scholarly journals Structural insight into the dual function of LbpB in mediating Neisserial pathogenesis

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Ravi Yadav ◽  
Srinivas Govindan ◽  
Courtney Daczkowski ◽  
Andrew Mesecar ◽  
Srinivas Chakravarthy ◽  
...  
Keyword(s):  
Antimicrobial Peptide ◽  
Iron Acquisition ◽  
Bound State ◽  
Size Exclusion ◽  
Dual Function ◽  
Binding Studies ◽  
Cationic Antimicrobial Peptide ◽  
X Ray Scattering ◽  
Exclusion Chromatography ◽  
Insight Into

Lactoferrin-binding protein B (LbpB) is a lipoprotein present on the surface of Neisseria that has been postulated to serve dual functions during pathogenesis in both iron acquisition from lactoferrin (Lf), and in providing protection against the cationic antimicrobial peptide lactoferricin (Lfcn). While previous studies support a dual role for LbpB, exactly how these ligands interact with LbpB has remained unknown. Here, we present the structures of LbpB from N. meningitidis and N. gonorrhoeae in complex with human holo-Lf, forming a 1:1 complex and confirmed by size-exclusion chromatography small-angle X-ray scattering. LbpB consists of N- and C-lobes with the N-lobe interacting extensively with the C-lobe of Lf. Our structures provide insight into LbpB’s preference towards holo-Lf, and our mutagenesis and binding studies show that Lf and Lfcn bind independently. Our studies provide the molecular details for how LbpB serves to capture and preserve Lf in an iron-bound state for delivery to the membrane transporter LbpA for iron piracy, and as an antimicrobial peptide sink to evade host immune defenses.

scholarly journals Structural insight into the dual function of LbpB in mediating Neisserial pathogenesis

2021 ◽  
Author(s):  
Nicholas Noinaj ◽  
Ravi Yadav ◽  
Srinivas Govindan ◽  
Courtney Daczkowski ◽  
Andrew Mesecar ◽  
...  
Keyword(s):  
Antimicrobial Peptide ◽  
Iron Acquisition ◽  
Bound State ◽  
Dual Function ◽  
Membrane Transporter ◽  
Binding Studies ◽  
Cationic Antimicrobial Peptide ◽  
Structural Insight ◽  
Insight Into ◽  
Dual Functions

Lactoferrin binding protein B (LbpB) is a lipoprotein present on the surface of Neisseria that has been postulated to serve dual functions during pathogenesis in both iron acquisition from lactoferrin, and in providing protection against the cationic antimicrobial peptide lactoferricin. Here, we present the structures of LbpB from N. meningitidis and N. gonorrhoeae in complex with human holo-lactoferrin, forming a 1:1 complex and confirmed by SEC-SAXS. LbpB consists of N- and C-lobes with the N-lobe interacting extensively with the C-lobe of lactoferrin. Our structures provides insight into LbpB's preference towards holo-lactoferrin, and our mutagenesis and binding studies show that lactoferrin and lactoferricin bind independently. Our studies provide the molecular details for how LbpB serves to capture and preserve lactoferrin in an iron-bound state for delivery to the membrane transporter LbpA for iron piracy, and as an antimicrobial peptide sink to evade host immune defenses.

scholarly journals PHF13 is a molecular reader and transcriptional co-regulator of H3K4me2/3

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Ho-Ryun Chung ◽  
Chao Xu ◽  
Alisa Fuchs ◽  
Andreas Mund ◽  
Martin Lange ◽  
...  
Keyword(s):  
Dna Damage Response ◽  
Size Exclusion ◽  
X Ray ◽  
Chip Sequencing ◽  
X Ray Crystallography ◽  
Genome Wide ◽  
Damage Response ◽  
Exclusion Chromatography ◽  
Insight Into ◽  
Binding Cell

PHF13 is a chromatin affiliated protein with a functional role in differentiation, cell division, DNA damage response and higher chromatin order. To gain insight into PHF13's ability to modulate these processes, we elucidate the mechanisms targeting PHF13 to chromatin, its genome wide localization and its molecular chromatin context. Size exclusion chromatography, mass spectrometry, X-ray crystallography and ChIP sequencing demonstrate that PHF13 binds chromatin in a multivalent fashion via direct interactions with H3K4me2/3 and DNA, and indirectly via interactions with PRC2 and RNA PolII. Furthermore, PHF13 depletion disrupted the interactions between PRC2, RNA PolII S5P, H3K4me3 and H3K27me3 and resulted in the up and down regulation of genes functionally enriched in transcriptional regulation, DNA binding, cell cycle, differentiation and chromatin organization. Together our findings argue that PHF13 is an H3K4me2/3 molecular reader and transcriptional co-regulator, affording it the ability to impact different chromatin processes.

scholarly journals Sorafenib as an Inhibitor of RUVBL2

Biomolecules ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 605 ◽  
Author(s):  
Nardin Nano ◽  
Francisca Ugwu ◽  
Thiago V. Seraphim ◽  
Tangzhi Li ◽  
Gina Azer ◽  
...  
Keyword(s):  
Atpase Activity ◽  
Competitive Inhibitor ◽  
Telomerase Activity ◽  
Size Exclusion ◽  
Scattering Data ◽  
Cellular Processes ◽  
Dna Damage Signaling ◽  
X Ray Scattering ◽  
Exclusion Chromatography ◽  
Aaa Atpases

RUVBL1 and RUVBL2 are highly conserved ATPases that belong to the AAA+ (ATPases Associated with various cellular Activities) superfamily and are involved in various complexes and cellular processes, several of which are closely linked to oncogenesis. The proteins were implicated in DNA damage signaling and repair, chromatin remodeling, telomerase activity, and in modulating the transcriptional activities of proto-oncogenes such as c-Myc and β-catenin. Moreover, both proteins were found to be overexpressed in several different types of cancers such as breast, lung, kidney, bladder, and leukemia. Given their various roles and strong involvement in carcinogenesis, the RUVBL proteins are considered to be novel targets for the discovery and development of therapeutic cancer drugs. Here, we describe the identification of sorafenib as a novel inhibitor of the ATPase activity of human RUVBL2. Enzyme kinetics and surface plasmon resonance experiments revealed that sorafenib is a weak, mixed non-competitive inhibitor of the protein’s ATPase activity. Size exclusion chromatography and small angle X-ray scattering data indicated that the interaction of sorafenib with RUVBL2 does not cause a significant effect on the solution conformation of the protein; however, the data suggested that the effect of sorafenib on RUVBL2 activity is mediated by the insertion domain in the protein. Sorafenib also inhibited the ATPase activity of the RUVBL1/2 complex. Hence, we propose that sorafenib could be further optimized to be a potent inhibitor of the RUVBL proteins.

scholarly journals Solution structures of long-acting insulin analogues and their complexes with albumin

2019 ◽  
Vol 75 (3) ◽  
pp. 272-282 ◽  
Author(s):  
Line A. Ryberg ◽  
Pernille Sønderby ◽  
Fabian Barrientos ◽  
Jens T. Bukrinski ◽  
Günther H. J. Peters ◽  
...  
Keyword(s):  
Solution Structure ◽  
Insulin Analogues ◽  
Size Exclusion ◽  
Life Extension ◽  
Once Daily ◽  
Solution Structures ◽  
X Ray Scattering ◽  
Exclusion Chromatography ◽  
Self Association ◽  
Long Acting

The lipidation of peptide drugs is one strategy to obtain extended half-lives, enabling once-daily or even less frequent injections for patients. The half-life extension results from a combination of self-association and association with human serum albumin (albumin). The self-association and association with albumin of two insulin analogues, insulin detemir and insulin degludec, were investigated by small-angle X-ray scattering (SAXS) and dynamic light scattering (DLS) in phenolic buffers. Detemir shows concentration-dependent self-association, with an equilibrium between hexamer, dihexamer, trihexamer and larger species, while degludec appears as a dihexamer independent of concentration. The solution structure of the detemir trihexamer has a bent shape. The stoichiometry of the association with albumin was studied using DLS. For albumin–detemir the molar stoichiometry was determined to be 1:6 (albumin:detemir ratio) and for albumin–degludec it was between 1:6 and 1:12 (albumin:degludec ratio). Batch SAXS measurements of a 1:6 albumin:detemir concentration series revealed a concentration dependence of complex formation. The data allowed the modelling of a complex between albumin and a detemir hexamer and a complex consisting of two albumins binding to opposite ends of a detemir dihexamer. Measurements of size-exclusion chromatography coupled to SAXS revealed a complex between a degludec dihexamer and albumin. Based on the results, equilibria for the albumin–detemir and albumin–degludec mixtures are proposed.

scholarly journals Trefoil Factor Family (TFF) Modules Are Characteristic Constituents of Separate Mucin Complexes in the Xenopus laevis Integumentary Mucus: In Vitro Binding Studies with FIM-A.1

2020 ◽  
Vol 21 (7) ◽  
pp. 2400 ◽  
Author(s):  
René Stürmer ◽  
Jana Reising ◽  
Werner Hoffmann
Keyword(s):  
Molecular Mass ◽  
Complex I ◽  
Size Exclusion ◽  
Trefoil Factor ◽  
Binding Studies ◽  
In Vitro Binding ◽  
Vitro Binding ◽  
Exclusion Chromatography ◽  
Trefoil Factor Family

The skin of the frog Xenopus laeevis is protected from microbial infections by a mucus barrier that contains frog integumentary mucins (FIM)-A.1, FIM-B.1, and FIM-C.1. These gel-forming mucins are synthesized in mucous glands consisting of ordinary mucous cells and one or more cone cells at the gland base. FIM-A.1 and FIM-C.1 are unique because their cysteine-rich domains belong to the trefoil factor family (TFF). Furthermore, FIM-A.1 is unusually short (about 400 amino acid residues). In contrast, FIM-B.1 contains cysteine-rich von Willebrand D (vWD) domains. Here, we separate skin extracts by the use of size exclusion chromatography and analyze the distribution of FIM-A.1 and FIM-C.1. Two mucin complexes were detected, i.e., a high-molecular-mass Complex I, which contains FIM-C.1 and little FIM-A.1, whereas Complex II is of lower molecular mass and contains the bulk of FIM-A.1. We purified FIM-A.1 by a combination of size-exclusion chromatography (SEC) and anion-exchange chromatography and performed first in vitro binding studies with radioactively labeled FIM-A.1. Binding of 125I-labeled FIM-A.1 to the high-molecular-mass Complex I was observed. We hypothesize that the presence of FIM-A.1 in Complex I is likely due to lectin interactions, e.g., with FIM-C.1, creating a complex mucus network.

scholarly journals Size-exclusion chromatography small-angle X-ray scattering of water soluble proteins on a laboratory instrument

2018 ◽  
Vol 51 (6) ◽  
pp. 1623-1632 ◽  
Author(s):  
Saskia Bucciarelli ◽  
Søren Roi Midtgaard ◽  
Martin Nors Pedersen ◽  
Søren Skou ◽  
Lise Arleth ◽  
...  
Keyword(s):  
Size Exclusion Chromatography ◽  
Small Angle ◽  
Size Exclusion ◽  
Scattering Data ◽  
X Ray ◽  
Laboratory Instrument ◽  
X Ray Scattering ◽  
Home Institution ◽  
Exclusion Chromatography ◽  
Ray Scattering

Coupling of size-exclusion chromatography with biological solution small-angle X-ray scattering (SEC-SAXS) on dedicated synchrotron beamlines enables structural analysis of challenging samples such as labile proteins and low-affinity complexes. For this reason, the approach has gained increased popularity during the past decade. Transportation of perishable samples to synchrotrons might, however, compromise the experiments, and the limited availability of synchrotron beamtime renders iterative sample optimization tedious and lengthy. Here, the successful setup of laboratory-based SEC-SAXS is described in a proof-of-concept study. It is demonstrated that sufficient quality data can be obtained on a laboratory instrument with small sample consumption, comparable to typical synchrotron SEC-SAXS demands. UV/vis measurements directly on the SAXS exposure cell ensure accurate concentration determination, crucial for direct molecular weight determination from the scattering data. The absence of radiation damage implies that the sample can be fractionated and subjected to complementary analysis available at the home institution after SEC-SAXS. Laboratory-based SEC-SAXS opens the field for analysis of biological samples at the home institution, thus increasing productivity of biostructural research. It may further ensure that synchrotron beamtime is used primarily for the most suitable and optimized samples.

scholarly journals Newly developed Laboratory-based Size exclusion chromatography Small-angle x-ray scattering System (La-SSS)

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Rintaro Inoue ◽  
Tatsuo Nakagawa ◽  
Ken Morishima ◽  
Nobuhiro Sato ◽  
Aya Okuda ◽  
...  
Keyword(s):  
Size Exclusion Chromatography ◽  
Small Angle ◽  
Size Exclusion ◽  
Scattering System ◽  
X Ray ◽  
X Ray Scattering ◽  
Exclusion Chromatography ◽  
Ray Scattering

scholarly journals Mode of induction of platelet-derived extracellular vesicles is a critical determinant of their phenotype and function

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
P. M. Ferreira ◽  
E. Bozbas ◽  
S. D. Tannetta ◽  
N. Alroqaiba ◽  
R. Zhou ◽  
...  
Keyword(s):  
Extracellular Vesicles ◽  
Size Exclusion ◽  
Biological Functions ◽  
Critical Determinant ◽  
Agonist Stimulation ◽  
Exclusion Chromatography ◽  
Average Size ◽  
And Function ◽  
Free Plasma ◽  
Insight Into

Abstract Platelet-derived extracellular vesicles (PDEVs) are the most abundant amongst all types of EVs in the circulation. However, the mechanisms leading to PDEVs release, their role in coagulation and phenotypic composition are poorly understood. PDEVs from washed platelets were generated using different stimuli and were characterised using nanoparticle tracking analysis. Procoagulant properties were evaluated by fluorescence flow cytometry and calibrated automated thrombography. EVs from plasma were isolated and concentrated using a novel protocol involving a combination of size exclusion chromatography and differential centrifugation, which produces pure and concentrated EVs. Agonist stimulation enhanced PDEV release, but did not alter the average size of EVs compared to those produced by unstimulated platelets. Agonist stimulation led to lower negatively-charged phospholipid externalization in PDEVs, which was reflected in the lower procoagulant activity compared to those generated without agonist stimulation. Circulating EVs did not have externalized negatively-charged phospholipids. None of the 4 types of EVs presented tissue factor. The mechanism by which PDEV formation is induced is a critical determinant of its phenotype and function. Importantly, we have developed methods to obtain clean, concentrated and functional EVs derived from platelet-free plasma and washed platelets, which can be used to provide novel insight into their biological functions.

Σύνθεση γραμμικών και αστεροειδών πολυμερών αποτελούμενα από συστάδες με υψηλή παράμετρο αλληλεπίδρασης Flory-Huggins χ

2020 ◽  
Author(s):  
Μαρία-Μαλβίνα Σταθουράκη
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Magnetic Resonance Spectroscopy ◽  
Ring Opening ◽  
Ring Opening Polymerization ◽  
Size Exclusion ◽  
Resonance Spectroscopy ◽  
X Ray ◽  
X Ray Scattering ◽  
Exclusion Chromatography

Σκοπό της διατριβής αυτής αποτελεί η σύνθεση και η μελέτη της αυτοοργάνωσης γραμμικών και αστεροειδών συμπολυμερών με υψηλή παράμετρο αλληλεπιδρασης Flory-Huggins, χ. Τα πολυμερή αυτά, λόγω της μικρής αναμιξιμότητας που παρουσιάζουν τα συστατικά τους, έχουν την δυνατότητα σε μικρά μοριακά βάρη να μπορούν να σχηματίζουν πολύ μικρές και καλά καθορισμένες δομές κατά το μικροφασικό διαχωρισμό. Αρχικά, πραγματοποιήθηκε η σύνθεση των γραμμικών δισυσταδικών συμπολυμερών πολυ(2-βινυλοπυριδίνης)-b-πολυ(l-λακτιδίου) (P2VP-b-PLLA) και των τρισυσταδικών πολυ(l-λακτιδίου)-b-πολύ(διμεθυλοσιλοξάνη)-b-πολύ(l-λακτιδίου) (PLLA-b-PDMS-b-PLLA), καθώς και γραμμικών και αστεροειδών συμπολυμερών πολύ(στυρένιο)-b-πολυ(μονομεθακρυλική γλυκερόλη), PS-b-PGMA, (πολυστυρένιο)2(πολυ(μονομεθακρυλική γλυκερόλη)), (PS)2(PGMA), και (πολυστυρένιο)3(πολυ(μονομεθακρυλική γλυκερόλη)), (PS)3(PGMA), σε διάφορες αναλογίες μοριακών βαρών των συστατικών τους. Χρησιμοποιήθηκαν τεχνικές ζωντανού ανιοντικού πολυμερισμού για τη σύνθεση της P2VP, καθώς και για τη σύνθεση των αστεροειδών πολυμερών, ενώ η σύνθεση των PLLA πραγματοποιήθηκε με χρήση πολυμερισμού διάνοιξης δακτυλίου (Ring Opening Polymerization, ROP). Ο μοριακός χαρακτηρισμός των πολυμερών έγινε μέσω Χρωματογραφίας Αποκλεισμού Μεγεθών (Size Exclusion Chromatography, SEC) και Φασματοσκοπίας Πυρηνικού Μαγνητικού Συντονισμού Πρωτονίου (Nuclear Magnetic Resonance Spectroscopy, 1H-NMR). Τέλος, τίθενται τα αποτελέσματα που αφορούν τα γεωμετρικά χαρακτηριστικά (μέγεθος, μορφολογία) των περιοδικών νανοδομών που σχηματίζουν στο τήγμα τα συμπολυμερή, μέσω σκέδασης ακτίνων Χ σε μικρές γωνίες (Small-angle X-ray Scattering, SAXS).

Sign in / Sign up

Export Citation Format

Share Document