scholarly journals Conformational Search on the Lewis X Structure by Molecular Dynamic: Study of Tri- and Pentasaccharide

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
N. Khebichat ◽  
K. Nekkaz ◽  
S. Ghalem
Keyword(s):  
Md Simulation ◽  
Leukocyte Adhesion ◽  
Conformational Search ◽  
Water Model ◽  
Biological Processes ◽  
Differentiation Antigen ◽  
Lewis X ◽  
Endothelial Leukocyte Adhesion Molecule ◽  
Explicit Water ◽  
Antigen Tumor

Carbohydrates play vital roles in many biological processes, such as recognition, adhesion, and signalling between cells. The Lewis X determinant is a trisaccharide fragment implicated as a specific differentiation antigen, tumor antigen, and key component of the ligand for the endothelial leukocyte adhesion molecule, so it is necessary or essential to determine and to know their conformational and structural properties. In this work, conformational analysis was performed using molecular dynamics (MD) simulation with the AMBER10 program package in order to study the dynamic behavior of of the Lewis X trisaccharide (β-D-Gal-(1,4)-[α-L-Fuc-(1,3)]-β-D-GlcNAc-OMe) and the Lewis X pentasaccharide (β-D-Gal-(1,4)-[α-L-Fuc-(1,3)]-β-D-GlcNAc-(1,3)-β-D-Gal-(1,4)-β-D-Glu-OMe) in explicit water model at 300 K for 10 ns using the GLYCAM 06 force field.

scholarly journals The selectin GMP-140 binds to sialylated, fucosylated lactosaminoglycans on both myeloid and nonmyeloid cells.

1991 ◽  
Vol 115 (2) ◽  
pp. 557-564 ◽  
Author(s):  
Q Zhou ◽  
K L Moore ◽  
D F Smith ◽  
A Varki ◽  
R P McEver ◽  
...  
Keyword(s):  
Leukocyte Adhesion ◽  
Structural Features ◽  
Sialyl Lewis X ◽  
Lewis X ◽  
Ligand Interaction ◽  
Sialyl Lewis ◽  
Activated Platelets ◽  
Granule Membrane ◽  
Myeloid Leukocytes ◽  
Endothelial Leukocyte Adhesion Molecule

Granule membrane protein-140 (GMP-140) is an inducible receptor for myeloid leukocytes on activated platelets and endothelium. Like other selectins, GMP-140 recognizes specific oligosaccharide ligands. However, prior data on the nature of these ligands are contradictory. We investigated the structural features required for ligand interaction with GMP-140 using purified GMP-140, cells naturally expressing specific oligosaccharides, and cells expressing cloned glycosyltransferases. Like the related selectin endothelial leukocyte adhesion molecule-1 (ELAM-1), GMP-140 recognizes alpha(2-3)sialylated, alpha(1-3)fucosylated lactosaminoglycans on both myeloid and nonmyeloid cells, including the sequence Neu5Ac alpha 2-3Gal beta 1-4(Fuc alpha 1-3)GlcNac beta-R (sialyl Lewis x). Recognition requires sialic acid, because cells expressing large amounts of Lewis x, but not sialyl Lewis x, do not interact with GMP-140. Although sialyl Lewis x is expressed by both myeloid HL-60 cells and CHO cells transfected with an alpha 1-3/4 fucosyltransferase, GMP-140 binds with significantly higher affinity to HL-60 cells. Thus, the sialyl Lewis x tetrasaccharide may require additional structural modifications or specific presentations in order for leukocytes in flowing blood to interact rapidly and with high affinity to GMP-140 on activated platelets or endothelium.

Effects of Nano-Nozzles Cross-Sectional Geometry on Fluid Flow: Molecular Dynamic Simulation

2017 ◽  
Vol 34 (5) ◽  
pp. 667-678 ◽  
Author(s):  
H. Nowruzi ◽  
H. Ghassemi
Keyword(s):  
Fluid Flow ◽  
Velocity Profile ◽  
Cross Sections ◽  
Md Simulation ◽  
Flow Behavior ◽  
Water Model ◽  
Physical Parameters ◽  
Cross Sectional ◽  
Behavior Characteristics ◽  
Fanning Friction Factor

AbstractNano-nozzles are an essential part of the nano electromechanical systems (NEMS). Cross-sectional geometry of nano-nozzles has a significant role on the fluid flow inside them. So, main purpose of the present study is related to the effects of different symmetrical cross-sections on the fluid flow behavior inside of nano-nozzles. To this accomplishment, five different cross-sectional geometries (equilateral triangle, square, regular hexagon, elliptical and circular) are investigated by using molecular dynamics (MD) simulation. In addition, TIP4P is used for atomistic water model. In order to evaluate the fluid flow behavior, non-dimensional physical parameters such as Fanning friction factor, velocity profile and density number are analyzed. Obtained results are shown that the flow behavior characteristics appreciably depend on the geometry of nano-nozzle's cross-section. Velocity profile and density number for five different cross sections of nano-nozzle at three various measurement gauges are presented and discussed.

Molecular dynamics study of the hydrophobic 6,6-ionene oligocation in aqueous solution with sodium halides

2010 ◽  
Vol 82 (10) ◽  
pp. 1943-1955 ◽  
Author(s):  
Maksym Druchok ◽  
Vojko Vlachy
Keyword(s):  
Molecular Dynamics ◽  
Md Simulation ◽  
Distribution Functions ◽  
Low Molecular Weight ◽  
Specific Effects ◽  
Sodium Cations ◽  
Counter Ions ◽  
Sodium Halides ◽  
Explicit Water ◽  
Pair Distribution Functions

An explicit water molecular dynamics (MD) simulation is presented of a solution modeling aliphatic 6,6-ionene oligocations mixed with low-molecular-weight electrolytes. In all cases, the co-ions were sodium cations and the counterions were fluoride, chloride, bromide, or iodide anions. The simple point charge/extended (SPC/E) model was used to describe water. The results of the simulation at T = 278 K (the data for 298 K were obtained earlier) and T = 318 K are presented in the form of pair distributions between various atoms and/or between ions in the system. We were interested in how temperature variation modifies the ion-specific effects, revealed by the various pair distribution functions (PDFs). The results were compared with previous calculations for the less hydrophobic 3,3-ionene solutions. Simulations of 6,6-ionene solutions containing mixtures of fluoride and iodide counter-ions at T = 298 K were also presented.

Human monocytes bind to two cytokine-induced adhesive ligands on cultured human endothelial cells: endothelial-leukocyte adhesion molecule-1 and vascular cell adhesion molecule-1

Blood ◽  
1991 ◽  
Vol 77 (10) ◽  
pp. 2266-2271 ◽  
Author(s):  
T Carlos ◽  
N Kovach ◽  
B Schwartz ◽  
M Rosa ◽  
B Newman ◽  
...  
Keyword(s):  
Adhesion Molecule ◽  
Cell Adhesion Molecule ◽  
Leukocyte Adhesion ◽  
Vascular Cell Adhesion ◽  
Vascular Cell ◽  
Leukocyte Adhesion Molecule ◽  
Endothelial Leukocyte Adhesion Molecule ◽  
Adhesive Proteins ◽  
Cell Adhesion Molecule 1 ◽  
Monocyte Adherence

Abstract Vascular cell adhesion molecule-1 (VCAM-1) and endothelial-leukocyte adhesion molecule-1 (ELAM-1) are adhesive proteins induced on endothelium by cytokines. We examined the contribution of these adhesive proteins to human peripheral blood monocyte adherence to endothelium using transfected Chinese hamster ovary (CHO) cells stably expressing these proteins and monoclonal antibodies (MoAbs) to ELAM-1, VCAM-1, or CD49d/CD29 (VLA-4), the leukocyte receptor for VCAM-1. Monocytes bound to CHO cells transfected with cDNA of ELAM-1 or VCAM-1. Binding to ELAM-1 was inhibited by MoAb to ELAM-1 and binding to VCAM-1 was inhibited by MoAb to VCAM-1 or the alpha-chain of very late activation antigen-4 (VLA-4) (CD49d). Additive inhibition of adherence to unstimulated human umbilical vein endothelium (HUVE) was observed when monocytes were pretreated with both MoAb to CD49d and MoAb to CD18, the common beta-chain of the leukocyte beta 2 integrin receptors. Adherence of monocytes to HUVE stimulated by recombinant human tumor necrosis factor-alpha was not reduced by MoAbs to CD18, CD49d, or ELAM- 1 when used singly, but combinations of these MoAbs produced significant inhibition. We conclude that multiple receptor-ligand systems are involved in monocyte adherence to endothelium.

scholarly journals Soluble CD14 participates in the response of cells to lipopolysaccharide.

1992 ◽  
Vol 176 (6) ◽  
pp. 1665-1671 ◽  
Author(s):  
E A Frey ◽  
D S Miller ◽  
T G Jahr ◽  
A Sundan ◽  
V Bazil ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Leukocyte Adhesion ◽  
Umbilical Vein ◽  
Cell Types ◽  
Mononuclear Phagocytes ◽  
Soluble Cd14 ◽  
Bovine Endothelial Cells ◽  
Endothelial Leukocyte Adhesion Molecule ◽  
Umbilical Vein Endothelial Cells ◽  
Serum Dependent

CD14 is a 55-kD protein found both as a glycosylphosphatidyl inositol-linked protein on the surface of mononuclear phagocytes and as a soluble protein in the blood. CD14 on the cell membrane (mCD14) has been shown to serve as a receptor for complexes of lipopolysaccharide (LPS) with LPS binding protein, but a function for soluble CD14 (sCD14) has not been described. Here we show that sCD14 enables responses to LPS by cells that do not express CD14. We have examined induction of endothelial-leukocyte adhesion molecule 1 expression by human umbilical vein endothelial cells, interleukin 6 secretion by U373 astrocytoma cells, and cytotoxicity of bovine endothelial cells. None of these cell types express mCD14, yet all respond to LPS in a serum-dependent fashion, and all responses are completely blocked by anti-CD14 antibodies. Immunodepletion of sCD14 from serum prevents responses to LPS, and the responses are restored by addition of sCD14. These studies suggest that a surface anchor is not needed for the function of CD14 and further imply that sCD14 must bind to additional proteins on the cell surface to associate with the cell and transduce a signal. They also indicate that sCD14 may have an important role in potentiating responses to LPS in cells lacking mCD14.

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