scholarly journals Structural Basis of Functional Group Activation by Sulfotransferases in Complex Metabolic Pathways

2012 ◽  
Vol 7 (12) ◽  
pp. 1994-2003 ◽  
Author(s):  
Jennifer Gehret McCarthy ◽  
Eli B. Eisman ◽  
Sarang Kulkarni ◽  
Lena Gerwick ◽  
William H. Gerwick ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Functional Group ◽  
Structural Basis

Prediction of Small Molecules Metabolic Pathways Based on Functional Group Composition

2009 ◽  
Vol 16 (8) ◽  
pp. 969-976 ◽  
Author(s):  
Jin Lu ◽  
Bing Niu ◽  
Liang Liu ◽  
Wen-Cong Lu ◽  
Yu-Dong Cai
Keyword(s):  
Small Molecules ◽  
Metabolic Pathways ◽  
Functional Group ◽  
Group Composition

Prediction of compounds’ biological function (metabolic pathways) based on functional group composition

2008 ◽  
Vol 12 (2) ◽  
pp. 131-137 ◽  
Author(s):  
Yu-Dong Cai ◽  
Ziliang Qian ◽  
Lin Lu ◽  
Kai-Yan Feng ◽  
Xin Meng ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Functional Group ◽  
Group Composition ◽  
Biological Function

scholarly journals Promiscuity in the Archaea: The enzymology of their metabolic pathways

2005 ◽  
Vol 27 (1) ◽  
pp. 17-21 ◽  
Author(s):  
Michael J. Danson ◽  
David W. Hough
Keyword(s):  
Metabolic Pathway ◽  
Metabolic Pathways ◽  
Hyperthermophilic Archaea ◽  
Structural Basis ◽  
Central Metabolism ◽  
Central Metabolic Pathway ◽  
Living Organisms ◽  
Single Set

The pathways of central metabolism provide the metabolic connections between the catabolic (degradative) and anabolic (biosynthetic) routes in all living organisms. In hyperthermophilic Archaea, we have discovered a promiscuous central metabolic pathway that catabolizes a variety of sugars using a single set of enzymes. This article explores the structural basis of this promiscuity in enzymes that have to maintain their integrity at temperatures approaching 100°C.

l-Arginine inhibits vasopressin-stimulated mesangial cell Ca2+

1998 ◽  
Vol 275 (2) ◽  
pp. C352-C357 ◽  
Author(s):  
Leah Balsam ◽  
Nasrin Nikbakht
Keyword(s):  
Amino Acids ◽  
Filtration Rate ◽  
Functional Group ◽  
Mesangial Cell ◽  
No Synthase ◽  
Structural Basis ◽  
Intracellular Ca ◽  
Cationic Amino Acids ◽  
Synthase Inhibitor ◽  
Progression Of Renal Disease

l-Arginine (l-Arg) affects various parameters that modulate the progression of renal disease. These same factors [e.g., glomerular filtration rate, changes in mesangial cell (MC) tension, and production of NO] are all controlled at least in part by changes in MC intracellular Ca2+concentration ([Ca2+]i). We therefore evaluated the effect of l-Arg on MC [Ca2+]i. We found thatl-Arg inhibits the vasopressin-stimulated rise in MC [Ca2+]i both in rat and murine cell cultures. This effect does not appear to be due to metabolism of l-Arg to either NO or l-ornithine (l-Orn). Blocking the metabolism of l-Arg with N ω-monomethyl-l-arginine, an NO synthase inhibitor, or with 20 mM l-valine (l-Val), an inhibitor of Orn formation, does not reverse the inhibition. However, other cationic amino acids, as well guanidine, the functional group ofl-Arg, all inhibit the vasopressin-stimulated rise in [Ca2+]i, consistent with a structural basis for this effect. We conclude that 1)l-Arg inhibits vasopressin-stimulated murine and rat MC [Ca2+]irise, 2) this inhibition is not mediated by metabolism of l-Arg to either NO or l-Orn, and 3) the effect ofl-Arg is due to its cationic functional group, guanidine.

Organization of tight junctions in the choroid plexus epithelium

1978 ◽  
Vol 36 (2) ◽  
pp. 336-337
Author(s):  
B. Van Deurs ◽  
J. K. Koehler
Keyword(s):  
Choroid Plexus ◽  
Present Report ◽  
Freeze Fracture ◽  
Barrier Properties ◽  
Cell Junctions ◽  
Structural Basis ◽  
Apical Surface ◽  
Choroid Plexus Epithelium ◽  
Solid Nitrogen ◽  
Special Composition

The choroid plexus epithelium constitutes a blood-cerebrospinal fluid (CSF) barrier, and is involved in regulation of the special composition of the CSF. The epithelium is provided with an ouabain-sensitive Na/K-pump located at the apical surface, actively pumping ions into the CSF. The choroid plexus epithelium has been described as “leaky” with a low transepithelial resistance, and a passive transepithelial flux following a paracellular route (intercellular spaces and cell junctions) also takes place. The present report describes the structural basis for these “barrier” properties of the choroid plexus epithelium as revealed by freeze fracture.Choroid plexus from the lateral, third and fourth ventricles of rats were used. The tissue was fixed in glutaraldehyde and stored in 30% glycerol. Freezing was performed either in liquid nitrogen-cooled Freon 22, or directly in a mixture of liquid and solid nitrogen prepared in a special vacuum chamber. The latter method was always used, and considered necessary, when preparations of complementary (double) replicas were made.

High resolution spot scan imaging of frozen, hydrated actin bundles with 400kV electrons

1992 ◽  
Vol 50 (1) ◽  
pp. 512-513
Author(s):  
J. Jakana ◽  
M.F. Schmid ◽  
P. Matsudaira ◽  
W. Chiu
Keyword(s):  
High Resolution ◽  
Binding Proteins ◽  
Actin Binding ◽  
Eukaryotic Cells ◽  
Dimensional Structure ◽  
Structural Basis ◽  
Actin Bundle ◽  
Actin Bundles ◽  
3 Dimensional ◽  
Macromolecular Assembly

Actin is a protein found in all eukaryotic cells. In its polymerized form, the cells use it for motility, cytokinesis and for cytoskeletal support. An example of this latter class is the actin bundle in the acrosomal process from the Limulus sperm. The different functions actin performs seem to arise from its interaction with the actin binding proteins. A 3-dimensional structure of this macromolecular assembly is essential to provide a structural basis for understanding this interaction in relationship to its development and functions.

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).

Electron diffraction detection of ordliking in annealed PbTe thin film

1990 ◽  
Vol 48 (4) ◽  
pp. 1018-1019
Author(s):  
Karimat El-Sayed
Keyword(s):  
Thin Film ◽  
Electron Diffraction ◽  
Lead Telluride ◽  
Structural Basis ◽  
Face Centered Cubic ◽  
X Ray ◽  
Polycrystalline Thin Films ◽  
Stage Process ◽  
Diffraction Patterns ◽  
Face Centered

Lead telluride is an important semiconductor of many applications. Many Investigators showed that there are anamolous descripancies in most of the electrophysical properties of PbTe polycrystalline thin films on annealing. X-Ray and electron diffraction studies are being undertaken in the present work in order to explain the cause of this anamolous behaviour.Figures 1-3 show the electron diffraction of the unheated, heated in air at 100°C and heated in air at 250°C respectively of a 300°A polycrystalline PbTe thin film. It can be seen that Fig. 1 is a typical [100] projection of a face centered cubic with unmixed (hkl) indices. Fig. 2 shows the appearance of faint superlattice reflections having mixed (hkl) indices. Fig. 3 shows the disappearance of thf superlattice reflections and the appearance of polycrystalline PbO phase superimposed on the [l00] PbTe diffraction patterns. The mechanism of this three stage process can be explained on structural basis as follows :

Structures of c-di-GMP/cGAMP degrading phosphodiesterase VcEAL: identification of a novel conformational switch and its implication

2019 ◽  
Vol 476 (21) ◽  
pp. 3333-3353 ◽  
Author(s):  
Malti Yadav ◽  
Kamalendu Pal ◽  
Udayaditya Sen
Keyword(s):  
Active Site ◽  
Metal Binding ◽  
Metal Ion ◽  
Triosephosphate Isomerase ◽  
Catalytic Mechanism ◽  
Degradation Mechanism ◽  
Structural Basis ◽  
Conserved Residues ◽  
Phosphodiester Bond ◽  
Cyclic Dinucleotides

Cyclic dinucleotides (CDNs) have emerged as the central molecules that aid bacteria to adapt and thrive in changing environmental conditions. Therefore, tight regulation of intracellular CDN concentration by counteracting the action of dinucleotide cyclases and phosphodiesterases (PDEs) is critical. Here, we demonstrate that a putative stand-alone EAL domain PDE from Vibrio cholerae (VcEAL) is capable to degrade both the second messenger c-di-GMP and hybrid 3′3′-cyclic GMP–AMP (cGAMP). To unveil their degradation mechanism, we have determined high-resolution crystal structures of VcEAL with Ca2+, c-di-GMP-Ca2+, 5′-pGpG-Ca2+ and cGAMP-Ca2+, the latter provides the first structural basis of cGAMP hydrolysis. Structural studies reveal a typical triosephosphate isomerase barrel-fold with substrate c-di-GMP/cGAMP bound in an extended conformation. Highly conserved residues specifically bind the guanine base of c-di-GMP/cGAMP in the G2 site while the semi-conserved nature of residues at the G1 site could act as a specificity determinant. Two metal ions, co-ordinated with six stubbornly conserved residues and two non-bridging scissile phosphate oxygens of c-di-GMP/cGAMP, activate a water molecule for an in-line attack on the phosphodiester bond, supporting two-metal ion-based catalytic mechanism. PDE activity and biofilm assays of several prudently designed mutants collectively demonstrate that VcEAL active site is charge and size optimized. Intriguingly, in VcEAL-5′-pGpG-Ca2+ structure, β5–α5 loop adopts a novel conformation that along with conserved E131 creates a new metal-binding site. This novel conformation along with several subtle changes in the active site designate VcEAL-5′-pGpG-Ca2+ structure quite different from other 5′-pGpG bound structures reported earlier.

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