Structure superimposition and degree of sequence identity.

<p>Three-dimensional structural alignments and sequence identity of members of the galectin family based on RMSD calculated by using the PDBeFold webserver <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059761#pone.0059761-Krissinel1" target="_blank">[49]</a>.</p

Understanding the Specificity of Human Galectin-8C Domain Interactions with Its Glycan Ligands Based on Molecular Dynamics Simulations

<div><p>Human Galectin-8 (Gal-8) is a member of the galectin family which shares an affinity for β-galactosides. The tandem-repeat Gal-8 consists of a N- and a C-terminal carbohydrate recognition domain (N- and C-CRD) joined by a linker peptide of various length. Despite their structural similarity both CRDs recognize different oligosaccharides. While the molecular requirements of the N-CRD for high binding affinity to sulfated and sialylated glycans have recently been elucidated by crystallographic studies of complexes with several oligosaccharides, the binding specificities of the C-CRD for a different set of oligosaccharides, as derived from experimental data, has only been explained in terms of the three-dimensional structure for the complex C-CRD with lactose. In this study we performed molecular dynamics (MD) simulations using the recently released crystal structure of the Gal-8C-CRD to analyse the three-dimensional conditions for its specific binding to a variety of oligosaccharides as previously defined by glycan-microarray analysis. The terminal β-galactose of disaccharides (LacNAc, lacto-N-biose and lactose) and the internal β-galactose moiety of blood group antigens A and B (BGA, BGB) as well as of longer linear oligosaccharide chains (di-LacNAc and lacto-N-neotetraose) are interacting favorably with conserved amino acids (H53, R57, N66, W73, E76). Lacto-N-neotetraose and di-LacNAc as well as BGA and BGB are well accommodated. BGA and BGB showed higher affinity than LacNAc and lactose due to generally stronger hydrogen bond interactions and water mediated hydrogen bonds with α1-2 fucose respectively. Our results derived from molecular dynamics simulations are able to explain the glycan binding specificities of the Gal-8C-CRD in comparison to those of the Gal-8N -CRD.</p> </div

Environmental context of major steps of human evolution in NE Africa during the Holocene.

<p>A: Percentage of C4 plants, as estimated from the δ¹³C of higher-plants n-alkanes (see Fig. 2). B: Sediment source as estimated from the radiogenic Sr isotope signature of the detrital sediment fraction. C: Phases of human evolution, as compiled from ref. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0115958#pone.0115958-GiffordGonzalez1" target="_blank">[5]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0115958#pone.0115958-Garcea1" target="_blank">[8]</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0115958#pone.0115958-Shanahan1" target="_blank">[54]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0115958#pone.0115958-Dunne1" target="_blank">[56]</a>.</p

Superimposition of Gal-8N and -C domain.

<p>Ribbon representation of superimposed Gal-8N and -C domain. The N domain is shown in pink color code whereas the C domain is in cyan. Lactose is shown as stick model in yellow color. The variable loop between S3–S4 shows difference in length between Gal-8C and -N.</p

Set of oligosaccharide ligands.

<p>List of oligosaccharides used in MD simulations for study of interactions with the Gal-8C domain.</p

Changes in precipitation, vegetation and erosion dynamics in the Nile watershed during the Holocene.

<p>A: Summer (June-August) insolation at 20°N <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0115958#pone.0115958-Laskar1" target="_blank">[59]</a> (dashed line) and oxygen isotope signature of the surface seawater (δ¹⁸O_SW) at the location of our core, which reflects changes in sea-surface salinity and river runoff (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0115958#pone.0115958.s001" target="_blank">S1 Fig</a>.) and has been controlled by orbitally-induced changes in precipitation. B:. Paleo-precipitation records obtained from a speleothem on the Oman Peninsula (δ¹⁸O), rainfall regime of which has been under influence of the Indian monsoon system <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0115958#pone.0115958-Fleitmann1" target="_blank">[10]</a> and obtained from marine sediments off the coast of Somalia (δD of n-alkanes), the rainfall regimes of which has been under the influence of deep-convection in the Indian Ocean <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0115958#pone.0115958-Tierney1" target="_blank">[11]</a>. C: Stable carbon isotope composition of higher-plant n-alkanes reflecting the proportion of C₄ (mainly grasses) versus C₃ plants (trees/shrubs). D: BIT index recording changes in the relative contribution of soil organic matter input. E: Radiogenic Sr and Nd isotope signatures of the bulk detrital fraction of the sediments documenting changes in sediment provenance. F: Sedimentation rates. Radiocarbon dates are indicated at the bottom of the panel as red triangles and black rectangles at the bottom of the figure indicate the laminated parts of the core (see “<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0115958#s2" target="_blank">Material and Methods</a>” section and ref. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0115958#pone.0115958-Blanchet1" target="_blank">[13]</a>).</p

Torsional analysis of bound ligands.

<p>Average glycosidic torsion angles for bound ligands in the Gal-8C domain (standard deviation). φ and ψ values for glycosidic linkages using the NMR definition as H1-C1-O1-C_x and C1-O1-C_x-H_x respectively.</p

Map of the present-day land cover in northern Africa.

<p>A: Location and averaged radiogenic isotope composition of the three main sources of sediments to the Nile deep-sea fan <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0115958#pone.0115958-Padoan1" target="_blank">[44]</a>. B: Types of vegetation and estimated percentage of trees at present in Northern Africa <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0115958#pone.0115958-Mayaux1" target="_blank">[58]</a>. The gray color represents the Sahara Desert, which is presently non-vegetated. The course of the Nile River is represented by the dark blue line. The location of core P362/2-33 is indicated by the red star. The present-day northern reach of the summer and winter African Rain Belt (ARB) are depicted as red and blue dashed lines, respectively.</p

Ligand binding of the galectin-8C domain.

<p>The Gal-8C binding site with (<b>A</b>) LacNAc, II, (<b>B</b>) di-LacNAc, (<b>C</b>) Lactose, (<b>D</b>) Lacto-N-neotetrose, (<b>E</b>) BGA, and (<b>F</b>) BGB. Ligands are shown as stick models and the surface of the protein-binding site in violet color. The ligands are color-coded (β-galactose: red; N-acetyl-glucosamine: green; glucose: blue; fucose: cyan; α-galactose and α- N-acetyl-galactosamine: yellow; downstream hydroxy group: white. Hydrogen bonds are shown as yellow dotted line. A snapshot which contains a maximum number of intermolecular hydrogen bonds is displayed. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059761#pone.0059761.s007" target="_blank"><b>File S1</b></a> for details of hydrogen bond interactions of each complex. The figure was designed using PyMOL Molecular Graphics System (DeLano Scientific, Palo Alto, CA).</p

Oligosaccharides ranked by calculated binding energy towards the Gal-8C domain.

<p>The values are derived from MMGBSA energies and entropy values calculated using NMode.</p