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Maestro B, Zamora-Carreras H, Jiménez MÁ, Sanz JM. Inter-hairpin linker sequences determine the structure of the ββ-solenoid fold: a "bottom-up" study of pneumococcal LytA choline-binding module. Int J Biol Macromol 2021; 190:679-692. [PMID: 34506863 DOI: 10.1016/j.ijbiomac.2021.08.223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/29/2021] [Accepted: 08/31/2021] [Indexed: 11/24/2022]
Abstract
The ββ-solenoid structures are part of many proteins involved in the recognition of bacterial cell wall. They are elongated polypeptides consisting of repeated β-hairpins connected by linker sequences and disposed around a superhelical axis stabilised by short-range interactions. Among the most studied ββ-solenoids are those belonging to the family of choline-binding modules (CBMs) from the respiratory pathogen Streptococcus pneumoniae (pneumococcus) and its bacteriophages, and their properties have been employed to develop several biotechnological and biomedical tools. We have carried out a theoretical, spectroscopic and thermodynamic study of the ββ-solenoid structure of the CBM from the pneumococcal LytA autolysin using peptides of increasing length containing 1-3 repeats of this structure. Our results show that hints of native-like tertiary structure are only observed with a minimum of three β-hairpins, corresponding to one turn of the solenoid superhelix, and identify the linker sequences between hairpins as the major directors of the solenoid folding. This study paves the way for the rational structural engineering of ββ-solenoids aimed to find novel applications.
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Affiliation(s)
- Beatriz Maestro
- Centro de Investigaciones Biológicas Margarita Salas, Spanish National Research Council (CSIC), Madrid, Spain; Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universidad Miguel Hernández, Elche, Spain
| | - Héctor Zamora-Carreras
- Instituto de Química-Física "Rocasolano", Spanish National Research Council (CSIC), Madrid, Spain; Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - M Ángeles Jiménez
- Instituto de Química-Física "Rocasolano", Spanish National Research Council (CSIC), Madrid, Spain.
| | - Jesús M Sanz
- Centro de Investigaciones Biológicas Margarita Salas, Spanish National Research Council (CSIC), Madrid, Spain; Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universidad Miguel Hernández, Elche, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain.
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Xu X, Qu R, Wu W, Jiang C, Shao D, Shi J. Applications of microbial co-cultures in polyketides production. J Appl Microbiol 2020; 130:1023-1034. [PMID: 32897644 DOI: 10.1111/jam.14845] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/28/2020] [Accepted: 08/31/2020] [Indexed: 12/21/2022]
Abstract
Polyketides are a large group of natural biomolecules that are normally produced by bacteria, fungi and plants. These molecules have clinical importance due to their anti-cancer, anti-microbial, anti-oxidant and anti-inflammatory properties. Polyketides are biosynthesized from units of acyl-CoA by different polyketide synthases (PKSs), which display wide diversity of functional domains and mechanisms of action between fungi and bacteria. Co-culture of different micro-organisms can produce novel products distinctive from those produced during single cultures. This study compared the new polyketides produced in such co-culture systems and discusses aspects of the cultivation systems, product structures and identification techniques. Current results indicate that the formation of new polyketides may be the result of activation of previously silent PKSs genes induced during co-culture. This review indicated a potential way to produce pure therapeutic polyketides by microbial fermentation and a potential way to develop functional foods and agricultural products using co-co-culture of different micro-organisms. It also pointed out a new perspective for studies on the process of functional foods, especially those involving multiple micro-organisms.
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Affiliation(s)
- X Xu
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - R Qu
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - W Wu
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - C Jiang
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - D Shao
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - J Shi
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
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Choline Binding Proteins from Streptococcus pneumoniae: A Dual Role as Enzybiotics and Targets for the Design of New Antimicrobials. Antibiotics (Basel) 2016; 5:antibiotics5020021. [PMID: 27314398 PMCID: PMC4929436 DOI: 10.3390/antibiotics5020021] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 05/04/2016] [Accepted: 05/16/2016] [Indexed: 12/20/2022] Open
Abstract
Streptococcus pneumoniae (pneumococcus) is an important pathogen responsible for acute invasive and non-invasive infections such as meningitis, sepsis and otitis media, being the major cause of community-acquired pneumonia. The fight against pneumococcus is currently hampered both by insufficient vaccine coverage and by rising antimicrobial resistances to traditional antibiotics, making necessary the research on novel targets. Choline binding proteins (CBPs) are a family of polypeptides found in pneumococcus and related species, as well as in some of their associated bacteriophages. They are characterized by a structural organization in two modules: a functional module (FM), and a choline-binding module (CBM) that anchors the protein to the choline residues present in the cell wall through non-covalent interactions. Pneumococcal CBPs include cell wall hydrolases, adhesins and other virulence factors, all playing relevant physiological roles for bacterial viability and virulence. Moreover, many pneumococcal phages also make use of hydrolytic CBPs to fulfill their infectivity cycle. Consequently, CBPs may play a dual role for the development of novel antipneumococcal drugs, both as targets for inhibitors of their binding to the cell wall and as active cell lytic agents (enzybiotics). In this article, we review the current state of knowledge about host- and phage-encoded pneumococcal CBPs, with a special focus on structural issues, together with their perspectives for effective anti-infectious treatments.
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Zamora-Carreras H, Maestro B, Strandberg E, Ulrich AS, Sanz JM, Jiménez MÁ. Micelle-Triggered β-Hairpin to α-Helix Transition in a 14-Residue Peptide from a Choline-Binding Repeat of the Pneumococcal Autolysin LytA. Chemistry 2015; 21:8076-89. [PMID: 25917218 PMCID: PMC4471590 DOI: 10.1002/chem.201500447] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Indexed: 11/08/2022]
Abstract
Choline-binding modules (CBMs) have a ββ-solenoid structure composed of choline-binding repeats (CBR), which consist of a β-hairpin followed by a short linker. To find minimal peptides that are able to maintain the CBR native structure and to evaluate their remaining choline-binding ability, we have analysed the third β-hairpin of the CBM from the pneumococcal LytA autolysin. Circular dichroism and NMR data reveal that this peptide forms a highly stable native-like β-hairpin both in aqueous solution and in the presence of trifluoroethanol, but, strikingly, the peptide structure is a stable amphipathic α-helix in both zwitterionic (dodecylphosphocholine) and anionic (sodium dodecylsulfate) detergent micelles, as well as in small unilamellar vesicles. This β-hairpin to α-helix conversion is reversible. Given that the β-hairpin and α-helix differ greatly in the distribution of hydrophobic and hydrophilic side chains, we propose that the amphipathicity is a requirement for a peptide structure to interact and to be stable in micelles or lipid vesicles. To our knowledge, this "chameleonic" behaviour is the only described case of a micelle-induced structural transition between two ordered peptide structures.
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Affiliation(s)
- Héctor Zamora-Carreras
- Instituto de Química Física Rocasolano (IQFR), Consejo Superior de Investigaciones Científicas (CSIC), Serrano 119, 28006-Madrid (Spain)
| | - Beatriz Maestro
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202-Alicante (Spain)
| | - Erik Strandberg
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), P.O.B. 3640, 76021 Karlsruhe (Germany)
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), P.O.B. 3640, 76021 Karlsruhe (Germany)
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe (Germany)
| | - Jesús M Sanz
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, 03202-Alicante (Spain)
| | - M Ángeles Jiménez
- Instituto de Química Física Rocasolano (IQFR), Consejo Superior de Investigaciones Científicas (CSIC), Serrano 119, 28006-Madrid (Spain).
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Stability, denaturation and refolding of Mycobacterium tuberculosis MfpA, a DNA mimicking protein that confers antibiotic resistance. Biophys Chem 2011; 159:33-40. [PMID: 21605934 DOI: 10.1016/j.bpc.2011.04.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 04/25/2011] [Accepted: 04/25/2011] [Indexed: 11/20/2022]
Abstract
MfpA from Mycobacterium tuberculosis is a founding member of the pentapeptide repeat class of proteins (PRP) that is believed to confer bacterial resistance to the drug fluoroquinolone by mimicking the size, shape and surface charge of duplex DNA. We show that phenylalanine side chain stacking stabilizes the N-terminus of MfpA's pentapeptide thus extending the DNA mimicry analogy. The Lumry-Eyring model was applied to multiple spectral measures of MfpA denaturation revealing that the MfpA dimer dissociates to monomers which undergo a structural transition that leads to aggregation. MfpA retains high secondary and tertiary structure content under denaturing conditions. Dimerization stabilizes MfpA's pentapeptide repeat fold. The high Arrhenius activation energy of the barrier to aggregate formation rationalizes its stability. The mechanism of MfpA denaturation and refolding is a 'double funnel' energy landscape where the 'native' and 'aggregate' funnels are separated by the high barrier that is not overcome during in vitro refolding.
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Fano M, van de Weert M, Moeller EH, Kruse NA, Frokjaer S. Ionic strength-dependent denaturation of Thermomyces lanuginosus lipase induced by SDS. Arch Biochem Biophys 2010; 506:92-8. [PMID: 21093408 DOI: 10.1016/j.abb.2010.11.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2010] [Revised: 11/09/2010] [Accepted: 11/11/2010] [Indexed: 11/29/2022]
Abstract
Triglyceride lipase from Thermomyces lanuginosus (TlL) has been reported to be resistant to denaturation by sodium dodecyl sulfate (SDS). We have found that at neutral pH, structural integrity is strongly dependent on ionic strength. In 10mM phosphate buffer and SDS, the lipase exhibits a far-UV CD spectrum similar to other proteins denatured in this surfactant while the near-UV CD spectrum shows a complete loss of tertiary structure, observations supported by steady state fluorescence spectroscopy. However, when increasing the ionic strength by the addition of NaCl, the lipase was rendered resistant towards SDS denaturation, as observed by all techniques employed. The effect of salt on the critical micelle concentration (CMC) of SDS was observed to correlate with the effect on the degree of SDS-induced denaturation. This finding is compatible with the notion that the concentration of SDS monomers is a crucial factor for SDS-lipase interactions. The presented results are important for the understanding and improvement of protein stability in surfactant systems.
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Affiliation(s)
- Mathias Fano
- Department of Pharmaceutics and Analytical Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Denmark.
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Maestro B, Santiveri CM, Jiménez MA, Sanz JM. Structural autonomy of a β-hairpin peptide derived from the pneumococcal choline-binding protein LytA. Protein Eng Des Sel 2010; 24:113-22. [DOI: 10.1093/protein/gzq087] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Schneider GF, Shaw BF, Lee A, Carillho E, Whitesides GM. Pathway for unfolding of ubiquitin in sodium dodecyl sulfate, studied by capillary electrophoresis. J Am Chem Soc 2009; 130:17384-93. [PMID: 19035631 DOI: 10.1021/ja804736t] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
This paper characterizes the complexes formed by a small protein, ubiquitin (UBI), and a negatively charged surfactant, sodium dodecyl sulfate (SDS), using capillary electrophoresis (CE), circular dichroism (CD), and amide hydrogen-deuterium exchange (HDX; as monitored by mass spectroscopy, MS). Capillary electrophoresis of complexes of UBI and SDS, at apparent equilibrium, at concentrations of SDS ranging from sub-micellar and sub-denaturing to micellar and denaturing, revealed multiple complexes of UBI and SDS of the general composition UBI-SDS(n). Examination of electrophoretic mobilities of complexes of UBI and SDS as a function of the concentration of SDS provided a new way to characterize the interaction of this protein with SDS and established key characteristics of this system: e.g., the reversibility of the formation of the complexes, their approximate chemical compositions, and the pathway of SDS binding to UBI. The work identified, in addition to SDS-saturated UBI, at least six groups of complexes of UBI with SDS, within which four groups were populated with complexes of distinct stoichiometries: UBI-SDS(approximately 11), UBI-SDS(approximately 25), UBI-SDS(approximately 33), and UBI-SDS(approximately 42). CD spectroscopy and amide HDX of the UBI-SDS(n) complexes suggested that many of the UBI-SDS(n) complexes (n > 11) have greater alpha-helical content than native UBI. Capillary electrophoresis provides a level of detail about interactions of proteins and SDS that has not previously been accessible, and CE is an analytical and biophysical method for studies of interactions of proteins and surfactants that is both convenient and practical. This study sheds light on the formation of the enigmatic protein-SDS complexes formed during SDS polyacrylamide gel electrophoresis and brings a new tool to the study of proteins and detergents.
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Affiliation(s)
- Grégory F Schneider
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
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Hernández-Rocamora VM, Maestro B, Mollá-Morales A, Sanz JM. Rational stabilization of the C-LytA affinity tag by protein engineering. Protein Eng Des Sel 2008; 21:709-20. [PMID: 18840883 DOI: 10.1093/protein/gzn046] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The C-LytA protein constitutes the choline-binding module of the LytA amidase from Streptococcus pneumoniae. Owing to its affinity for choline and analogs, it is regularly used as an affinity tag for the purification of proteins in a single chromatographic step. In an attempt to build a robust variant against thermal denaturation, we have engineered several salt bridges on the protein surface. All the stabilizing mutations were pooled in a single variant, C-LytAm7, which contained seven changes: Y25K, F27K, M33E, N51K, S52K, T85K and T108K. The mutant displays a 7 degrees C thermal stabilization compared with the wild-type form, together with a complete reversibility upon heating and a higher kinetic stability. Moreover, the accumulation of intermediates in the unfolding of C-LytA is virtually abolished for C-LytAm7. The differences in stability become more evident when the proteins are bound to a DEAE-cellulose affinity column, as most of wild-type C-LytA is denatured at approximately 65 degrees C, whereas C-LytAm7 may stand temperatures up to 90 degrees C. Finally, the change in the isoelectric point of C-LytAm7 enhances its solubility at acidic pHs. Therefore, C-LytAm7 behaves as an improved affinity tag and supports the engineering of surface salt bridges as an effective approach for protein stabilization.
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Affiliation(s)
- Víctor M Hernández-Rocamora
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Avda Universidad s/n, Elche 03202, Spain
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Andersen KK, Westh P, Otzen DE. Global study of myoglobin-surfactant interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:399-407. [PMID: 18069862 DOI: 10.1021/la702890y] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Surfactants interact with proteins in multifarious ways which depend on surfactant concentration and structure. To obtain a global overview of this process, we have analyzed the interaction of horse myoglobin (Mb) with an anionic (SDS) and cationic (CTAC) surfactant, using both equilibrium titration techniques and stopped-flow kinetics. Binding and kinetics of conformational changes can be divided into a number of different regions (five below the cmc and one above) with very distinct features (broadly similar between the two surfactants, despite their difference in head group and chain length), which nuance the classical view of biphasic binding prior to micellization. In stage A, fairly weak interactions lead to a linear decrease in thermal stability. This gives way to a more cooperative process in stage B, where aggregates (presumably hemimicelles) start to form on the protein surface, leading to global denaturation (loss of a thermal transition) and biphasic unfolding kinetics. This is consolidated in stage C with titratable surfactant adsorption. Adsorption of this surfactant species leads to significant changes in kinetics, namely, inhibition of unfolding kinetics in CTAC and altered unfolding amplitudes in SDS, though the process is still biphasic in both surfactants. Stage D commences the reduction in exothermic binding signals, leading to further uptake of 5 (SDS) or 31 (CTAC) surfactant molecules without any major changes in protein conformation. In stage E many more surfactant molecules (46 SDS and 39 CTAC) are bound, presumably as quasi-micellar structures, and we observe a very slow unfolding phase in SDS, which disappears as we reach the cmc. Above the cmc, the unfolding rates remain essentially constant in SDS, but increase significantly in CTAC, possibly because binding of bulk micelles removes the inhibition by hemimicellar aggregates. Our work highlights the fascinating richness of conformational changes that proteins can undergo in the presence of molecules with self-assembling properties.
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Affiliation(s)
- Kell K Andersen
- Interdisciplinary Nanoscience Centre, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
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