1
|
Riu F, Ruda A, Ibba R, Sestito S, Lupinu I, Piras S, Widmalm G, Carta A. Antibiotics and Carbohydrate-Containing Drugs Targeting Bacterial Cell Envelopes: An Overview. Pharmaceuticals (Basel) 2022; 15:942. [PMID: 36015090 PMCID: PMC9414505 DOI: 10.3390/ph15080942] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 02/07/2023] Open
Abstract
Certain bacteria constitute a threat to humans due to their ability to escape host defenses as they easily develop drug resistance. Bacteria are classified into gram-positive and gram-negative according to the composition of the cell membrane structure. Gram-negative bacteria have an additional outer membrane (OM) that is not present in their gram-positive counterpart; the latter instead hold a thicker peptidoglycan (PG) layer. This review covers the main structural and functional properties of cell wall polysaccharides (CWPs) and PG. Drugs targeting CWPs are discussed, both noncarbohydrate-related (β-lactams, fosfomycin, and lipopeptides) and carbohydrate-related (glycopeptides and lipoglycopeptides). Bacterial resistance to these drugs continues to evolve, which calls for novel antibacterial approaches to be developed. The use of carbohydrate-based vaccines as a valid strategy to prevent bacterial infections is also addressed.
Collapse
Affiliation(s)
- Federico Riu
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Via Muroni 23/A, 07100 Sassari, Italy; (F.R.); (I.L.); (S.P.); (A.C.)
| | - Alessandro Ruda
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden; (A.R.); (G.W.)
| | - Roberta Ibba
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Via Muroni 23/A, 07100 Sassari, Italy; (F.R.); (I.L.); (S.P.); (A.C.)
| | - Simona Sestito
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, Via Vienna 2, 07100 Sassari, Italy;
| | - Ilenia Lupinu
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Via Muroni 23/A, 07100 Sassari, Italy; (F.R.); (I.L.); (S.P.); (A.C.)
| | - Sandra Piras
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Via Muroni 23/A, 07100 Sassari, Italy; (F.R.); (I.L.); (S.P.); (A.C.)
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden; (A.R.); (G.W.)
| | - Antonio Carta
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Via Muroni 23/A, 07100 Sassari, Italy; (F.R.); (I.L.); (S.P.); (A.C.)
| |
Collapse
|
2
|
Ramos Y, Sansone S, Morales DK. Sugarcoating it: Enterococcal polysaccharides as key modulators of host-pathogen interactions. PLoS Pathog 2021; 17:e1009822. [PMID: 34499702 PMCID: PMC8428557 DOI: 10.1371/journal.ppat.1009822] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Yusibeska Ramos
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, New York, United States of America
| | - Stephanie Sansone
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, New York, United States of America
- Department of Urology, Weill Cornell Medicine, New York, New York, United States of America
| | - Diana K. Morales
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, New York, United States of America
- * E-mail:
| |
Collapse
|
3
|
Senturk H, Eksin E, Işık Ö, İlaslan Z, Mısırlı F, Erdem A. Impedimetric aptasensor for lysozyme detection based on carbon nanofibres enriched screen-printed electrodes. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2021.138078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
4
|
Liu T, Marcinko TM, Vachet RW. Protein-Ligand Affinity Determinations Using Covalent Labeling-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1544-1553. [PMID: 32501685 PMCID: PMC7332385 DOI: 10.1021/jasms.0c00131] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Determining the binding affinity is an important aspect of characterizing protein-ligand complexes. Here, we describe an approach based on covalent labeling (CL)-mass spectrometry (MS) that can accurately provide protein-ligand dissociation constants (Kd values) using diethylpyrocarbonate (DEPC) as the labeling reagent. Even though DEPC labeling reactions occur on a time scale that is similar to the dissociation/reassociation rates of many protein-ligand complexes, we demonstrate that relatively accurate binding constants can still be obtained as long as the extent of protein labeling is kept below 30%. Using two well-established model systems and one insufficiently characterized system, we find that Kd values can be determined that are close to values obtained in previous measurements. The CL-MS-based strategy that is described here should serve as an alternative for characterizing protein-ligand complexes that are challenging to measure by other methods. Moreover, this method has the potential to provide, simultaneously, the affinity and binding site information.
Collapse
Affiliation(s)
| | | | - Richard W. Vachet
- Corresponding author: Prof. Richard W. Vachet, Department of Chemistry, University of Massachusetts, Amherst, MA 01003, , Phone: (413) 545-2733
| |
Collapse
|
5
|
Marchenkova MA, Kuranova IP, Timofeev VI, Boikova AS, Dorovatovskii PV, Dyakova YA, Ilina KB, Pisarevskiy YV, Kovalchuk MV. The binding of precipitant ions in the tetragonal crystals of hen egg white lysozyme. J Biomol Struct Dyn 2019; 38:5159-5172. [PMID: 31760865 DOI: 10.1080/07391102.2019.1696706] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The bonds between lysozyme molecules and precipitant ions in single crystals grown with chlorides of several metals are analysed on the basis of crystal structure data. Crystals of tetragonal hen egg lysozyme (HEWL) were grown with chlorides of several alkali and transition metals (LiCl, NaCl, KCl, NiCl2 and CuCl2) as precipitants and the three-dimensional structures were determined at 1.35 Å resolution by X-ray diffraction method. The positions of metal and chloride ions attached to the protein were located, divided into three groups and analysed. Some of them, in accordance with the recently proposed and experimentally confirmed crystal growth model, provide connections in protein dimers and octamers that are precursor clusters in the crystallization lysozyme solution. The first group, including Cu+2, Ni+2 and Na+1 cations, binds specifically to the protein molecule. The second group consists of metal and chloride ions bound inside the dimers and octamers. The third group of ions can participate in connections between the octamers that are suggested as building units during the crystal growth. The arrangement of chloride and metal ions associated with lysozyme molecule at all stages of the crystallization solution formation and crystal growth is discussed.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Margarita A Marchenkova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation
| | - Inna P Kuranova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation
| | - Vladimir I Timofeev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation
| | - Anastasiia S Boikova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation
| | | | - Yulia A Dyakova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation
| | - Kseniia B Ilina
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation
| | - Yury V Pisarevskiy
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation
| | - Mikhail V Kovalchuk
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre "Kurchatov Institute", Moscow, Russian Federation.,The Faculty of Physics, St. Petersburg State University, St. Petersburg, Russian Federation
| |
Collapse
|
6
|
Abstract
Staphylococcus aureus has become a serious threat to human health. In addition to having increased antibiotic resistance, the bacterium is a master at adapting to its host by evading almost every facet of the immune system, the so-called immune evasion proteins. Many of these immune evasion proteins target neutrophils, the most important immune cells in clearing S. aureus infections. The neutrophil attacks pathogens via a plethora of strategies. Therefore, it is no surprise that S. aureus has evolved numerous immune evasion strategies at almost every level imaginable. In this review we discuss step by step the aspects of neutrophil-mediated killing of S. aureus, such as neutrophil activation, migration to the site of infection, bacterial opsonization, phagocytosis, and subsequent neutrophil-mediated killing. After each section we discuss how S. aureus evasion molecules are able to resist the neutrophil attack of these different steps. To date, around 40 immune evasion molecules of S. aureus are known, but its repertoire is still expanding due to the discovery of new evasion proteins and the addition of new functions to already identified evasion proteins. Interestingly, because the different parts of neutrophil attack are redundant, the evasion molecules display redundant functions as well. Knowing how and with which proteins S. aureus is evading the immune system is important in understanding the pathophysiology of this pathogen. This knowledge is crucial for the development of therapeutic approaches that aim to clear staphylococcal infections.
Collapse
|
7
|
Nguyen GH, Tran TN, Podgorski MN, Bell SG, Supuran CT, Donald WA. Nanoscale Ion Emitters in Native Mass Spectrometry for Measuring Ligand-Protein Binding Affinities. ACS CENTRAL SCIENCE 2019; 5:308-318. [PMID: 30834319 PMCID: PMC6396573 DOI: 10.1021/acscentsci.8b00787] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Indexed: 05/20/2023]
Abstract
Electrospray ionization (ESI) mass spectrometry (MS) is a crucial method for rapidly determining the interactions between small molecules and proteins with ultrahigh sensitivity. However, nonvolatile molecules and salts that are often necessary to stabilize the native structures of protein-ligand complexes can readily adduct to protein ions, broaden spectral peaks, and lower signal-to-noise ratios in native MS. ESI emitters with narrow tip diameters (∼250 nm) were used to significantly reduce the extent of adduction of salt and nonvolatile molecules to protein complexes to more accurately measure ligand-protein binding constants than by use of conventional larger-bore emitters under these conditions. As a result of decreased salt adduction, peaks corresponding to protein-ligand complexes that differ in relative molecular weight by as low as 0.06% can be readily resolved. For low-molecular-weight anion ligands formed from sodium salts, anion-bound and unbound protein ions that differ in relative mass by 0.2% were completely baseline resolved using nanoscale emitters, which was not possible under these conditions using conventional emitters. Owing to the improved spectral resolution obtained using narrow-bore emitters and an analytically derived equation, K d values were simultaneously obtained for at least six ligands to a single druggable protein target from one spectrum for the first time. This research suggests that ligand-protein binding constants can be directly and accurately measured from solutions with high concentrations of nonvolatile buffers and salts by native MS.
Collapse
Affiliation(s)
- Giang
T. H. Nguyen
- School
of Chemistry, University of New South Wales, Dalton Building, Sydney, New South Wales 2052, Australia
| | - Thinh N. Tran
- School
of Electrical Engineering and Telecommunications, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Matthew N. Podgorski
- Department
of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Stephen G. Bell
- Department
of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Claudiu T. Supuran
- Department
of Neuroscience, Psychology, Drug Research and Child’s Health,
Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - William A. Donald
- School
of Chemistry, University of New South Wales, Dalton Building, Sydney, New South Wales 2052, Australia
- Phone: +61 (2) 9385 8827. E-mail:
| |
Collapse
|
8
|
Optimization of a dual-functional biocatalytic system for continuous hydrolysis of lactose in milk. J Biosci Bioeng 2019; 127:38-44. [DOI: 10.1016/j.jbiosc.2018.07.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 06/17/2018] [Accepted: 07/10/2018] [Indexed: 01/16/2023]
|
9
|
Archer JJ, Karki S, Shi F, Sistani H, Levis RJ. Quantification of Protein-Ligand Interactions by Laser Electrospray Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1484-1492. [PMID: 29654537 DOI: 10.1007/s13361-018-1935-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 03/01/2018] [Accepted: 03/02/2018] [Indexed: 06/08/2023]
Abstract
Laser electrospray mass spectrometry (LEMS) measurement of the dissociation constant (Kd) for hen egg white lysozyme (HEWL) and N,N',N″-triacetylchitotriose (NAG3) revealed an apparent Kd value of 313.2 ± 25.9 μM for the ligand titration method. Similar measurements for N,N',N″,N″'-tetraacetylchitotetraose (NAG4) revealed an apparent Kd of 249.3 ± 13.6 μM. An electrospray ionization mass spectrometry (ESI-MS) experiment determined a Kd value of 9.8 ± 0.6 μM. In a second LEMS approach, a calibrated measurement was used to determine a Kd value of 6.8 ± 1.5 μM for NAG3. The capture efficiency of LEMS was measured to be 3.6 ± 1.8% and is defined as the fraction of LEMS sample detected after merging with the ESI plume. When the dilution is factored into the ligand titration measurement, the adjusted Kd value was 11.3 μM for NAG3 and 9.0 μM for NAG4. The calibration method for measuring Kd developed in this study can be applied to solutions containing unknown analyte concentrations. Graphical Abstract.
Collapse
Affiliation(s)
- Jieutonne J Archer
- Department of Chemistry and Center for Advanced Photonics Research, Temple University, Philadelphia, PA, 19122, USA
| | - Santosh Karki
- Department of Chemistry and Center for Advanced Photonics Research, Temple University, Philadelphia, PA, 19122, USA
| | - Fengjian Shi
- Department of Chemistry and Center for Advanced Photonics Research, Temple University, Philadelphia, PA, 19122, USA
| | - Habiballah Sistani
- Department of Chemistry and Center for Advanced Photonics Research, Temple University, Philadelphia, PA, 19122, USA
| | - Robert J Levis
- Department of Chemistry and Center for Advanced Photonics Research, Temple University, Philadelphia, PA, 19122, USA.
| |
Collapse
|
10
|
Du FK, Zhang H, Tan XC, Yan J, Liu M, Chen X, Wu YY, Feng DF, Chen QY, Cen JM, Liu SG, Qiu YQ, Han HY. Ru(bpy) 32+-Silica@Poly-L-lysine-Au as labels for electrochemiluminescence lysozyme aptasensor based on 3D graphene. Biosens Bioelectron 2018; 106:50-56. [PMID: 29414088 DOI: 10.1016/j.bios.2018.01.059] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 01/21/2018] [Accepted: 01/26/2018] [Indexed: 12/11/2022]
Abstract
In this work, the feasibility of a novel sensitive electrochemiluminescence aptasensor for the detection of lysozyme using Ru(bpy)32+-Silica@Poly-L-lysine-Au (RuSiNPs@PLL-Au) nanocomposites labeling as an indicator was demonstrated. The substrate electrode of the aptasensor was prepared by depositing gold nanoparticles (AuNPs) on 3D graphene-modified electrode. The lysozyme binding aptamer (LBA) was attached to the 3D graphene/AuNPs electrode through gold-thiol affinity, hybridized with a complementary single-strand DNA (CDNA) of the lysozyme aptamer labeled by RuSiNPs@PLL-Au as an electrochemiluminescence intensity amplifier. Thanks to the synergistic amplification of the 3D graphene, the AuNPs and RuSiNPs@PLL-Au NPs linked to Ru(bpy)32+-ECL further enhanced the ECL intensity of the aptasensor. In presence of lysozyme, the CDNA segment of the self-assembled duplex was displaced by the lysozyme, resulting in decreased electrochemiluminescence signal. Under the optimized conditions, the decrease in electrochemiluminescence intensity varied proportionally with the logarithmic concentration of the lysozyme from 2.25 × 10-12 to 5.0 × 10-8 mol L-1, and the detection limit was estimated to 7.5 × 10-13 mol L-1. The aptasensor was further tested in real samples and found reliable for the detection of lysozyme, thus holding great potential application in food safety researches and bioassay analysis.
Collapse
Affiliation(s)
- Fang-Kai Du
- Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Guangxi Colleges and Universities for food safety and pharmaceutical analytical chemistry, School of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning 530008, PR China
| | - Hui Zhang
- Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Guangxi Colleges and Universities for food safety and pharmaceutical analytical chemistry, School of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning 530008, PR China
| | - Xue-Cai Tan
- Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Guangxi Colleges and Universities for food safety and pharmaceutical analytical chemistry, School of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning 530008, PR China.
| | - Jun Yan
- Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Guangxi Colleges and Universities for food safety and pharmaceutical analytical chemistry, School of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning 530008, PR China
| | - Min Liu
- Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Guangxi Colleges and Universities for food safety and pharmaceutical analytical chemistry, School of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning 530008, PR China
| | - Xiao Chen
- Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Guangxi Colleges and Universities for food safety and pharmaceutical analytical chemistry, School of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning 530008, PR China
| | - Ye-Yu Wu
- Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Guangxi Colleges and Universities for food safety and pharmaceutical analytical chemistry, School of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning 530008, PR China
| | - De-Fen Feng
- Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Guangxi Colleges and Universities for food safety and pharmaceutical analytical chemistry, School of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning 530008, PR China
| | - Quan-You Chen
- Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Guangxi Colleges and Universities for food safety and pharmaceutical analytical chemistry, School of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning 530008, PR China
| | - Jian-Mei Cen
- Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Guangxi Colleges and Universities for food safety and pharmaceutical analytical chemistry, School of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning 530008, PR China
| | - Shao-Gang Liu
- Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Guangxi Colleges and Universities for food safety and pharmaceutical analytical chemistry, School of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning 530008, PR China
| | - Yu-Qin Qiu
- Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Guangxi Colleges and Universities for food safety and pharmaceutical analytical chemistry, School of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning 530008, PR China
| | - He-You Han
- Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Guangxi Colleges and Universities for food safety and pharmaceutical analytical chemistry, School of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning 530008, PR China; State Key Laboratory of Agricultural Microbiology, College of Science, College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| |
Collapse
|
11
|
Label-Free Aptasensor for Lysozyme Detection Using Electrochemical Impedance Spectroscopy. SENSORS 2018; 18:s18020354. [PMID: 29373502 PMCID: PMC5855017 DOI: 10.3390/s18020354] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 01/16/2018] [Accepted: 01/23/2018] [Indexed: 11/17/2022]
Abstract
This research develops a label-free aptamer biosensor (aptasensor) based on graphite-epoxy composite electrodes (GECs) for the detection of lysozyme protein using Electrochemical Impedance Spectroscopy (EIS) technique. The chosen immobilization technique was based on covalent bonding using carbodiimide chemistry; for this purpose, carboxylic moieties were first generated on the graphite by electrochemical grafting. The detection was performed using [Fe(CN)6]3−/[Fe(CN)6]4− as redox probe. After recording the frequency response, values were fitted to its electric model using the principle of equivalent circuits. The aptasensor showed a linear response up to 5 µM for lysozyme and a limit of detection of 1.67 µM. The sensitivity of the established method was 0.090 µM−1 in relative charge transfer resistance values. The interference response by main proteins, such as bovine serum albumin and cytochrome c, has been also characterized. To finally verify the performance of the developed aptasensor, it was applied to wine analysis.
Collapse
|
12
|
Fluorescence switch biosensor based on quantum dots and gold nanoparticles for discriminative detection of lysozyme. Int J Biol Macromol 2017; 103:1155-1161. [DOI: 10.1016/j.ijbiomac.2017.05.144] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 05/22/2017] [Accepted: 05/23/2017] [Indexed: 11/23/2022]
|
13
|
Novel peptide motifs from lysozyme suppress pro-inflammatory cytokines in macrophages by antagonizing toll-like receptor and LPS-scavenging action. Eur J Pharm Sci 2017; 107:240-248. [PMID: 28711715 DOI: 10.1016/j.ejps.2017.07.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 06/29/2017] [Accepted: 07/06/2017] [Indexed: 02/07/2023]
Abstract
Lysozyme is commonly found in spots where bacterial infections are most likely to enter the body. Earlier we found that lysozyme possesses five antimicrobial peptide motifs in its N-terminal region which can be generated by newborn pepsin. In this study, we explore the role of these peptides in the anti-inflammatory activity of lysozyme. The five peptides, helix1 (H1), helix2 (H2), H1 and H2 connected with a loop (HLH), H2 extended with either 2 β-strands (H2-S12) or 3 β-strands (H2-S13), were synthesized and examined for anti-inflammatory action. The five peptides dose-dependently decreased, to different degrees, expression of pro-inflammatory cytokines, TNF-α, IL-6 and IL-1β, in lipopolysaccharide (LPS)- or interferon-gamma (INF-γ)-stimulated mouse macrophage cells (RAW264.7). The HLH peptide and its individual helices (H1 and H2) were markedly the most potent anti-inflammatory. When macrophage cells were stimulated with live bacteria (E. coli), H1 peptide was the most powerful suppressor of TNF-α and IL-6 expression, providing evidence that the peptide is able to antagonize the pathogen-induced inflammatory response. Receptor binding assay and docking simulation provided evidence that H1 peptide bind specifically to the pocket for endotoxin binding of the toll-like receptor 4 (TLR-4) of macrophage. The results demonstrate, for the first time, the molecular basis of anti-inflammatory action of lysozyme that N-terminal helical peptides are the main contributors. This exciting finding offers new classes of therapeutic peptides with potential in the treatment of infection-induced inflammatory diseases.
Collapse
|
14
|
Yao Y, Richards MR, Kitova EN, Klassen JS. Influence of Sulfolane on ESI-MS Measurements of Protein-Ligand Affinities. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:498-506. [PMID: 26667179 DOI: 10.1007/s13361-015-1312-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 11/22/2015] [Accepted: 11/24/2015] [Indexed: 06/05/2023]
Abstract
The results of an investigation into the influence of sulfolane, a commonly used supercharging agent, on electrospray ionization mass spectrometry (ESI-MS) measurements of protein-ligand affinities are described. Binding measurements carried out on four protein-carbohydrate complexes, lysozyme with β-D-GlcNAc-(1→4)-β-D-GlcNAc-(1→4)-β-D-GlcNAc-(1→4)-D-GlcNAc, a single chain variable fragment and α-D-Gal-(1→2)-[α-D-Abe-(1→3)]-α-D-Man-OCH3, cholera toxin B subunit homopentamer with β-D-Gal-(1→3)-β-D-GalNAc-(1→4)[α-D-Neu5Ac-(2→3)]-β-D-Gal-(1→4)-β-D-Glc, and a fragment of galectin 3 and α-L-Fuc-(1→2)-β-D-Gal-(1→3)-β-D-GlcNAc-(1→3)-β-D-Gal-(1→4)-β-D-Glc, revealed that sulfolane generally reduces the apparent (as measured by ESI-MS) protein-ligand affinities. To establish the origin of this effect, a detailed study was undertaken using the lysozyme-tetrasaccharide interaction as a model system. Measurements carried out using isothermal titration calorimetry (ITC), circular dichroism, and nuclear magnetic resonance spectroscopies reveal that sulfolane reduces the binding affinity in solution but does not cause any significant change in the higher order structure of lysozyme or to the intermolecular interactions. These observations confirm that changes to the structure of lysozyme in bulk solution are not responsible for the supercharging effect induced by sulfolane. Moreover, the agreement between the ESI-MS and ITC-derived affinities indicates that there is no dissociation of the complex during ESI or in the gas phase (i.e., in-source dissociation). This finding suggests that supercharging of lysozyme by sulfolane is not related to protein unfolding during the ESI process. Binding measurements performed using liquid sample desorption ESI-MS revealed that protein supercharging with sulfolane can be achieved without a reduction in affinity.
Collapse
Affiliation(s)
- Yuyu Yao
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Michele R Richards
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Elena N Kitova
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - John S Klassen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada.
| |
Collapse
|
15
|
Tiwari JN, Vij V, Kemp KC, Kim KS. Engineered Carbon-Nanomaterial-Based Electrochemical Sensors for Biomolecules. ACS NANO 2016; 10:46-80. [PMID: 26579616 DOI: 10.1021/acsnano.5b05690] [Citation(s) in RCA: 270] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The study of electrochemical behavior of bioactive molecules has become one of the most rapidly developing scientific fields. Biotechnology and biomedical engineering fields have a vested interest in constructing more precise and accurate voltammetric/amperometric biosensors. One rapidly growing area of biosensor design involves incorporation of carbon-based nanomaterials in working electrodes, such as one-dimensional carbon nanotubes, two-dimensional graphene, and graphene oxide. In this review article, we give a brief overview describing the voltammetric techniques and how these techniques are applied in biosensing, as well as the details surrounding important biosensing concepts of sensitivity and limits of detection. Building on these important concepts, we show how the sensitivity and limit of detection can be tuned by including carbon-based nanomaterials in the fabrication of biosensors. The sensing of biomolecules including glucose, dopamine, proteins, enzymes, uric acid, DNA, RNA, and H2O2 traditionally employs enzymes in detection; however, these enzymes denature easily, and as such, enzymeless methods are highly desired. Here we draw an important distinction between enzymeless and enzyme-containing carbon-nanomaterial-based biosensors. The review ends with an outlook of future concepts that can be employed in biosensor fabrication, as well as limitations of already proposed materials and how such sensing can be enhanced. As such, this review can act as a roadmap to guide researchers toward concepts that can be employed in the design of next generation biosensors, while also highlighting the current advancements in the field.
Collapse
Affiliation(s)
- Jitendra N Tiwari
- Center for Superfunctional Materials, Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST) , Ulsan 689-798, Korea
| | - Varun Vij
- Center for Superfunctional Materials, Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST) , Ulsan 689-798, Korea
| | - K Christian Kemp
- Center for Superfunctional Materials, Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST) , Ulsan 689-798, Korea
| | - Kwang S Kim
- Center for Superfunctional Materials, Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST) , Ulsan 689-798, Korea
| |
Collapse
|
16
|
Label free aptasensor for Lysozyme detection: A comparison of the analytical performance of two aptamers. Bioelectrochemistry 2015; 105:72-7. [PMID: 26011131 DOI: 10.1016/j.bioelechem.2015.05.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 05/11/2015] [Accepted: 05/11/2015] [Indexed: 01/07/2023]
|
17
|
Ocaña C, Hayat A, Mishra R, Vasilescu A, del Valle M, Marty JL. A novel electrochemical aptamer-antibody sandwich assay for lysozyme detection. Analyst 2015; 140:4148-53. [PMID: 25905497 DOI: 10.1039/c5an00243e] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper, we have reported a novel electrochemical aptamer-antibody based sandwich biosensor for the detection of lysozyme. In the sensing strategy, an anti-lysozyme aptamer was immobilized onto the carbon electrode surface by covalent binding via diazonium salt chemistry. After incubating with a target protein (lysozyme), a biotinylated antibody was used to complete the sandwich format. The subsequent additions of avidin-alkaline phosphatase as an enzyme label, and a 1-naphthyl phosphate substrate (1-NPP) allowed us to determine the concentration of lysozyme (Lys) via Differential Pulse Voltammetry (DPV) of the generated enzyme reaction product, 1-naphthol. Using this strategy, a wide detection range from 5 fM to 5 nM was obtained for a target lysozyme, with a detection limit of 4.3 fM. The control experiments were carried out by using bovine serum albumin (BSA), cytochrome c and casein. The results showed that the proposed biosensor had good specificity, stability and reproducibility for lysozyme analysis. In addition, the biosensor was applied for detecting lysozyme in spiked wine samples, and very good recovery rates were obtained in the range from 95.2 to 102.0% for lysozyme detection. This implies that the proposed sandwich biosensor is a promising analytical tool for the analysis of lysozyme in real samples.
Collapse
Affiliation(s)
- Cristina Ocaña
- Sensors and Biosensors Group, Department of Chemistry, UniversitatAutònoma de Barcelona, 08193 Bellaterra, Spain
| | | | | | | | | | | |
Collapse
|
18
|
Payne CM, Knott BC, Mayes HB, Hansson H, Himmel ME, Sandgren M, Ståhlberg J, Beckham GT. Fungal Cellulases. Chem Rev 2015; 115:1308-448. [DOI: 10.1021/cr500351c] [Citation(s) in RCA: 533] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Christina M. Payne
- Department
of Chemical and Materials Engineering and Center for Computational
Sciences, University of Kentucky, 177 F. Paul Anderson Tower, Lexington, Kentucky 40506, United States
| | - Brandon C. Knott
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| | - Heather B. Mayes
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Henrik Hansson
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Michael E. Himmel
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Mats Sandgren
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Jerry Ståhlberg
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Gregg T. Beckham
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| |
Collapse
|
19
|
Yao Y, Shams-Ud-Doha K, Daneshfar R, Kitova EN, Klassen JS. Quantifying protein-carbohydrate interactions using liquid sample desorption electrospray ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:98-106. [PMID: 25315460 DOI: 10.1007/s13361-014-1008-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 09/03/2014] [Accepted: 09/05/2014] [Indexed: 06/04/2023]
Abstract
The application of liquid sample desorption electrospray ionization mass spectrometry (liquid sample DESI-MS) for quantifying protein-carbohydrate interactions in vitro is described. Association constants for the interactions between lysozyme and β-D-GlcNAc-(1 → 4)-β-D-GlcNAc-(1 → 4)-D-GlcNAc and β-D-GlcNAc-(1 → 4)-β-D-GlcNAc-(1 → 4)-β-D-GlcNAc-(1 → 4)-D-GlcNAc, and between a single chain antibody and α-D-Galp-(1 → 2)-[α-D-Abep-(1 → 3)]-α-D-Manp-OCH3 and β-D-Glcp-(1 → 2)-[α-D-Abep-(1 → 3)]-α-D-Manp-OCH3 measured using liquid sample DESI-MS were found to be in good agreement with values measured by isothermal titration calorimetry and the direct ESI-MS assay. The reference protein method, which was originally developed to correct ESI mass spectra for the occurrence of nonspecific ligand-protein binding, was shown to reliably correct liquid sample DESI mass spectra for nonspecific binding. The suitability of liquid sample DESI-MS for quantitative binding measurements carried out using solutions containing high concentrations of the nonvolatile biological buffer phosphate buffered saline (PBS) was also explored. Binding of lysozyme to β-D-GlcNAc-(1 → 4)-β-D-GlcNAc-(1 → 4)-D-GlcNAc in aqueous solutions containing up to 1× PBS was successfully monitored using liquid sample DESI-MS; with ESI-MS the binding measurements were limited to concentrations less than 0.02 X PBS.
Collapse
Affiliation(s)
- Yuyu Yao
- Alberta Glycomics Center and Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | | | | | | | | |
Collapse
|
20
|
Sohya S, Kamioka T, Fujita C, Maki T, Ohta Y, Kuroda Y. Biochemical and biophysical characterization of an unexpected bacteriolytic activity of VanX, a member of the vancomycin-resistance vanA gene cluster. J Biol Chem 2014; 289:35686-94. [PMID: 25294880 DOI: 10.1074/jbc.m114.590265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
VanX is a d-alanyl-d-alanine (d-Ala-d-Ala) dipeptidase encoded in the vancomycin-resistance vanA gene cluster. Here we report that strong bacteriolysis occurred when isolated VanX was expressed in Escherichia coli at temperatures lower than 30 °C, which was unexpected because the vanA operon confers vancomycin resistance by protecting the cell wall. Therefore, we monitored cell lysis by measuring sample turbidity with absorbance at 590 nm and VanX expression using SDS-PAGE. No cell lysis was observed when VanX was expressed, even in large quantities, in the cell inclusion bodies at 37 °C, suggesting that a natively folded VanX is required for lysis. In addition, VanX mutants with suppressed dipeptidase activity did not lyse E. coli cells, confirming that bacteriolysis originated from the dipeptidase activity of VanX. We also observed shape changes in E. coli cells undergoing VanX-mediated lysis with optical microscopy and classified these changes into three classes: bursting, deformation, and leaking fluid. Optical microscopic image analysis fully corroborated our interpretation of the turbidity changes in the samples. From a practical perspective, the finding that VanX expressed in isolation induces cell lysis suggests that inhibitors of VanA and VanH that act downstream from VanX could provide a new class of therapeutic chemicals against bacteria expressing the vancomycin-resistance gene cluster.
Collapse
Affiliation(s)
- Shihori Sohya
- From the Department of Biotechnology and Life Science, Graduate School of Engineering, and
| | - Tetsuya Kamioka
- From the Department of Biotechnology and Life Science, Graduate School of Engineering, and
| | - Chisako Fujita
- From the Department of Biotechnology and Life Science, Graduate School of Engineering, and
| | - Tei Maki
- Research Center for Science and Technology, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi, Tokyo, 184-8588 Japan, and JEOL Ltd., EM Business Unit, 3-1-2 Musashino, Akishima, Tokyo 196-8558, Japan
| | - Yoshihiro Ohta
- From the Department of Biotechnology and Life Science, Graduate School of Engineering, and
| | - Yutaka Kuroda
- From the Department of Biotechnology and Life Science, Graduate School of Engineering, and
| |
Collapse
|
21
|
Maple HJ, Scheibner O, Baumert M, Allen M, Taylor RJ, Garlish RA, Bromirski M, Burnley RJ. Application of the Exactive Plus EMR for automated protein-ligand screening by non-covalent mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:1561-8. [PMID: 24861608 DOI: 10.1002/rcm.6925] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 04/14/2014] [Accepted: 04/16/2014] [Indexed: 05/12/2023]
Abstract
RATIONALE Non-covalent mass spectrometry (MS) offers considerable potential for protein-ligand screening in drug discovery programmes. However, there are some limitations with the time-of-flight (TOF) instrumentation typically employed that restrict the application of non-covalent MS in industrial laboratories. METHODS An Exactive Plus EMR mass spectrometer was investigated for its ability to characterise non-covalent protein-small molecule interactions. Nano-electrospray ionisation (nanoESI) infusion was achieved with a TriVersa NanoMate. The transport multipole and ion lens voltages, dissociation energies and pressure in the Orbitrap™ were optimised. Native MS was performed, with ligand titrations to judge retention of protein-ligand interactions, serial dilutions of native proteins as an indication of sensitivity, and a heterogeneous protein analysed for spectral resolution. RESULTS Interactions between native proteins and ligands are preserved during analysis on the Exactive Plus EMR, with the binding affinities determined in good agreement with expected values. High spectral resolution allows baseline separation of adduct ions, which should improve the accuracy and limit of detection for measuring ligand interactions. Data are also presented showing baseline resolution of glycoforms of a highly glycosylated protein, allowing binding of a fragment molecule to be detected. CONCLUSIONS The high sensitivity and spectral resolution achievable with the Orbitrap technology confer significant advantages over TOF mass spectrometers, and offer a solution to current limitations regarding throughput, data analysis and sample requirements. A further benefit of improved spectral resolution is the possibility of using heterogeneous protein samples such as glycoproteins for fragment screening. This would significantly expand the scope of applicability of non-covalent MS in the pharmaceutical and other industries.
Collapse
|
22
|
Matsuda Y, Itaya H, Kitahara Y, Theresia NM, Kutukova EA, Yomantas YAV, Date M, Kikuchi Y, Wachi M. Double mutation of cell wall proteins CspB and PBP1a increases secretion of the antibody Fab fragment from Corynebacterium glutamicum. Microb Cell Fact 2014; 13:56. [PMID: 24731213 PMCID: PMC4021378 DOI: 10.1186/1475-2859-13-56] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 03/17/2014] [Indexed: 12/16/2022] Open
Abstract
Background Among other advantages, recombinant antibody-binding fragments (Fabs) hold great clinical and commercial potential, owing to their efficient tissue penetration compared to that of full-length IgGs. Although production of recombinant Fab using microbial expression systems has been reported, yields of active Fab have not been satisfactory. We recently developed the Corynebacterium glutamicum protein expression system (CORYNEX®) and demonstrated improved yield and purity for some applications, although the system has not been applied to Fab production. Results The Fab fragment of human anti-HER2 was successfully secreted by the CORYNEX® system using the conventional C. glutamicum strain YDK010, but the productivity was very low. To improve the secretion efficiency, we investigated the effects of deleting cell wall-related genes. Fab secretion was increased 5.2 times by deletion of pbp1a, encoding one of the penicillin-binding proteins (PBP1a), mediating cell wall peptidoglycan (PG) synthesis. However, this Δpbp1a mutation did not improve Fab secretion in the wild-type ATCC13869 strain. Because YDK010 carries a mutation in the cspB gene encoding a surface (S)-layer protein, we evaluated the effect of ΔcspB mutation on Fab secretion from ATCC13869. The Δpbp1a mutation showed a positive effect on Fab secretion only in combination with the ΔcspB mutation. The ΔcspBΔpbp1a double mutant showed much greater sensitivity to lysozyme than either single mutant or the wild-type strain, suggesting that these mutations reduced cell wall resistance to protein secretion. Conclusion There are at least two crucial permeability barriers to Fab secretion in the cell surface structure of C. glutamicum, the PG layer, and the S-layer. The ΔcspBΔpbp1a double mutant allows efficient Fab production using the CORYNEX® system.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Masaaki Wachi
- Department of Bioengineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.
| |
Collapse
|
23
|
Erdem A, Eksin E, Muti M. Chitosan-graphene oxide based aptasensor for the impedimetric detection of lysozyme. Colloids Surf B Biointerfaces 2013; 115:205-11. [PMID: 24362059 DOI: 10.1016/j.colsurfb.2013.11.037] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 11/18/2013] [Accepted: 11/20/2013] [Indexed: 01/16/2023]
Abstract
An impedimetric detection of lysozyme (LYS) was performed for the first time in this study at the surface of chitosan-graphene oxide (CHIT-GO) modified sensor based on the specific interaction process between DNA aptamer and its cognate protein, LYS. The amino linked DNA aptamer (APT) was covalently immobilized without using any chemical agents onto the surface of pencil graphite electrode (PGE). These PGEs are inexpensive and simple to use, and thus, they can be furtherly developed for a single-use application in a portable protein chip device. The electrochemical impedance spectroscopy (EIS) technique was used herein to analyze (i) the surface characterization of unmodified PGE and CHIT-GO modified PGE, and also (ii) the interaction between APT and LYS. The limit of detection (DL) was found as 0.38 μg/mL (equals to 28.53 nM). This impedimetric LYS aptasensor exhibited a higher selectivity toward thrombin and bovine serum albumin, even in the mixture samples.
Collapse
Affiliation(s)
- Arzum Erdem
- Ege University, Faculty of Pharmacy, Analytical Chemistry Department, Bornova, 35100, Izmir, Turkey.
| | - Ece Eksin
- Ege University, Faculty of Pharmacy, Analytical Chemistry Department, Bornova, 35100, Izmir, Turkey
| | - Mihrican Muti
- Ege University, Faculty of Pharmacy, Analytical Chemistry Department, Bornova, 35100, Izmir, Turkey; Adnan Menderes University, Faculty of Science, Chemistry Department, 09010, Aydın, Turkey
| |
Collapse
|
24
|
Spaan AN, Surewaard BGJ, Nijland R, van Strijp JAG. Neutrophils versus Staphylococcus aureus: a biological tug of war. Annu Rev Microbiol 2013; 67:629-50. [PMID: 23834243 DOI: 10.1146/annurev-micro-092412-155746] [Citation(s) in RCA: 236] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The pathogen Staphylococcus aureus is well adapted to its human host. Neutrophil-mediated killing is a crucial defense system against S. aureus; however, the pathogen has evolved many strategies to resist killing. We first describe the discrete steps of neutrophil activation and migration to the site of infection and the killing of microbes by neutrophils in general. We then highlight the different approaches utilized by S. aureus to resist the different steps of neutrophil attack. Various molecules are discussed in their evolutionary context. Most of the molecules secreted by S. aureus to combat neutrophil attacks at the site of infection show clear human specificity. Many elements of human neutrophil defenses appear redundant, and so the evasion strategies of staphylococci display redundant functions as well. All efforts by S. aureus to resist neutrophil-mediated killing stress the importance of these mechanisms in the pathophysiology of staphylococcal diseases. However, the highly human-specific nature of most host-pathogen interactions hinders the in vivo establishment of their contribution to staphylococcal pathophysiology.
Collapse
Affiliation(s)
- András N Spaan
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; , , ,
| | | | | | | |
Collapse
|
25
|
Protein-specific force field derived from the fragment molecular orbital method can improve protein-ligand binding interactions. J Comput Chem 2013; 34:1251-7. [DOI: 10.1002/jcc.23250] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 01/15/2013] [Accepted: 01/22/2013] [Indexed: 11/07/2022]
|
26
|
Cubrilovic D, Zenobi R. Influence of dimehylsulfoxide on protein-ligand binding affinities. Anal Chem 2013; 85:2724-30. [PMID: 23347283 DOI: 10.1021/ac303197p] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Because of its favorable physicochemical properties, DMSO is the standard solvent for sample storage and handling of compounds in drug discovery. To date, little attention was given to how DMSO influences protein-ligand binding strengths. In this study we investigated the effects of DMSO on different noncovalent protein-ligand complexes, in particular in terms of the binding affinities, which we determined using nanoESI-MS. For the investigation, three different protein-ligand complexes were chosen: trypsin-Pefabloc, lysozyme-tri-N-acetylchitotriose (NAG3), and carbonic anhydrase-chlorothiazide. The DMSO content in the nanoESI buffer was increased systematically from 0.5 to 8%. For all three model systems, it was shown that the binding affinity decreases upon addition of DMSO. Even 0.5-1% DMSO alters the KD values, in particular for the tight binding system carbonic anhydrase-chlorothiazide. The determined dissociation constant (KD) is up to 10 times higher than for a DMSO-free sample in the case of carbonic anhydrase-chlorothiazide binding. For the trypsin-Pefabloc and lysozyme-NAG3 complexes, the dissociation constants are 7 and 3 times larger, respectively, in the presence of DMSO. This work emphasizes the importance of effects of DMSO as a co-solvent for quantification of protein-ligand binding strengths in the early stages of drug discovery.
Collapse
Affiliation(s)
- Dragana Cubrilovic
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | | |
Collapse
|
27
|
Jaquillard L, Saab F, Schoentgen F, Cadene M. Improved accuracy of low affinity protein-ligand equilibrium dissociation constants directly determined by electrospray ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:908-922. [PMID: 22430390 DOI: 10.1007/s13361-011-0305-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 11/07/2011] [Accepted: 11/23/2011] [Indexed: 05/31/2023]
Abstract
There is continued interest in the determination by ESI-MS of equilibrium dissociation constants (K(D)) that accurately reflect the affinity of a protein-ligand complex in solution. Issues in the measurement of K(D) are compounded in the case of low affinity complexes. Here we present a K(D) measurement method and corresponding mathematical model dealing with both gas-phase dissociation (GPD) and aggregation. To this end, a rational mathematical correction of GPD (f(sat)) is combined with the development of an experimental protocol to deal with gas-phase aggregation. A guide to apply the method to noncovalent protein-ligand systems according to their kinetic behavior is provided. The approach is validated by comparing the K(D) values determined by this method with in-solution K(D) literature values. The influence of the type of molecular interactions and instrumental setup on f(sat) is examined as a first step towards a fine dissection of factors affecting GPD. The method can be reliably applied to a wide array of low affinity systems without the need for a reference ligand or protein.
Collapse
Affiliation(s)
- Lucie Jaquillard
- Centre de Biophysique Moléculaire, CNRS UPR 4301, affiliated with Université d'Orléans, rue Charles-Sadron, 45071 Orléans, Cedex 2, France
| | | | | | | |
Collapse
|
28
|
Maple HJ, Garlish RA, Rigau-Roca L, Porter J, Whitcombe I, Prosser CE, Kennedy J, Henry AJ, Taylor RJ, Crump MP, Crosby J. Automated Protein–Ligand Interaction Screening by Mass Spectrometry. J Med Chem 2012; 55:837-51. [DOI: 10.1021/jm201347k] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Hannah J. Maple
- School of Chemistry, University of Bristol, Cantock’s
Close, Clifton, Bristol BS8 1TS, United Kingdom
| | - Rachel A. Garlish
- UCB Pharma, 216 Bath Road, Slough, Berkshire SL1 4EN, United Kingdom
| | - Laura Rigau-Roca
- School of Chemistry, University of Bristol, Cantock’s
Close, Clifton, Bristol BS8 1TS, United Kingdom
| | - John Porter
- UCB Pharma, 216 Bath Road, Slough, Berkshire SL1 4EN, United Kingdom
| | - Ian Whitcombe
- UCB Pharma, 216 Bath Road, Slough, Berkshire SL1 4EN, United Kingdom
| | | | - Jeff Kennedy
- UCB Pharma, 216 Bath Road, Slough, Berkshire SL1 4EN, United Kingdom
| | - Alistair J. Henry
- UCB Pharma, 216 Bath Road, Slough, Berkshire SL1 4EN, United Kingdom
| | - Richard J. Taylor
- UCB Pharma, 216 Bath Road, Slough, Berkshire SL1 4EN, United Kingdom
| | - Matthew P. Crump
- School of Chemistry, University of Bristol, Cantock’s
Close, Clifton, Bristol BS8 1TS, United Kingdom
| | - John Crosby
- School of Chemistry, University of Bristol, Cantock’s
Close, Clifton, Bristol BS8 1TS, United Kingdom
| |
Collapse
|
29
|
Ibrahim HR, Imazato K, Ono H. Human lysozyme possesses novel antimicrobial peptides within its N-terminal domain that target bacterial respiration. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2011; 59:10336-10345. [PMID: 21851100 DOI: 10.1021/jf2020396] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Human milk lysozyme is thought to be a key defense factor in protecting the gastrointestinal tract of newborns against bacterial infection. Recently, evidence was found that pepsin, under conditions relevant to the newborn stomach, cleaves chicken lysozyme (cLZ) at specific loops to generate five antimicrobial peptide motifs. This study explores the antimicrobial role of the corresponding peptides of human lysozyme (hLZ), the actual protein in breast milk. Five peptide motifs of hLZ, one helix-loop-helix (HLH), its two helices (H1 and H2), and two helix-sheet motifs, H2-β-strands 1-2 (H2-S12) or H2-β-strands 1-3 (H2-S13), were synthesized and examined for antimicrobial action. The five peptides of hLZ exhibit microbicidal activity to various degrees against several bacterial strains. The HLH peptide and its N-terminal helix (H1) were significantly the most potent bactericidal to Gram-positive and Gram-negative bacteria and the fungus Candida albicans . Outer and inner membrane permeabilization studies, as well as measurements of transmembrane electrochemical potentials, provided evidence that HLH peptide and its N-terminal helix (H1) kill bacteria by crossing the outer membrane of Gram-negative bacteria via self-promoted uptake and are able to dissipate the membrane potential-dependent respiration of Gram-positive bacteria. This finding is the first to describe that hLZ possesses multiple antimicrobial peptide motifs within its N-terminal domain, providing insight into new classes of antibiotic peptides with potential use in the treatment of infectious diseases.
Collapse
Affiliation(s)
- Hisham R Ibrahim
- Department of Biochemistry and Biotechnology, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan.
| | | | | |
Collapse
|
30
|
Hopper JTS, Oldham NJ. Alkali metal cation-induced destabilization of gas-phase protein-ligand complexes: consequences and prevention. Anal Chem 2011; 83:7472-9. [PMID: 21863818 DOI: 10.1021/ac201686f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electrospray ionization, now a well established technique for studying noncovalent protein-ligand interactions, is prone to production of alkali metal adducts. Here it is shown that this adduction significantly destabilizes the interactions between two model proteins and their ligands and that destabilization correlates with cation size. For both the [FKBP·FK506] and [lysozyme·NAG(n)] systems, dissociation of the metalated complex occurs at markedly lower collision energies than their purely protonated equivalents. Dependency upon size of the metal(+) demonstrates the importance of electrostatic charge density during the dissociation process. Differences in the gas phase basicities (GBapp) of the multiply charged protein ions and proton and sodium affinities of the ligands explain the observed charge partitioning during dissociation of the complexes. Ion mobility-mass spectrometry measurements demonstrate that metal cation adduction does not induce a significant increase in unfolding of the polypeptides, indicating that this is not the principal mechanism responsible for destabilization. Destabilizing effects can be largely reduced by exposing the electrospray to solvent (e.g., acetonitrile) vapor, a method that acts to reduce the amount of adduct formation as well as decrease the charge states of the resulting ions. This approach leads to more accurate determination of apparent K(D)s in the presence of trace alkali metals.
Collapse
Affiliation(s)
- Jonathan T S Hopper
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD
| | | |
Collapse
|
31
|
Chen Z, Li L, Zhao H, Guo L, Mu X. Electrochemical impedance spectroscopy detection of lysozyme based on electrodeposited gold nanoparticles. Talanta 2010; 83:1501-6. [PMID: 21238744 DOI: 10.1016/j.talanta.2010.11.042] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2010] [Revised: 11/15/2010] [Accepted: 11/18/2010] [Indexed: 01/29/2023]
Abstract
A simple, highly sensitive, and label-free electrochemical impedance spectroscopy (EIS) aptasensor based on an anti-lysozyme-aptamer as a molecular recognition element, was developed for the detection of lysozyme. Improvement in sensitivity was achieved by utilizing gold nanoparticles (AuNPs), which were electrodeposited onto the surface of a gold electrode, as a platform for immobilization of the aptamer. To quantify the amount of lysozyme, changes in the interfacial electron transfer resistance (R(et)) of the aptasensor were monitored using the redox couple of an [Fe(CN)(6)](3-/4-) probe. The R(et) increased with lysozyme concentration. The plot of R(et) against the logarithm of lysozyme concentration is linear over the range from 0.1 pM to 500 pM with a detection limit of 0.01 pM. The aptasensor also showed good selectivity for lysozyme without being affected by the presence of other proteins.
Collapse
Affiliation(s)
- Zhengbo Chen
- School of Chemistry and Environment, Beijing University of Aeronautics and Astronautics, Haidian District, Beijing, China
| | | | | | | | | |
Collapse
|
32
|
Norberg AL, Karlsen V, Hoell IA, Bakke I, Eijsink VGH, Sørlie M. Determination of substrate binding energies in individual subsites of a family 18 chitinase. FEBS Lett 2010; 584:4581-5. [PMID: 20965174 DOI: 10.1016/j.febslet.2010.10.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 10/11/2010] [Accepted: 10/13/2010] [Indexed: 10/18/2022]
Abstract
Thermodynamic parameters for binding of N-acetylglucosamine (GlcNAc) oligomers to a family 18 chitinase, ChiB of Serratia marcescens, have been determined using isothermal titration calorimetry. Binding studies with oligomers of different lengths showed that binding to subsites -2 and +1 is driven by a favorable enthalpy change, while binding to the two other most important subsites, +2 and +3, is driven by entropy with unfavorable enthalpy. These remarkable unfavorable enthalpy changes are most likely due to favorable enzyme-substrate interactions being offset by unfavorable enthalpic effects of the conformational changes that accompany substrate-binding.
Collapse
Affiliation(s)
- Anne Line Norberg
- Department of Chemistry, Biotechnology, and Food Science, The Norwegian University of Life Sciences, 1432 Ås, Norway
| | | | | | | | | | | |
Collapse
|
33
|
Saharay M, Guo H, Smith JC. Catalytic mechanism of cellulose degradation by a cellobiohydrolase, CelS. PLoS One 2010; 5:e12947. [PMID: 20967294 PMCID: PMC2953488 DOI: 10.1371/journal.pone.0012947] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Accepted: 08/20/2010] [Indexed: 12/02/2022] Open
Abstract
The hydrolysis of cellulose is the bottleneck in cellulosic ethanol production. The cellobiohydrolase CelS from Clostridium thermocellum catalyzes the hydrolysis of cello-oligosaccharides via inversion of the anomeric carbon. Here, to examine key features of the CelS-catalyzed reaction, QM/MM (SCCDFTB/MM) simulations are performed. The calculated free energy profile for the reaction possesses a 19 kcal/mol barrier. The results confirm the role of active site residue Glu87 as the general acid catalyst in the cleavage reaction and show that Asp255 may act as the general base. A feasible position in the reactant state of the water molecule responsible for nucleophilic attack is identified. Sugar ring distortion as the reaction progresses is quantified. The results provide a computational approach that may complement the experimental design of more efficient enzymes for biofuel production.
Collapse
Affiliation(s)
- Moumita Saharay
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Hong Guo
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Jeremy C. Smith
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America
| |
Collapse
|
34
|
Production of chitooligosaccharides and their potential applications in medicine. Mar Drugs 2010; 8:1482-517. [PMID: 20559485 PMCID: PMC2885077 DOI: 10.3390/md8051482] [Citation(s) in RCA: 407] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Revised: 04/14/2010] [Accepted: 04/23/2010] [Indexed: 01/17/2023] Open
Abstract
Chitooligosaccharides (CHOS) are homo- or heterooligomers of N-acetylglucosamine and D-glucosamine. CHOS can be produced using chitin or chitosan as a starting material, using enzymatic conversions, chemical methods or combinations thereof. Production of well-defined CHOS-mixtures, or even pure CHOS, is of great interest since these oligosaccharides are thought to have several interesting bioactivities. Understanding the mechanisms underlying these bioactivities is of major importance. However, so far in-depth knowledge on the mode-of-action of CHOS is scarce, one major reason being that most published studies are done with badly characterized heterogeneous mixtures of CHOS. Production of CHOS that are well-defined in terms of length, degree of N-acetylation, and sequence is not straightforward. Here we provide an overview of techniques that may be used to produce and characterize reasonably well-defined CHOS fractions. We also present possible medical applications of CHOS, including tumor growth inhibition and inhibition of T(H)2-induced inflammation in asthma, as well as use as a bone-strengthener in osteoporosis, a vector for gene delivery, an antibacterial agent, an antifungal agent, an anti-malaria agent, or a hemostatic agent in wound-dressings. By using well-defined CHOS-mixtures it will become possible to obtain a better understanding of the mechanisms underlying these bioactivities.
Collapse
|
35
|
26kDa endochitinase from barley seeds: Real-time monitoring of the enzymatic reaction and substrate binding experiments using electrospray ionization mass spectrometry. J Biotechnol 2009; 143:274-83. [DOI: 10.1016/j.jbiotec.2009.08.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2008] [Revised: 07/30/2009] [Accepted: 08/03/2009] [Indexed: 11/19/2022]
|
36
|
Characterization of the Interactions of Lysozyme with DNA by Surface Plasmon Resonance and Circular Dichroism Spectroscopy. Appl Biochem Biotechnol 2008; 158:631-41. [DOI: 10.1007/s12010-008-8348-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Accepted: 08/18/2008] [Indexed: 10/21/2022]
|
37
|
Henning Cederkvist F, Parmer MP, Vårum KM, Eijsink VG, Sørlie M. Inhibition of a family 18 chitinase by chitooligosaccharides. Carbohydr Polym 2008. [DOI: 10.1016/j.carbpol.2008.01.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
38
|
|
39
|
Jecklin MC, Touboul D, Bovet C, Wortmann A, Zenobi R. Which electrospray-based ionization method best reflects protein-ligand interactions found in solution? a comparison of ESI, nanoESI, and ESSI for the determination of dissociation constants with mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:332-43. [PMID: 18083584 DOI: 10.1016/j.jasms.2007.11.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Revised: 11/08/2007] [Accepted: 11/08/2007] [Indexed: 05/24/2023]
Abstract
We present a comparison of three different electrospray-based ionization techniques for the investigation of noncovalent complexes with mass spectrometry. The features and characteristics of standard electrospray ionization (ESI), chip-based nanoESI, and electrosonic spray ionization (ESSI) mounted onto a hybrid quadrupole time-of-flight mass spectrometer were compared in their performance to determine the dissociation constant (KD) of the model system hen egg white lysozyme (HEWL) binding to N,N',N''-triacetylchitotriose (NAG3). The best KD value compared with solution data were found for ESSI, 19.4 +/- 3.6 microM. Then, we determined the KDs of the two nucleotide binding sites of adenylate kinase (AK), where we obtained KDs of 2.2 +/- 0.8 microM for the first and 19.5 +/- 8.0 microM for the second binding site using ESSI. We found a weak charge state dependence of the KD for both protein-ligand systems, where for all ionization techniques the KD value decreases with increasing charge state. We demonstrate that ESSI is very gentle and insensitive to instrumental parameters, and the KD obtained is in good agreement with solution phase results from the literature. In addition, we tried to determine the KD for the lymphocyte-specific kinase LCK binding to a kinase inhibitor using nanoESI due to the very low amount of sample available. In this case, we found KD values with a strong charge state dependence, which were in no case close to literature values for solution phase.
Collapse
|
40
|
Sami AJ, Haider MK. Identification of novel catalytic features of endo-beta-1,4-glucanase produced by mulberry longicorn beetle Apriona germari. J Zhejiang Univ Sci B 2007; 8:765-70. [PMID: 17910121 PMCID: PMC1997232 DOI: 10.1631/jzus.2007.b0765] [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] [Indexed: 01/09/2023]
Abstract
Mulberry longicorn beetle, Apriona germari, has been reported to produce two endo-beta-1,4-glucanases or AgEGases (accession Nos. Q6SS52 and Q5XQD1). AgEGase sequence contains catalytic motif (amino acid residues 37-48), which is the characteristic of family Glycohydrolase 45 and is identified as the substrate binding site. The application of bioinformatics approaches includes sequence analysis, structural modeling and inhibitor docking to relate the structure and function of AgEGases. We have dissected the sequence and structure of AgEGase catalytic motif and compared it with crystal structure of Humicola insolens endoglucanases V. The results show an involvement of sulfur containing amino acid residues in the active site of the enzyme. Cys residues and position of disulfide bonds are highly conserved between the two structures of endoglucanases of A. germari. Surface calculation of AgEGase structure in the absence of Cys residues reveals greater accessibility of the catalytic site to the substrate involving Asp42, a highly conserved residue. For the inhibition study, tannin-based structure was docked into the catalytic site of AgEGase using ArgusLab 4.0 and it resulted in a stable complex formation. It is suggested that the inhibition could occur through formation of a stable transition state analog-enzyme complex with the tannin-based inhibitor, as observed with other insect cellulases in our laboratory.
Collapse
Affiliation(s)
- Amtul Jamil Sami
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore 54594, Pakistan.
| | | |
Collapse
|
41
|
Herbert S, Bera A, Nerz C, Kraus D, Peschel A, Goerke C, Meehl M, Cheung A, Götz F. Molecular basis of resistance to muramidase and cationic antimicrobial peptide activity of lysozyme in staphylococci. PLoS Pathog 2007; 3:e102. [PMID: 17676995 PMCID: PMC1933452 DOI: 10.1371/journal.ppat.0030102] [Citation(s) in RCA: 182] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2007] [Accepted: 06/04/2007] [Indexed: 12/19/2022] Open
Abstract
It has been shown recently that modification of peptidoglycan by O-acetylation renders pathogenic staphylococci resistant to the muramidase activity of lysozyme. Here, we show that a Staphylococcus aureus double mutant defective in O-acetyltransferase A (OatA), and the glycopeptide resistance-associated two-component system, GraRS, is much more sensitive to lysozyme than S. aureus with the oatA mutation alone. The graRS single mutant was resistant to the muramidase activity of lysozyme, but was sensitive to cationic antimicrobial peptides (CAMPs) such as the human lysozyme-derived peptide 107R-A-W-V-A-W-R-N-R115 (LP9), polymyxin B, or gallidermin. A comparative transcriptome analysis of wild type and the graRS mutant revealed that GraRS controls 248 genes. It up-regulates global regulators (rot, sarS, or mgrA), various colonization factors, and exotoxin-encoding genes, as well as the ica and dlt operons. A pronounced decrease in the expression of the latter two operons explains why the graRS mutant is also biofilm-negative. The decrease of the dlt transcript in the graRS mutant correlates with a 46.7% decrease in the content of esterified d-alanyl groups in teichoic acids. The oatA/dltA double mutant showed the highest sensitivity to lysozyme; this mutant completely lacks teichoic acid–bound d-alanine esters, which are responsible for the increased susceptibility to CAMPs and peptidoglycan O-acetylation. Our results demonstrate that resistance to lysozyme can be dissected into genes mediating resistance to its muramidase activity (oatA) and genes mediating resistance to CAMPs (graRS and dlt). The two lysozyme activities act synergistically, as the oatA/dltA or oatA/graRS double mutants are much more susceptible to lysozyme than each of the single mutants. In humans, lysozyme plays an important role in the suppression of bacterial infections. However, some bacterial pathogens, such as Staphylococcus aureus, are completely resistant to lysozyme. Here we demonstrate that lysozyme acts on S. aureus in two ways: as a muramidase (cell wall lytic enzyme) and as a cationic antimicrobial peptide (CAMP). S. aureus has developed resistance mechanisms against both activities by modifying distinct cell wall structures. Modification of the peptidoglycan by O-acetylation (OatA) renders the cells resistant to the muramidase activity. Modification of teichoic acids by d-alanine esterification (Dlt) renders the cells resistant to lysozyme's CAMPs and other CAMPs. Transcriptome analysis of the glycopeptide resistance-associated (GraRS) two-component system revealed that this global regulator controls 248 genes such as other global regulators, colonization factors, or exotoxin-encoding genes. Since GraRS also upregulates the dlt operon, it was not surprising that in the graRS mutant teichoic acid d-alanylation is markedly decreased, which explains its increased sensitivity to CAMPs. By comparative analysis of mutants we were able to dissect genes that were responsive to the dual activities of lysozyme. Here we show how efficiently S. aureus is protected from the human defense system, which enables this pathogen to cause persistent infections.
Collapse
Affiliation(s)
- Silvia Herbert
- Microbial Genetics Department, University of Tübingen, Tübingen, Germany
| | - Agnieszka Bera
- Microbial Genetics Department, University of Tübingen, Tübingen, Germany
| | - Christiane Nerz
- Microbial Genetics Department, University of Tübingen, Tübingen, Germany
| | - Dirk Kraus
- Medical Microbiology and Hygiene Department, University of Tübingen, Tübingen, Germany
| | - Andreas Peschel
- Medical Microbiology and Hygiene Department, University of Tübingen, Tübingen, Germany
| | - Christiane Goerke
- Medical Microbiology and Hygiene Department, University of Tübingen, Tübingen, Germany
| | - Michael Meehl
- Department of Microbiology, Dartmouth Medical School, Hanover, New Hampshire, United States of America
| | - Ambrose Cheung
- Department of Microbiology, Dartmouth Medical School, Hanover, New Hampshire, United States of America
| | - Friedrich Götz
- Microbial Genetics Department, University of Tübingen, Tübingen, Germany
- * To whom correspondence should be addressed. E-mail:
| |
Collapse
|
42
|
Veros CT, Oldham NJ. Quantitative determination of lysozyme-ligand binding in the solution and gas phases by electrospray ionisation mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2007; 21:3505-10. [PMID: 17922488 DOI: 10.1002/rcm.3232] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Affinity constants for the binding of a range of substrate and non-substrate oligosaccharides to hen egg white lysozyme were determined by direct observation of the protein.ligand complexes using electrospray ionisation mass spectrometry (ESI-MS) with a chip-based nano-ESI source. The values obtained for a series of beta-1,4-N-acetylglucosamine oligomers (NAGn) were found to be in good agreement with those determined by fluorescence measurement. Oligomers of alpha-1,4-glucose (Glcn), which are believed to bind to lysozyme non-specifically, exhibited a 10(6)- to 10(8)-fold lower affinity for the enzyme. Lysozyme.NAGn complexes displayed an increase in Ka from n=2 to n=4, but then reached a plateau. In contrast non-specific lysozyme.Glcn complexes showed no such trend. Determination of gas-phase complex stability was achieved by quantitative collision-induced dissociation (CID) and infrared multiphoton dissociation (IRMPD) measurements. The collision energy (Ec50) or laser power (IRMPD50) required to dissociate precursor ions to 50% of their original intensity was determined for lysozyme.NAGn and Glcn complexes using the [M+8H]8+ charge state. An excellent correlation between trends in Ka and gas-phase stability was seen for NAGn oligomers bound to lysozyme, whereas no such relationship was observed with the non-specific, weaker lysozyme.Glcn complexes. These results illustrate that ESI-MS can be used to quantify the interactions between lysozyme and oligosaccharides in both the solution and gas phase and that measurement of gas-phase complex stability by CID or IRMPD can provide information about specific solution binding events.
Collapse
Affiliation(s)
- Christopher T Veros
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | | |
Collapse
|
43
|
Wade MH, de Feijter AW, Frame MK. Quantitative fluorescence imaging techniques for the study of organization and signaling mechanisms in cells. METHODS OF BIOCHEMICAL ANALYSIS 2006; 37:117-41. [PMID: 8309365 DOI: 10.1002/9780470110584.ch3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- M H Wade
- Meridian Instruments, Okemos, Michigan
| | | | | |
Collapse
|
44
|
Dennhart N, Letzel T. Mass spectrometric real-time monitoring of enzymatic glycosidic hydrolysis, enzymatic inhibition and enzyme complexes. Anal Bioanal Chem 2006; 386:689-98. [PMID: 16924382 DOI: 10.1007/s00216-006-0604-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2006] [Revised: 05/30/2006] [Accepted: 06/08/2006] [Indexed: 11/28/2022]
Abstract
The mass spectrometric development of an enzymatic assay resulting in enzymatic activity, its reaction pathway and its dissociation constant are described for the first time within a single experiment. The method combines the performance of a mass spectrometry-compatible enzyme assay with the direct detection of specific enzyme complexes using hen egg white lysozyme as a model. The continuous liquid-flow technique applied, when hyphenated with electrospray ionization (ESI)-time-of-flight (ToF)-mass spectrometry (MS), permitted the simultaneous detection of several substances involved in product screening as well as the direct observation of dissociation constants. Dissociation constants for the product inhibitor N, N', N''-triacetylchitotriose were calculated using a Scatchard plot (12 x 10(-6) M) and the law of mass action (18-24 x 10(-6) M), and these are in good agreement with constants obtained in earlier mass spectrometric (6-18 x 10(-6) M) or spectroscopic (6-8 x 10(-6) M) studies. Finally, the enzymatic hydrolysis of glycosidic substrate was monitored by ESI-ToF-MS in the presence of various inhibitors, thus leading to decreased activities in terms of their enzyme affinities. The associated inhibitor-enzyme complexes could be detected for up to lower micromolar K( d ) values.
Collapse
Affiliation(s)
- Nicole Dennhart
- Biopolymer Chemistry, Analytical Research Group, Department for Basic Life Sciences, Technical University of Munich, Weihenstephaner Berg 3, 85354, Freising-Weihenstephan, Germany
| | | |
Collapse
|
45
|
Nishimura SI, Nagahori N, Takaya K, Tachibana Y, Miura N, Monde K. Direct observation of sugar-protein, sugar-sugar, and sugar-water complexes by cold-spray ionization time-of-flight mass spectrometry. Angew Chem Int Ed Engl 2006; 44:571-5. [PMID: 15597388 DOI: 10.1002/anie.200461867] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Shin-Ichiro Nishimura
- Division of Biological Sciences, Graduate School of Science, Frontier Research Center for Post-Genome Science and Technology, Hokkaido University, Sapporo 001-0021, Japan.
| | | | | | | | | | | |
Collapse
|
46
|
Nishimura SI, Nagahori N, Takaya K, Tachibana Y, Miura N, Monde K. Direct Observation of Sugar-Protein, Sugar-Sugar, and Sugar-Water Complexes by Cold-Spray Ionization Time-of-Flight Mass Spectrometry. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200461867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
47
|
Ibrahim HR, Thomas U, Pellegrini A. A helix-loop-helix peptide at the upper lip of the active site cleft of lysozyme confers potent antimicrobial activity with membrane permeabilization action. J Biol Chem 2001; 276:43767-74. [PMID: 11560930 DOI: 10.1074/jbc.m106317200] [Citation(s) in RCA: 207] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recently, we have found that partially unfolded lysozyme exerts broad spectrum antimicrobial action in vitro against Gram-negative and Gram-positive bacteria independent of its catalytic activity. In parallel, an internal peptide (residues 98-112) of hen egg white lysozyme, obtained after digestion with clostripain, possessed broad spectrum antimicrobial action in vitro. This internal peptide is part of a helix-loop-helix domain (87-114 sequence of hen lysozyme) located at the upper lip of the active site cleft of lysozyme. The helix-loop-helix (HLH) structures are known motifs commonly found in membrane-active and DNA-binding proteins. To evaluate the contribution of the HLH peptide to the antimicrobial properties of lysozyme, the HLH sequence and its secondary structure derivatives of chicken and human lysozyme were synthesized and tested for antimicrobial activity against several bacterial strains. We found that the full HLH peptide of both chicken and human lysozymes was potently microbicidal against both Gram-positive and Gram-negative bacteria and the fungus Candida albicans. The N-terminal helix of HLH was specifically bactericidal to Gram-positive bacteria, whereas the C-terminal helix was bactericidal to all tested strains. Outer and inner membrane permeabilization studies, as well as measurements of transmembrane electrochemical potentials, provided evidence that HLH peptide and its C-terminal helix domain kill Gram-negative bacteria by crossing the outer membrane via self-promoted uptake and causing damage to the inner membrane through channel formation. The results are discussed in terms of proposed mechanisms for the catalytically independent antimicrobial activity of lysozyme that offer a new strategy for the design of potential antimicrobial drugs in the treatment of infectious diseases.
Collapse
Affiliation(s)
- H R Ibrahim
- Department of Biochemistry and Biotechnology, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan.
| | | | | |
Collapse
|
48
|
Mine S, Ueda T, Hashimoto Y, Imoto T. Analysis of the internal motion of free and ligand-bound human lysozyme by use of 15N NMR relaxation measurement: a comparison with those of hen lysozyme. Protein Sci 2000; 9:1669-84. [PMID: 11045614 PMCID: PMC2144705 DOI: 10.1110/ps.9.9.1669] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Human lysozyme has a structure similar to that of hen lysozyme and differs in amino acid sequence by 51 out of 129 residues with one insertion at the position between 47 and 48 in hen lysozyme. The backbone dynamics of free or (NAG)3-bound human lysozyme has been determined by measurements of 15N nuclear relaxation. The relaxation data were analyzed using the Lipari-Szabo formalism and were compared with those of hen lysozyme, which was already reported (Mine S et al.. 1999, J Mol Biol 286:1547-1565). In this paper, it was found that the backbone dynamics of free human and hen lysozymes showed very similar behavior except for some residues, indicating that the difference in amino acid sequence did not affect the behavior of entire backbone dynamics, but the folded pattern was the major determinant of the internal motion of lysozymes. On the other hand, it was also found that the number of residues in (NAG)3-bound human and hen lysozymes showed an increase or decrease in the order parameters at or near active sites on the binding of (NAG)3, indicating the increase in picosecond to nanosecond. These results suggested that the immobilization of residues upon binding (NAG)3 resulted in an entropy penalty and that this penalty was compensated by mobilizing other residues. However, compared with the internal motions between both ligand-bound human and hen lysozymes, differences in dynamic behavior between them were found at substrate binding sites, reflecting a subtle difference in the substrate-binding mode or efficiency of activity between them.
Collapse
Affiliation(s)
- S Mine
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | | | | | | |
Collapse
|
49
|
Northrop DB, Simpson FB. Beyond enzyme kinetics: direct determination of mechanisms by stopped-flow mass spectrometry. Bioorg Med Chem 1997; 5:641-4. [PMID: 9158861 DOI: 10.1016/s0968-0896(97)00020-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The development of soft ionization techniques has made mass spectrometry an efficient and essential tool for the determinations of the primary structures of peptides and proteins. Recently the technique has been extended at an explosive rate to noncovalent structures as well as dynamics of protein-protein interactions. We propose here that interfacing mass spectrometry with a stopped-flow mixing device and applying these new techniques of soft ionization to enzymes undergoing catalysis will provide direct access to enzyme mechanisms, both kinetic mechanisms (which describe the comings and goings of substrates, products, and inhibitors) and chemical mechanisms (which describe the order of breaking and making chemical bonds). Transient-state measurements will provide the order of reaction events; steady-state measurements will provide the distribution and therefore the relative energy level of enzyme forms participating in those events; combining transient-state and steady-state measurements is therefore expected to provide sufficient information to construct a free energy diagram of the enzyme-catalyzed reaction.
Collapse
Affiliation(s)
- D B Northrop
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin, Madison 53706, USA
| | | |
Collapse
|
50
|
Przybylski M, Glocker MO. Elektrospray-Massenspektrometrie von Biomakromoleülkomplexen mit nichtkovalenten Wechselwirkungen – neue analytische Perspektiven für supramolekulare Chemie und molekulare Erkennungsprozesse. Angew Chem Int Ed Engl 1996. [DOI: 10.1002/ange.19961080804] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|