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.

Current Trends in Biotherapeutic Higher Order Structure Characterization by Irreversible Covalent Footprinting Mass Spectrometry

2019 ◽  
Vol 26 (1) ◽  
pp. 35-43 ◽  
Author(s):  
Natalie K. Garcia ◽  
Galahad Deperalta ◽  
Aaron T. Wecksler
Keyword(s):  
Mass Spectrometry ◽  
Protein Structure ◽  
Protein Interactions ◽  
Quaternary Structure ◽  
Solvent Accessibility ◽  
Higher Order ◽  
Structure Characterization ◽  
Order Structure ◽  
Protein Footprinting ◽  
Wide Range

Background: Biotherapeutics, particularly monoclonal antibodies (mAbs), are a maturing class of drugs capable of treating a wide range of diseases. Therapeutic function and solutionstability are linked to the proper three-dimensional organization of the primary sequence into Higher Order Structure (HOS) as well as the timescales of protein motions (dynamics). Methods that directly monitor protein HOS and dynamics are important for mapping therapeutically relevant protein-protein interactions and assessing properly folded structures. Irreversible covalent protein footprinting Mass Spectrometry (MS) tools, such as site-specific amino acid labeling and hydroxyl radical footprinting are analytical techniques capable of monitoring the side chain solvent accessibility influenced by tertiary and quaternary structure. Here we discuss the methodology, examples of biotherapeutic applications, and the future directions of irreversible covalent protein footprinting MS in biotherapeutic research and development. Conclusion: Bottom-up mass spectrometry using irreversible labeling techniques provide valuable information for characterizing solution-phase protein structure. Examples range from epitope mapping and protein-ligand interactions, to probing challenging structures of membrane proteins. By paring these techniques with hydrogen-deuterium exchange, spectroscopic analysis, or static-phase structural data such as crystallography or electron microscopy, a comprehensive understanding of protein structure can be obtained.

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.

Purification and properties of crustacyanin

1966 ◽  
Vol 164 (994) ◽  
pp. 130-151 ◽  
Keyword(s):  
Molecular Weight ◽  
Quaternary Structure ◽  
Gel Filtration ◽  
Potassium Thiocyanate ◽  
Starch Gel Electrophoresis ◽  
Prosthetic Group ◽  
Reversible Dissociation ◽  
Purification And Properties ◽  
Starch Gel ◽  
Quaternary Structures

Crustacyanin, the blue carapace pigment of the common lobster Homarus gammarus (L.), has been purified and crystallized. This chromoprotein has a minimum molecular weight of 36 000 based on the content of the carotenoid prosthetic group astaxanthin. The molecular weight in gel filtration measurements is about 650 000, corresponding to some 18 molecules of astaxanthin per molecule of protein. Crustacyanin, on dialysis against water, dissociates into particles of about 35 000 molecular weight, each apparently bearing one molecule of carotenoid. The dissociation is accompanied by a shift in the principal maximum of the absorption spectrum from 633 to 595 nm and is reversed upon addition of salt. Reversible dissociation also occurs in the presence of 3 M urea, 1 M potassium thiocyanate, 10% (v/v) dioxan or 10% (v/v) acetone. When the carotenoid is removed from crustacyanin with acetone, the resul­tant apoprotein has a mean molecular weight of about 20 000. It may be resolved by starch gel electrophoresis into several components of which two predominate. Crustacyanin, indistinguishable from the native material, can be reconstituted from apoprotein and carotenoid. Evidence from the behaviour of crustacyanin and its apoprotein at surfaces indicates that the tertiary and quaternary structures of the native protein are stabilized by the carotenoid. It is suggested that the quaternary structure of crustacyanin is induced by an interaction of the carotenoid molecules of the subunits, which in turn causes a change in configuration of the protein favourable to aggregation. The result is a micelle-like structure with a hydrophobic carotenoid core.

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 Molecular dynamics and experimental investigation of H2 and O2 diffusion in [Fe]-hydrogenase

2005 ◽  
Vol 33 (1) ◽  
pp. 80-82 ◽  
Author(s):  
J. Cohen ◽  
K. Kim ◽  
M. Posewitz ◽  
M.L. Ghirardi ◽  
K. Schulten ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Experimental Investigation ◽  
Protein Structure ◽  
Active Site ◽  
Essential Role ◽  
Clostridium Pasteurianum ◽  
Prosthetic Group ◽  
Theoretical Investigations ◽  
O2 Diffusion

The [Fe]-hydrogenase enzymes are highly efficient H2 catalysts found in ecologically and phylogenetically diverse microorganisms, including the photosynthetic green alga, Chlamydomonas reinhardtii. Although these enzymes can occur in several forms, H2 catalysis takes place at a unique [FeS] prosthetic group or H-cluster, located at the active site. Significant to the function of hydrogenases is how the surrounding protein structure facilitates substrate-product transfer, and protects the active site H-cluster from inactivation. To elucidate the role of protein structure in O2 inactivation of [Fe]-hydrogenases, experimental and theoretical investigations have been performed. Molecular dynamics was used to comparatively investigate O2 and H2 diffusion in CpI ([Fe]-hydrogenase I from Clostridium pasteurianum). Our preliminary results suggest that H2 diffuses more easily and freely than O2, which is restricted to a small number of allowed pathways to and from the active site. These O2 pathways are located in the conserved active site domain, shown experimentally to have an essential role in active site protection.

scholarly journals The structure of the Moco carrier protein from Rippkaea orientalis

2020 ◽  
Vol 76 (9) ◽  
pp. 453-463 ◽  
Author(s):  
Joern Krausze ◽  
Thomas W. Hercher ◽  
Archna Archna ◽  
Tobias Kruse
Keyword(s):  
Quaternary Structure ◽  
Chloride Ions ◽  
Free Form ◽  
Carrier Protein ◽  
Prosthetic Group ◽  
Computational Docking ◽  
Recombinant Production ◽  
Enzymatic Function ◽  
Nucleotide Binding Proteins ◽  
Positively Charged

The molybdenum cofactor (Moco) is the prosthetic group of all molybdenum-dependent enzymes except for nitrogenase. The multistep biosynthesis pathway of Moco and its function in molybdenum-dependent enzymes are already well understood. The mechanisms of Moco transfer, storage and insertion, on the other hand, are not. In the cell, Moco is usually not found in its free form and remains bound to proteins because of its sensitivity to oxidation. The green alga Chlamydomonas reinhardtii harbors a Moco carrier protein (MCP) that binds and protects Moco but is devoid of enzymatic function. It has been speculated that this MCP acts as a means of Moco storage and transport. Here, the search for potential MCPs has been extended to the prokaryotes, and many MCPs were found in cyanobacteria. A putative MCP from Rippkaea orientalis (RoMCP) was selected for recombinant production, crystallization and structure determination. RoMCP has a Rossmann-fold topology that is characteristic of nucleotide-binding proteins and a homotetrameric quaternary structure similar to that of the MCP from C. reinhardtii. In each protomer, a positively charged crevice was identified that accommodates up to three chloride ions, hinting at a potential Moco-binding site. Computational docking experiments supported this notion and gave an impression of the RoMCP–Moco complex.

Quaternary structure of Limulus polyphemus hemocyanin

1978 ◽  
Vol 36 (2) ◽  
pp. 176-177
Author(s):  
T. Wichertjes ◽  
E.J. Kwak ◽  
E.F.J. Van Bruggen
Keyword(s):  
Electron Microscopy ◽  
Functional Properties ◽  
Horseshoe Crab ◽  
Temperature Jump ◽  
Quaternary Structure ◽  
Crystallographic Analysis ◽  
Limulus Polyphemus ◽  
Oxygen Binding ◽  
X Ray ◽  
Intact Molecule

Hemocyanin of the horseshoe crab (Limulus polyphemus) has been studied in nany ways. Recently the structure, dissociation and reassembly was studied using electron microscopy of negatively stained specimens as the method of investigation. Crystallization of the protein proved to be possible and X-ray crystallographic analysis was started. Also fluorescence properties of the hemocyanin after dialysis against Tris-glycine buffer + 0.01 M EDTA pH 8.9 (so called “stripped” hemocyanin) and its fractions II and V were studied, as well as functional properties of the fractions by NMR. Finally the temperature-jump method was used for assaying the oxygen binding of the dissociating molecule and of preparations of isolated subunits. Nevertheless very little is known about the structure of the intact molecule. Schutter et al. suggested that the molecule possibly consists of two halves, combined in a staggered way, the halves themselves consisting of four subunits arranged in a square.

Characterization of Tamm-Horsfall Urinary Glycoprotein

1973 ◽  
Vol 31 ◽  
pp. 420-421
Author(s):  
John P. Robinson ◽  
J. David Puett
Keyword(s):  
Electron Microscopy ◽  
Circular Dichroism ◽  
Secondary Structure ◽  
Quaternary Structure ◽  
Normal Adult ◽  
Morphological Properties ◽  
Adult Males ◽  
Circular Dichroïsm ◽  
Urinary Glycoprotein

Much work has been reported on the chemical, physical and morphological properties of urinary Tamm-Horsfall glycoprotein (THG). Although it was once reported that cystic fibrotic (CF) individuals had a defective THG, more recent data indicate that THG and CF-THG are similar if not identical.No studies on the conformational aspects have been reported on this glycoprotein using circular dichroism (CD). We examined the secondary structure of THG and derivatives under various conditions and have correlated these results with quaternary structure using electron microscopy.THG was prepared from normal adult males and CF-THG from a 16-year old CF female by the method of Tamm and Horsfall. CF female by the method of Tamm and Horsfall.

Electron Microscopy and image reconstruction reveal the structural basis for spectrin's elastic properties

1992 ◽  
Vol 50 (1) ◽  
pp. 510-511
Author(s):  
Amy M. McGough ◽  
Robert Josephs
Keyword(s):  
Electron Microscopy ◽  
Elastic Properties ◽  
Conformational Changes ◽  
Quaternary Structure ◽  
Three Dimensional ◽  
Membrane Skeleton ◽  
Projection Algorithm ◽  
Structural Basis ◽  
Iterative Approximation ◽  
Membrane Skeletons

The remarkable deformability of the erythrocyte derives in large part from the elastic properties of spectrin, the major component of the membrane skeleton. It is generally accepted that spectrin's elasticity arises from marked conformational changes which include variations in its overall length (1). In this work the structure of spectrin in partially expanded membrane skeletons was studied by electron microscopy to determine the molecular basis for spectrin's elastic properties. Spectrin molecules were analysed with respect to three features: length, conformation, and quaternary structure. The results of these studies lead to a model of how spectrin mediates the elastic deformation of the erythrocyte.Membrane skeletons were isolated from erythrocyte membrane ghosts, negatively stained, and examined by transmission electron microscopy (2). Particle lengths and end-to-end distances were measured from enlarged prints using the computer program MACMEASURE. Spectrin conformation (straightness) was assessed by calculating the particles’ correlation length by iterative approximation (3). Digitised spectrin images were correlation averaged or Fourier filtered to improve their signal-to-noise ratios. Three-dimensional reconstructions were performed using a suite of programs which were based on the filtered back-projection algorithm and executed on a cluster of Microvax 3200 workstations (4).

The Nature of Oxide Surfaces: Topographic and Electronic Structure

1993 ◽  
Vol 51 ◽  
pp. 966-967
Author(s):  
Dawn A. Bonnell ◽  
Yong Liang
Keyword(s):  
Transition Metal Oxides ◽  
Electronic Structures ◽  
Recent Progress ◽  
Spatial Localization ◽  
Level Of Detail ◽  
Scanning Tunneling ◽  
Oxide Surfaces ◽  
Tunneling Microscopy ◽  
Considerable Effort ◽  
Complete Understanding

Recent progress in the application of scanning tunneling microscopy (STM) and tunneling spectroscopy (STS) to oxide surfaces has allowed issues of image formation mechanism and spatial resolution limitations to be addressed. As the STM analyses of oxide surfaces continues, it is becoming clear that the geometric and electronic structures of these surfaces are intrinsically complex. Since STM requires conductivity, the oxides in question are transition metal oxides that accommodate aliovalent dopants or nonstoichiometry to produce mobile carriers. To date, considerable effort has been directed toward probing the structures and reactivities of ZnO polar and nonpolar surfaces, TiO2 (110) and (001) surfaces and the SrTiO3 (001) surface, with a view towards integrating these results with the vast amount of previous surface analysis (LEED and photoemission) to build a more complete understanding of these surfaces. However, the spatial localization of the STM/STS provides a level of detail that leads to conclusions somewhat different from those made earlier.

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