scholarly journals Chemically Denatured Structures of Porcine Pepsin using Small-Angle X-ray Scattering

Polymers ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 2104
Author(s):  
Yecheol Rho ◽  
Jun Ha Kim ◽  
Byoungseok Min ◽  
Kyeong Sik Jin
Keyword(s):  
Small Angle ◽  
Conformational Transition ◽  
Early Stage ◽  
3D Structure ◽  
Three Dimensional ◽  
Porcine Pepsin ◽  
X Ray ◽  
X Ray Scattering ◽  
Wide Range ◽  
Ray Scattering

Porcine pepsin is a gastric aspartic proteinase that reportedly plays a pivotal role in the digestive process of many vertebrates. We have investigated the three-dimensional (3D) structure and conformational transition of porcine pepsin in solution over a wide range of denaturant urea concentrations (0–10 M) using Raman spectroscopy and small-angle X-ray scattering. Furthermore, 3D GASBOR ab initio structural models, which provide an adequate conformational description of pepsin under varying denatured conditions, were successfully constructed. It was shown that pepsin molecules retain native conformation at 0–5 M urea, undergo partial denaturation at 6 M urea, and display a strongly unfolded conformation at 7–10 M urea. According to the resulting GASBOR solution models, we identified an intermediate pepsin conformation that was dominant during the early stage of denaturation. We believe that the structural evidence presented here provides useful insights into the relationship between enzymatic activity and conformation of porcine pepsin at different states of denaturation.

scholarly journals Synthesis and Advanced Characterization of Polymer-Protein Core-Shell Nanoparticles

Catalysts ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 730
Author(s):  
Erik Sarnello ◽  
Tao Li
Keyword(s):  
Particle Size ◽  
Small Angle ◽  
Core Shell ◽  
Assembly Process ◽  
Shell Nanoparticles ◽  
X Ray ◽  
X Ray Scattering ◽  
Wide Range ◽  
Core Shell Nanoparticles ◽  
Ray Scattering

Enzyme immobilization techniques are widely researched due to their wide range of applications. Polymer–protein core–shell nanoparticles (CSNPs) have emerged as a promising technique for enzyme/protein immobilization via a self-assembly process. Based on the desired application, different sizes and distribution of the polymer–protein CSNPs may be required. This work systematically studies the assembly process of poly(4-vinyl pyridine) and bovine serum albumin CSNPs. Average particle size was controlled by varying the concentrations of each reagent. Particle size and size distributions were monitored by dynamic light scattering, ultra-small-angle X-ray scattering, small-angle X-ray scattering and transmission electron microscopy. Results showed a wide range of CSNPs could be assembled ranging from an average radius as small as 52.3 nm, to particles above 1 µm by adjusting reagent concentrations. In situ X-ray scattering techniques monitored particle assembly as a function of time showing the initial particle growth followed by a decrease in particle size as they reach equilibrium. The results outline a general strategy that can be applied to other CSNP systems to better control particle size and distribution for various applications.

X-ray imaging with ultra-small-angle X-ray scattering as a contrast mechanism

2004 ◽  
Vol 37 (5) ◽  
pp. 757-765 ◽  
Author(s):  
L. E. Levine ◽  
G. G. Long
Keyword(s):  
Small Angle ◽  
Imaging Technique ◽  
Three Dimensional ◽  
Sample Volume ◽  
Contrast Imaging ◽  
X Ray ◽  
X Ray Scattering ◽  
X Ray Imaging ◽  
Contrast Mechanism ◽  
Ray Scattering

A new transmission X-ray imaging technique using ultra-small-angle X-ray scattering (USAXS) as a contrast mechanism is described. USAXS imaging can sometimes provide contrast in cases where radiography and phase-contrast imaging are unsuccessful. Images produced at different scattering vectors highlight different microstructural features within the same sample volume. When used in conjunction with USAXS scans, USAXS imaging provides substantial quantitative and qualitative three-dimensional information on the sizes, shapes and spatial arrangements of the scattering objects. The imaging technique is demonstrated on metal and biological samples.

A multi-length-scale USAXS/SAXS facility: 10–50 keV small-angle X-ray scattering instrument

2013 ◽  
Vol 46 (5) ◽  
pp. 1508-1512 ◽  
Author(s):  
Byron Freelon ◽  
Kamlesh Suthar ◽  
Jan Ilavsky
Keyword(s):  
Small Angle ◽  
Soft Matter ◽  
High Energy ◽  
X Rays ◽  
X Ray ◽  
X Ray Scattering ◽  
Wide Range ◽  
And Performance ◽  
New Facility ◽  
Ray Scattering

Coupling small-angle X-ray scattering (SAXS) and ultra-small-angle X-ray scattering (USAXS) provides a powerful system of techniques for determining the structural organization of nanostructured materials that exhibit a wide range of characteristic length scales. A new facility that combines high-energy (HE) SAXS and USAXS has been developed at the Advanced Photon Source (APS). The application of X-rays across a range of energies, from 10 to 50 keV, offers opportunities to probe structural behavior at the nano- and microscale. An X-ray setup that can characterize both soft matter or hard matter and high-Zsamples in the solid or solution forms is described. Recent upgrades to the Sector 15ID beamline allow an extension of the X-ray energy range and improved beam intensity. The function and performance of the dedicated USAXS/HE-SAXS ChemMatCARS-APS facility is described.

scholarly journals Development of combined microstructure and structure characterization facility forin situandoperandostudies at the Advanced Photon Source

2018 ◽  
Vol 51 (3) ◽  
pp. 867-882 ◽  
Author(s):  
Jan Ilavsky ◽  
Fan Zhang ◽  
Ross N. Andrews ◽  
Ivan Kuzmenko ◽  
Pete R. Jemian ◽  
...  
Keyword(s):  
Small Angle ◽  
National Laboratory ◽  
Argonne National Laboratory ◽  
Incident Beam ◽  
Evolutionary Development ◽  
X Ray ◽  
X Ray Scattering ◽  
Wide Range ◽  
Photon Source ◽  
Ray Scattering

Following many years of evolutionary development, first at the National Synchrotron Light Source, Brookhaven National Laboratory, and then at the Advanced Photon Source (APS), Argonne National Laboratory, the APS ultra-small-angle X-ray scattering (USAXS) facility has been transformed by several new developments. These comprise a conversion to higher-order crystal optics and higher X-ray energies as the standard operating mode, rapid fly scan measurements also as a standard operational mode, automated contiguous pinhole small-angle X-ray scattering (SAXS) measurements at intermediate scattering vectors, and associated rapid wide-angle X-ray scattering (WAXS) measurements for X-ray diffraction without disturbing the sample geometry. With each mode using the USAXS incident beam optics upstream of the sample, USAXS/SAXS/WAXS measurements can now be made within 5 min, allowingin situandoperandomeasurement capabilities with great flexibility under a wide range of sample conditions. These developments are described, together with examples of their application to investigate materials phenomena of technological importance. Developments of two novel USAXS applications, USAXS-based X-ray photon correlation spectroscopy and USAXS imaging, are also briefly reviewed.

scholarly journals Inter-α-inhibitor heavy chain-1 has an integrin-like 3D structure mediating immune regulatory activities and matrix stabilization during ovulation

2020 ◽  
Vol 295 (16) ◽  
pp. 5278-5291 ◽  
Author(s):  
David C. Briggs ◽  
Alexander W. W. Langford-Smith ◽  
Holly L. Birchenough ◽  
Thomas A. Jowitt ◽  
Cay M. Kielty ◽  
...  
Keyword(s):  
Small Angle ◽  
Metal Ion ◽  
Alternative Pathway ◽  
3D Structure ◽  
Complement C3 ◽  
Dependent Manner ◽  
X Ray ◽  
X Ray Scattering ◽  
Matrix Stabilization ◽  
Ray Scattering

Inter-α-inhibitor is a proteoglycan essential for mammalian reproduction and also plays a less well-characterized role in inflammation. It comprises two homologous “heavy chains” (HC1 and HC2) covalently attached to chondroitin sulfate on the bikunin core protein. Before ovulation, HCs are transferred onto the polysaccharide hyaluronan (HA) to form covalent HC·HA complexes, thereby stabilizing an extracellular matrix around the oocyte required for fertilization. Additionally, such complexes form during inflammatory processes and mediate leukocyte adhesion in the synovial fluids of arthritis patients and protect against sepsis. Here using X-ray crystallography, we show that human HC1 has a structure similar to integrin β-chains, with a von Willebrand factor A domain containing a functional metal ion-dependent adhesion site (MIDAS) and an associated hybrid domain. A comparison of the WT protein and a variant with an impaired MIDAS (but otherwise structurally identical) by small-angle X-ray scattering and analytical ultracentrifugation revealed that HC1 self-associates in a cation-dependent manner, providing a mechanism for HC·HA cross-linking and matrix stabilization. Surprisingly, unlike integrins, HC1 interacted with RGD-containing ligands, such as fibronectin, vitronectin, and the latency-associated peptides of transforming growth factor β, in a MIDAS/cation-independent manner. However, HC1 utilizes its MIDAS motif to bind to and inhibit the cleavage of complement C3, and small-angle X-ray scattering–based modeling indicates that this occurs through the inhibition of the alternative pathway C3 convertase. These findings provide detailed structural and functional insights into HC1 as a regulator of innate immunity and further elucidate the role of HC·HA complexes in inflammation and ovulation.

Simulation of small-angle X-ray scattering from thylakoid membranes

2009 ◽  
Vol 42 (4) ◽  
pp. 649-659 ◽  
Author(s):  
J. J. K. Kirkensgaard ◽  
J. K. Holm ◽  
J. K. Larsen ◽  
D. Posselt
Keyword(s):  
Experimental Data ◽  
Small Angle ◽  
Virtual Instrument ◽  
Three Dimensional ◽  
Thylakoid Membranes ◽  
Three Dimensional Model ◽  
General Applicability ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

Small-angle X-ray scattering (SAXS) patterns are calculated from a three-dimensional model of photosynthetic thylakoid membranes. The intricate structure of the thylakoids is represented by sampling random `electron density points' on geometric surfaces. The simulation setup works as a virtual instrument, allowing direct comparison with experimental data. The simulations qualitatively reproduce experimental data and thus clarify the structural origin of the scattering features. This is used to explain recent SAXS measurements and as a guideline for new experiments and future quantitative modeling. The setup has general applicability for model testing purposes when modeling scattering from membrane systems of complex geometries.

scholarly journals Two practical Java software tools for small-angle X-ray scattering analysis of biomolecules

2014 ◽  
Vol 47 (2) ◽  
pp. 810-815 ◽  
Author(s):  
Andreas Hofmann ◽  
Andrew E. Whitten
Keyword(s):  
Small Angle ◽  
Three Dimensional ◽  
Small Angle Scattering ◽  
Ease Of Use ◽  
Scattering Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Angle Scattering ◽  
Three Dimensional Models ◽  
Ray Scattering

Small-angle X-ray scattering has established itself as a common technique in structural biology research. Here, two novel Java applications to aid modelling of three-dimensional macromolecular structures based on small-angle scattering data are described.MolScatis an application that computes small-angle scattering intensities from user-provided three-dimensional models. The program can fit the theoretical scattering intensities to experimental X-ray scattering data.SAFIRis a program for interactive rigid-body modelling into low-resolution shapes restored from small-angle scattering data. The program has been designed with an emphasis on ease of use and intuitive handling. An embedded version ofMolScatis used to enable quick evaluation of the fit between the model and experimental scattering data.SAFIRalso provides options to refine macromolecular complexes with optional user-specified restraints against scattering data by means of a Monte Carlo approach.

Four steps for revealing and adjusting the 3D structure of aptamers in solution by small-angle X-ray scattering and computer simulation

2019 ◽  
Vol 411 (25) ◽  
pp. 6723-6732 ◽  
Author(s):  
Felix N. Tomilin ◽  
Roman Moryachkov ◽  
Irina Shchugoreva ◽  
Vladimir N. Zabluda ◽  
Georgy Peters ◽  
...  
Keyword(s):  
Computer Simulation ◽  
Small Angle ◽  
3D Structure ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

Simulations of the transmission small angle x-ray scattering for three-dimensional architectures

2021 ◽  
Author(s):  
Tianjuan Yang ◽  
Jiahao Zhang ◽  
Jianyuan Ma ◽  
Shiyuan Liu ◽  
Xiuguo Chen
Keyword(s):  
Small Angle ◽  
Three Dimensional ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering
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