Graduate School of Pharmaceutical Sciences, Kumamoto University , 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Koki Wada
- Nihon Shokuhin Kako Co., Ltd. , 30 Tajima, Fuji, Shizuoka 417-8539, Japan
| | - Keiichi Motoyama
- Graduate School of Pharmaceutical Sciences, Kumamoto University , 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Hidetoshi Arima
- Graduate School of Pharmaceutical Sciences, Kumamoto University , 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan.,Program for Leading Graduate Schools "HIGO (Health life science: Interdisciplinary and Glocal Oriented) Program", Kumamoto University , 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
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18
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Das I, Panja S, Halder M. Modulation and Salt-Induced Reverse Modulation of the Excited-State Proton-Transfer Process of Lysozymized Pyranine: The Contrasting Scenario of the Ground-State Acid–Base Equilibrium of the Photoacid. J Phys Chem B 2016; 120:7076-87. [DOI: 10.1021/acs.jpcb.6b04111] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Ishita Das
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Sudipta Panja
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Mintu Halder
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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19
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Lopes ALK, Cardoso J, Dos Santos FRCC, Silva ACG, Stets MI, Zanchin NIT, Soares MJ, Krieger MA. Development of a magnetic separation method to capture sepsis associated bacteria in blood. J Microbiol Methods 2016; 128:96-101. [PMID: 27432342 DOI: 10.1016/j.mimet.2016.07.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 07/14/2016] [Accepted: 07/15/2016] [Indexed: 12/21/2022]
Abstract
Bloodstream infections are important public health problems, associated with high mortality due to the inability to detect the pathogen quickly in the early stages of infection. Such inability has led to a growing interest in the development of a rapid, sensitive, and specific assay to detect these pathogens. In an effort to improve diagnostic efficiency, we present here a magnetic separation method for bacteria that is based on mutated lysozyme (LysE35A) to capture S. aureus from whole blood. LysE35A-coated beads were able to bind different MSSA and MRSA isolates in the blood and also other six Gram-positive and two Gram-negative species in whole blood. This system was capable to bind bacteria at low concentrations (10CFU/ml) in spiked blood. Samples captured with the mutated lysozyme showed more responsive amplification of the 16S gene than whole blood at concentrations of 10(3)-10(5)CFU. These data demonstrate detection of S. aureus directly in blood samples, without in vitro cultivation. Our results show that capture with LysE35A-coated beads can be useful to develop a point of care diagnostic system for rapid and sensitive detection of pathogens in clinical settings.
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Affiliation(s)
- Ana Luisa Kalb Lopes
- Instituto de Biologia Molecular do Paraná, Department of Research and Development, Prof. Algacyr Munhoz Mader Street 3775, 81350-010 Curitiba, PR, Brazil.
| | - Josiane Cardoso
- Instituto de Biologia Molecular do Paraná, Department of Research and Development, Prof. Algacyr Munhoz Mader Street 3775, 81350-010 Curitiba, PR, Brazil
| | | | - Ana Claudia Graziani Silva
- Instituto de Biologia Molecular do Paraná, Department of Research and Development, Prof. Algacyr Munhoz Mader Street 3775, 81350-010 Curitiba, PR, Brazil
| | - Maria Isabel Stets
- Instituto de Biologia Molecular do Paraná, Department of Research and Development, Prof. Algacyr Munhoz Mader Street 3775, 81350-010 Curitiba, PR, Brazil
| | - Nilson Ivo Tonin Zanchin
- Laboratory of Proteomic and Protein Engineering, Carlos Chagas Institute, Fiocruz, Prof. Algacyr Munhoz Mader Street 3775, 81350-010 Curitiba, PR, Brazil
| | - Maurilio José Soares
- Laboratory of Cell Biology, Carlos Chagas Institute, Fiocruz, Prof. Algacyr Munhoz Mader Street 3775, 81350-010 Curitiba, PR, Brazil
| | - Marco Aurélio Krieger
- Instituto de Biologia Molecular do Paraná, Department of Research and Development, Prof. Algacyr Munhoz Mader Street 3775, 81350-010 Curitiba, PR, Brazil
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20
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Lee JW, Kim HI. Investigating acid-induced structural transitions of lysozyme in an electrospray ionization source. Analyst 2015; 140:661-9. [PMID: 25429398 DOI: 10.1039/c4an01794c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The effect of acids on the structure of lysozyme (Lyz) during electrospray ionization (ESI) was studied by comparing the solution and gas-phase structures of Lyz. Investigation using circular dichroism spectroscopy and small-angle X-ray scattering demonstrated that the folded conformation of Lyz was maintained in pH 2.2 solutions containing different acids. On the other hand, analysis of the charge state distributions and ion mobility (IM) distributions, combined with molecular dynamics simulations, demonstrated that the gas phase structures of Lyz depend on the pKa of the acid used to acidify the protein solution. Formic acid and acetic acid, which are weak acids (pKa > 3.5), induce unfolding of Lyz during ESI, presumably because the undissociated weak acids provide protons to maintain the acidic groups within Lyz protonated and prevent the formation of salt bridges. However, HCl suppressed the formation of the unfolded conformers because the acid is already dissociated in solution, and chloride anions within the ESI droplet can interact with Lyz to reduce the intramolecular electrostatic repulsion. These trends in the IM distributions are observed for all charge states, demonstrating the significance of the acid effect on the structure of Lyz during ESI.
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Affiliation(s)
- Jong Wha Lee
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 790-784, South Korea.
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21
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Matano M, Nakajima K, Kashiwagi Y, Udaka S, Maehashi K. Sweetness characterization of recombinant human lysozyme. Comp Biochem Physiol B Biochem Mol Biol 2015; 188:8-14. [DOI: 10.1016/j.cbpb.2015.05.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 05/18/2015] [Accepted: 05/21/2015] [Indexed: 11/26/2022]
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22
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Kawaguchi Y, Yoneda K, Torikata T, Araki T. Asp48 function in the hydrogen-bonding network involving Asp52 of hen egg-white lysozyme. Biosci Biotechnol Biochem 2015; 79:196-204. [DOI: 10.1080/09168451.2014.963502] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Abstract
To characterize the hydrogen-bonding network in lysozyme, we focused on the residue of Asp48 located at the active site in hen egg-white lysozyme. We constructed a mutant lysozyme (D48A) and analyzed using (GlcNAc)3 and chitin-affinity chromatography. The substrate binding of subsites D–F in D48A and the activity against (GlcNAc)5 were decreased. The parameters of substrate binding and rate constants obtained from computer simulations confirmed these changes. In the crystal structure, (GlcNAc)4 was located at the same position as wildtype. However, the side chains of Arg45 and Thr47 at subsites E–F were moved by the replacement. Further, the loss of the hydrogen bond between Asp48 and Ser50 changed the hydrogen-bonding network, and this resulted in an alteration of the side chain of Asn59. This result suggests that the hydrogen-bonding network plays a crucial in the function of Asp52 and of transglycosylation at subsites E–F.
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Affiliation(s)
- Yuya Kawaguchi
- Department of Bioscience, School of Agriculture, Tokai University, Kumamoto, Japan
| | - Kazunari Yoneda
- Department of Bioscience, School of Agriculture, Tokai University, Kumamoto, Japan
| | - Takao Torikata
- Department of Bioscience, School of Agriculture, Tokai University, Kumamoto, Japan
| | - Tomohiro Araki
- Department of Bioscience, School of Agriculture, Tokai University, Kumamoto, Japan
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23
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Jash C, Payghan PV, Ghoshal N, Suresh Kumar G. Binding of the Iminium and Alkanolamine Forms of Sanguinarine to Lysozyme: Spectroscopic Analysis, Thermodynamics, and Molecular Modeling Studies. J Phys Chem B 2014; 118:13077-91. [DOI: 10.1021/jp5068704] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Chandrima Jash
- Biophysical Chemistry Laboratory, Chemistry Division and ‡Structural Biology
and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Pavan V. Payghan
- Biophysical Chemistry Laboratory, Chemistry Division and ‡Structural Biology
and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Nanda Ghoshal
- Biophysical Chemistry Laboratory, Chemistry Division and ‡Structural Biology
and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Chemistry Division and ‡Structural Biology
and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
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24
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25
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Savage AE, Kiemnec-Tyburczy KM, Ellison AR, Fleischer RC, Zamudio KR. Conservation and divergence in the frog immunome: pyrosequencing and de novo assembly of immune tissue transcriptomes. Gene 2014; 542:98-108. [PMID: 24680726 DOI: 10.1016/j.gene.2014.03.051] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 03/06/2014] [Accepted: 03/26/2014] [Indexed: 11/17/2022]
Abstract
BACKGROUND Frogs are a diverse group of vertebrates for which limited genomic resources are available. Natural frog populations face a multitude of threats, including habitat degradation, infectious disease, and environmental change. Characterizing the functional genomics of anuran tissues in general - and the immune system in particular - will enhance our knowledge of genetic and epigenetic responses to environmental threats and inform conservation and recovery efforts. RESULTS To increase the number of species with genomic datasets and characterize gene expression in immune-related tissues, we sequenced the transcriptomes of three tissues from two frogs (Espadarana prosoblepon and Lithobates yavapaiensis) on the Roche 454 GS FLX platform. Our sequencing produced 8881 E. prosoblepon and 5428 L. yavapaiensis annotated gene products after de novo assembly and Gene Ontology classification. Transcripts of the innate and acquired immune system were expressed in all three tissues. Inflammatory response and acquired immunity transcripts were significantly more diverged between E. prosoblepon and L. yavapaiensis compared to innate immunity and immune system development transcripts. Immune-related transcripts did not show an overall elevated rate of functional evolution, with the exception of glycosyl proteases, which include lysozymes, central bacterial and fungal-killing enzymes of the innate immune system. CONCLUSIONS The three frog transcriptomes provide more than 600 Mbp of new genomic data, and will serve as a valuable framework for future comparative studies of non-model anurans. Additionally, we show that immune gene divergence varies by functional group and that transcriptome studies can be useful in comparing rates of evolutionary change across gene families.
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Affiliation(s)
- Anna E Savage
- Center for Conservation and Evolutionary Genetics, Smithsonian Institution, Washington, DC 20013, United States; Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, United States.
| | - Karen M Kiemnec-Tyburczy
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, United States.
| | - Amy R Ellison
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, United States.
| | - Robert C Fleischer
- Center for Conservation and Evolutionary Genetics, Smithsonian Institution, Washington, DC 20013, United States.
| | - Kelly R Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, United States.
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26
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Niu J, Zhu Y, Xie Y, Song L, Shi L, Lan J, Liu B, Li X, Huang Z. Solid-phase polyethylene glycol conjugation using hydrophobic interaction chromatography. J Chromatogr A 2013; 1327:66-72. [PMID: 24411087 DOI: 10.1016/j.chroma.2013.12.049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 12/11/2013] [Accepted: 12/14/2013] [Indexed: 02/04/2023]
Abstract
PEGylation is a widely applied approach to improve the pharmacokinetic and pharmacodynamic properties of protein therapeutics. The current solution-phase PEGylation protocols often suffer from poor yield of homogeneously PEGylated bioactive products and hence fall short of being commercially attractive. To improve upon these techniques, here we developed a novel, solid-phase PEGylation methodology using a hydrophobic interaction chromatography (HIC) resin. Two variations of the HIC-based PEGylation are described that are tailored towards conjugation of proteins with hydrophobicity index above (lysozyme) and below (fibroblast growth factor 1, FGF-1) that of the mPEG-butyraldehyde (mPEG) chain used. In the case of lysozyme, the protein was first immobilized on the HIC, and the HIC-bound protein was then conjugated by passing over the column. In the case of FGF-1, the mPEG solution was first immobilized on the HIC, and the FGF-1 solution was then passed through the column. Circular dichroism (CD) spectroscopy demonstrated HIC-based PEGylation almost retained the secondary structures of proteins. Bioactivity assay showed that the recovery of activity of HIC-based PEGylated rhFGF-1 (i.e. 92%) was higher than that of liquid-phase PEGylated rhFGF-1 (i.e. 61%), while HIC-based PEGylated lysozyme showed the same activity recovery (i.e. 7%) as the liquid-phase PEGylated form. For specific proteins, the HIC-based solid-phase PEGylation maybe offer a more promising alternative than the current PEGylation methods and is expected to have a major impact in the area of protein-based therapeutics.
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Affiliation(s)
- Jianlou Niu
- School of Pharmacy, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China; Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu 610041, Sichuan, China
| | - Yanlin Zhu
- School of Pharmacy, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China
| | - Yaoyao Xie
- School of Pharmacy, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China
| | - Lintao Song
- School of Pharmacy, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China
| | - Lu Shi
- School of Pharmacy, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China
| | - Junjie Lan
- School of Pharmacy, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China
| | - Bailin Liu
- Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu 610041, Sichuan, China
| | - Xiaokun Li
- School of Pharmacy, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China
| | - Zhifeng Huang
- School of Pharmacy, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China.
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27
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Hinds Vaughan N, Smith SL. Isolation and characterization of a c-type lysozyme from the nurse shark. FISH & SHELLFISH IMMUNOLOGY 2013; 35:1824-1828. [PMID: 24084042 DOI: 10.1016/j.fsi.2013.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 08/29/2013] [Accepted: 09/02/2013] [Indexed: 06/02/2023]
Abstract
Lysozyme is a ubiquitous antibacterial enzyme that occurs in numerous invertebrate and vertebrate species. Three forms have been described c-type, g-type and i-type which differ in primary structure. Shark lysozyme has not been characterized; here we report on the isolation and characterization of lysozyme from unstimulated shark (Ginglymostoma cirratum) leukocytes and provide amino acid sequence data across the highly conserved active site of the molecule identifying it to be a c-type lysozyme. A leukocyte lysate was applied either (a) to the first of two sequential DE-52 cellulose columns or alternatively, (b) to a DEAE-Sepharose column. Lysozyme activity in lysate and active fractions was identified by zones of lysis of Micrococcus lysodeikticus cell walls on lysoplates and zones of growth inhibition in agar diffusion assays using Planococcus citreus as the target organism. SDS-PAGE analysis revealed a 14 kDa protein which was identified as lysozyme by mass spectroscopic analysis of peptides, reactivity against anti-HEWL antibodies on a Western blot, hydrolysis of M. lysodeikticus cell walls, and inhibition of growth of P. citreus on AU-gel blots in which the area of growth inhibition correlated to a 14 kDa protein.
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Affiliation(s)
- Nichole Hinds Vaughan
- Department of Biological Sciences, Florida International University, 11200 S.W. 8th Street, Miami, FL 33199, USA
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28
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Umasuthan N, Bathige SDNK, Kasthuri SR, Wan Q, Whang I, Lee J. Two duplicated chicken-type lysozyme genes in disc abalone Haliotis discus discus: molecular aspects in relevance to structure, genomic organization, mRNA expression and bacteriolytic function. FISH & SHELLFISH IMMUNOLOGY 2013; 35:284-299. [PMID: 23664908 DOI: 10.1016/j.fsi.2013.04.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Revised: 04/16/2013] [Accepted: 04/22/2013] [Indexed: 06/02/2023]
Abstract
Lysozymes are crucial antibacterial proteins that are associated with catalytic cleavage of peptidoglycan and subsequent bacteriolysis. The present study describes the identification of two lysozyme genes from disc abalone Haliotis discus discus and their characterization at sequence-, genomic-, transcriptional- and functional-levels. Two cDNAs and BAC clones bearing lysozyme genes were isolated from abalone transcriptome and BAC genomic libraries, respectively and sequences were determined. Corresponding deduced amino acid sequences harbored a chicken-type lysozyme (LysC) family profile and exhibited conserved characteristics of LysC family members including active residues (Glu and Asp) and GS(S/T)DYGIFQINS motif suggested that they are LysC counterparts in disc abalone and designated as abLysC1 and abLysC2. While abLysC1 represented the homolog recently reported in Ezo abalone [1], abLysC2 shared significant identity with LysC homologs. Unlike other vertebrate LysCs, coding sequence of abLysCs were distributed within five exons interrupted by four introns. Both abLysCs revealed a broader mRNA distribution with highest levels in mantle (abLysC1) and hepatopancreas (abLysC2) suggesting their likely main role in defense and digestion, respectively. Investigation of temporal transcriptional profiles post-LPS and -pathogen challenges revealed induced-responses of abLysCs in gills and hemocytes. The in vitro muramidase activity of purified recombinant (r) abLysCs proteins was evaluated, and findings indicated that they are active in acidic pH range (3.5-6.5) and over a broad temperature range (20-60 °C) and influenced by ionic strength. When the antibacterial spectra of (r)abLysCs were examined, they displayed differential activities against both Gram positive and Gram negative strains providing evidence for their involvement in bacteriolytic function in abalone physiology.
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Affiliation(s)
- Navaneethaiyer Umasuthan
- Department of Marine Life Sciences, School of Marine Biomedical Sciences, Jeju National University, Jeju Self-Governing Province 690-756, Republic of Korea
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Ratzka C, Gross R, Feldhaar H. Gene expression analysis of the endosymbiont-bearing midgut tissue during ontogeny of the carpenter ant Camponotus floridanus. JOURNAL OF INSECT PHYSIOLOGY 2013; 59:611-623. [PMID: 23570961 DOI: 10.1016/j.jinsphys.2013.03.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 03/27/2013] [Accepted: 03/29/2013] [Indexed: 06/02/2023]
Abstract
Insects have frequently evolved mutualistic relationships with extracellular and/or intracellular bacterial endosymbionts. Infection with endosymbionts seems to affect several cellular functions of the host such as immune pathways, oxidative stress regulation and autophagy. Our current knowledge about specific host factors leading to endosymbiont tolerance and/or control is still scarce and is based on very few associations between insect hosts and bacteria only. Camponotus floridanus ants harbour the obligate intracellular bacterium Blochmannia floridanus within specialized midgut cells called bacteriocytes. The number of Blochmannia endosymbionts within the midgut tissue increases strongly during host development and reaches a maximum at the late pupal stage, where the entire midgut is transformed into a symbiotic organ. After eclosion of workers the number of Blochmannia strongly decreases again. We chose 15 candidate genes from C. floridanus likely to be involved in host-symbiont interactions based on their significant homology to previously investigated symbiosis-relevant genes from other insects. We determined the expression of these genes in the endosymbiont-bearing midgut tissue in comparison to the residual body tissue at different developmental stages of C. floridanus in order to reveal changes in gene expression correlating with changes in endosymbiont number per host. Strikingly, two pattern recognition receptors (amidase PGRP-LB and PGRP-SC2) were highly expressed in the midgut tissue at the pupal stage, potentially down-modulating the IMD pathway to enable endosymbiont tolerance. Moreover, we investigated the immune gene expression in response to bacterial challenge at the pupal stage. Results showed that the midgut tissue differs in expression pattern in contrast to the residual body. Our results support a key role for amidase PGRPs, especially PGRP-LB, in regulation of the immune response towards endosymbionts in C. floridanus and suggest an involvement of the lysosomal system in control of Blochmannia endosymbionts.
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Affiliation(s)
- Carolin Ratzka
- Lehrstuhl für Mikrobiologie, Biozentrum, Universität Würzburg, Germany.
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New sub-family of lysozyme-like proteins shows no catalytic activity: crystallographic and biochemical study of STM3605 protein from Salmonella Typhimurium. ACTA ACUST UNITED AC 2013; 14:1-10. [PMID: 23572252 DOI: 10.1007/s10969-013-9151-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 03/28/2013] [Indexed: 01/24/2023]
Abstract
Phage viruses that infect prokaryotes integrate their genome into the host chromosome; thus, microbial genomes typically contain genetic remnants of both recent and ancient phage infections. Often phage genes occur in clusters of atypical G+C content that reflect integration of the foreign DNA. However, some phage genes occur in isolation without other phage gene neighbors, probably resulting from horizontal gene transfer. In these cases, the phage gene product is unlikely to function as a component of a mature phage particle, and instead may have been co-opted by the host for its own benefit. The product of one such gene from Salmonella enterica serovar Typhimurium, STM3605, encodes a protein with modest sequence similarity to phage-like lysozyme (N-acetylmuramidase) but appears to lack essential catalytic residues that are strictly conserved in all lysozymes. Close homologs in other bacteria share this characteristic. The structure of the STM3605 protein was characterized by X-ray crystallography, and functional assays showed that it is a stable, folded protein whose structure closely resembles lysozyme. However, this protein is unlikely to hydrolyze peptidoglycan. Instead, STM3605 is presumed to have evolved an alternative function because it shows some lytic activity and partitions to micelles.
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Leysen S, Vanderkelen L, Weeks SD, Michiels CW, Strelkov SV. Structural basis of bacterial defense against g-type lysozyme-based innate immunity. Cell Mol Life Sci 2013; 70:1113-22. [PMID: 23086131 PMCID: PMC11113182 DOI: 10.1007/s00018-012-1184-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 09/21/2012] [Accepted: 09/27/2012] [Indexed: 10/27/2022]
Abstract
Gram-negative bacteria can produce specific proteinaceous inhibitors to defend themselves against the lytic action of host lysozymes. So far, four different lysozyme inhibitor families have been identified. Here, we report the crystal structure of the Escherichia coli periplasmic lysozyme inhibitor of g-type lysozyme (PliG-Ec) in complex with Atlantic salmon g-type lysozyme (SalG) at a resolution of 0.95 Å, which is exceptionally high for a complex of two proteins. The structure reveals for the first time the mechanism of g-type lysozyme inhibition by the PliG family. The latter contains two specific conserved regions that are essential for its inhibitory activity. The inhibitory complex formation is based on a double 'key-lock' mechanism. The first key-lock element is formed by the insertion of two conserved PliG regions into the active site of the lysozyme. The second element is defined by a distinct pocket of PliG accommodating a lysozyme loop. Computational analysis indicates that this pocket represents a suitable site for small molecule binding, which opens an avenue for the development of novel antibacterial agents that suppress the inhibitory activity of PliG.
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Affiliation(s)
- S. Leysen
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, Herestraat 49 bus 822, 3000 Leuven, Belgium
| | - L. Vanderkelen
- Laboratory of Food Microbiology, Leuven Food Science and Nutrition Research Centre (LFoRCe), Katholieke Universiteit Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
| | - S. D. Weeks
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, Herestraat 49 bus 822, 3000 Leuven, Belgium
| | - C. W. Michiels
- Laboratory of Food Microbiology, Leuven Food Science and Nutrition Research Centre (LFoRCe), Katholieke Universiteit Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
| | - S. V. Strelkov
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, Herestraat 49 bus 822, 3000 Leuven, Belgium
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Ogata M, Umemoto N, Ohnuma T, Numata T, Suzuki A, Usui T, Fukamizo T. A novel transition-state analogue for lysozyme, 4-O-β-tri-N-acetylchitotriosyl moranoline, provided evidence supporting the covalent glycosyl-enzyme intermediate. J Biol Chem 2013; 288:6072-82. [PMID: 23303182 DOI: 10.1074/jbc.m112.439281] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
4-O-β-Di-N-acetylchitobiosyl moranoline (2) and 4-O-β-tri-N-acetylchitotriosyl moranoline (3) were produced by lysozyme-mediated transglycosylation from the substrates tetra-N-acetylchitotetraose, (GlcNAc)4, and moranoline, and the binding modes of 2 and 3 to hen egg white lysozyme (HEWL) was examined by inhibition kinetics, isothermal titration calorimetry (ITC), and x-ray crystallography. Compounds 2 and 3 specifically bound to HEWL, acting as competitive inhibitors with Ki values of 2.01 × 10(-5) and 1.84 × 10(-6) m, respectively. From ITC analysis, the binding of 3 was found to be driven by favorable enthalpy change (ΔHr°), which is similar to those obtained for 2 and (GlcNAc)4. However, the entropy loss (-TΔSr°) for the binding of 3 was smaller than those of 2 and (GlcNAc)4. Thus the binding of 3 was found to be more favorable than those of the others. Judging from the Kd value of 3 (760 nm), the compound appears to have the highest affinity among the lysozyme inhibitors identified to date. X-ray crystal structure of HEWL in a complex with 3 showed that compound 3 binds to subsites -4 to -1 and the moranoline moiety adopts an undistorted (4)C1 chair conformation almost overlapping with the -1 sugar covalently bound to Asp-52 of HEWL (Vocadlo, Davies, G. J., Laine, R., and Withers, S. G. (2001) Nature 412, 835-838). From these results, we concluded that compound 3 serves as a transition-state analogue for lysozyme providing additional evidence supporting the covalent glycosyl-enzyme intermediate in the catalytic reaction.
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Affiliation(s)
- Makoto Ogata
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, Shizuoka 422-8529, Japan
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Amino acid sequence of Egyptian goose egg-white lysozyme and effects of amino acid substitution on the enzymatic activity. Biosci Biotechnol Biochem 2012; 76:691-8. [PMID: 22484934 DOI: 10.1271/bbb.110819] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The amino acid sequence of Egyptian goose lysozyme (EGL) from egg-white and its enzymatic properties were analyzed. The established sequence had the highest similarity to wood duck lysozyme (WDL) with five amino acid substitutions, and had eighteen substitutions difference from hen egg-white lysozyme (HEL). Tyr34 and Gly37 were found at subsites E and F of the active site when compared with HEL. The experimental time-course characteristics of EGL against the N-acetylglucosamine pentamer substrate, (GlcNAc)(5), revealed higher production of (GlcNAc)(4) and lower production of (GlcNAc)(2) when compared with HEL. The saccharide-binding ability of subsites A-C in EGL was also found to be weaker than in HEL. An analysis of the enzymatic reactions of five mutants in respect of positions 34, 37 and 71 in HEL indicated the time-course characteristics of EGL to be caused by the combination of three substitutions (F34Y, N37G and G71R) between HEL and EGL. A computer simulation of the EGL-catalyzed reaction suggested that the time-course characteristics of EGL resulted from the difference in the binding free energy for subsites A, B, E and F and the rate constant of transglycosylation between EGL and HEL.
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34
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A lysozyme and magnetic bead based method of separating intact bacteria. Anal Bioanal Chem 2011; 401:253-65. [DOI: 10.1007/s00216-011-5065-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 04/11/2011] [Accepted: 04/26/2011] [Indexed: 11/26/2022]
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Voet A, Callewaert L, Ulens T, Vanderkelen L, Vanherreweghe JM, Michiels CW, De Maeyer M. Structure based discovery of small molecule suppressors targeting bacterial lysozyme inhibitors. Biochem Biophys Res Commun 2011; 405:527-32. [PMID: 21256115 DOI: 10.1016/j.bbrc.2011.01.053] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 01/15/2011] [Indexed: 11/28/2022]
Abstract
The production of lysozyme inhibitors, competitively binding to the lysozyme active site, is a bacterial strategy to prevent the lytic activity of host lysozymes. Therefore, suppression of the lysozyme-inhibitor interaction is an interesting new approach for drug development since restoration of the bacterial lysozyme sensitivity will support bacterial clearance from the infected sites. Using molecular modelling techniques the interaction of the Salmonella PliC inhibitor with c-type lysozyme was studied and a protein-protein interaction based pharmacophore model was created. This model was used as a query to identify molecules, with potential affinity for the target, and subsequently, these molecules were filtered using molecular docking. The retained molecules were validated as suppressors of lysozyme inhibitory proteins using in vitro experiments revealing four active molecules.
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Affiliation(s)
- Arnout Voet
- Laboratory for Biomolecular Modelling and BioMacS, Katholieke Universiteit Leuven, Celestijnenlaan 200G bus 2403, 3001 Heverlee, Leuven, Belgium.
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Sudiarta IP, Fukushima T, Sekiguchi J. Bacillus subtilis CwlP of the SP-{beta} prophage has two novel peptidoglycan hydrolase domains, muramidase and cross-linkage digesting DD-endopeptidase. J Biol Chem 2010; 285:41232-43. [PMID: 20980266 DOI: 10.1074/jbc.m110.156273] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
For bacteria and bacteriophages, cell wall digestion by hydrolases is a very important event. We investigated one of the proteins involved in cell wall digestion, the yomI gene product (renamed CwlP). The gene is located in the SP-β prophage region of the Bacillus subtilis chromosome. Inspection of the Pfam database indicates that CwlP contains soluble lytic transglycosylase (SLT) and peptidase M23 domains, which are similar to Escherichia coli lytic transglycosylase Slt70, and the Staphylococcus aureus Gly-Gly endopeptidase LytM, respectively. The SLT domain of CwlP exhibits hydrolytic activity toward the B. subtilis cell wall; however, reverse phase (RP)-HPLC and mass spectrometry revealed that the CwlP-SLT domain has only muramidase activity. In addition, the peptidase M23 domain of CwlP exhibited hydrolytic activity and could cleave d-Ala-diaminopimelic acid cross-linkage, a property associated with dd-endopeptidases. Remarkably, the M23 domain of CwlP possessed a unique Zn(2+)-independent endopeptidase activity; this contrasts with all other characterized M23 peptidases (and enzymes similar to CwlP), which are Zn(2+) dependent. Both domains of CwlP could hydrolyze the peptidoglycan and cell wall of B. subtilis. However, the M23 domain digested neither the peptidoglycans nor the cell walls of S. aureus or Streptococcus thermophilus. The effect of defined point mutations in conserved amino acid residues of CwlP is also determined.
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Affiliation(s)
- I Putu Sudiarta
- Interdisciplinary Graduate School of Science and Technology, Department of Life Sciences, Research Center for Human and Environmental Sciences, Shinshu University, Nagano 386-8567, Japan
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Maruyama Y, Ochiai A, Itoh T, Mikami B, Hashimoto W, Murata K. Mutational studies of the peptidoglycan hydrolase FlgJ of Sphingomonas sp. strain A1. J Basic Microbiol 2010; 50:311-7. [PMID: 20586063 DOI: 10.1002/jobm.200900249] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The flagellar protein FlgJ, a member of glycoside hydrolase family 73, has N- and C-terminal domains that are responsible for flagellar rod assembly and peptidoglycan hydrolysis, respectively. The crystal structure of the C-terminal domain of SPH1045 (SPH1045-C), the FlgJ from Sphingomonas sp. strain A1, showed a long cleft formed by two lobes, alpha and beta. In this study, seven site-specific mutants of residues in the cleft were prepared and analyzed. Enzyme activity was reduced most significantly in mutants E185A and Y281A, followed by E224A. A comparison of the crystal structure of the inactive mutant E185A with that of other related enzymes revealed that Glu185 is structurally reasonable as the proton donor and that Tyr281 is close to Glu185. Glu224 is, however, far from the catalytic site, which is inconsistent with the decreased activity exhibited by E224A. The structural flexibility of Glu224 and its neighboring residues observed in SPH1045-C may indicate that this region is able to change its conformation upon substrate binding.
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Affiliation(s)
- Yukie Maruyama
- Laboratory of Basic and Applied Molecular Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
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Ponkham P, Daduang S, Kitimasak W, Krittanai C, Chokchaichamnankit D, Srisomsap C, Svasti J, Kawamura S, Araki T, Thammasirirak S. Complete amino acid sequence of three reptile lysozymes. Comp Biochem Physiol C Toxicol Pharmacol 2010; 151:75-83. [PMID: 19747569 DOI: 10.1016/j.cbpc.2009.08.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2008] [Revised: 08/23/2009] [Accepted: 08/30/2009] [Indexed: 11/19/2022]
Abstract
To study the structure and function of reptile lysozymes, we have reported their purification, and in this study we have established the amino acid sequence of three egg white lysozymes in soft-shelled turtle eggs (SSTL A and SSTL B from Trionyx sinensis, ASTL from Amyda cartilaginea) by using the rapid peptide mapping method. The established amino acid sequence of SSTL A, SSTL B, and ASTL showed substitutions of 43, 42, and 44 residues respectively when compared with the HEWL (hen egg white lysozyme) sequence. In these reptile lysozymes, SSTL A had one substitution compared with SSTL B (Gly126Asp) and had an N-terminal extra Gly and 11 substitutions compared with ASTL. SSTL B had an N-terminal extra Gly and 10 residues different from ASTL. The sequence of SSTL B was identical to soft-shelled turtle lysozyme from STL (Trionyx sinensis japonicus). The Ile residue at position 93 of ASTL is the first report in all C-type lysozymes. Furthermore, amino acid substitutions (Phe34His, Arg45Tyr, Thr47Arg, and Arg114Tyr) were also found at subsites E and F when compared with HEWL. The time course using N-acetylglucosamine pentamer as a substrate exhibited a reduction of the rate constant of glycosidic cleavage and increase of binding free energy for subsites E and F, which proved the contribution for amino acids mentioned above for substrate binding at subsites E and F. Interestingly, the variable binding free energy values occurred on ASTL, may be contributed from substitutions at outside of subsites E and F.
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Affiliation(s)
- Pornpimol Ponkham
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
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Bublitz M, Polle L, Holland C, Heinz DW, Nimtz M, Schubert WD. Structural basis for autoinhibition and activation of Auto, a virulence-associated peptidoglycan hydrolase ofListeria monocytogenes. Mol Microbiol 2009; 71:1509-22. [DOI: 10.1111/j.1365-2958.2009.06619.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Fukushima T, Kitajima T, Yamaguchi H, Ouyang Q, Furuhata K, Yamamoto H, Shida T, Sekiguchi J. Identification and characterization of novel cell wall hydrolase CwlT: a two-domain autolysin exhibiting n-acetylmuramidase and DL-endopeptidase activities. J Biol Chem 2008; 283:11117-25. [PMID: 18305117 DOI: 10.1074/jbc.m706626200] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A cell wall hydrolase homologue, Bacillus subtilis YddH (renamed CwlT), was determined to be a novel cell wall lytic enzyme. The cwlT gene is located in the region of an integrative and conjugative element (ICEBs1), and a cwlT-lacZ fusion experiment revealed the significant expression when mitomycin C was added to the culture. Judging from the Pfam data base, CwlT (cell wall lytic enzyme T (Two-catalytic domains)) has two hydrolase domains that exhibit high amino acid sequence similarity to dl-endopeptidases and relatively low similarity to lytic transglycosylases at the C and N termini, respectively. The purified C-terminal domain of CwlT (CwlT-C-His) could hydrolyze the linkage of d-gamma-glutamyl-meso-diaminopimelic acid in B. subtilis peptidoglycan, suggesting that the C-terminal domain acts as a dl-endopeptidase. On the other hand, the purified N-terminal domain (CwlT-N-His) could also hydrolyze the peptidoglycan of B. subtilis. However, on reverse-phase HPLC and mass spectrometry (MS) and MS-MS analyses of the reaction products by CwlT-N-His, this domain was determined to act as an N-acetylmuramidase and not a lytic transglycosylase. Moreover, the site-directed mutagenesis analysis revealed that Glu-87 and Asp-94 are sites related with the cell wall lytic activity. Because the amino acid sequence of the N-terminal domain of CwlT exhibits low similarity compared with those of the soluble lytic transglycosylase and muramidase (goose lysozyme), this domain represents "a new category of cell wall hydrolases."
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Affiliation(s)
- Tatsuya Fukushima
- Department of Bioscience and Textile Technology, Interdisciplinary Graduate School of Science and Technology, Shinshu University, 3-15-1 Tokida, Ueda, Nagano 386-8567, Japan
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de la Mora J, Ballado T, González-Pedrajo B, Camarena L, Dreyfus G. The flagellar muramidase from the photosynthetic bacterium Rhodobacter sphaeroides. J Bacteriol 2007; 189:7998-8004. [PMID: 17873041 PMCID: PMC2168687 DOI: 10.1128/jb.01073-07] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have characterized open reading frame RSP0072, which is located within the flgG operon in Rhodobacter sphaeroides. The amino acid sequence analysis of this gene product showed the presence of a soluble lytic transglycosylase domain. The deletion of the N-terminal region (90 amino acids) of the product of RSP0072 yields a leaky nonmotile phenotype, as determined by swarm assays in soft agar. Electron micrographs revealed the lack of flagella in mutant cells. The purified wild-type protein showed lytic activity on extracts of Micrococcus luteus. In contrast, no lytic activity was observed when the residues E57 or E83 were replaced by alanine. Affinity blotting suggests that the protein encoded by RSP0072 interacts with the flagellar rod-scaffolding protein FlgJ, which lacks the muramidase domain present in FlgJ of many bacteria. We propose that the product of RSP0072 is a flagellar muramidase that is exported to the periplasm via the Sec pathway, where it interacts with FlgJ to open a gap in the peptidoglycan layer for the subsequent penetration of the nascent flagellar structure.
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Affiliation(s)
- Javier de la Mora
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apdo. Postal 70-243 Cd. Universitaria, México DF 04510, México
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Gandhe AS, Janardhan G, Nagaraju J. Immune upregulation of novel antibacterial proteins from silkmoths (Lepidoptera) that resemble lysozymes but lack muramidase activity. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2007; 37:655-66. [PMID: 17550822 DOI: 10.1016/j.ibmb.2007.03.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2007] [Revised: 03/19/2007] [Accepted: 03/21/2007] [Indexed: 05/15/2023]
Abstract
Study on immune proteins in domesticated and wild silkmoths Bombyx mori and Antheraea mylitta, respectively, led to identification of a new class of antimicrobial proteins. We designated them as lysozyme-like proteins (LLPs) owing to their partial similarity with lysozymes. However, lack of characteristic catalytic amino acid residues essential for muramidase activity in LLPs puts them functionally apart from classical lysozymes. Two LLPs, one from B. mori (BLLP1) and the other from A. mylitta (ALLP1) expressed in a recombinant system, exhibited a broad-spectrum antibacterial action. Further investigation of the antibacterial mechanism revealed that BLLP1 is bacteriostatic rather than bactericidal against Escherichia coli and Micrococcus luteus. Substantial increase in hemolymph bacterial load was observed in B. mori upon RNA interference mediated in vivo knockdown of BLLP1. We demonstrate that the antibacterial mechanism of this protein depends on peptidoglycan binding unlike peptidoglycan hydrolysis or membrane permeabilization as observed with lysozymes and most other antimicrobial peptides. To our knowledge, this is the first report on functional analysis of novel, non-catalytic lysozyme-like family of antibacterial proteins that are quite apart functionally from classical lysozymes. The present analysis holds promise for functional annotation of similar proteins from other organisms.
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Affiliation(s)
- Archana S Gandhe
- Laboratory of Molecular Genetics, Centre for DNA Fingerprinting and Diagnostics, ECIL Road, Nacharam, Hyderabad 500076, India
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Li S, Li B, Fei Y, Jiang D, Sheng Y, Sun Y, Zhang J. Exon grafting yields a “two active-site” lysozyme. Biochem Biophys Res Commun 2007; 358:997-1001. [PMID: 17524359 DOI: 10.1016/j.bbrc.2007.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2007] [Accepted: 05/02/2007] [Indexed: 10/23/2022]
Abstract
The design of enzymes with enhanced stability and activity has long been a goal in protein engineering. We report a strategy to engineer an additional active site for human lysozyme, grafted the entire human lysozyme exon 2, which encodes the catalytically competent domain, into the gene at a position corresponding to an exposed loop region in the translated protein. Exon 2 grafting created a novel lysozyme with twice the activity of the wild type enzyme, equal activity came from each of the two active sites. We dissected the contributions of each active site using site-directed mutagenesis of the catalytic doublets of (E35A/D53A), circular dichroism, fluorescence spectra, and molecular modeling. Temperature and pH stability of the "two active-site" enzyme were similar to those of wild-type lysozyme. Thus, we provide a novel strategy for engineering the active site of enzymes.
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Affiliation(s)
- Shuang Li
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, PR China
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Chijiiwa Y, Kawamura S, Torikata T, Araki T. Amino acid sequence and activity of green turtle (Chelonia mydas) lysozyme. Protein J 2007; 25:336-44. [PMID: 16947076 DOI: 10.1007/s10930-006-9019-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Green turtle lysozyme purified from egg white was sequenced and analyzed its activity. Lysozyme was reduced and pyridylethylated or carboxymethylated to digest with trypsin, chymotrypsin and V8 protease. The peptides yielded were purified by RP-HPLC and sequenced. Every trypsin peptide was overlapped by chymotrypsin peptides and V8 protease peptides. This lysozyme is composed of 130 amino acids including an insertion of a Gly residue between 47 and 48 residues when compared with chicken lysozyme. The amino acid substitutions were found at subsites E and F. Namely Phe34, Arg45, Thr47, and Arg114 were replaced by Tyr, Tyr, Pro, and Asn, respectively. The time course using N-acetylglucosamine pentamer as a substrate showed a reduction of the rate constant of glycosidic cleavage and transglycosylation and increase of binding free energy for subsite E, which proved the contribution of amino acids mentioned above for substrate binding at subsites E and F.
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Affiliation(s)
- Yuki Chijiiwa
- Department of Bioscience, School of Agriculture, Kyushu Tokai University, Kumamoto, Minamiaso, 869-1404, Japan
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Kawamura S, Ohno K, Ohkuma M, Chijiiwa Y, Torikata T. Experimental Verification of the Crucial Roles of Glu73 in the Catalytic Activity and Structural Stability of Goose Type Lysozyme. ACTA ACUST UNITED AC 2006; 140:75-85. [PMID: 16877771 DOI: 10.1093/jb/mvj125] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The roles of Glu(73), which has been proposed to be a catalytic residue of goose type (G-type) lysozyme based on X-ray structural studies, were investigated by means of its replacement with Gln, Asp, and Ala using ostrich egg-white lysozyme (OEL) as a model. No remarkable differences in secondary structure or substrate binding ability were observed between the wild type and Glu(73)-mutated proteins, as evaluated by circular dichroism (CD) spectroscopy and chitin-coated celite chromatography. Substitution of Glu(73) with Gln or Ala abolished the enzymatic activity toward both the bacterial cell substrate and N-acetylglucosamine pentamer, (GlcNAc)(5), while substitution with Asp did not abolish but drastically reduced the activity of OEL. These results demonstrate that the carboxyl group of Glu(73) is directly involved in the catalytic action of G-type lysozyme. Furthermore, the stabilities of all three mutants, which were determined from the thermal and guanidine hydrochloride (GdnHCl) unfolding curves, respectively, were significantly decreased relative to those of the wild type. The results obtained clearly indicate the crucially important roles of Glu(73) in the structural stability as well as in the catalytic activity of G-type lysozyme.
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Affiliation(s)
- Shunsuke Kawamura
- Department of Bioscience, School of Agriculture, Kyushu Tokai University, Aso, Kumamoto 869-1404.
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47
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Keep NH, Ward JM, Cohen-Gonsaud M, Henderson B. Wake up! Peptidoglycan lysis and bacterial non-growth states. Trends Microbiol 2006; 14:271-6. [PMID: 16675219 DOI: 10.1016/j.tim.2006.04.003] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2006] [Revised: 03/02/2006] [Accepted: 04/20/2006] [Indexed: 11/27/2022]
Abstract
When stressed, bacteria can enter various non-dividing states, which are medically important. For example, dormancy is used by Mycobacterium tuberculosis to evade host responses. A major breakthrough has been the discovery of resuscitation-promoting factor (Rpf) from Micrococcus luteus, which is an extremely potent anti-dormancy factor. Mycobacteria have multiple proteins that contain this domain. Surprisingly, the highly conserved resuscitation-promoting factor domain has strong structural similarities to lysozyme and soluble lytic transglycosylases, and it has been demonstrated that resuscitation-promoting factors cleave peptidoglycan. This suggests that the activation of dormant cells requires peptidoglycan hydrolysis, which either alters the mechanical properties of the cell wall to facilitate cell division or releases lysis products that function as anti-dormancy signals.
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Affiliation(s)
- Nicholas H Keep
- School of Crystallography and Institute of Structural Molecular Biology, Birkbeck, University of London, Malet Street, London, UK, WC1E 7HX
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Li B, Calvo E, Marinotti O, James AA, Paskewitz SM. Characterization of the c-type lysozyme gene family in Anopheles gambiae. Gene 2005; 360:131-9. [PMID: 16137842 DOI: 10.1016/j.gene.2005.07.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2005] [Accepted: 07/01/2005] [Indexed: 11/19/2022]
Abstract
Seven new c-type lysozyme genes were found using the Anopheles gambiae genome sequence, increasing to eight the total number of genes in this family identified in this species. The eight lysozymes in An. gambiae have considerable variation in gene structure and expression patterns. Lys c-6 has the most unusual primary amino acid structure as the predicted protein consists of five lysozyme-like domains. Transcript abundance of each c-type lysozyme was determined by semiquantitative RT-PCR. Lys c-1, c-6 and c-7 are expressed constitutively in all developmental stages from egg to adult. Lys c-2 and c-4 also are found in all stages, but with relatively much higher levels in adults. Conversely, Lys c-3 and c-8 transcripts are highest in larvae. Lys c-1, c-6 and c-7 transcripts are found in nearly all the adult tissue samples examined while Lys c-2 and Lys c-4 are more restricted in their expression. Lys c-1 and c-2 transcripts are clearly immune responsive and are increased significantly 6-12 h post challenge with bacteria. The functional adaptive changes that may have evolved during the expansion of this gene family are briefly discussed in terms of the expression patterns, gene and protein structures.
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Affiliation(s)
- Bin Li
- Department of Entomology, University of Wisconsin, 237 Russell Labs, 1630 Linden Dr, Madison, Wisconsin 53706, USA
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Mandal A, Klotz KL, Shetty J, Jayes FL, Wolkowicz MJ, Bolling LC, Coonrod SA, Black MB, Diekman AB, Haystead TAJ, Flickinger CJ, Herr JC. SLLP1, a unique, intra-acrosomal, non-bacteriolytic, c lysozyme-like protein of human spermatozoa. Biol Reprod 2003; 68:1525-37. [PMID: 12606493 DOI: 10.1095/biolreprod.102.010108] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
We report the presence of a unique, non-bacteriolytic, c (chicken or conventional type) lysozyme-like protein, SLLP1, in the acrosome of human sperm. C lysozymes are bacteriolytic and can also bind to N-acetylglucosamines linked by beta-1,4 glycosidic bonds. Most of the invariant residues (17 out of 20), including all the cysteines, were conserved in SLLP1, but the two catalytic residues E35 and D52 of c lysozymes were replaced with T and N, respectively. The full-length cDNA encodes a protein of 215 aa with a predicted protease cleavage site between A87 and K88. The processed form of SLLP1, which showed an exon-intron organization similar to human c lysozyme, was the major isoform in the acrosome of ejaculated sperm. As expected, based on its sequence, the mature protein secreted from yeast showed no bacteriolytic activity. A significant decrease (54%, P < or = 0.001) in the number of sperm bound to zona-free hamster eggs was observed in the presence of antisera to recombinant SLLP1. SLLP1 mRNA (size, approximately 1 kb) appeared to be expressed only in the testis and in the Burkitt lymphoma Raji cell line. The gene SPACA3 encodes SLLP1 and contains five exons at locus 17q11.2. Because of its typical c lysozyme-like sequence, genomic organization, conservation of putative substrate-binding sites even in the absence of catalytic residues, and localization in the acrosomal matrix, we hypothesize that, after acrosome reaction, SLLP1 could be a potential receptor for the egg oligosaccharide residue N-acetylglucosamine, which is present in the extracellular matrix over the egg plasma membrane, within the perivitelline space, pores of zona pellucida, and cumulus layers.
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Affiliation(s)
- Arabinda Mandal
- Center for Research in Contraceptive and Reproductive Health, Department of Cell Biology, University of Virginia, Charlottesville 22908, USA
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Rambow-Larsen AA, Weiss AA. The PtlE protein of Bordetella pertussis has peptidoglycanase activity required for Ptl-mediated pertussis toxin secretion. J Bacteriol 2002; 184:2863-9. [PMID: 12003925 PMCID: PMC135057 DOI: 10.1128/jb.184.11.2863-2869.2002] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pertussis toxin of Bordetella pertussis is secreted by a type IV secretion system comprised of the products of the nine ptl (pertussis toxin liberation) genes. These proteins are believed to form a complex spanning both the inner and outer membranes and passing through the peptidoglycan layer. Peptidoglycan acts as a barrier for transport through the periplasm of large folded molecules. Assembled pertussis toxin and the secretion component proteins PtlC through PtlH are too large to diffuse through intact peptidoglycan. Therefore, we hypothesized that the Ptl system contains a peptidoglycanase activity. The PtlE protein was found to exhibit a sequence match to the active site of glycohydrolase enzymes. An N-terminally polyhistidine-tagged PtlE fusion protein, constructed and expressed in Escherichia coli and in B. pertussis, exhibited peptidoglycanase activity on activity gels. A fusion protein with alanine substitutions at the putative active site residues (aspartic acid at position 53 and glutamic acid at position 62) lacked peptidoglycanase activity. B. pertussis strains with the amino acid substitutions were deficient for pertussis toxin secretion. Based on these results, we concluded that PtlE is a peptidoglycanase responsible for the local removal or rearrangement of the peptidoglycan layer during Ptl secretion complex assembly.
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Affiliation(s)
- Amy A Rambow-Larsen
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati, Cincinnati, Ohio 45267, USA
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