1
|
Nasiri A, Golestani N, Rajabi S, Hashemi M. Facile and green synthesis of recyclable, environmentally friendly, chemically stable, and cost-effective magnetic nanohybrid adsorbent for tetracycline adsorption. Heliyon 2024; 10:e24179. [PMID: 38293470 PMCID: PMC10825349 DOI: 10.1016/j.heliyon.2024.e24179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/19/2023] [Accepted: 01/04/2024] [Indexed: 02/01/2024] Open
Abstract
Antibiotic contamination of water sources, particularly tetracycline (TC) contamination, has emerged as one of the global issues that needs action. In this research, ZnCoFe2O4@Chitosan (Ch) as a magnetic nanohybrid adsorbent was synthesized using the microwave-assisted co-precipitation method, and their efficiency for the TC adsorption process was investigated. FESEM (Field Emission Scanning Electron Microscope), EDX (Energy Dispersive X-ray), Mapping and line Scan, XRD (X-Ray Diffraction), FTIR (Fourier Transform Infrared Spectrometer), VSM (Vibrating Sample Magnetometer), Thermogravimetric analysis (TGA) and BET (Brunauer Emmett Teller) techniques were used to check and verify its physical and chemical properties. The removal of TC via the adsorption process from synthetic and real wastewater samples was investigated. The factors determining the TC adsorption process, comprising tetracycline concentration (5-30 mg/L), adsorbent dosage (0.7-2 g/L), contact time (2-45 min), and pH (3-11), were evaluated. The removal effectiveness for the synthetic sample and the real wastewater sample was 93 % and 80 %, respectively, under the ideal TC adsorption process parameters of pH 3, adsorbent dosage 1 g/L, TC initial concentration 5 mg/L, and contact time 30 min. According to kinetic and equilibrium studies, the adsorption of TC by ZnCoFe2O4@Ch follows pseudo-second-order kinetics and the Freundlich isotherm. Additionally, it was determined through the analysis of thermodynamic data that the process of exothermic adsorption is spontaneous and is followed by a decrease in disorder (ΔH = -15.16 kJ/mol, ΔS = -28.69 kJ/mol, and ΔG = -6.62 kJ/mol). After five cycles of recovery and regeneration, the ZnCoFe2O4@Ch magnetic nanocomposite was able to remove 65 % of the TC pollutant and had good chemical stability. The results showed that the magnetic nano-adsorbent ZnCoFe2O4@Ch is a novel magnetic nano-adsorbent with high adsorption capacity that can be utilized to eliminate pharmaceutical contaminants from aqueous solutions.
Collapse
Affiliation(s)
- Alireza Nasiri
- Environmental Health Engineering Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Najmeh Golestani
- Environmental Health Engineering Research Center, Kerman University of Medical Sciences, Kerman, Iran
- Department of Environmental Health Engineering, Kerman University of Medical Sciences, Kerman, Iran
| | - Saeed Rajabi
- Environmental Health Engineering Research Center, Kerman University of Medical Sciences, Kerman, Iran
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Environmental Health Engineering, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Majid Hashemi
- Environmental Health Engineering Research Center, Kerman University of Medical Sciences, Kerman, Iran
- Department of Environmental Health Engineering, Kerman University of Medical Sciences, Kerman, Iran
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran
| |
Collapse
|
2
|
Massaro M, Cagnoni AJ, Medrano FJ, Pérez-Sáez JM, Abdullayev S, Belkhadem K, Mariño KV, Romero A, Roy R, Rabinovich GA. Selective modifications of lactose and N-acetyllactosamine with sulfate and aromatic bulky groups unveil unique structural insights in galectin-1-ligand recognition. Bioorg Med Chem 2023; 94:117480. [PMID: 37774448 DOI: 10.1016/j.bmc.2023.117480] [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: 07/15/2023] [Revised: 09/01/2023] [Accepted: 09/18/2023] [Indexed: 10/01/2023]
Abstract
Galectins, a family of endogenous glycan-binding proteins, play crucial roles in a broad range of physiological and pathological processes. Galectin-1 (Gal-1), a proto-type member of this family, is overexpressed in several cancers and plays critical roles in tumor-immune escape, angiogenesis and metastasis. Thus, generation of high-affinity Gal-1 inhibitors emerges as an attractive therapeutic approach for a wide range of neoplastic conditions. Small-molecule carbohydrate inhibitors based on lactose (Lac) and N-acetyllactosamine (LacNAc) structures have been tested showing different results. In this study, we evaluated Lac- and LacNAc-based compounds with specific chemical modifications at key positions as Gal-1 ligands by competitive solid-phase assays (SPA) and isothermal titration calorimetry (ITC). Both assays showed excellent correlation, highlighting that lactosides bearing bulky aromatic groups at the anomeric carbon and sulfate groups at the O3' position exhibited the highest binding affinities. To dissect the atomistic determinants for preferential affinity of the different tested Gal-1 ligands, molecular docking simulations were conducted and PRODIGY-LIG structure-based method was employed to predict binding affinity in protein-ligand complexes. Notably, calculated binding free energies derived from the molecular docking were in accordance with experimental values determined by SPA and ITC, showing excellent correlation between theoretical and experimental approaches. Moreover, this analysis showed that 3'-O-sulfate groups interact with residues of the Gal-1 subsite B, mainly with Asn33, while the ester groups of the aromatic anomeric group interact with Gly69 and Thr70 at Gal-1 subsite E, extending deeper into the pocket, which could account for the enhanced binding affinity. This study contributes to the rational design of highly optimized Gal-1 inhibitors to be further studied in cancer models and other pathologic conditions.
Collapse
Affiliation(s)
- Mora Massaro
- Laboratorio de Glicomedicina, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1428 Ciudad de Buenos Aires, Argentina; Laboratorio de Glicómica Funcional y Molecular, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1428 Ciudad de Buenos Aires, Argentina
| | - Alejandro J Cagnoni
- Laboratorio de Glicomedicina, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1428 Ciudad de Buenos Aires, Argentina; Laboratorio de Glicómica Funcional y Molecular, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1428 Ciudad de Buenos Aires, Argentina
| | - Francisco J Medrano
- Centro de Investigaciones Biológicas "Margarita Salas" (CIB), CSIC, E-28040 Madrid, Spain
| | - Juan M Pérez-Sáez
- Laboratorio de Glicomedicina, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1428 Ciudad de Buenos Aires, Argentina
| | - Shuay Abdullayev
- Glycosciences and Nanomaterials Laboratory, Université du Québec à Montréal, Succ. Centre-Ville, P.O. Box 8888, Montréal, QC H3C 3P8, Canada
| | - Karima Belkhadem
- Glycosciences and Nanomaterials Laboratory, Université du Québec à Montréal, Succ. Centre-Ville, P.O. Box 8888, Montréal, QC H3C 3P8, Canada
| | - Karina V Mariño
- Laboratorio de Glicómica Funcional y Molecular, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1428 Ciudad de Buenos Aires, Argentina
| | - Antonio Romero
- Centro de Investigaciones Biológicas "Margarita Salas" (CIB), CSIC, E-28040 Madrid, Spain.
| | - René Roy
- Glycosciences and Nanomaterials Laboratory, Université du Québec à Montréal, Succ. Centre-Ville, P.O. Box 8888, Montréal, QC H3C 3P8, Canada.
| | - Gabriel A Rabinovich
- Laboratorio de Glicomedicina, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1428 Ciudad de Buenos Aires, Argentina; Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428 Ciudad de Buenos Aires, Argentina.
| |
Collapse
|
3
|
Blachnio M, Zienkiewicz-Strzalka M, Derylo-Marczewska A, Nosach LV, Voronin EF. Chitosan-Silica Composites for Adsorption Application in the Treatment of Water and Wastewater from Anionic Dyes. Int J Mol Sci 2023; 24:11818. [PMID: 37511577 PMCID: PMC10380244 DOI: 10.3390/ijms241411818] [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: 06/30/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
A series of new types of composites (biopolymer-silica materials) are proposed as selective and effective adsorbents. A new procedure for the synthesis of chitosan-nanosilica composites (ChNS) and chitosan-silica gel composites (ChSG) using geometrical modification of silica and mechanosorption of chitosan is applied. The highest adsorption efficiency was achieved at pH = 2, hence the desirability of modifications aimed at stabilizing chitosan in such conditions. The amount of chitosan in the synthesis grew to 1.8 times the adsorption capacity for the nanosilica-supported materials and 1.6 times for the silica gel-based composites. The adsorption kinetics of anionic dyes (acid red AR88) was faster for ChNS than for ChSG, which results from a silica-type effect. The various structural, textural, and physicochemical aspects of the chitosan-silica adsorbents were analyzed via small-angle X-ray scattering, scanning electron microscopy, low-temperature gas (nitrogen) adsorption, and potentiometric titration, as well as their adsorption effectiveness towards selected dyes. This indicates the synergistic effect of the presence of dye-binding groups of the chitosan component, and the developed interfacial surface of the silica component in composites.
Collapse
Affiliation(s)
- Magdalena Blachnio
- Faculty of Chemistry, Maria Curie-Sklodowska University, M. Curie-Sklodowska Sq. 3, 20-031 Lublin, Poland
| | | | - Anna Derylo-Marczewska
- Faculty of Chemistry, Maria Curie-Sklodowska University, M. Curie-Sklodowska Sq. 3, 20-031 Lublin, Poland
| | - Liudmyla V Nosach
- Chuiko Institute of Surface Chemistry, National Academy of Sciences of Ukraine, 17 General Naumov Str., 03164 Kyiv, Ukraine
| | - Eugeny F Voronin
- Chuiko Institute of Surface Chemistry, National Academy of Sciences of Ukraine, 17 General Naumov Str., 03164 Kyiv, Ukraine
| |
Collapse
|
4
|
CuCoFe2O4@MC/AC as a new hybrid magnetic nanocomposite for metronidazole removal from wastewater: Bioassay and toxicity of effluent. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2022.121366] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
5
|
Porciúncula-González C, Cagnoni AJ, Fontana C, Mariño KV, Saenz-Méndez P, Giacomini C, Irazoqui G. Structural insights in galectin-1-glycan recognition: Relevance of the glycosidic linkage and the N-acetylation pattern of sugar moieties. Bioorg Med Chem 2021; 44:116309. [PMID: 34293617 DOI: 10.1016/j.bmc.2021.116309] [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: 02/04/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 10/20/2022]
Abstract
Galectins, soluble lectins widely expressed intra- and extracellularly in different cell types, play major roles in deciphering the cellular glycocode. Galectin-1 (Gal-1), a prototype member of this family, presents a carbohydrate recognition domain (CRD) with specific affinity for β-galactosides such as N-acetyllactosamine (β-d-Galp-(1 → 4)-d-GlcpNAc), and mediate numerous physiological and pathological processes. In this work, Gal-1 binding affinity for β-(1 → 6) galactosides, including β-d-Galp-(1 → 6)-β-d-GlcpNAc-(1 → 4)-d-GlcpNAc was evaluated, and their performance was compared to that of β-(1 → 4) and β-(1 → 3) galactosides. To this end, the trisaccharide β-d-Galp-(1 → 6)-β-d-GlcpNAc-(1 → 4)-d-GlcpNAc was enzymatically synthesized, purified and structurally characterized. To evaluate the affinity of Gal-1 for the galactosides, competitive solid phase assays (SPA) and isothermal titration calorimetry (ITC) studies were carried out. The experimental dissociation constants and binding energies obtained were compared to those calculated by molecular docking. These analyses evidenced the critical role of the glycosidic linkage between the terminal galactopyranoside residue and the adjacent monosaccharide, as galactosides bearing β-(1 → 6) glycosidic linkages showed dissociation constants six- and seven-fold higher than those involving β-(1 → 4) and β-(1 → 3) linkages, respectively. Moreover, docking experiments revealed the presence of hydrogen bond interactions between the N-acetyl group of the glucosaminopyranose moiety of the evaluated galactosides and specific amino acid residues of Gal-1, relevant for galectin-glycan affinity. Noticeably, the binding free energies (ΔGbindcalc) derived from the molecular docking were in good agreement with experimental values determined by ITC measurements (ΔGbindexp), evidencing a good correlation between theoretical and experimental approaches, which validates the in silico simulations and constitutes an important tool for the rational design of future optimized ligands.
Collapse
Affiliation(s)
- Cecilia Porciúncula-González
- Laboratorio de Bioquímica, Departamento de Biociencias, Facultad de Química, UdelaR, Gral. Flores, 2124, 11800 Montevideo, Uruguay; Computational Chemistry and Biology Group, DETEMA, Facultad de Química, UdelaR, Isidoro de María 1614, 11800 Montevideo, Uruguay; Graduate Program in Chemistry, Facultad de Química, Universidad de la República, Uruguay
| | - Alejandro J Cagnoni
- Laboratorio de Glicómica Funcional y Molecular, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1428ADN Buenos Aires, Argentina
| | - Carolina Fontana
- Laboratorio de Espectroscopía y Fisicoquímica Orgánica, Departamento de Química del Litoral, CENUR Litoral Norte (S.R.A. Facultad de Química), UdelaR, Ruta 3 km 363, 60000 Paysandú, Uruguay
| | - Karina V Mariño
- Laboratorio de Glicómica Funcional y Molecular, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1428ADN Buenos Aires, Argentina
| | - Patricia Saenz-Méndez
- Computational Chemistry and Biology Group, DETEMA, Facultad de Química, UdelaR, Isidoro de María 1614, 11800 Montevideo, Uruguay; Department of Engineering and Chemical Sciences, Faculty of Health, Science and Technology, Karlstad University, Universitetsgatan 2, 651 88 Karlstad, Sweden
| | - Cecilia Giacomini
- Laboratorio de Bioquímica, Departamento de Biociencias, Facultad de Química, UdelaR, Gral. Flores, 2124, 11800 Montevideo, Uruguay
| | - Gabriela Irazoqui
- Laboratorio de Bioquímica, Departamento de Biociencias, Facultad de Química, UdelaR, Gral. Flores, 2124, 11800 Montevideo, Uruguay.
| |
Collapse
|
6
|
Hena S, Gutierrez L, Croué JP. Removal of metronidazole from aqueous media by C. vulgaris. JOURNAL OF HAZARDOUS MATERIALS 2020; 384:121400. [PMID: 31624001 DOI: 10.1016/j.jhazmat.2019.121400] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/22/2019] [Accepted: 10/04/2019] [Indexed: 06/10/2023]
Abstract
This current study investigated the removal of metronidazole from aqueous media by C. vulgaris. Two different initial sizes of inoculum (0.05 and 0.5 g L-1) were tested for a wide concentration range of metronidazole (1-50 μM). The effect of metronidazole concentrations on biomass production was studied for 20 days. The exopolymeric substances (EPS) were quantified and correlated with the removal of antibiotics from aqueous media. Specifically, MDZ stimulated the production of EPS in C. vulgaris, which played the major role in the adsorption of this antibiotic. Also, metronidazole significantly influenced the zeta potential of C. vulgaris in the test cultures, indicating a change in surface characteristics. This decrease in surface negative charge caused auto-flocculation phenomena at a stationary phase. Chronic and acute toxicity experiments showed that metronidazole was harmful to C. vulgaris at stationary phase. Results from this study would advance our knowledge on the treatment of metronidazole-contaminated waters with C. vulgaris as a green technology-oriented process.
Collapse
Affiliation(s)
- Sufia Hena
- Curtin Water Quality Research Centre, Department of Chemistry, Curtin University, Australia
| | - Leo Gutierrez
- Facultad del Mar y Medio Ambiente, Universidad del Pacifico, Ecuador
| | - Jean-Philippe Croué
- Curtin Water Quality Research Centre, Department of Chemistry, Curtin University, Australia; Institut de Chimie des Milieux et des Matériaux IC2MP UMR 7285 CNRS, Université de Poitiers, France.
| |
Collapse
|
7
|
Acheson JF, Derewenda ZS, Zimmer J. Architecture of the Cellulose Synthase Outer Membrane Channel and Its Association with the Periplasmic TPR Domain. Structure 2019; 27:1855-1861.e3. [PMID: 31604608 PMCID: PMC6939607 DOI: 10.1016/j.str.2019.09.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/12/2019] [Accepted: 09/16/2019] [Indexed: 02/06/2023]
Abstract
Extracellular bacterial cellulose contributes to biofilm stability and to the integrity of the bacterial cell envelope. In Gram-negative bacteria, cellulose is synthesized and secreted by a multi-component cellulose synthase complex. The BcsA subunit synthesizes cellulose and also transports the polymer across the inner membrane. Translocation across the outer membrane occurs through the BcsC porin, which extends into the periplasm via 19 tetra-tricopeptide repeats (TPR). We present the crystal structure of a truncated BcsC, encompassing the last TPR repeat and the complete outer membrane channel domain, revealing a 16-stranded, β barrel pore architecture. The pore is blocked by an extracellular gating loop, while the extended C terminus inserts deeply into the channel and positions a conserved Trp residue near its extracellular exit. The channel is lined with hydrophilic and aromatic residues suggesting a mechanism for facilitated cellulose diffusion based on aromatic stacking and hydrogen bonding.
Collapse
Affiliation(s)
- Justin F Acheson
- University of Virginia, School of Medicine, Department of Molecular Physiology and Biological Physics, Charlottesville, VA 22903, USA
| | - Zygmunt S Derewenda
- University of Virginia, School of Medicine, Department of Molecular Physiology and Biological Physics, Charlottesville, VA 22903, USA
| | - Jochen Zimmer
- University of Virginia, School of Medicine, Department of Molecular Physiology and Biological Physics, Charlottesville, VA 22903, USA.
| |
Collapse
|
8
|
Caffalette CA, Corey RA, Sansom MSP, Stansfeld PJ, Zimmer J. A lipid gating mechanism for the channel-forming O antigen ABC transporter. Nat Commun 2019; 10:824. [PMID: 30778065 PMCID: PMC6379404 DOI: 10.1038/s41467-019-08646-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/23/2019] [Indexed: 12/15/2022] Open
Abstract
Extracellular glycan biosynthesis is a widespread microbial protection mechanism. In Gram-negative bacteria, the O antigen polysaccharide represents the variable region of outer membrane lipopolysaccharides. Fully assembled lipid-linked O antigens are translocated across the inner membrane by the WzmWzt ABC transporter for ligation to the lipopolysaccharide core, with the transporter forming a continuous transmembrane channel in a nucleotide-free state. Here, we report its structure in an ATP-bound conformation. Large structural changes within the nucleotide-binding and transmembrane regions push conserved hydrophobic residues at the substrate entry site towards the periplasm and provide a model for polysaccharide translocation. With ATP bound, the transporter forms a large transmembrane channel with openings toward the membrane and periplasm. The channel's periplasmic exit is sealed by detergent molecules that block solvent permeation. Molecular dynamics simulation data suggest that, in a biological membrane, lipid molecules occupy this periplasmic exit and prevent water flux in the transporter's resting state.
Collapse
Affiliation(s)
- Christopher A Caffalette
- Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | | | - Jochen Zimmer
- Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
| |
Collapse
|
9
|
Zimmer J. Structural features underlying recognition and translocation of extracellular polysaccharides. Interface Focus 2019; 9:20180060. [PMID: 30842868 DOI: 10.1098/rsfs.2018.0060] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/02/2019] [Indexed: 12/31/2022] Open
Abstract
Essentially all living systems produce complex carbohydrates as an energy source, structural component, protective coat or adhesive for cell attachment. Many polysaccharides are displayed on the cell surface or are threaded through proteinaceous tunnels for degradation. Dictated by their chemical composition and mode of polymerization, the physical properties of complex carbohydrates differ substantially, from amphipathic water-insoluble polymers to highly hydrated hydrogel-forming macromolecules. Accordingly, diverse recognition and translocation mechanisms evolved to transport polysaccharides to their final destinations. This review will summarize and compare diverse polysaccharide transport mechanisms implicated in the biosynthesis and degradation of cell surface polymers in pro- and eukaryotes.
Collapse
Affiliation(s)
- Jochen Zimmer
- University of Virginia, 480 Ray C. Hunt Dr., Charlottesville, VA 22903, USA
| |
Collapse
|
10
|
Bartolome JP, Fragoso A. Preparation of stable aqueous dispersions of carbon nano-onions via supramolecular crown ether-ammonium interactions with aminated biocompatible polymers. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.08.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
11
|
Chawla M, Chermak E, Zhang Q, Bujnicki JM, Oliva R, Cavallo L. Occurrence and stability of lone pair-π stacking interactions between ribose and nucleobases in functional RNAs. Nucleic Acids Res 2017; 45:11019-11032. [PMID: 28977572 PMCID: PMC5737201 DOI: 10.1093/nar/gkx757] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 08/17/2017] [Indexed: 12/13/2022] Open
Abstract
The specific folding pattern and function of RNA molecules lies in various weak interactions, in addition to the strong base-base pairing and stacking. One of these relatively weak interactions, characterized by the stacking of the O4' atom of a ribose on top of the heterocycle ring of a nucleobase, has been known to occur but has largely been ignored in the description of RNA structures. We identified 2015 ribose-base stacking interactions in a high-resolution set of non-redundant RNA crystal structures. They are widespread in structured RNA molecules and are located in structural motifs other than regular stems. Over 50% of them involve an adenine, as we found ribose-adenine contacts to be recurring elements in A-minor motifs. Fewer than 50% of the interactions involve a ribose and a base of neighboring residues, while approximately 30% of them involve a ribose and a nucleobase at least four residues apart. Some of them establish inter-domain or inter-molecular contacts and often implicate functionally relevant nucleotides. In vacuo ribose-nucleobase stacking interaction energies were calculated by quantum mechanics methods. Finally, we found that lone pair-π stacking interactions also occur between ribose and aromatic amino acids in RNA-protein complexes.
Collapse
Affiliation(s)
- Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Thuwal 23955-6900, Saudi Arabia.,Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Edrisse Chermak
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Thuwal 23955-6900, Saudi Arabia.,Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Qingyun Zhang
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Thuwal 23955-6900, Saudi Arabia
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland.,Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143 Naples, Italy.,King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal 23955-6900, Saudi Arabia
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Thuwal 23955-6900, Saudi Arabia.,Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| |
Collapse
|
12
|
Schade J, Weidenmaier C. Cell wall glycopolymers of Firmicutes and their role as nonprotein adhesins. FEBS Lett 2016; 590:3758-3771. [PMID: 27396949 DOI: 10.1002/1873-3468.12288] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 06/27/2016] [Accepted: 07/05/2016] [Indexed: 12/12/2022]
Abstract
Cell wall glycopolymers (CWGs) of gram-positive bacteria have gained increasing interest with respect to their role in colonization and infection. In most gram-positive pathogens they constitute a large fraction of the cell wall biomass and represent major cell envelope determinants. Depending on their chemical structure they modulate interaction with complement factors and play roles in immune evasion or serve as nonprotein adhesins that mediate, especially under dynamic conditions, attachment to different host cell types. In particular, covalently peptidoglycan-attached CWGs that extend well above the cell wall seem to interact with glyco-receptors on host cell surfaces. For example, in the case of Staphylococcus aureus, the cell wall-attached teichoic acid (WTA) has been identified as a major CWG adhesin. A recent report indicates that a type-F scavenger receptor, termed SR-F1 (SREC-I), is the predominant WTA receptor in the nasal cavity and that WTA-SREC-I interaction plays an important role in S. aureus nasal colonization. Therefore, understanding the role of CWGs in complex processes that mediate colonization and infection will allow novel insights into the mechanisms of host-microbiota interaction.
Collapse
Affiliation(s)
- Jessica Schade
- Interfaculty Institute for Microbiology and Infection Medicine (IMIT), University of Tübingen, Germany
| | - Christopher Weidenmaier
- Interfaculty Institute for Microbiology and Infection Medicine (IMIT), University of Tübingen, Germany.,German Center for Infection Research (DZIF), Partnersite Tübingen, Germany
| |
Collapse
|
13
|
Bell A, Heath M, Hewings S, Skinner M. The adsorption of allergoids and 3-O-desacyl-4′-monophosphoryl lipid A (MPL®) to microcrystalline tyrosine (MCT) in formulations for use in allergy immunotherapy. J Inorg Biochem 2015; 152:147-53. [DOI: 10.1016/j.jinorgbio.2015.08.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 07/29/2015] [Accepted: 08/05/2015] [Indexed: 12/17/2022]
|
14
|
Abstract
Cellulose is the most abundant biopolymer on Earth, and certain organisms from bacteria to plants and animals synthesize cellulose as an extracellular polymer for various biological functions. Humans have used cellulose for millennia as a material and an energy source, and the advent of a lignocellulosic fuel industry will elevate it to the primary carbon source for the burgeoning renewable energy sector. Despite the biological and societal importance of cellulose, the molecular mechanism by which it is synthesized is now only beginning to emerge. On the basis of recent advances in structural and molecular biology on bacterial cellulose synthases, we review emerging concepts of how the enzymes polymerize glucose molecules, how the nascent polymer is transported across the plasma membrane, and how bacterial cellulose biosynthesis is regulated during biofilm formation. Additionally, we review evolutionary commonalities and differences between cellulose synthases that modulate the nature of the cellulose product formed.
Collapse
Affiliation(s)
- Joshua T. McNamara
- Center for Membrane Biology, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908
| | - Jacob L.W. Morgan
- Center for Membrane Biology, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908
| | - Jochen Zimmer
- Center for Membrane Biology, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908
| |
Collapse
|
15
|
Wilson KA, Wetmore SD. A Survey of DNA–Protein π–Interactions: A Comparison of Natural Occurrences and Structures, and Computationally Predicted Structures and Strengths. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-14163-3_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
|
16
|
Wilson KA, Kellie JL, Wetmore SD. DNA-protein π-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or deoxyribose sugar. Nucleic Acids Res 2014; 42:6726-41. [PMID: 24744240 PMCID: PMC4041443 DOI: 10.1093/nar/gku269] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Four hundred twenty-eight high-resolution DNA-protein complexes were chosen for a bioinformatics study. Although 164 crystal structures (38% of those searched) contained no interactions, 574 discrete π-contacts between the aromatic amino acids and the DNA nucleobases or deoxyribose were identified using strict criteria, including visual inspection. The abundance and structure of the interactions were determined by unequivocally classifying the contacts as either π-π stacking, π-π T-shaped or sugar-π contacts. Three hundred forty-four nucleobase-amino acid π-π contacts (60% of all interactions identified) were identified in 175 of the crystal structures searched. Unprecedented in the literature, 230 DNA-protein sugar-π contacts (40% of all interactions identified) were identified in 137 crystal structures, which involve C-H···π and/or lone-pair···π interactions, contain any amino acid and can be classified according to sugar atoms involved. Both π-π and sugar-π interactions display a range of relative monomer orientations and therefore interaction energies (up to -50 (-70) kJ mol(-1) for neutral (charged) interactions as determined using quantum chemical calculations). In general, DNA-protein π-interactions are more prevalent than perhaps currently accepted and the role of such interactions in many biological processes may yet to be uncovered.
Collapse
Affiliation(s)
- Katie A Wilson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB, T1K 3M4, Canada
| | - Jennifer L Kellie
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB, T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB, T1K 3M4, Canada
| |
Collapse
|
17
|
Mechanism of activation of bacterial cellulose synthase by cyclic di-GMP. Nat Struct Mol Biol 2014; 21:489-96. [PMID: 24704788 PMCID: PMC4013215 DOI: 10.1038/nsmb.2803] [Citation(s) in RCA: 220] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 03/05/2014] [Indexed: 02/08/2023]
Abstract
The bacterial signaling molecule cyclic-di-GMP stimulates the synthesis of bacterial cellulose, frequently found in biofilms. Bacterial cellulose is synthesized and translocated across the inner membrane by a complex of the cellulose synthase BcsA and BcsB subunits. Here we present crystal structures of the cyclic-di-GMP-activated BcsA–B complex. The structures reveal that cyclic-di-GMP releases an auto-inhibited state of the enzyme by breaking a salt bridge which otherwise tethers a conserved gating loop that controls access to and substrate coordination at the active site. Disrupting the salt bridge by mutagenesis generates a constitutively active cellulose synthase. Additionally, the cyclic-di-GMP activated BcsA–B complex contains a nascent cellulose polymer whose terminal glucose unit rests at a novel location above BcsA’s active site where it is positioned for catalysis. Our mechanistic insights are the first examples of how cyclic-di-GMP allosterically modulates enzymatic functions.
Collapse
|
18
|
Stanca-Kaposta EC, Carçabal P, Cocinero EJ, Hurtado P, Simons JP. Carbohydrate-aromatic interactions: vibrational spectroscopy and structural assignment of isolated monosaccharide complexes with p-hydroxy toluene and N-acetyl l-tyrosine methylamide. J Phys Chem B 2013; 117:8135-42. [PMID: 23773008 DOI: 10.1021/jp404527s] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The nature of carbohydrate binding first to p-hydroxy toluene and then the capped amino acid, N-acetyl l-tyrosine methyl amide (AcTyrNHMe), has been investigated in a solvent-free environment under molecular beam conditions. A combination of double resonance IR-UV spectroscopy and quantum chemical calculations has established the structures of complexes with the α and β anomers of methyl d-gluco- and d-galacto- and l-fucopyranosides (α/βMeGlc, MeGal, MeFuc). The new results, when combined with dispersion-corrected DFT calculations, reveal gas phase structures which are dominated by hydrogen bonding but also with evidence of CH-π bonded interactions in complexes with α/βMeGal. These adopt stacked intermolecular structures in marked contrast to those with α/βMeGlc; p-OH → O bonds linking AcTyrNHMe, or p-hydroxy toluene, to the carbohydrate provide an anchor that facilitates further binding, both through OH → O and NH → O hydrogen bonds to the peptide backbone and through CH-π dispersion interactions with the aromatic side group. "Stacked" structures associated with dispersion interactions with the aromatic ring are not detected in the corresponding complexes of capped phenylalanine, despite their common occurrence in bound carbohydrate-protein structures.
Collapse
Affiliation(s)
- E Cristina Stanca-Kaposta
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | | | | | | | | |
Collapse
|