Modelling competition between the siderophore ferrioxamine B and humic like binding sites in seawater v1

2021 ◽  
Author(s):  
Kechen Zhu ◽  
Martha Gledhill
Keyword(s):  
Binding Sites ◽  
Major Ions ◽  
Side Reaction ◽  
Iron Solubility ◽  
Desferrioxamine B ◽  
Thermodynamic Constants ◽  
Reaction Coefficient ◽  
Ferrioxamine B ◽  
Donnan Model

Here we archive a protocol that can be used to determine competition between a siderophore (ferrioxamine B) and humic like binding sites that are present in marine DOM. We use the NICA-Donnan model to describe binding by humic like binding sites in DOM. Constants for Fe binding to marine DOM are taken from Zhu et al., (2021). Thermodynamic constants describing binding between major ions, iron and ferrioxamine B are taken from Schijf and Burns, (2016). References Schijf, J., Burns, S.M., 2016. Determination of the Side-Reaction Coefficient of Desferrioxamine B in Trace-Metal-Free Seawater. Front. Mar. Sci. 3, 117. https://doi.org/10.3389/fmars.2016.00117 Zhu, K., Birchill, A.J., Milne, A., Ussher, S.J., Humphreys, M.P., Carr, N., Mahaffey, C., Lohan, M.C., Achterberg, E.P., Gledhill, M., 2021a. Equilbrium calculations of iron speciation and apparent iron solubility in the Celtic Sea at ambient pH using the NICA-Donnan model. Mar. Chem

Conformation of Ribosomes from Escherichia Coli

1974 ◽  
Vol 32 ◽  
pp. 210-211
Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Binding Sites ◽  
Ribosomal Proteins ◽  
Fluorescent Dyes ◽  
Protein Biosynthesis ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Dimensional Structure ◽  
Complete Understanding ◽  
And Function

The present knowledge of the three-dimensional structure of ribosomes is far too limited to enable a complete understanding of the various roles which ribosomes play in protein biosynthesis. The spatial arrangement of proteins and ribonuclec acids in ribosomes can be analysed in many ways. Determination of binding sites for individual proteins on ribonuclec acid and locations of the mutual positions of proteins on the ribosome using labeling with fluorescent dyes, cross-linking reagents, neutron-diffraction or antibodies against ribosomal proteins seem to be most successful approaches. Structure and function of ribosomes can be correlated be depleting the complete ribosomes of some proteins to the functionally inactive core and by subsequent partial reconstitution in order to regain active ribosomal particles.

Determination of copper binding sites in peptides containing basic residues: a combined experimental and theoretical study

2001 ◽  
Vol 204 (1-3) ◽  
pp. 31-46 ◽  
Author(s):  
Brian K. Bluhm ◽  
Sharon J. Shields ◽  
Craig A. Bayse ◽  
Michael B. Hall ◽  
David H. Russell
Keyword(s):  
Binding Sites ◽  
Theoretical Study ◽  
Copper Binding ◽  
Determination Of Copper ◽  
Copper Binding Sites

scholarly journals Determination of the alpha-actinin-binding site on actin filaments by cryoelectron microscopy and image analysis.

1994 ◽  
Vol 126 (2) ◽  
pp. 433-443 ◽  
Author(s):  
A McGough ◽  
M Way ◽  
D DeRosier
Keyword(s):  
Image Analysis ◽  
Smooth Muscle ◽  
Binding Sites ◽  
Actin Filaments ◽  
Three Dimensional ◽  
Actin Binding ◽  
Dimensional Structure ◽  
Outer Face ◽  
Actin Binding Domain

The three-dimensional structure of actin filaments decorated with the actin-binding domain of chick smooth muscle alpha-actinin (alpha A1-2) has been determined to 21-A resolution. The shape and location of alpha A1-2 was determined by subtracting maps of F-actin from the reconstruction of decorated filaments. alpha A1-2 resembles a bell that measures approximately 38 A at its base and extends 42 A from its base to its tip. In decorated filaments, the base of alpha A1-2 is centered about the outer face of subdomain 2 of actin and contacts subdomain 1 of two neighboring monomers along the long-pitch (two-start) helical strands. Using the atomic model of F-actin (Lorenz, M., D. Popp, and K. C. Holmes. 1993. J. Mol. Biol. 234:826-836.), we have been able to test directly the likelihood that specific actin residues, which have been previously identified by others, interact with alpha A1-2. Our results indicate that residues 86-117 and 350-375 comprise distinct binding sites for alpha-actinin on adjacent actin monomers.

Determination of spatial domains of zygotic gene expression in the Drosophila embryo by the affinity of binding sites for the bicoid morphogen

Nature ◽  
1989 ◽  
Vol 340 (6232) ◽  
pp. 363-367 ◽  
Author(s):  
Wolfgang Driever ◽  
Gudrun Thoma ◽  
Christiane Nüsslein-Volhard
Keyword(s):  
Gene Expression ◽  
Binding Sites ◽  
Drosophila Embryo ◽  
Zygotic Gene ◽  
Spatial Domains

scholarly journals Interaction of rice (Oryza sativa) lectin with N-acetylglucosaminides. Fluorescence studies

1985 ◽  
Vol 229 (3) ◽  
pp. 687-692 ◽  
Author(s):  
F Tabary ◽  
J P Frénoy
Keyword(s):  
Oryza Sativa ◽  
Binding Sites ◽  
Wheat Germ ◽  
Equilibrium Dialysis ◽  
Blue Shift ◽  
Association Constants ◽  
Fluorescence Studies ◽  
Saccharide Binding ◽  
Binding Enthalpy

The interaction of lectin isolated from rice (Oryza sativa) embryos with N-acetylglucosaminides was studied by equilibrium dialysis and fluorescence. Equilibrium dialysis with 4-methylumbelliferyl-(GlcNac)2 showed that rice lectin (Mr 38000) contains four equivalent saccharide-binding sites. Addition of the N-acetylglucosaminides GlcNac, (GlcNac)2 and (GlcNac)3 enhanced the intrinsic fluorescence of rice lectin and this was accompanied by a 10nm blue-shift of its maximum fluorescence with (GlcNac)2 and (GlcNac)3. These changes in intensity allowed determination of the association constants, which increased with the number of saccharide units: at 20 degrees C, Ka = (1.3 +/- 0.1) X 10(3), (5.1 +/- 0.4) X 10(4) and (2.6 +/- 0.1) X 10(5) M−1 for GlcNac, (GlcNac)2 and (GlcNac)3 respectively. The binding enthalpy, delta H0, for the three glucosaminides were very low and ranged from −12.1 to −20.6 kJ X mol-1. The results are compared with those obtained with wheat-germ agglutinin, another GlcNac-specific gramineaous lectin.

Determination of hydrogen atom binding sites on Ru(001) by HREELS

1983 ◽  
Vol 133 (2-3) ◽  
pp. A375
Author(s):  
M.A. Barteau ◽  
J.Q. Broughton ◽  
D. Menzel
Keyword(s):  
Hydrogen Atom ◽  
Binding Sites
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