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Ó'Fágáin C. Protein Stability: Enhancement and Measurement. Methods Mol Biol 2023; 2699:369-419. [PMID: 37647007 DOI: 10.1007/978-1-0716-3362-5_18] [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] [Indexed: 09/01/2023]
Abstract
This chapter defines protein stability, emphasizes its importance, and surveys the field of protein stabilization, with summary reference to a selection of 2014-2021 publications. One can enhance stability, particularly by protein engineering strategies but also by chemical modification and by other means. General protocols are set out on how to measure a given protein's (i) kinetic thermal stability and (ii) oxidative stability and (iii) how to undertake chemical modification of a protein in solution.
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Affiliation(s)
- Ciarán Ó'Fágáin
- School of Biotechnology, Dublin City University, Dublin, Ireland.
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2
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Ma Q, Lei H, Cao Y. Intramolecular covalent bonds in Gram-positive bacterial surface proteins. Chembiochem 2022; 23:e202200316. [PMID: 35801833 DOI: 10.1002/cbic.202200316] [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: 06/03/2022] [Revised: 07/07/2022] [Indexed: 11/09/2022]
Abstract
Gram-positive bacteria experience considerable mechanical perturbation when adhering to host surfaces during colonization and infection. They have evolved various adhesion proteins that are mechanically robust to ensure strong surface adhesion. Recently, it was discovered that these adhesion proteins contain rare, extra intramolecular covalent bonds that stabilize protein structures and participate in surface bonding. These intramolecular covalent bonds include isopeptides, thioesters, and ester bonds, which often form spontaneously without the need for additional enzymes. With the development of single-molecule force spectroscopy techniques, the detailed mechanical roles of these intramolecular covalent bonds have been revealed. In this review, we summarize the recent advances in this area of research, focusing on the link between the mechanical stability and function of these covalent bonds in Gram-positive bacterial surface proteins. We also highlight the potential impact of these discoveries on the development of novel antibiotics and chemical biology tools.
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Affiliation(s)
- Quan Ma
- Nanjing University, Department of Physics, CHINA
| | - Hai Lei
- Nanjing University, Department of Physics, CHINA
| | - Yi Cao
- Nanjing University, Department of Physics, 22 Hankou Road, 210093, Nanjing, CHINA
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3
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Abstract
Intramolecular isopeptide bonds, formed autocatalytically between Lys and Asn/Asp side chains, are widely present in the immunoglobulin-like domains of Gram-positive bacterial adhesins, including Group A Streptococcus, and confer considerable mechanical and chemical stability. These properties make them attractive for applications in biotechnology. Here, we detail the practical considerations that are involved in engineering isopeptide bonds into Ig-like proteins, including the choice of a site where bond-forming residues could be introduced and the appropriate methodology for mutagenesis. We specify how to determine whether an isopeptide bond has formed, what strategies can be adopted to overcome problems, and how to monitor the stability of the engineered protein.
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4
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Nakata M, Kreikemeyer B. Genetics, Structure, and Function of Group A Streptococcal Pili. Front Microbiol 2021; 12:616508. [PMID: 33633705 PMCID: PMC7900414 DOI: 10.3389/fmicb.2021.616508] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/18/2021] [Indexed: 12/12/2022] Open
Abstract
Streptococcus pyogenes (Group A Streptococcus; GAS) is an exclusively human pathogen. This bacterial species is responsible for a large variety of infections, ranging from purulent but mostly self-limiting oropharynx/skin diseases to streptococcal sequelae, including glomerulonephritis and rheumatic fever, as well as life-threatening streptococcal toxic-shock syndrome. GAS displays a wide array of surface proteins, with antigenicity of the M protein and pili utilized for M- and T-serotyping, respectively. Since the discovery of GAS pili in 2005, their genetic features, including regulation of expression, and structural features, including assembly mechanisms and protein conformation, as well as their functional role in GAS pathogenesis have been intensively examined. Moreover, their potential as vaccine antigens has been studied in detail. Pilus biogenesis-related genes are located in a discrete section of the GAS genome encoding fibronectin and collagen binding proteins and trypsin-resistant antigens (FCT region). Based on the heterogeneity of genetic composition and DNA sequences, this region is currently classified into nine distinguishable forms. Pili and fibronectin-binding proteins encoded in the FCT region are known to be correlated with infection sites, such as the skin and throat, possibly contributing to tissue tropism. As also found for pili of other Gram-positive bacterial pathogens, GAS pilin proteins polymerize via isopeptide bonds, while intramolecular isopeptide bonds present in the pilin provide increased resistance to degradation by proteases. As supported by findings showing that the main subunit is primarily responsible for T-serotyping antigenicity, pilus functions and gene expression modes are divergent. GAS pili serve as adhesins for tonsillar tissues and keratinocyte cell lines. Of note, a minor subunit is considered to have a harpoon function by which covalent thioester bonds with host ligands are formed. Additionally, GAS pili participate in biofilm formation and evasion of the immune system in a serotype/strain-specific manner. These multiple functions highlight crucial roles of pili during the onset of GAS infection. This review summarizes the current state of the art regarding GAS pili, including a new mode of host-GAS interaction mediated by pili, along with insights into pilus expression in terms of tissue tropism.
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Affiliation(s)
- Masanobu Nakata
- Department of Oral Microbiology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology and Hygiene, University of Rostock, Rostock, Germany
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5
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Wang JL, Chen WG, Zhang JJ, Xu CJ. Nogo-A-Δ20/EphA4 interaction antagonizes apoptosis of neural stem cells by integrating p38 and JNK MAPK signaling. J Mol Histol 2021; 52:521-537. [PMID: 33555537 DOI: 10.1007/s10735-021-09960-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 01/25/2021] [Indexed: 11/26/2022]
Abstract
Nogo-A protein consists of two main extracellular domains: Nogo-66 (rat amino acid [aa] 1019-1083) and Nogo-A-Δ20 (extracellular, active 180 amino acid Nogo-A region), which serve as strong inhibitors of axon regeneration in the adult CNS (Central Nervous System). Although receptors S1PR2 and HSPGs have been identified as Nogo-A-Δ20 binding proteins, it remains at present elusive whether other receptors directly interacting with Nogo-A-Δ20 exist, and decrease cell death. On the other hand, the key roles of EphA4 in the regulation of glioblastoma, axon regeneration and NSCs (Neural Stem Cells) proliferation or differentiation are well understood, but little is known the relationship between EphA4 and Nogo-A-Δ20 in NSCs apoptosis. Thus, we aim to determine whether Nogo-A-Δ20 can bind to EphA4 and affect survival of NSCs. Here, we discover that EphA4, belonging to a member of erythropoietin-producing hepatocellular (Eph) receptors family, could be acting as a high affinity ligand for Nogo-A-Δ20. Trans-membrane protein of EphA4 is needed for Nogo-A-Δ20-triggered inhibition of NSCs apoptosis, which are mediated by balancing p38 inactivation and JNK MAPK pathway activation. Finally, we predict at the atomic level that essential residues Lys-205, Ile-190, Pro-194 in Nogo-A-Δ20 and EphA4 residues Gln-390, Asn-425, Pro-426 might play critical roles in Nogo-A-Δ20/EphA4 binding via molecular docking.
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Affiliation(s)
- Jun-Ling Wang
- Center for Reproductive Medicine, Affiliated Hospital 1 of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China
| | - Wei-Guang Chen
- Department of Histology & Embryology, School of Basic Medical Science, Wenzhou Medical University, Cha Shan University Town, No.1 Central North Road, Wenzhou, 325035, Zhejiang, People's Republic of China
| | - Jia-Jia Zhang
- School of 1St Clinical Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, People's Republic of China
| | - Chao-Jin Xu
- Department of Histology & Embryology, School of Basic Medical Science, Wenzhou Medical University, Cha Shan University Town, No.1 Central North Road, Wenzhou, 325035, Zhejiang, People's Republic of China.
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6
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Zhang F, Zhang W. Encrypting Chemical Reactivity in Protein Sequences toward
Information‐Coded
Reactions
†. CHINESE J CHEM 2020. [DOI: 10.1002/cjoc.202000083] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Fan Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 China
| | - Wen‐Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 China
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Mitkowski P, Jagielska E, Nowak E, Bujnicki JM, Stefaniak F, Niedziałek D, Bochtler M, Sabała I. Structural bases of peptidoglycan recognition by lysostaphin SH3b domain. Sci Rep 2019; 9:5965. [PMID: 30979923 PMCID: PMC6461655 DOI: 10.1038/s41598-019-42435-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 03/29/2019] [Indexed: 11/09/2022] Open
Abstract
Staphylococcus simulans lysostaphin cleaves pentaglycine cross-bridges between stem peptides in the peptidoglycan of susceptible staphylococci, including S. aureus. This enzyme consists of an N-terminal catalytic domain and a cell wall binding domain (SH3b), which anchors the protein to peptidoglycan. Although structures of SH3bs from lysostaphin are available, the binding modes of peptidoglycan to these domains are still unclear. We have solved the crystal structure of the lysostaphin SH3b domain in complex with a pentaglycine peptide representing the peptidoglycan cross-bridge. The structure identifies a groove between β1 and β2 strands as the pentaglycine binding site. The structure suggests that pentaglycine specificity of the SH3b arises partially directly by steric exclusion of Cβ atoms in the ligand and partially indirectly due to the selection of main chain conformations that are easily accessible for glycine, but not other amino acid residues. We have revealed further interactions of SH3b with the stem peptides with the support of bioinformatics tools. Based on the structural data we have attempted engineering of the domain specificity and have investigated the relevance of the introduced substitutions on the domain binding and specificity, also in the contexts of the mature lysostaphin and of its bacteriolytic activity.
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Affiliation(s)
- Paweł Mitkowski
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Elżbieta Jagielska
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Elżbieta Nowak
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Janusz M Bujnicki
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.,Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Filip Stefaniak
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Dorota Niedziałek
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
| | - Matthias Bochtler
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.,Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
| | - Izabela Sabała
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
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8
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Wang XW, Zhang WB. Chemical Topology and Complexity of Protein Architectures. Trends Biochem Sci 2018; 43:806-817. [DOI: 10.1016/j.tibs.2018.07.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/01/2018] [Accepted: 07/03/2018] [Indexed: 12/16/2022]
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Cao Y, Liu D, Zhang WB. Supercharging SpyCatcher toward an intrinsically disordered protein with stimuli-responsive chemical reactivity. Chem Commun (Camb) 2018; 53:8830-8833. [PMID: 28692103 DOI: 10.1039/c7cc04507g] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We report a supercharged, intrinsically disordered protein, SpyCatcher(-), possessing stimuli-responsive reactivity toward SpyTag with tunable yields ranging from 4% to 98% depending on pH, temperature, ionic strength, etc. The CD and NMR studies reveal that the reaction occurs through a folded intermediate formed probably via a different mechanism from that of SpyCatcher.
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Affiliation(s)
- Yang Cao
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China.
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10
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Hong Q, Zhou S, Zhao H, Peng J, Li Y, Shang Y, Wu M, Zhang W, Lu S, Li S, Yu S, Wang W, Wang Q. Allergenicity of recombinant Humulus japonicus pollen allergen 1 after combined exposure to ozone and nitrogen dioxide. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 234:707-715. [PMID: 29241157 DOI: 10.1016/j.envpol.2017.11.078] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/07/2017] [Accepted: 11/24/2017] [Indexed: 06/07/2023]
Abstract
Ozone (O3) and nitrogen dioxide (NO2) are thought to play primary roles in aggravating air pollution-induced health problems. However, the effects of joint O3/NO2 on the allergenicity of pollen allergens are unclear. Humulus japonicus pollen allergen 1 (Hum j1) is a profilin protein that causes widespread pollinosis in eastern Asia. In order to study the effects of combined O3/NO2 on the allergenicity of Hum j1, tandem six-histidine peptide tag (His6)-fused recombinant Hum j1 (rHum j1) was expressed in a prokaryotic system and purified through His6 affinity chromatography. The purified rHum j1 was used to immunize SD rats. Rat sera with high titers of IgG and IgE antibodies against rHum j1 were used for allergenicity quantification. The rHum j1 was exposed to O3/NO2, and changes in allergenicity of the exposed rHum j1 were assayed using the immunized rat antibodies. Tandem LC-MS/LC (liquid chromatography-mass spectrometer/liquid chromatography spectrometer) chromatography and UV and circular dichroism (CD) spectroscopy were used to study the structural changes in rHum j1. Our data demonstrated that a novel disulfide bond between the sulfhydryl groups of two neighboring cysteine molecules was formed after the rHum j1 exposure to joint O3/NO2, and therefore IgE-binding affinity was increased and the allergenicity was reinforced. Our results provided clues to elucidate the mechanism behind air pollution-induced increase in pollinosis prevalence.
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Affiliation(s)
- Qiang Hong
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China; School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Shumin Zhou
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Hui Zhao
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
| | - Jiaxian Peng
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
| | - Yang Li
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Yu Shang
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Minghong Wu
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
| | - Wei Zhang
- School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Senlin Lu
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China.
| | - Shuijun Li
- Shanghai Xuhui Center Hospital, Shanghai 200031, China
| | - Shen Yu
- Shanghai Xuhui Center Hospital, Shanghai 200031, China
| | - Weiqian Wang
- School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Qingyue Wang
- School of Science and Engineering, Saitama University, Saitama 338-8570, Japan.
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11
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Unleashing chemical power from protein sequence space toward genetically encoded “click” chemistry. CHINESE CHEM LETT 2017. [DOI: 10.1016/j.cclet.2017.08.052] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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