Ovorubin, a chromoprotein from the eggs of the gastropod mollusc Pomacea canaliculata

1958 ◽  
Vol 149 (937) ◽  
pp. 571-587 ◽  
Keyword(s):  
Molecular Weight ◽  
Protein Structure ◽  
High Stability ◽  
Carotenoid Content ◽  
Pomacea Canaliculata ◽  
Carbohydrate Component ◽  
Prosthetic Group ◽  
Gastropod Mollusc ◽  
Protein Molecules ◽  
Prosobranch Snail

The eggs of Pomacea canaliculata australis (d’Orbigny), an amphibious freshwater prosobranch snail, have, as the most important nitrogenous constituent of the jelly surrounding the ovum, a red glycoprotein with a carotenoid prosthetic group. This protein, to which the name ovorubin has been given, has a high stability to denaturation by heat and by adsorption at interfaces. It is partially utilized during development of the ovum, although about two-thirds of the original ovorubin content of the egg is found in the visceral hump of the newly hatched animal. The carotenoid component is probably an ester or ether of astaxanthin, highly labile to alkali in the cold. The minimum molecular weight, calculated from the carotenoid content, lies in the region of 330 000. The carbohydrate component represents about 20% of the molecule. The carotenoid and the glycoprotein may readily be separated and recombined. Experiments on the apo-glycoprotein and the reconstituted caroteno-protein indicate that the carotenoid stabilizes the native configuration of the protein structure. It is suggested that stabilization of the configurations of protein molecules may be one of the roles of carotenoids in nature.

scholarly journals ‘Tanned’ gelatin spheres and granules for exclusion chromatography

1968 ◽  
Vol 108 (4) ◽  
pp. 641-646 ◽  
Author(s):  
A. Polson ◽  
W. Katz
Keyword(s):  
Molecular Weight ◽  
Polyethylene Glycol ◽  
High Molecular Weight ◽  
Weight Fraction ◽  
High Flow ◽  
High Molecular Weight Fraction ◽  
Flow Rates ◽  
Protein Molecules ◽  
Exclusion Chromatography

1. The preparation of tanned gelatin spheres and granules from high-molecular-weight gelatin is described. This material is comparatively hard, giving high flow rates, is insoluble in water at temperatures between 0° and 100° and is resistant to digestion by trypsin and chymotrypsin. The high-molecular-weight fraction of gelatin was prepared by precipitation with polyethylene glycol, and the spheres and granules prepared from this fraction were hardened and insolubilized by tanning with either formalin or chromium salts or both. 2. The spheres and granules were used successfully for the separation of protein molecules and other protein-aceous materials ranging in molecular weight from 200 to greater than 6000000. This gel exclusion material has several properties superior to those of other products used for similar purposes. Further, it was noticed that the porosity of the spheres differed considerably from that of the granules.

scholarly journals Arrangement of high molecular weight associated proteins on purified mammalian brain microtubules.

1977 ◽  
Vol 72 (3) ◽  
pp. 642-654 ◽  
Author(s):  
L A Amos
Keyword(s):  
Molecular Weight ◽  
High Molecular Weight ◽  
Mammalian Brain ◽  
Lateral Interactions ◽  
High Molecular Weight Protein ◽  
Protein Molecules ◽  
Associated Proteins ◽  
Weight Protein ◽  
High Molecular Weight Proteins ◽  
Brain Microtubules

The arrangement of the high molecular weight proteins associated with the walls of reconstituted mammalian brain microtubules has been investigated by electron microscopy of negatively stained preparations. The images are found to be consistent with an arrangement whereby the high molecular weight molecules are spaced 12 tubulin dimers apart, i.e., 960 A, along each protofilament of the microtubule, in agreement with the relative stoichiometry of tubulin and high molecular weight protein. Molecules on neighbouring protofilaments seem to be staggered so that they give rise to a helical superlattice, which can be superimposed on the underlying tubulin lattice. In micrographs of disintegrating tubules there is some indication of lateral interactions between neighbouring high molecular weight molecules. When the microtubules are depolymerized into a mixture of short spirals and rings, the high molecular weight proteins appear to remain attached to their respective protofilaments.

scholarly journals The purification and properties of butyryl-coenzyme A dehydrogenase from Peptostreptococcus elsdenii

1971 ◽  
Vol 125 (3) ◽  
pp. 879-887 ◽  
Author(s):  
Paul C. Engel ◽  
V. Massey
Keyword(s):  
Molecular Weight ◽  
Amino Acid ◽  
Simple Procedure ◽  
Potassium Bromide ◽  
Prosthetic Group ◽  
Pig Liver ◽  
Peak Absorption ◽  
Purification And Properties ◽  
Green Form ◽  
Spectrophotometric Titrations

Butyryl-CoA dehydrogenase prepared by a simple procedure from Peptostreptococcus elsdenii has a molecular weight of approx. 150000. The enzyme has FAD as its prosthetic group. The amino acid analysis is reported. This enzyme, like most of the corresponding mammalian ones, is green. The absorption band at 710nm can be abolished irreversibly by dithionite reduction and air reoxidation; it can be abolished reversibly by phenylmercuric acetate or potassium bromide. The enzyme as isolated appears to be a mixture of a green and a yellow form, both of which are active. This view is supported by the variable ‘greenness’ of different preparations and the biphasic curve obtained in anaerobic spectrophotometric titrations with dithionite. It can be calculated from the titration results that fully green enzyme would have a peak-to-peak absorption ratio (E710/E430) as great as 0.54. The green form is much less rapidly reduced by dithionite than the yellow form, but is nevertheless much more readily reduced by dithionite than the enzyme from pig liver. It is also more readily reoxidized by air and shows less tendency to form a semiquinone. Treatment with sodium borohydride produces an unusual reduced species that is probably the 3,4-dihydroflavin.

Controlling the Diffusive Field to Grow a Higher Quality Protein Crystal in Microgravity

2012 ◽  
Vol 323-325 ◽  
pp. 549-554 ◽  
Author(s):  
Hiroaki Tanaka ◽  
Koji Inaka ◽  
Naoki Furubayashi ◽  
Mari Yamanaka ◽  
Sachiko Takahashi ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Three Dimensional ◽  
Protein Crystal ◽  
Microgravity Environment ◽  
High Quality ◽  
X Ray ◽  
Crystallization Experiments ◽  
Protein Molecules ◽  
Filtering Effect ◽  
Internal Order

Growing high quality crystals is a bottleneck in the multi-stepped process of three-dimensional structural analyses of protein. It is known that a microgravity environment may maintain ideal depletion zones of protein and impurity around a growing crystal and the filtering effect of these depletion zones may contribute to obtaining high-resolution X-ray diffracting crystals with superior internal order. The effects of these depletion zones around growing crystals are thought to be the main mechanisms for the improvement of crystal quality in microgravity. A competition between the diffusion of protein molecules in the solution (indexed by the diffusion coefficient, D) and the adsorption of those into the growing crystal (indexed by the kinetic coeffcient, β) decides the extent of depletion zones. Lower D values and higher β values indicate that these effects are more obvious in numerical analyses. Therefore we use the D/β value as an index for these effects. The most effective method of lowering the D/β value is using viscous precipitant reagents, such as a high molecular weight polyethylene glycol (PEG) to decrease the D value and using highly homogenous protein samples to increase the β value. In this report, we briefly introduce simple yet practical methods of estimating D and β values followed by a numerical analysis to understand the filtration effects, and the results of crystallization experiments in microgravity when controlling the diffusive field around the growing crystals using the D/β value as an index.

scholarly journals Abstract P-5: Neural Network Approaches to Classify 3D Protein Structures from the Data of X-ray Laser Radiation Diffraction from Single Particles

2021 ◽  
Vol 11 (Suppl_1) ◽  
pp. S13-S13
Author(s):  
Valery Novoseletsky ◽  
Mikhail Lozhnikov ◽  
Grigoriy Armeev ◽  
Aleksandr Kudriavtsev ◽  
Alexey Shaytan ◽  
...  
Keyword(s):  
Neural Network ◽  
Protein Structure ◽  
Image Classification ◽  
Structure Determination ◽  
Protein Structures ◽  
Protein Structure Determination ◽  
Family Type ◽  
X Ray ◽  
Protein Molecules ◽  
Diffraction Patterns

Background: Protein structure determination using X-ray free-electron laser (XFEL) includes analysis and merging a large number of snapshot diffraction patterns. Convolutional neural networks are widely used to solve numerous computer vision problems, e.g. image classification, and can be used for diffraction pattern analysis. But the task of protein structure determination with the use of CNNs only is not yet solved. Methods: We simulated the diffraction patterns using the Condor software library and obtained more than 1000 diffraction patterns for each structure with simulation parameters resembling real ones. To classify diffraction patterns, we tried two approaches, which are widely known in the area of image classification: a classic VGG network and residual networks. Results: 1. Recognition of a protein class (GPCRs vs globins). Globins and GPCR-like proteins are typical α-helical proteins. Each of these protein families has a large number of representatives (including those with known structure) but we used only 8 structures from every family. 12,000 of diffraction patterns were used for training and 4,000 patterns for testing. Results indicate that all considered networks are able to recognize the protein family type with high accuracy. 2. Recognition of the number of protein molecules in the liposome. We considered the usage of lyposomes as carriers of membrane or globular proteins for sample delivery in XFEL experiments in order to improve the X-ray beam hit rate. Three sets of diffractograms for liposomes of various radius were calculated, including diffractograms for empty liposomes, liposomes loaded with 5 bacteriorhodopsin molecules, and liposomes loaded with 10 bacteriorhodopsin molecules. The training set consisted of 23625 diffraction patterns, and test set of 7875 patterns. We found that all networks used in our study were able to identify the number of protein molecules in liposomes independent of the liposome radius. Our findings make this approach rather promising for the usage of liposomes as protein carriers in XFEL experiments. Conclusion: Thus, the performed numerical experiments show that the use of neural network algorithms for the recognition of diffraction images from single macromolecular particles makes it possible to determine changes in the structure at the angstrom scale.

scholarly journals Crystal Structures of [Fe]-Hydrogenase from Methanolacinia paynteri Suggest a Path of the FeGP-Cofactor Incorporation Process

Inorganics ◽  
2020 ◽  
Vol 8 (9) ◽  
pp. 50
Author(s):  
Gangfeng Huang ◽  
Francisco Javier Arriaza-Gallardo ◽  
Tristan Wagner ◽  
Seigo Shima
Keyword(s):  
Crystal Structure ◽  
Protein Structure ◽  
Guanosine Monophosphate ◽  
Amino Group ◽  
Prosthetic Group ◽  
Closed Conformation ◽  
Open Conformation ◽  
Local Protein Structure ◽  
Local Protein

[Fe]-hydrogenase (Hmd) catalyzes the reversible heterolytic cleavage of H2, and hydride transfer to methenyl-tetrahydromethanopterin (methenyl-H4MPT+). The iron-guanylylpyridinol (FeGP) cofactor, the prosthetic group of Hmd, can be extracted from the holoenzyme and inserted back into the protein. Here, we report the crystal structure of an asymmetric homodimer of Hmd from Methanolacinia paynteri (pHmd), which was composed of one monomer in the open conformation with the FeGP cofactor (holo-form) and a second monomer in the closed conformation without the cofactor (apo-form). In addition, we report the symmetric pHmd-homodimer structure in complex with guanosine monophosphate (GMP) or guanylylpyridinol (GP), in which each ligand was bound to the protein, where the GMP moiety of the FeGP-cofactor is bound in the holo-form. Binding of GMP and GP modified the local protein structure but did not induce the open conformation. The amino-group of the Lys150 appears to interact with the 2-hydroxy group of pyridinol ring in the pHmd–GP complex, which is not the case in the structure of the pHmd–FeGP complex. Lys150Ala mutation decreased the reconstitution rate of the active enzyme with the FeGP cofactor at the physiological pH. These results suggest that Lys150 might be involved in the FeGP-cofactor incorporation into the Hmd protein in vivo.

scholarly journals Flavin-dependent alcohol oxidase from the yeast Pichia pinus. Spatial localization of the coenzyme FAD in the protein structure: hot-tritium bombardment and ESR experiments

1995 ◽  
Vol 310 (2) ◽  
pp. 601-604 ◽  
Author(s):  
A Z Averbakh ◽  
N D Pekel ◽  
V I Seredenko ◽  
A V Kulikov ◽  
R I Gvozdev ◽  
...  
Keyword(s):  
Protein Structure ◽  
Quaternary Structure ◽  
Specific Radioactivity ◽  
Alcohol Oxidase ◽  
Spatial Localization ◽  
Prosthetic Group ◽  
Tritium Planigraphy ◽  
Pichia Pinus

The spatial localization of the coenzyme FAD in the quaternary structure of the alcohol oxidase from the yeast Pichia pinus was studied by tritium planigraphy and ESR methods. In the present paper we measured the specific radioactivity of FAD labelled as a part of the alcohol oxidase complex. The specific-radioactivity ratio for two FAD portions (FMN and AMP) was calculated. ESR experiments show 4 A (0.4 nm) to be the depth of immersion of paramagnetic isoalloxazines into alcohol oxidase octamer molecules. It is suggested that FAD molecules are bound to the surface of the octamer, rather than to the subunit interfaces. The orientation of the prosthetic group FAD in the alcohol oxidase protein is discussed.

scholarly journals Oxidant-Mediated Protein Amino Acid Conversion

Antioxidants ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 50 ◽  
Author(s):  
Yuichiro Suzuki
Keyword(s):  
Protein Structure ◽  
Amino Acid ◽  
Biological System ◽  
Redox Regulation ◽  
Amino Acid Sequences ◽  
Biological Oxidation ◽  
Oxidation Reactions ◽  
Protein Amino Acid ◽  
Peroxiredoxin 6 ◽  
Protein Molecules

Biological oxidation plays important roles in the pathogenesis of various diseases and aging. Carbonylation is one mode of protein oxidation. It has been reported that amino acids that are susceptible to carbonylation are arginine (Arg), proline (Pro), lysine, and threonine residues. The carbonylation product of both Arg and Pro residues is glutamyl semialdehyde. While chemically the oxidation reactions of neither Pro to glutamyl semialdehyde nor Arg to glutamyl semialdehyde are reversible, experimental results from our laboratory suggest that the biological system may drive the reduction of glutamyl semialdehyde to Pro in the protein structure. Further, glutamyl semialdehyde can be oxidized to become glutamic acid (Glu). Therefore, I hypothesize that biological oxidation post-translationally converts Arg to Pro, Arg to Glu, and Pro to Glu within the protein structure. Our mass spectrometry experiments provided evidence that, in human cells, 5–10% of peroxiredoxin 6 protein molecules have Pro-45 replaced by Glu. This concept of protein amino acid conversion challenges the dogma that amino acid sequences are strictly defined by nucleic acid sequences. I propose that, in the biological system, amino acid replacements can occur post-translationally through redox regulation, and protein molecules with non-DNA coding sequences confer functions.

Sign in / Sign up

Export Citation Format

Share Document