scholarly journals Structural similarities in the CPC clip motif explain peptide-binding promiscuity between glycosaminoglycans and lipopolysaccharides

2017 ◽  
Vol 14 (136) ◽  
pp. 20170423 ◽  
Author(s):  
David Pulido ◽  
Rocío Rebollido-Rios ◽  
Javier Valle ◽  
David Andreu ◽  
Ester Boix ◽  
...  
Keyword(s):  
Binding Sites ◽  
Three Dimensional ◽  
The Body ◽  
Heparin Binding ◽  
Structural Determinants ◽  
E Coli ◽  
High Affinity ◽  
Structural Framework ◽  
And Control ◽  
Proteins And Peptides

Lipopolysaccharides (LPSs) and glycosaminoglycans (GAGs) are polymeric structures containing negatively charged disaccharide units that bind to specialized proteins and peptides in the human body and control fundamental processes such as inflammation and coagulation. Surprisingly, some proteins can bind both LPSs and GAGs with high affinity, suggesting that a cross-communication between these two pathways can occur. Here, we explore whether GAGs and LPSs can share common binding sites in proteins and what are the structural determinants of this binding. We found that the LPS-binding peptide YI12WF, derived from protein FhuA, can bind both heparin and E. coli LPS with high affinity. Most interestingly, mutations decreasing heparin binding in the peptide also reduce LPS affinity. We show that such mutations involve the CPC clip motif in the peptide, a small three-dimensional signature required for heparin binding. Overall, we conclude that negatively charged polysaccharide-containing polymers such as GAGs and LPSs can compete for similar binding sites in proteins, and that the CPC clip motif is essential to bind both ligands. Our results provide a structural framework to explain why these polymers can cross-interact with the same proteins and peptides and thus contribute to the regulation of apparently unrelated processes in the body.

scholarly journals Експериментальне зараження поросят вірусом епідемічної діареї свиней

2017 ◽  
Vol 19 (77) ◽  
pp. 208-213
Author(s):  
D. Masiuk ◽  
A. Sosnitskiy ◽  
A. Kokarev ◽  
S. Koliada
Keyword(s):  
Real Time ◽  
The Body ◽  
Control Group ◽  
Rt Pcr ◽  
Internal Organs ◽  
Real Time System ◽  
E Coli ◽  
Neonatal Piglets ◽  
And Control ◽  
Experimental Group

There were infected neonatal piglets in the first days of their lives PED virus suspension derived from pigs previously PED patients. Diagnosis for PED in piglets donor virus PED was inserted complex method for clinical and epizootic performance and confirmed the identification PEDV by PCR-RT using the test system «EZ-RED/TGE/PDCoV MPX 1.0 Real time RT-PCR» company Tetracore (USA) Thermocyclers CFX 96 Real-Time System company BIO RAD (USA). Homogenate small intestine of pigs PEDV donor, prepared in a blender for PCR in a thick band of 18 animal carcasses, frozen at -18 °C without cryopreservation and kept 359 days. Before infecting pigs and strip defrost by RT-PCR identified the concentration of the virus genome equivalents (GE) without establishing viable virions quantitative pathogen. For Sample 20 selected analog neonatal piglets, divided them into 3 experimental groups (group 1 – 5 piglets, group 2 – 5 piglets and group 3 – 7 piglets) and one control (3 piglets). Research pigs infected per os virus-containing suspension with a concentration PEDV 1.03×106 GE/cm3. The dose for infection first group was 6 cm3 (6.18×106 GE/cm3), for the second – 5 cm3 (5,15 × 106 GE/cm3), for the third – 4 cm3 (4.12 GE×106/cm3) homogenate. The fourth group – control (not infected). All the pigs were in identical conditions that fully meet the physiological needs of the body. Of the 17 infected pigs only 2 was infected PEDV. PED was confirmed by laboratory methods. In bacteriological examination of internal organs of pigs that came out of a research experiment and control group were diagnosed colibacteriosis. In the control group was isolated from heart and intestinal non-pathogenic for white mice E. coli. From pigs 1 and 2 research groups has been allocated to white mice nonpathogenic E. coli, is set colibacteriosis; 2 experimental group found in one pig hemolytic E. coli; 3 experimental group from the internal organs of pigs in conjunction with non-pathogenic for mice intestinal former cane isolated Klesiella spp., is diagnosed with mixed infection (E. coli, Klesiella spp.). From the intestine of experimental and control pigs do not identified beneficial microflora – aerococcus, lactobacteria, bifidobacteria and cultured putrefactive anaerobic spore facultative and non spore microflora.

Mechanisms of helical swimming: asymmetries in the morphology, movement and mechanics of larvae of the ascidian Distaplia occidentalis

2001 ◽  
Vol 204 (17) ◽  
pp. 2959-2973 ◽  
Author(s):  
Matthew J. McHenry
Keyword(s):  
Body Shape ◽  
Three Dimensional ◽  
The Body ◽  
Hydrodynamic Theory ◽  
Helical Motion ◽  
Body Rotation ◽  
Oblique Angle ◽  
Free Swimming ◽  
Three Point Bending ◽  
And Control

SUMMARY A great diversity of unicellular and invertebrate organisms swim along a helical path, but it is not well understood how asymmetries in the body shape or the movement of propulsive structures affect a swimmer’s ability to perform the body rotation necessary to move helically. The present study found no significant asymmetries in the body shape of ascidian larvae (Distaplia occidentalis) that could operate to rotate the body during swimming. By recording the three-dimensional movement of free-swimming larvae, it was found that the tail possessed two bends, each with constant curvature along their length. As these bends traveled posteriorly, the amplitude of curvature changes was significantly greater in the concave-left direction than in the concave-right direction. In addition to this asymmetry, the tail oscillated at an oblique angle to the midline of the trunk. These asymmetries generated a yawing moment that rotated the body in the counterclockwise direction from a dorsal view, according to calculations from hydrodynamic theory. The tails of resting larvae were bent in the concave-left direction with a curvature statistically indistinguishable from the median value for tail curvature during swimming. The flexural stiffness of the tails of larvae, measured in three-point bending, may be great enough to allow the resting curvature of the tail to have an effect on the symmetry of kinematics. This work suggests that asymmetrical tail motion is an important mechanism for generating a yawing moment during swimming in ascidian larvae and that these asymmetries may be caused by the tail’s bent shape. Since helical motion requires that moments also be generated in the pitching or rolling directions, other mechanisms are required to explain fully how ascidian larvae generate and control helical swimming.

scholarly journals Mechanism of thrombin binding to endothelial cells

Blood ◽  
1983 ◽  
Vol 61 (2) ◽  
pp. 368-372 ◽  
Author(s):  
PT Bauer ◽  
R Machovich ◽  
P Aranyi ◽  
KG Buki ◽  
E Csonka ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Binding Sites ◽  
Antithrombin Iii ◽  
Affinity Binding ◽  
Heparin Binding ◽  
High Affinity Binding ◽  
Aortic Endothelial Cells ◽  
High Affinity ◽  
Lysine Residues ◽  
Two Populations

Abstract The interaction of human alpha-thrombin with mini-pig aortic endothelial cells was studied using 125I-labeled enzyme. Equilibrium between bound and free thrombin was attained within 1 min, and the Klotz-Hunston equations indicated two populations of binding sites. Approximately 30,000 sites/cell belonged to the high-affinity class with a Kd of about 3 x 10(-8) M. Modification of two lysine residues of thrombin with pyridoxal 5′-phosphate (PLP2-thrombin) destroyed the high- affinity binding and about three-fourths of the low-affinity bindings. When the lysine residue of thrombin involved in heparin binding was protected with heparin against chemical modification (PLP-thrombin), the modified enzyme remained similar to the native one with respect to cellular binding, with some loss of low-affinity binding only. Heparin, in a tenfold molar excess to enzyme, inhibited the binding of the native as well as the PLP-thrombin, whereas it did not influence the interaction between PLP2-thrombin and the cell. Since heparin might interfere with both the enzyme and the cell, the binding of heparin to endothelial cells was also examined. The results revealed that 3H- heparin also bound to cells. This binding was characterized by a Kd of 3 x 10(-7) M, approximately 10(6) sites/cell. Furthermore, thrombin bound to endothelial cells was released by antithrombin III. On the basis of these and other data in the literature, a model is proposed for the mechanism of the binding of thrombin to endothelial cells.

scholarly journals Biosynthesis of heparin. Use of Escherichia coli K5 capsular polysaccharide as a model substrate in enzymic polymer-modification reactions

1991 ◽  
Vol 275 (1) ◽  
pp. 151-158 ◽  
Author(s):  
M Kusche ◽  
H H Hannesson ◽  
U Lindahl
Keyword(s):  
Escherichia Coli ◽  
Structural Analysis ◽  
Binding Sites ◽  
Proteinase Inhibitor ◽  
Capsular Polysaccharide ◽  
Polymer Modification ◽  
Sulphated Polysaccharide ◽  
E Coli ◽  
High Affinity ◽  
K5 Polysaccharide

A capsular polysaccharide from Escherichia coli K5 was previously found to have the same structure, [-(4)beta GlcA(1)→(4)alpha GlcNAc(1)-]n, as that of the non-sulphated precursor polysaccharide in heparin biosynthesis [Vann, Schmidt, Jann & Jann (1981) Eur. J. Biochem. 116, 359-364]. The K5 polysaccharide was N-deacetylated (by hydrazinolysis) and N-sulphated, and was then incubated with detergent-solubilized enzymes from a heparin-producing mouse mastocytoma, in the presence of adenosine 3′-phosphate 5′-phospho[35S] sulphate ([35S]PAPS). Structural analysis of the resulting 35S-labelled polysaccharide revealed the formation of all the major disaccharide units found in heparin. The identification of 2-O-[35S]sulphated IdoA (L-iduronic acid) as well as 6-O-[35S]sulphated GlcNSO3 units demonstrated that the modified K5 polysaccharide served as a substrate in the hexuronosyl C-5-epimerase and the major O-sulphotransferase reactions involved in the biosynthesis of heparin. The GlcA units of the native (N-acetylated) E. coli polysaccharide were attacked by the epimerase only when PAPS was present in the incubations, whereas those of the chemically N-sulphated polysaccharide were epimerized also in the absence of PAPS, in accord with the notion that N-sulphate groups are required for epimerization. With increasing concentrations of PAPS, the mono-O-sulphated disaccharide unit-IdoA(2-OSO3)-GlcNSO3- was progressively converted into the di-O-sulphated species -IdoA(2-OSO3)-GlcNSO3(6-OSO3)-. A small proportion of the 35S-labelled polysaccharide was found to bind with high affinity to the proteinase inhibitor antithrombin. This proportion increased with increasing concentration of PAPS up to a level corresponding to approximately 1-2% of the total incorporated 35S. The solubilized enzymes thus catalysed all the reactions required for the generation of functional antithrombin-binding sites.

scholarly journals Characterization of Ca2+ interactions with matrix metallopeptidase-12: implications for matrix metallopeptidase regulation

2006 ◽  
Vol 398 (3) ◽  
pp. 393-398 ◽  
Author(s):  
Thomas Gossas ◽  
U. Helena Danielson
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Calcium Binding ◽  
Three Dimensional ◽  
Zinc Ion ◽  
Affinity Binding ◽  
High Affinity Binding ◽  
High Affinity ◽  
High Affinity Binding Site ◽  
Matrix Metallopeptidase

Matrix metallopeptidase-12 (MMP-12) binds three calcium ions and a zinc ion, in addition to the catalytic zinc ion. These ions are thought to have a structural role, stabilizing the active conformation of the enzyme. To characterize the importance of Ca2+ binding for MMP-12 activity and the properties of the different Ca2+ sites, the activity as a function of [Ca2+] and the effect of pH was investigated. The enzymatic activity was directly correlated to calcium binding and a Langmuir isotherm for three binding sites described the activity as a function of [Ca2+]. The affinities for two of the binding sites were quantified at several pH values. At pH 7.5, the KD was 0.1 mM for the high-affinity binding site, 5 mM for the intermediate-affinity binding site and >100 mM for the low-affinity binding site. For all three sites, the affinity for calcium decreased with reduced pH, in accordance with the loss of interactions upon protonation of the calcium-co-ordinating aspartate and glutamate carboxylates at acidic pH. The pKa values of the calcium binding sites with the highest and intermediate affinities were determined to be 4.3 and 6.5 respectively. Optimal pH for catalysis was above 7.5. The low-, intermediate- and high-affinity binding sites were assigned on the basis of analysis of three-dimensional-structures of MMP-12. The strong correlation between MMP-12 activity and calcium binding for the physiologically relevant [Ca2+] and pH ranges studied suggest that Ca2+ may be involved in controlling the activity of MMP-12.

scholarly journals Strength and Service Life of a Steam Turbine Stop and Control Valve Body

2021 ◽  
Vol 24 (4) ◽  
pp. 61-70 ◽  
Author(s):  
Andrii S. Koliadiuk ◽  
◽  
Mykola H. Shulzhenko ◽  
Oleksandr M. Hubskyi ◽  
◽  
...  
Keyword(s):  
Service Life ◽  
Steam Turbine ◽  
Three Dimensional ◽  
The Body ◽  
Valve Body ◽  
Control Valves ◽  
Operating Modes ◽  
And Control ◽  
Inlet Chamber ◽  
Creep Strains

The stability of operation of steam turbines depends (along with other factors) on the reliable operation of their steam distribution systems, which are based on stop and control valves. This paper considers the strength of the elements of the K-325-23.5 steam turbine valves, in whose bodies, after 30 thousand hours of operation, cracks came to be observed. Previously determined were the nature of gas-dynamic processes in the flow paths of the valves and the temperature state of the valve body in the main stationary modes of operation. To do this, a combined problem of steam flow and thermal conductivity in stop and control valves was solved in a three-dimensional formulation by the finite element method. Different positions of the valve elements were considered taking into account the filter sieve. The assessment of the thermal stress state of the valve body showed that the maximum stresses in different operating modes do not exceed the yield strength. Therefore, the assessment of the creep of the valve body material is important to determine the valve body damage and service life. Modeling the creep of the stop and control valves of the turbine was performed on the basis of three-dimensional models, using the theory of hardening, with the components of unstable and steady creep strains taken into account. The creep was determined at the maximum power of the turbine for all the stationary operating modes. The maximum calculated values of creep strains are concentrated in the valve body branch pipes before the control valves and in the steam inlet chamber, where in practice fatigue defects are observed. However, even for 300 thousand hours of operation of the turbine (with a conditional maximum power) in stationary modes, creep strains do not exceed admissible values. The damage and service life of the valve bodies were assessed by two methods developed at A. Pidhornyi Institute of Mechanical Engineering Problems of the NAS of Ukraine (2011), and I. Polzunov Scientific and Design Association on Research and Design of Power Equipment. (NPO CKTI) – 1986. The results of assessing the damage and the turbine valve body wear from the effects of cyclic loading and creep of the turbine in stationary modes for 40, 200 and 300 thousand hours show that the thermal conditions of the body in the steam inlet chamber are not violated (without taking into account possible body defects after manufacture). The damage in valve body branch pipes after 300 thousand hours of operation exceeds the admissible value, with account taken of the safety margin. At the same time, the damage from creep in stationary operating modes is about 70% of the total damage. The maximum values of damage are observed in the areas of the body where there are defects during the operation of the turbine steam distribution system. The difference between the results of both methods in relation to their average value is ~20%.

scholarly journals Mechanism of thrombin binding to endothelial cells

Blood ◽  
1983 ◽  
Vol 61 (2) ◽  
pp. 368-372
Author(s):  
PT Bauer ◽  
R Machovich ◽  
P Aranyi ◽  
KG Buki ◽  
E Csonka ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Binding Sites ◽  
Antithrombin Iii ◽  
Affinity Binding ◽  
Heparin Binding ◽  
High Affinity Binding ◽  
Aortic Endothelial Cells ◽  
High Affinity ◽  
Lysine Residues ◽  
Two Populations

The interaction of human alpha-thrombin with mini-pig aortic endothelial cells was studied using 125I-labeled enzyme. Equilibrium between bound and free thrombin was attained within 1 min, and the Klotz-Hunston equations indicated two populations of binding sites. Approximately 30,000 sites/cell belonged to the high-affinity class with a Kd of about 3 x 10(-8) M. Modification of two lysine residues of thrombin with pyridoxal 5′-phosphate (PLP2-thrombin) destroyed the high- affinity binding and about three-fourths of the low-affinity bindings. When the lysine residue of thrombin involved in heparin binding was protected with heparin against chemical modification (PLP-thrombin), the modified enzyme remained similar to the native one with respect to cellular binding, with some loss of low-affinity binding only. Heparin, in a tenfold molar excess to enzyme, inhibited the binding of the native as well as the PLP-thrombin, whereas it did not influence the interaction between PLP2-thrombin and the cell. Since heparin might interfere with both the enzyme and the cell, the binding of heparin to endothelial cells was also examined. The results revealed that 3H- heparin also bound to cells. This binding was characterized by a Kd of 3 x 10(-7) M, approximately 10(6) sites/cell. Furthermore, thrombin bound to endothelial cells was released by antithrombin III. On the basis of these and other data in the literature, a model is proposed for the mechanism of the binding of thrombin to endothelial cells.

scholarly journals High-resolution, genome-wide mapping of positive supercoiling in chromosomes

2021 ◽  
Author(s):  
Monica S. Guo ◽  
Ryo Kawamura ◽  
Megan Littlehale ◽  
John F. Marko ◽  
Michael T. Laub
Keyword(s):  
High Resolution ◽  
Chromatin Immunoprecipitation ◽  
Binding Sites ◽  
Three Dimensional ◽  
Domain Model ◽  
Bacterial Protein ◽  
E Coli ◽  
Genome Wide ◽  
Powerful Approach ◽  
Positive Supercoiling

AbstractSupercoiling impacts DNA replication, transcription, protein binding to DNA, and the three-dimensional organization of chromosomes. However, there are currently no methods to directly interrogate or map positive supercoils, so their distribution in genomes remains unknown. Here, we describe a method, GapR-seq, based on the chromatin immunoprecipitation of GapR, a bacterial protein that preferentially recognizes overtwisted DNA, for generating high-resolution maps of positive supercoiling. Applying this method to E. coli and S. cerevisiae, we find that positive supercoiling is widespread, associated with transcription, and particularly enriched between convergently-oriented genes, consistent with the “twin-domain” model of supercoiling. In yeast, we also find positive supercoils associated with centromeres, cohesin binding sites, autonomously replicating sites, and the borders of R-loops (DNA-RNA hybrids). Our results suggest that GapR-seq is a powerful approach, likely applicable in any organism, to investigate aspects of chromosome structure and organization not accessible by Hi-C or other existing methods.

HEPARIN BINDING TO ENDOTHELIAL CELLS POTENTIATES THROMBINSTIMULATED PGI2 PRoDUCTION

1987 ◽  
Author(s):  
T Bårzu ◽  
P Molho ◽  
R Cariou ◽  
G Tobelem ◽  
J Caen
Keyword(s):  
Binding Sites ◽  
Umbilical Vein ◽  
Primary Cultures ◽  
Low Molecular Weight ◽  
Heparin Binding ◽  
Serum Free Medium ◽  
Free Medium ◽  
Specific Mechanism ◽  
High Affinity ◽  
Stimulation Of

We studied the consequences of hepari n (H) binding to endothel iaI cells (EC) on their basal and thrombin-stimulated PGI2 production. Primary cultures of human umbilical vein EC were incubated with different H concentrations, in serum free medium for 5 hrs. The amount of 6-keto-pGF1α was measured in the medium after 5 hrs with an enzyme-linked inmunoassay. At all concentrations used (0.75 to 75 μg/ml) H did not alter the 5-hour basal production of PGI2 (control, 10.1 α 1.4 ng/106 cells; H 15 μg/m1 ; 10.8 ± 2.7 ng/106 cells). Basal or thrombin (0.1 U/m])-rtimulated (10 min) pGI2 production was then determined using EC bearing only bound heparin. The low, unstimulated PGI2 release (0.412 ± 0.04 ng/106 cells) was not significantly changed in the presence of bound H, but the thrombin-stimulated release was potentiated.The KD for H binding to EC is 2.5 μg/ml. Thus at 3 μg/ml, half maximal saturation of binding sites and maximal potentiation of thrombin action were achieved. This concentration of bound H shifted the dose-response curve of thrombin induced PGI2 production to the left. Similar effect was obtained with half maximal saturating concentration of low molecular weight H (CY 222). Neither arachinodate nor LC4-induced PGI2 release were modified by H binding to EC, suggesting that potentiation is specific to thrombin. Since bound H was shown to not modify the high affinity thrombin binding to EC, the potentiating effect of bound H could related rather to interference with the specific mechanism of thrombin-stimulation of PGI2 production.

scholarly journals High-resolution, genome-wide mapping of positive supercoiling in chromosomes

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Monica S Guo ◽  
Ryo Kawamura ◽  
Megan L Littlehale ◽  
John F Marko ◽  
Michael T Laub
Keyword(s):  
High Resolution ◽  
Chromatin Immunoprecipitation ◽  
Binding Sites ◽  
Three Dimensional ◽  
Domain Model ◽  
Bacterial Protein ◽  
E Coli ◽  
Genome Wide ◽  
Powerful Approach ◽  
Positive Supercoiling

Supercoiling impacts DNA replication, transcription, protein binding to DNA, and the three-dimensional organization of chromosomes. However, there are currently no methods to directly interrogate or map positive supercoils, so their distribution in genomes remains unknown. Here, we describe a method, GapR-seq, based on the chromatin immunoprecipitation of GapR, a bacterial protein that preferentially recognizes overtwisted DNA, for generating high-resolution maps of positive supercoiling. Applying this method to E. coli and S. cerevisiae, we find that positive supercoiling is widespread, associated with transcription, and particularly enriched between convergently-oriented genes, consistent with the 'twin-domain' model of supercoiling. In yeast, we also find positive supercoils associated with centromeres, cohesin binding sites, autonomously replicating sites, and the borders of R-loops (DNA-RNA hybrids). Our results suggest that GapR-seq is a powerful approach, likely applicable in any organism, to investigate aspects of chromosome structure and organization not accessible by Hi-C or other existing methods.

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