| 1. |
- Bairy, Sneha, et al.
(författare)
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Automation aided optimization of cloning, expression and purification of enzymes of the bacterial sialic acid catabolic and sialylation pathways enzymes for structural studies.
- 2018
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Ingår i: Microbial biotechnology. - : Wiley. - 1751-7915. ; 11:2, s. 420-428
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Tidskriftsartikel (refereegranskat)abstract
- The process of obtaining a well-expressing, soluble and correctly folded constructs can be made easier and quicker by automating the optimization of cloning, expression and purification. While there are many semiautomated pipelines available for cloning, expression and purification, there is hardly any pipeline that involves complete automation. Here, we achieve complete automation of all the steps involved in cloning and invivo expression screening. This is demonstrated using 18 genes involved in sialic acid catabolism and the surface sialylation pathway. Our main objective was to clone these genes into a His-tagged Gateway vector, followed by their small-scale expression optimization invivo. The constructs that showed best soluble expression were then selected for purification studies and scaled up for crystallization studies. Our technique allowed us to quickly find conditions for producing significant quantities of soluble proteins in Escherichia coli, their large-scale purification and successful crystallization of a number of these proteins. The method can be implemented in other cases where one needs to screen a large number of constructs, clones and expression vectors for successful recombinant production of functional proteins.
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| 2. |
- Caing Carlsson, Rhawnie, et al.
(författare)
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Crystal structure of N-acetylmannosamine kinase from Fusobacterium nucleatum
- 2017
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Ingår i: Acta crystallographica. Section F, Structural biology communications. - 2053-230X. ; 73:6, s. 356-362
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Tidskriftsartikel (refereegranskat)abstract
- Sialic acids comprise a varied group of nine-carbon amino sugars that are widely distributed among mammals and higher metazoans. Some human commensals and bacterial pathogens can scavenge sialic acids from their environment and degrade them for use as a carbon and nitrogen source. The enzyme N-acetylmannosamine kinase (NanK; EC 2.7.1.60) belongs to the transcriptional repressors, uncharacterized open reading frames and sugar kinases (ROK) superfamily. NanK catalyzes the second step of the sialic acid catabolic pathway, transferring a phosphate group from adenosine 5′-triphosphate to the C6 position of N-acetylmannosamine to generate N-acetylmannosamine 6-phosphate. The structure of NanK from Fusobacterium nucleatum was determined to 2.23 Å resolution by X-ray crystallography. Unlike other NanK enzymes and ROK family members, F. nucleatum NanK does not have a conserved zinc-binding site. In spite of the absence of the zinc-binding site, all of the major structural features of enzymatic activity are conserved.
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| 3. |
- Caing Carlsson, Rhawnie
(författare)
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Structural Insight into the Bacterial Sialic Acid Catabolic Pathway
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- A genetically diverse community of commensal and pathogenic bacteria thrive in the digestive system and urogenital tracts of animals. Many of these bacteria forage sialic acid from mucosal cell surfaces. Bacteria have evolved a system that utilizes host-derived sialic acid either as an alternative food source (catabolic pathway) or for molecular mimicry to evade the host’s immune system (sialylation pathway). Their ability to utilize sialic acid confers a selective advantage by securing an ecological niche for colonization and persistence. Sialic acid catabolic and sialylation pathways are therefore potential targets for the development of novel antimicrobial therapies. This thesis presents work aimed at determining X-ray structures of sialic acid catabolic enzymes and sialic acid transporters. An automated pipeline was developed to optimize the cloning, expression and purification of enzymes involved in the sialic acid catabolic and sialylation pathways. This led to the large scale production and purification of Nan kinase from Fusobacterium nucleatum (Fn)NanK, an enzyme that phosphorylates ManNAc to ManNAc-6-P in the catabolic pathway. The apo structure of FnNanK was determined at 2.2 Å resolution and displays motifs characteristic of the repressor open reading frame kinase (ROK) superfamily. Despite lacking a zinc-binding region previously implicated in stabilizing the enzyme’s active site, FnNanK conserved all structural features required for enzymatic activity. A broad base strategy for the expression, solubilization and purification of a sialic acid TRAP transporter orthologues was pursued with the overriding goal of determining the crystal structure of a sialic acid TRAP transporter. Different constructs from four orthologues funneled down to the Pasteurella multocida TRAP transporter yielding crystals which diffracted to 11 Å resolution. New crystallization strategies or other structural approaches may be necessary to propel this project to structure determination. Finally, the crystal structure of the sialic acid transporter SiaT from Proteus mirabilis was determined at 1.9 Å with bound substrate. SiaT adopts an outward-facing conformation that provides novel insight into the alternate access mechanism employed by transporters with inverted topology. The crystal structure also reveals a second sodium-binding site that aids substrate binding and stabilizes the outward-facing conformation.
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| 4. |
- Chen, Yihong, et al.
(författare)
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Identification of an osteopontin-derived peptide that binds neuropilin-1 and activates vascular repair responses and angiogenesis
- 2024
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Ingår i: Pharmacological Research. - 1096-1186. ; 205
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Tidskriftsartikel (refereegranskat)abstract
- The osteopontin-derived peptide FOL-005 stimulates hair growth. Using ligand-receptor glyco-capture technology we identified neuropilin-1 (NRP-1), a known co-receptor for vascular endothelial growth factor (VEGF) receptors, as the most probable receptor for FOL-005 and the more stable analogue FOL-026. X-ray diffraction and microscale thermophoresis analysis revealed that FOL-026 shares binding site with VEGF in the NRP-1 b1-subdomain. Stimulation of human umbilical vein endothelial cells with FOL-026 resulted in phosphorylation of VEGFR-2, ERK1/2 and AKT, increased cell growth and migration, stimulation of endothelial tube formation and inhibition of apoptosis in vitro. FOL-026 also promoted angiogenesis in vivo as assessed by subcutaneous Matrigel plug and hind limb ischemia models. NRP-1 knock-down or treatment of NRP-1 antagonist EG00229 blocked the stimulatory effects of FOL-026 on endothelial cells. Exposure of human coronary artery smooth muscle cells to FOL-026 stimulated cell growth, migration, inhibited apoptosis, and induced VEGF gene expression and VEGFR-2/AKT phosphorylation by an NRP-1-dependent mechanism. RNA sequencing showed that FOL-026 activated pathways involved in tissue repair. These findings identify NRP-1 as the receptor for FOL-026 and show that its biological effects mimic that of growth factors binding to the VEGF receptor family. They also suggest that FOL-026 may have therapeutical potential in conditions that require vascular repair and/or enhanced angiogenesis.
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| 5. |
- Pippione, Agnese C., et al.
(författare)
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Hydroxyazole scaffold-based Plasmodium falciparum dihydroorotate dehydrogenase inhibitors : Synthesis, biological evaluation and X-ray structural studies
- 2019
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Ingår i: European Journal of Medicinal Chemistry. - : Elsevier BV. - 0223-5234 .- 1768-3254. ; 163, s. 266-280
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Tidskriftsartikel (refereegranskat)abstract
- Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) has been clinically validated as a target for antimalarial drug discovery, as a triazolopyrimidine class inhibitor (DSM265) is currently undergoing clinical development. Here, we have identified new hydroxyazole scaffold-based PfDHODH inhibitors belonging to two different chemical series. The first series was designed by a scaffold hopping strategy that exploits the use of hydroxylated azoles. Within this series, the hydroxythiadiazole 3 was identified as the best selective PfDHODH inhibitor (IC50 12.0 μM). The second series was designed by modulating four different positions of the hydroxypyrazole scaffold. In particular, hydroxypyrazoles 7e and 7f were shown to be active in the low μM range (IC50 2.8 and 5.3 μM, respectively). All three compounds, 3, 7e and 7f showed clear selectivity over human DHODH (IC50 > 200 μM), low cytotoxicity, and retained micromolar activity in P. falciparum-infected erythrocytes. The crystallographic structures of PfDHODH in complex with compounds 3 and 7e proved their binding mode, supplying essential data for future optimization of these scaffolds.
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| 6. |
- Wahlgren, Weixiao Yuan, 1970, et al.
(författare)
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Substrate-bound outward-open structure of a Na+-coupled sialic acid symporter reveals a new Na+ site.
- 2018
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- Many pathogenic bacteria utilise sialic acids as an energy source or use them as an external coating to evade immune detection. As such, bacteria that colonise sialylated environments deploy specific transporters to mediate import of scavenged sialic acids. Here, we report a substrate-bound 1.95Å resolution structure and subsequent characterisation of SiaT, a sialic acid transporter from Proteus mirabilis. SiaT is a secondary active transporter of the sodium solute symporter (SSS) family, which use Na+ gradients to drive the uptake of extracellular substrates. SiaT adopts the LeuT-fold and is in an outward-open conformation in complex with the sialic acid N-acetylneuraminic acid and two Na+ ions. One Na+ binds to the conserved Na2 site, while the second Na+ binds to a new position, termed Na3, which is conserved in many SSS family members. Functional and molecular dynamics studies validate the substrate-binding site and demonstrate that both Na+ sites regulate N-acetylneuraminic acid transport.
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