scholarly journals Characterization of the structure and redox behaviour of cytochrome c3 from Desulfovibrio baculatus by 1H-nuclear-magnetic-resonance spectroscopy

1993 ◽  
Vol 294 (3) ◽  
pp. 899-908 ◽  
Author(s):  
I B Coutinho ◽  
D L Turner ◽  
J LeGall ◽  
A V Xavier
Keyword(s):  
Chemical Shifts ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Resonance Spectroscopy ◽  
Cytochrome C3 ◽  
X Ray ◽  
1H Nuclear Magnetic Resonance ◽  
Proton Resonances ◽  
Nuclear Overhauser

Complete assignment of the aromatic and haem proton resonances in the cytochromes c3 isolated from Desulfovibrio baculatus strains (Norway 4, DSM 1741) and (DSM 1743) was achieved using one- and two-dimensional 1H n.m.r. Nuclear Overhauser enhancements observed between haem and aromatic resonances and between resonances due to different haems, together with the ring-current contributions to the chemical shifts of haem resonances, support the argument that the haem core architecture is conserved in the various cytochromes c3, and that the X-ray structure of the D. baculatus cytochrome c3 is erroneous. The relative orientation of the haems for both cytochromes was determined directly from n.m.r. data. The n.m.r. structures have a resolution of approximately 0.25 nm and are found to be in close agreement with the X-ray structure from D. vulgaris cytochrome c3. The proton assignments were used to relate the highest potential to a specific haem in the three-dimensional structure by monitoring the chemical-shift variation of several haem resonances throughout redox titrations followed by 1H n.m.r. The haem with highest redox potential is not the same as that in other cytochromes c3.

scholarly journals Structural characterization of a Thorarchaeota profilin indicates eukaryotic-like features but with an extended N-terminus

2021 ◽  
Author(s):  
Celestine N Chi ◽  
Ravi Teja Inturi ◽  
Sandra Martinez Lara ◽  
Mahmoud Darweesh
Keyword(s):  
Common Ancestor ◽  
Three Dimensional ◽  
Eukaryotic Cell ◽  
Dimensional Structure ◽  
Resonance Spectroscopy ◽  
Last Eukaryotic Common Ancestor ◽  
Rigid Core ◽  
N Terminus ◽  
Metagenomics Analysis

The emergence of the first eukaryotic cell was preceded by evolutionary events which are still highly debatable. Recently, comprehensive metagenomics analysis has uncovered that the Asgard super-phylum is the closest yet known archaea host of eukaryotes. However, it remains to be established if a large number of eukaryotic signature proteins predicated to be encoded by the Asgard super-phylum are functional at least, in the context of a eukaryotic cell. Here, we determined the three-dimensional structure of profilin from Thorarchaeota by nuclear magnetic resonance spectroscopy and show that this profilin has a rigid core with a flexible N-terminus which was previously implicated in polyproline binding. In addition, we also show that thorProfilin co-localizes with eukaryotic actin in cultured HeLa cells. This finding reaffirm the notion that Asgardean encoded proteins possess eukaryotic-like characteristics and strengthen likely existence of a complex cytoskeleton already in a last eukaryotic common ancestor

X-ray nanotomography and focused-ion-beam sectioning for quantitative three-dimensional analysis of nanocomposites

2016 ◽  
Vol 23 (4) ◽  
pp. 990-996 ◽  
Author(s):  
Christopher E. Shuck ◽  
Mathew Frazee ◽  
Andrew Gillman ◽  
Matthew T. Beason ◽  
Ibrahim Emre Gunduz ◽  
...  
Keyword(s):  
Focused Ion Beam ◽  
Ion Beam ◽  
Three Dimensional ◽  
Nondestructive Method ◽  
Material Behavior ◽  
Dimensional Structure ◽  
X Ray ◽  
The Monte Carlo Method ◽  
Micrometer Size

Knowing the relationship between three-dimensional structure and properties is paramount for complete understanding of material behavior. In this work, the internal nanostructure of micrometer-size (∼10 µm) composite Ni/Al particles was analyzed using two different approaches. The first technique, synchrotron-based X-ray nanotomography, is a nondestructive method that can attain resolutions of tens of nanometers. The second is a destructive technique with sub-nanometer resolution utilizing scanning electron microscopy combined with an ion beam and `slice and view' analysis, where the sample is repeatedly milled and imaged. The obtained results suggest that both techniques allow for an accurate characterization of the larger-scale structures, while differences exist in the characterization of the smallest features. Using the Monte Carlo method, the effective resolution of the X-ray nanotomography technique was determined to be ∼48 nm, while focused-ion-beam sectioning with `slice and view' analysis was ∼5 nm.

scholarly journals Crystallization and preliminary X-ray characterization of MutT2, MSMEG_5148 fromMycobacterium smegmatis

2014 ◽  
Vol 70 (2) ◽  
pp. 190-192 ◽  
Author(s):  
S. M. Arif ◽  
P. B. Sang ◽  
U. Varshney ◽  
M. Vijayan
Keyword(s):  
Mycobacterium Smegmatis ◽  
Three Dimensional ◽  
Protein Molecule ◽  
Dimensional Structure ◽  
Molecular Replacement ◽  
Nudix Hydrolase ◽  
X Ray Diffraction ◽  
Orthorhombic Unit Cell ◽  
X Ray

Crystallization of MutT2, MSMEG_5148 fromMycobacterium smegmatis, has been carried out and the crystals have been characterized using X-ray diffraction. Matthews coefficient calculation suggests the possibility of one protein molecule in the asymmetric unit of the orthorhombic unit cell, space groupP21212 orP2122. Solution of the structure of the protein by molecular replacement using the known three-dimensional structure of a bacterial Nudix hydrolase is envisaged.

Conformational and Structural characterization of carbohydrates and their interactions studied by NMR

2021 ◽  
Vol 28 ◽  
Author(s):  
Francisco Javier Cañada ◽  
Ángeles Canales ◽  
Pablo Valverde ◽  
Beatriz Fernández de Toro ◽  
Mónica Martínez-Orts ◽  
...  
Keyword(s):  
Structural Information ◽  
Theoretical Calculations ◽  
Chemical Shifts ◽  
Structural Complexity ◽  
Coupling Constants ◽  
Resonance Spectroscopy ◽  
Additional Information ◽  
Nuclear Overhauser ◽  
Nuclear Overhauser Effects

: Carbohydrates, either free or as glycans conjugated with other biomolecules, participate in many essential biological processes. Their apparent simplicity in terms of chemical functionality hides an extraordinary diversity and structural complexity. Deeply deciphering at the atomic level their structures is essential to understand their biological function and activities, but it is still a challenging task in need of complementary approaches and no generalized procedures are available to address the study of such complex, natural glycans. The versatility of Nuclear Magnetic Resonance spectroscopy (NMR) often makes it the preferred choice to study glycans and carbohydrates in solution media. The most basic NMR parameters, namely chemical shifts, coupling constants and nuclear Overhauser effects, allow defining short or repetitive chain sequences and characterize their structures and local geometries either in the free state or when interacting with other biomolecules, rendering additional information on the molecular recognition processes. The increased accessibility to carbohydrate molecules extensively or selectively labeled with 13C boosts the resolution and detail that analyzed glycan structures can reach. In turn, structural information derived from NMR, complemented with molecular modeling and theoretical calculations can also provide dynamic information on the conformational flexibility of carbohydrate structures. Furthermore, using partially oriented media or paramagnetic perturbations, it has been possible to introduce additional long-range observables rendering structural information on longer and branched glycan chains. In this review, we provide examples of these studies and an overview of the recent and most relevant NMR applications in the glycobiology field.

scholarly journals Preparation and Characterization of Nano-size Polyreactive Blue MXR

2012 ◽  
Vol 9 (3) ◽  
pp. 1336-1341
Author(s):  
Joghee Suresh ◽  
Raja Gopal Rajiv Gandhi ◽  
Sundaram Gowri ◽  
Samayanan Selvam ◽  
Mahalingam Sundrarajan
Keyword(s):  
Average Particle Size ◽  
Three Dimensional ◽  
Colour Change ◽  
Dimensional Structure ◽  
Average Particle ◽  
X Ray ◽  
Force Microscopy ◽  
Atomic Force ◽  
Nano Size

Nanosize Polyreactive blue MXR dye was synthesized from reactive blue MXR dye in presence of potassium persulfate as catalyst. The formation of polyreactive blue MXR was indicated by colour change from blue to brown. The characterization techniques such as, Fourier transform infrared spectroscopy (FTIR), Atomic force microscopy (AFM), and X-ray diffractrometry (XRD) were used to characterize the formation of nanosize polyreactive blue MXR. The absence of asymmetric stretching of NH2 group in polymer dye FTIR spectrum confirmed the polymerization of dye was occurring. The average particle size of the polymer dye was found to be 18.11 nm according to Scherer formula.AFM analysis shows the three dimensional structure of polyreactive blue MXR.

Revealing gross three-dimensional structure in the SEM

1987 ◽  
Vol 45 ◽  
pp. 656-657
Author(s):  
Sterling P. Newberry
Keyword(s):  
Freeze Drying ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Small Object ◽  
Final Solution ◽  
Dimensional Representation ◽  
X Ray ◽  
Three Dimensional Representation ◽  
Freeze Dried ◽  
Critical Point Drying

The beautiful three dimensional representation of small object surfaces by the SEM leads one to search for ways to open up the sample and look inside. Could this be the answer to a better microscopy for gross biological 3-D structure? We know from X-Ray microscope images that Freeze Drying and Critical Point Drying give promise of adequately preserving gross structure. Can we slice such preparations open for SEM inspection? In general these preparations crush more readily than they slice. Russell and Dagihlian got around the problem by “deembedding” a section before imaging. This some what defeats the advantages of direct dry preparation, thus we are reluctant to accept it as the final solution to our problem. Alternatively, consider fig 1 wherein a freeze dried onion root has a window cut in its surface by a micromanipulator during observation in the SEM.

Characterization of Monoclonal Anti-human Factor VII Antibody (B101/B1) that Recognized Three-dimensional Structures near Arg at Position 79 in the First EGF-like Domain

1998 ◽  
Vol 79 (01) ◽  
pp. 104-109 ◽  
Author(s):  
Osamu Takamiya
Keyword(s):  
Monoclonal Antibodies ◽  
Tissue Factor ◽  
Human Factor ◽  
Solid Phase ◽  
Three Dimensional ◽  
Coagulation Factors ◽  
Factor Vii ◽  
Dimensional Structure ◽  
Epidermal Growth

SummaryMurine monoclonal antibodies (designated hVII-B101/B1, hVIIDC2/D4 and hVII-DC6/3D8) directed against human factor VII (FVII) were prepared and characterized, with more extensive characterization of hVII-B101/B1 that did not bind reduced FVIIa. The immunoglobulin of the three monoclonal antibodies consisted of IgG1. These antibodies did not inhibit procoagulant activities of other vitamin K-dependent coagulation factors except FVII and did not cross-react with proteins in the immunoblotting test. hVII-DC2/D4 recognized the light chain after reduction of FVIIa with 2-mercaptoethanol, and hVIIDC6/3D8 the heavy chain. hVII-B101/B1 bound FVII without Ca2+, and possessed stronger affinity for FVII in the presence of Ca2+. The Kd for hVII-B101/B1 to FVII was 1.75 x 10–10 M in the presence of 5 mM CaCl2. The antibody inhibited the binding of FVII to tissue factor in the presence of Ca2+. hVII-B101/B1 also inhibited the activation of FX by the complex of FVIIa and tissue factor in the presence of Ca2+. Furthermore, immunoblotting revealed that hVII-B101/B1 reacted with non-reduced γ-carboxyglutaminic acid (Gla)-domainless-FVII and/or FVIIa. hVII-B101/B1 showed a similar pattern to that of non-reduced proteolytic fragments of FVII by trypsin with hVII-DC2/D4 on immunoblotting test. hVII-B101/B1 reacted differently with the FVII from the dysfunctional FVII variant, FVII Shinjo, which has a substitution of Gln for Arg at residue 79 in the first epidermal growth factor (1st EGF)-like domain (Takamiya O, et al. Haemosta 25, 89-97,1995) compared with normal FVII, when used as a solid phase-antibody for ELISA by the sandwich method. hVII-B101/B1 did not react with a series of short peptide sequences near position 79 in the first EGF-like domain on the solid-phase support for epitope scanning. These results suggested that the specific epitope of the antibody, hVII-B101/B1, was located in the three-dimensional structure near position 79 in the first EGF-like domain of human FVII.

scholarly journals Characterization of Charge States in Conducting Organic Nanoparticles by X-ray Photoemission Spectroscopy

Materials ◽  
2021 ◽  
Vol 14 (8) ◽  
pp. 2058
Author(s):  
Jordi Fraxedas ◽  
Antje Vollmer ◽  
Norbert Koch ◽  
Dominique de Caro ◽  
Kane Jacob ◽  
...  
Keyword(s):  
Partial Oxidation ◽  
Chemical Shifts ◽  
Large Family ◽  
Photoemission Spectroscopy ◽  
Intrinsic Structure ◽  
X Ray ◽  
Level Lines ◽  
Donor And Acceptor ◽  
Electronic Configurations

The metallic and semiconducting character of a large family of organic materials based on the electron donor molecule tetrathiafulvalene (TTF) is rooted in the partial oxidation (charge transfer or mixed valency) of TTF derivatives leading to partially filled molecular orbital-based electronic bands. The intrinsic structure of such complexes, with segregated donor and acceptor molecular chains or planes, leads to anisotropic electronic properties (quasi one-dimensional or two-dimensional) and morphology (needle-like or platelet-like crystals). Recently, such materials have been synthesized as nanoparticles by intentionally frustrating the intrinsic anisotropic growth. X-ray photoemission spectroscopy (XPS) has emerged as a valuable technique to characterize the transfer of charge due to its ability to discriminate the different chemical environments or electronic configurations manifested by chemical shifts of core level lines in high-resolution spectra. Since the photoemission process is inherently fast (well below the femtosecond time scale), dynamic processes can be efficiently explored. We determine here the fingerprint of partial oxidation on the photoemission lines of nanoparticles of selected TTF-based conductors.

Three dimensional characterization of micronized soybean seeds using X-ray microtomography

2021 ◽  
Vol 127 ◽  
pp. 388-397
Author(s):  
Rani Puthukulangara Ramachandran ◽  
Chyngyz Erkinbaev ◽  
Sandeep Thakur ◽  
Jitendra Paliwal
Keyword(s):  
Three Dimensional ◽  
Soybean Seeds ◽  
X Ray
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