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

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.

[1]  F. Cañada,et al.  Structural aspects of binding of α-linked digalactosides to human galectin-1. , 2011, Glycobiology.

[2]  David F. Smith,et al.  Dimeric Galectin-8 Induces Phosphatidylserine Exposure in Leukocytes through Polylactosamine Recognition by the C-terminal Domain* , 2008, Journal of Biological Chemistry.

[3]  E. Korchagina,et al.  Carbohydrate specificity of chicken and human tandem-repeat-type galectins-8 in composition of cells , 2011, Biochemistry (Moscow).

[4]  A. Imberty,et al.  Structure and conformation of complex carbohydrates of glycoproteins, glycolipids, and bacterial polysaccharides. , 1999, Annual review of biophysics and biomolecular structure.

[5]  Ineo Ishizuka,et al.  The N-terminal carbohydrate recognition domain of galectin-8 recognizes specific glycosphingolipids with high affinity. , 2003, Glycobiology.

[6]  J. Jiménez-Barbero,et al.  Molecular recognition of the Thomsen-Friedenreich antigen-threonine conjugate by adhesion/growth regulatory galectin-3: nuclear magnetic resonance studies and molecular dynamics simulations. , 2012, Biochemistry.

[7]  Soichi Wakatsuki,et al.  Structural analysis of the recognition mechanism of poly-N-acetyllactosamine by the human galectin-9 N-terminal carbohydrate recognition domain. , 2008, Glycobiology.

[8]  Douglas N W Cooper,et al.  Galectinomics: finding themes in complexity. , 2002, Biochimica et biophysica acta.

[9]  E. Korchagina,et al.  Comparative study of the glycan specificities of cell-bound human tandem-repeat-type galectin-4, -8 and -9. , 2012, Glycobiology.

[10]  M. Eisenstein,et al.  It depends on the hinge: a structure-functional analysis of galectin-8, a tandem-repeat type lectin. , 2006, Glycobiology.

[11]  V. Hornak,et al.  Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.

[12]  Claus-Wilhelm von der Lieth,et al.  GlycoMapsDB: a database of the accessible conformational space of glycosidic linkages , 2007, Nucleic Acids Res..

[13]  T. Nonaka,et al.  Galectin-8-N-domain Recognition Mechanism for Sialylated and Sulfated Glycans* , 2011, The Journal of Biological Chemistry.

[14]  Marcelo A Martí,et al.  Characterization of the galectin-1 carbohydrate recognition domain in terms of solvent occupancy. , 2007, The journal of physical chemistry. B.

[15]  K Henrick,et al.  Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. , 2004, Acta crystallographica. Section D, Biological crystallography.

[16]  H. Yoshida,et al.  X-ray Structures of Human Galectin-9 C-terminal Domain in Complexes with a Biantennary Oligosaccharide and Sialyllactose* , 2010, The Journal of Biological Chemistry.

[17]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[18]  Hans-Joachim Gabius,et al.  Growth-regulatory human galectin-1: crystallographic characterisation of the structural changes induced by single-site mutations and their impact on the thermodynamics of ligand binding. , 2004, Journal of molecular biology.

[19]  L. Amzel,et al.  Disaccharide binding to galectin-1: free energy calculations and molecular recognition mechanism. , 2011, Biophysical journal.

[20]  Susanne Carlsson,et al.  Introduction to galectins , 1997, Glycoconjugate Journal.

[21]  Martin Frank,et al.  Bioinformatics and molecular modeling in glycobiology , 2010, Cellular and Molecular Life Sciences.

[22]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[23]  H Kaltner,et al.  A toolbox of lectins for translating the sugar code: the galectin network in phylogenesis and tumors. , 2012, Histology and histopathology.

[24]  Dario A. Estrin,et al.  An Integrated Computational Analysis of the Structure, Dynamics, and Ligand Binding Interactions of the Human Galectin Network , 2011, J. Chem. Inf. Model..

[25]  Karl Nicholas Kirschner,et al.  GLYCAM06: A generalizable biomolecular force field. Carbohydrates , 2008, J. Comput. Chem..

[26]  K. Katoh,et al.  MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. , 2002, Nucleic acids research.

[27]  Robert J Woods,et al.  Molecular dynamics simulations of galectin‐1‐oligosaccharide complexes reveal the molecular basis for ligand diversity , 2003, Proteins.

[28]  Markus Aebi,et al.  Structure and functional analysis of the fungal galectin CGL2. , 2004, Structure.

[29]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[30]  O. Campetella,et al.  Galectin-8 tandem-repeat structure is essential for T-cell proliferation but not for co-stimulation. , 2011, The Biochemical journal.

[31]  S. Sidhu,et al.  Phylogenetic analysis of the vertebrate galectin family. , 2004, Molecular biology and evolution.

[32]  A. M. Wu,et al.  Human galectin-3 (Mac-2 antigen): defining molecular switches of affinity to natural glycoproteins, structural and dynamic aspects of glycan binding by flexible ligand docking and putative regulatory sequences in the proximal promoter region. , 2011, Biochimica et biophysica acta.

[33]  S. Barondes,et al.  Crystallization and preliminary X-ray diffraction analysis of the human dimeric S-Lac lectin (L-14-II). , 1993, Journal of molecular biology.

[34]  M. Akke,et al.  The Carbohydrate-Binding Site in Galectin-3 Is Preorganized To Recognize a Sugarlike Framework of Oxygens: Ultra-High-Resolution Structures and Water Dynamics , 2011, Biochemistry.

[35]  H. Yoshida,et al.  X‐ray structure of a protease‐resistant mutant form of human galectin‐8 with two carbohydrate recognition domains , 2012, The FEBS journal.

[36]  R. Cummings,et al.  Affinity of galectin-8 and its carbohydrate recognition domains for ligands in solution and at the cell surface. , 2007, Glycobiology.

[37]  H. Gabius.  Influence of type of linkage and spacer on the interaction of beta-galactoside-binding proteins with immobilized affinity ligands. , 1990, Analytical biochemistry.

[38]  Wei Lang,et al.  Advancing glycomics: implementation strategies at the consortium for functional glycomics. , 2006, Glycobiology.

[39]  Christophe Meynier,et al.  Computational Studies of Human Galectin-1: Role of Conserved Tryptophan Residue in Stacking Interaction with Carbohydrate Ligands , 2009, Journal of biomolecular structure & dynamics.

[40]  S. Barondes,et al.  X-ray crystal structure of the human galectin-3 carbohydrate recognition domain at 2.1-A resolution. , 1998, The Journal of biological chemistry.

[41]  Toshihiko Oka,et al.  Oligosaccharide specificity of galectins: a search by frontal affinity chromatography. , 2002, Biochimica et biophysica acta.

[42]  David F. Smith,et al.  Innate immune lectins kill bacteria expressing blood group antigen , 2010, Nature Medicine.

[43]  S. Barondes,et al.  X-ray crystal structure of the human dimeric S-Lac lectin, L-14-II, in complex with lactose at 2.9-A resolution. , 1994, The Journal of biological chemistry.

[44]  Y. Zhuo,et al.  Emerging Role of α2,6-Sialic Acid as a Negative Regulator of Galectin Binding and Function* , 2010, The Journal of Biological Chemistry.