scholarly journals Biochemical and Biophysical Characterization of the dsDNA Packaging Motor from the Lactococcus lactis Bacteriophage Asccphi28

Viruses ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 15
Author(s):  
Emilio Reyes-Aldrete ◽  
Erik A. Dill ◽  
Cecile Bussetta ◽  
Michal R. Szymanski ◽  
Geoffrey Diemer ◽  
...  
Keyword(s):  
Lactococcus Lactis ◽  
Analytical Ultracentrifugation ◽  
Atp Hydrolysis ◽  
Size Exclusion ◽  
Radius Of Gyration ◽  
Biophysical Characterization ◽  
X Ray ◽  
Double Stranded Dna ◽  
Symmetric Complex

Double-stranded DNA viruses package their genomes into pre-assembled protein procapsids. This process is driven by macromolecular motors that transiently assemble at a unique vertex of the procapsid and utilize homomeric ring ATPases to couple genome encapsidation to ATP hydrolysis. Here, we describe the biochemical and biophysical characterization of the packaging ATPase from Lactococcus lactis phage asccφ28. Size-exclusion chromatography (SEC), analytical ultracentrifugation (AUC), small angle X-ray scattering (SAXS), and negative stain transmission electron microscopy (TEM) indicate that the ~45 kDa protein formed a 443 kDa cylindrical assembly with a maximum dimension of ~155 Å and radius of gyration of ~54 Å. Together with the dimensions of the crystallographic asymmetric unit from preliminary X-ray diffraction experiments, these results indicate that gp11 forms a decameric D5-symmetric complex consisting of two pentameric rings related by 2-fold symmetry. Additional kinetic analysis shows that recombinantly expressed gp11 has ATPase activity comparable to that of functional ATPase rings assembled on procapsids in other genome packaging systems. Hence, gp11 forms rings in solution that likely reflect the fully assembled ATPases in active virus-bound motor complexes. Whereas ATPase functionality in other double-stranded DNA (dsDNA) phage packaging systems requires assembly on viral capsids, the ability to form functional rings in solution imparts gp11 with significant advantages for high-resolution structural studies and rigorous biophysical/biochemical analysis.

scholarly journals Biochemical and Biophysical Characterization of the dsDNA packaging motor from the Lactococcus lactis bacteriophage asccphi28

2020 ◽  
Author(s):  
Emilio Reyes-Aldrete ◽  
Erik A. Dill ◽  
Cecile Bussetta ◽  
Michal R. Szymanski ◽  
Geoffrey Diemer ◽  
...  
Keyword(s):  
Lactococcus Lactis ◽  
Analytical Ultracentrifugation ◽  
Atp Hydrolysis ◽  
Size Exclusion ◽  
Radius Of Gyration ◽  
Biophysical Characterization ◽  
X Ray ◽  
Symmetric Complex ◽  
Exclusion Chromatography

AbstractDouble-stranded DNA viruses package their genomes into pre-assembled protein procapsids. This process is driven by macromolecular motors that transiently assemble at a unique vertex of the procapsid and utilize homomeric ring ATPases to couple genome encapsidation to ATP hydrolysis. Here we describe biochemical and biophysical characterization of the packaging ATPase from Lactococcus lactis phage asccφ28. Size-exclusion chromatography, analytical ultracentrifugation, small angle x-ray scattering, and negative stain TEM indicate that the ~45 kDa protein formed a 443 kDa cylindrical assembly with a maximum dimension of ~155 Å and radius of gyration of ~54 Å. Together with the dimensions of the crystallographic asymmetric unit from preliminary X-ray diffraction experiments, these results indicate that gp11 forms a decameric D5-symmetric complex consisting of two pentameric rings related by 2-fold symmetry. Additional kinetic analysis shows that recombinantly expressed gp11 has ATPase activity comparable to that of functional ATPase rings assembled on procapsids in other genome packaging systems. Hence, gp11 forms rings in solution that likely reflect the fully assembled ATPases in active virus-bound motor complexes. Whereas ATPase functionality in other dsDNA phage packaging systems requires assembly on viral capsids, the ability to form functional rings in solution imparts gp11 with significant advantages for high resolution structural studies and rigorous biophysical/biochemical analysis.

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 Dissociation Mechanics and Stability of Type a Botulinum Neurotoxin Complex by Means of Biophysical Evaluation

2022 ◽  
Author(s):  
Shavron Hada ◽  
Jae Chul Lee ◽  
Eun Chae Lee ◽  
Sunkyong Ji ◽  
Jeong Sun Nam ◽  
...  
Keyword(s):  
Light Scattering ◽  
Botulinum Neurotoxin ◽  
Type A ◽  
Size Exclusion ◽  
Enzyme Linked Immunosorbent Assay ◽  
Biophysical Characterization ◽  
Exclusion Chromatography ◽  
Associated Proteins ◽  
Dissociated State

Abstract Biophysical characterization of type A botulinum neurotoxin (BoNT/A) complex along with its thermodynamic stability was assessed through a combination of various methods. BoNT/A exists as large complexes in association with neurotoxin associated proteins (NAPs). To evaluate its biophysical behavior, size-exclusion chromatography (SEC), multi-angled light scattering (MALS), enzyme linked immunosorbent assay (ELISA), and dynamic light scattering (DLS) were utilized. Initially, a single peak (peak 1) of SEC was observed at pH 6.0, and an additional peak (peak 2) appeared at pH 7.4 with a decrement of peak 1. Through MALS and ELISA, the peak 2 was determined to be BoNT/A dissociated from its complex. The dissociation was accelerated by time and temperature. At 37°C, dissociated BoNT/A self-associated at pH 7.4 in the presence of polysorbate 20. On the other hand, the dissociation was partly reversible when titrated back to pH 6.0. Overall, BoNT/A was more stable when associated with NAPs at pH 6.0 compared to its dissociated state at pH 7.4. The conventional analytical methods could be utilized to relatively quantify its amount in different formulations.

scholarly journals Pre-clinical Biophysical Characterization of Therapeutic Antibodies in Human Serum by Analytical Ultracentrifugation

2018 ◽  
Vol 114 (3) ◽  
pp. 64a-65a
Author(s):  
Robert T. Wright ◽  
Walter F. Stafford ◽  
Peter J. Sherwood ◽  
David Hayes ◽  
John J. Correia
Keyword(s):  
Human Serum ◽  
Analytical Ultracentrifugation ◽  
Therapeutic Antibodies ◽  
Biophysical Characterization

Characterization of the sorbitol dehydrogenase SmoS from Sinorhizobium meliloti 1021

2021 ◽  
Vol 77 (3) ◽  
pp. 380-390
Author(s):  
MacLean G. Kohlmeier ◽  
Ben A. Bailey-Elkin ◽  
Brian L. Mark ◽  
Ivan J. Oresnik
Keyword(s):  
Sinorhizobium Meliloti ◽  
Model Organism ◽  
Time Frame ◽  
Industrial Applications ◽  
Size Exclusion ◽  
Ligand Docking ◽  
X Ray Diffraction ◽  
X Ray ◽  
Exclusion Chromatography

Sinorhizobium meliloti 1021 is a Gram-negative alphaproteobacterium with a robust capacity for carbohydrate metabolism. The enzymes that facilitate these reactions assist in the survival of the bacterium across a range of environmental niches, and they may also be suitable for use in industrial processes. SmoS is a dehydrogenase that catalyzes the oxidation of the commonly occurring sugar alcohols sorbitol and galactitol to fructose and tagatose, respectively, using NAD+ as a cofactor. The main objective of this study was to evaluate SmoS using biochemical techniques. The nucleotide sequence was codon-optimized for heterologous expression in Escherichia coli BL21 (DE3) Gold cells and the protein was subsequently overexpressed and purified. Size-exclusion chromatography and X-ray diffraction experiments suggest that SmoS is a tetramer. SmoS was crystallized, and crystals obtained in the absence of substrate diffracted to 2.1 Å resolution and those of a complex with sorbitol diffracted to 2.0 Å resolution. SmoS was characterized kinetically and shown to have a preference for sorbitol despite having a higher affinity for galactitol. Computational ligand-docking experiments suggest that tagatose binds the protein in a more energetically favourable complex than fructose, which is retained in the active site over a longer time frame following oxidation and reduces the rate of the reaction. These results supplement the inventory of biomolecules with potential for industrial applications and enhance the understanding of metabolism in the model organism S. meliloti.

scholarly journals Enhanced oligomerization of full-length RAGE by synergy of the interaction of its domains

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Alexander Moysa ◽  
Dietmar Hammerschmid ◽  
Roman H. Szczepanowski ◽  
Frank Sobott ◽  
Michal Dadlez
Keyword(s):  
Analytical Ultracentrifugation ◽  
Vascular Diseases ◽  
Native Mass Spectrometry ◽  
Full Length ◽  
Size Exclusion ◽  
Glycation End Products ◽  
Exclusion Chromatography ◽  
Hydrogen Deuterium

AbstractThe pattern recognition receptor RAGE (receptor for advanced glycation end-products) transmits proinflammatory signals in several inflammation-related pathological states, including vascular diseases, cancer, neurodegeneration and diabetes. Its oligomerization is believed to be important in signal transduction, but RAGE oligomeric structures and stoichiometries remain unclear. Different oligomerization modes have been proposed in studies involving different truncated versions of the extracellular parts of RAGE. Here, we provide basic characterization of the oligomerization patterns of full-length RAGE (including the transmembrane (TM) and cytosolic regions) and compare the results with oligomerization modes of its four truncated fragments. For this purpose, we used native mass spectrometry, analytical ultracentrifugation, and size-exclusion chromatography coupled with multi-angle light scattering. Our results confirm known oligomerization tendencies of separate domains and highlight the enhanced oligomerization properties of full-length RAGE. Mutational analyses within the GxxxG motif of the TM region show sensitivity of oligomeric distributions to the TM sequence. Using hydrogen–deuterium exchange, we mapped regions involved in TM-dependent RAGE oligomerization. Our data provide experimental evidence for the major role of the C2 and TM domains in oligomerization, underscoring synergy among different oligomerization contact regions along the RAGE sequence. These results also explain the variability of obtained oligomerization modes in RAGE fragments.

Masking of the Fc region in human IgG4 by constrained X-ray scattering modelling: implications for antibody function and therapy

2010 ◽  
Vol 432 (1) ◽  
pp. 101-114 ◽  
Author(s):  
Yuki Abe ◽  
Jayesh Gor ◽  
Daniel G. Bracewell ◽  
Stephen J. Perkins ◽  
Paul A. Dalby
Keyword(s):  
Concentration Dependence ◽  
Solution Structure ◽  
Analytical Ultracentrifugation ◽  
Sedimentation Coefficient ◽  
Radius Of Gyration ◽  
X Ray ◽  
X Ray Scattering ◽  
Starting Point ◽  
Self Association ◽  
Ray Scattering

Of the four human IgG antibody subclasses IgG1–IgG4, IgG4 is of interest in that it does not activate complement and exhibits atypical self-association, including the formation of bispecific antibodies. The solution structures of antibodies are critical to understand function and therapeutic applications. Thus IgG4 was studied by synchrotron X-ray scattering. The Guinier X-ray radius of gyration RG increased from 5.0 nm to 5.1 nm with an increase of concentration. The distance distribution function P(r) revealed a single peak at 0.3 mg/ml, which resolved into two peaks that shifted to smaller r values at 1.3 mg/ml, even though the maximum dimension of IgG4 was unchanged at 17 nm. This indicated a small concentration dependence of the IgG4 solution structure. By analytical ultracentrifugation, no concentration dependence in the sedimentation coefficient of 6.4 S was observed. Constrained scattering modelling resulted in solution structural determinations that showed that IgG4 has an asymmetric solution structure in which one Fab–Fc pair is closer together than the other pair, and the accessibility of one side of the Fc region is masked by the Fab regions. The averaged distances between the two Fab–Fc pairs change by 1–2 nm with the change in IgG4 concentration. The averaged conformation of the Fab regions appear able to hinder complement C1q binding to the Fc region and the self-association of IgG4 through the Fc region. The present results clarify IgG4 function and provide a starting point to investigate antibody stability.

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.

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