scholarly journals Impact of crystal packing on coiled-coil flexibility.

2014 ◽  
Vol 70 (a1) ◽  
pp. C1599-C1599
Author(s):  
François Ferron ◽  
David Blocquel ◽  
Johnny Habchi ◽  
Eric Durand ◽  
Marion Sevajol ◽  
...  
Keyword(s):  
Measles Virus ◽  
Quaternary Structure ◽  
Crystal Packing ◽  
Coiled Coil ◽  
Size Exclusion ◽  
X Ray ◽  
X Ray Scattering ◽  
Exclusion Chromatography ◽  
Partial Unfolding

The structural characterization of various constructs of the Measles virus (MeV) Phosphoprotein (P) multimerization domain (PMD) has brought to light significant discrepancies in the quaternary structure due to both crystal constraints and the flexible nature of this coiled-coil. Indeed, despite a conserved tetrameric parallel coiled-coil core, structural comparison unveiled significant deformations in the C-terminal extremities that even led to the partial unfolding of the coiled-coil. These deformations were induced by intermolecular interactions within the crystal, as well as by the crystallization condition. These deformations also suggest that PMD has the ability to adapt to external mechanical constrains. Using a combination of biophysical methods (size-exclusion chromatography, circular dichroism and small angle X-ray scattering), we assessed the differential flexibility of the C-terminal region of the MeV PMD in solution. Taken together, these results show that crystal packing can be used to "freeze" in a certain state, parts of proteins known to be in a dynamic folding-unfolding equilibrium. They also bring awareness that conclusions about function and mechanism based on analysis of a single crystal structure of a known dynamic protein can be easily biased, and they challenge to some extent the assumption that coiled-coil structures can be reliably predicted from the amino acid sequence.

Coiled-coil deformations in crystal structures: themeasles virusphosphoprotein multimerization domain as an illustrative example

2014 ◽  
Vol 70 (6) ◽  
pp. 1589-1603 ◽  
Author(s):  
David Blocquel ◽  
Johnny Habchi ◽  
Eric Durand ◽  
Marion Sevajol ◽  
François Ferron ◽  
...  
Keyword(s):  
Measles Virus ◽  
Quaternary Structure ◽  
Dynamic Equilibrium ◽  
Crystal Packing ◽  
Coiled Coil ◽  
Terminal Region ◽  
Size Exclusion ◽  
Structural Deformation ◽  
Structural Comparison ◽  
Exclusion Chromatography

The structures of two constructs of themeasles virus(MeV) phosphoprotein (P) multimerization domain (PMD) are reported and are compared with a third structure published recently by another group [Communieet al.(2013),J. Virol.87, 7166–7169]. Although the three structures all have a tetrameric and parallel coiled-coil arrangement, structural comparison unveiled considerable differences in the quaternary structure and unveiled that the three structures suffer from significant structural deformation induced by intermolecular interactions within the crystal. These results show that crystal packing can bias conclusions about function and mechanism based on analysis of a single crystal structure, and they challenge to some extent the assumption according to which coiled-coil structures can be reliably predicted from the amino-acid sequence. Structural comparison also highlighted significant differences in the extent of disorder in the C-terminal region of each monomer. The differential flexibility of the C-terminal region is also supported by size-exclusion chromatography and small-angle X-ray scattering studies, which showed that MeV PMD exists in solution as a dynamic equilibrium between two tetramers of different compaction. Finally, the possible functional implications of the flexibility of the C-terminal region of PMD are discussed.

scholarly journals Structural and functional characterization of TesB fromYersinia pestisreveals a unique octameric arrangement of hotdog domains

2015 ◽  
Vol 71 (4) ◽  
pp. 986-995 ◽  
Author(s):  
C. M. D. Swarbrick ◽  
M. A. Perugini ◽  
N. Cowieson ◽  
J. K. Forwood
Keyword(s):  
Analytical Ultracentrifugation ◽  
Quaternary Structure ◽  
Functional Characterization ◽  
Fatty Acyl ◽  
Size Exclusion ◽  
X Ray Scattering ◽  
Wide Range ◽  
Exclusion Chromatography ◽  
Enzyme Families

Acyl-CoA thioesterases catalyse the hydrolysis of the thioester bonds present within a wide range of acyl-CoA substrates, releasing free CoASH and the corresponding fatty-acyl conjugate. The TesB-type thioesterases are members of the TE4 thioesterase family, one of 25 thioesterase enzyme families characterized to date, and contain two fused hotdog domains in both prokaryote and eukaryote homologues. Only two structures have been elucidated within this enzyme family, and much of the current understanding of the TesB thioesterases has been based on theEscherichia colistructure.Yersinia pestis, a highly virulent bacterium, encodes only one TesB-type thioesterase in its genome; here, the structural and functional characterization of this enzyme are reported, revealing unique elements both within the protomer and quaternary arrangements of the hotdog domains which have not been reported previously in any thioesterase family. The quaternary structure, confirmed using a range of structural and biophysical techniques including crystallography, small-angle X-ray scattering, analytical ultracentrifugation and size-exclusion chromatography, exhibits a unique octameric arrangement of hotdog domains. Interestingly, the same biological unit appears to be present in both TesB structures solved to date, and is likely to be a conserved and distinguishing feature of TesB-type thioesterases. Analysis of theY. pestisTesB thioesterase activity revealed a strong preference for octanoyl-CoA and this is supported by structural analysis of the active site. Overall, the results provide novel insights into the structure of TesB thioesterases which are likely to be conserved and distinguishing features of the TE4 thioesterase family.

scholarly journals Characterization of the Micelle Formed by a Hydrophobically Modified Pullulan in Aqueous Solution: Size Exclusion Chromatography

Polymers ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1237
Author(s):  
Jia Yang ◽  
Takahiro Sato
Keyword(s):  
Size Exclusion Chromatography ◽  
Degree Of Polymerization ◽  
Size Exclusion ◽  
Radius Of Gyration ◽  
X Ray ◽  
X Ray Scattering ◽  
Hydrophobically Modified ◽  
Tiny Amount ◽  
Exclusion Chromatography

Size exclusion chromatography equipped with a multi-angle, light-scattering online detector (SEC-MALS) measurements were carried out on a hydrophobically modified pullulan (PUL-OSA) with degrees of substitution (DS) of 0.14, 0.2, and 0.3 in 0.01 M aqueous NaCl to obtain the degree of polymerization (N0) dependence of the radius of gyration (⟨S2⟩1/2) for PUL-OSA in the aqueous NaCl. The result was consistent with the loose flower necklace model proposed in a previous study, and the increase in the chain size with introducing OSA groups was explained by the backbone stiffness of the loose flower necklace formed by PUL-OSA. For PUL-OSA samples with DS = 0.2 and 0.3, ⟨S2⟩1/2 obtained by SEC-MALS in a high N0 region deviated downward from ⟨S2⟩1/2 expected by the loose flower necklace model. This deviation came from a tiny amount of the aggregating component of PUL-OSA, taking a branched architecture composed of loose flower necklaces. Although the aggregating component of PUL-OSA was also detected by previous small angle X-ray scattering measurements, its conformation was revealed in this study by SEC-MALS.

scholarly journals Evidence for an Elongated Dimeric Structure of Heparin-Binding Hemagglutinin from Mycobacterium tuberculosis

2008 ◽  
Vol 190 (13) ◽  
pp. 4749-4753 ◽  
Author(s):  
Carla Esposito ◽  
Maxim V. Pethoukov ◽  
Dmitri I. Svergun ◽  
Alessia Ruggiero ◽  
Carlo Pedone ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Virulence Factor ◽  
Biochemical Characterization ◽  
Coiled Coil ◽  
Heparin Binding ◽  
Truncated Form ◽  
X Ray ◽  
Dimeric Structure ◽  
X Ray Scattering

ABSTRACT Heparin-binding hemagglutinin (HBHA) is a virulence factor of tuberculosis which is responsible for extrapulmonary dissemination of this disease. A thorough biochemical characterization of HBHA has provided experimental evidence of a coiled-coil nature of HBHA. These data, together with the low-resolution structures of a full-length form and a truncated form of HBHA obtained by small-angle X-ray scattering, have unambiguously indicated that HBHA has a dimeric structure with an elongated shape.

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

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).

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