Comparative domain modeling of human EGF-like module EMR2 and study of interaction of the fourth domain of EGF with chondroitin 4-sulphate

Lomize, 1999, Structural organization of G-protein-coupled receptors, J Comput Aided Mol Des, 13, 325, 10.1023/A:1008050821744 Fotiadis, 2006, Structure of the rhodopsin dimer: a working model for G-protein-coupled receptors, Struct Biol, 16, 252 Robert, 2007, G-protein-coupled receptors and cancer, Nature, 7, 79 Klabunde, 2002, Drug Design Strategies for Targeting G-Protein-Coupled Receptors, ChemBioChem, 3, 928, 10.1002/1439-7633(20021004)3:10<928::AID-CBIC928>3.0.CO;2-5 Palczewski, 2000, Crystal Structure of Rhodopsin: A G Protein-Coupled Receptor, Science, 289, 739, 10.1126/science.289.5480.739 Marinissen, 2001, G-protein-coupled receptors and signaling networks: Emerging paradigms, Trends Pharmacol Sci, 22, 368, 10.1016/S0165-6147(00)01678-3 Stacey, 2003, The epidermal growth factor-like domains of the human EMR2 receptor mediate cell attachment through chondroitin sulfate glycosaminoglycans, Blood, 102, 2916, 10.1182/blood-2002-11-3540 Kwakkenbos, 2002, The human EGF-TM7 family member EMR2 is a heterodimeric receptor expressed on myeloid cells, J Leukoc Biol, 71, 854, 10.1189/jlb.71.5.854 Lin, 2000, Human EMR2, a Novel EGF-TM7 Molecule on Chromosome 19p13.1, is Closely Related to CD97, Genomics, 67, 188, 10.1006/geno.2000.6238 Chang, 2007, The human adhesion-GPCR EMR2, is differentially expressed during differentiation, maturation, and activation ofmyeloid cells. Biochem, Biophys Res Commun, 353, 133, 10.1016/j.bbrc.2006.11.148 Yona, 2007, Ligation of the adhesion-GPCR EMR2 regulates human neutrophil function, FASEB J, 22, 741, 10.1096/fj.07-9435com 1994, The European Polycystic Kidney Disease Consortium, Cell, 77, 881 1995, The International Polycystic Kidney Disease Consortium, Cell, 81, 289, 10.1016/0092-8674(95)90339-9 Mengerink, 2002, suREJ3, a polycystin-1 protein, is cleaved at the GPS domain and localizes to the acrosomal region of sea urchin sperm, J Biol Chem, 277, 943, 10.1074/jbc.M109673200 Hughes, 1999, Autosomal Dominant Polycystic Kidney Disease: Clues to Pathogenesis, Hum Mol Genet, 8, 543, 10.1093/hmg/8.3.543 Qian, 2002, Cleavage of polycystin-1 requires the receptor for egg jelly domain and is disrupted by human autosomal-dominant polycystic kidney disease 1-associated mutations, Proc Natl Acad Sci, 99, 16981, 10.1073/pnas.252484899 Weston, 2004, Mutations in the VLGR1 gene implicates G-protein signaling in the pathogenesis of Usher syndrome type II, Am J Hum Genet, 74, 357, 10.1086/381685 Piao, 2004, G protein-coupled receptor-dependent development of human frontal cortex, Science, 303, 2033, 10.1126/science.1092780 Larkin, 2007, Clustal W and Clustal X version 2.0, Bioinformatics, 23, 2947, 10.1093/bioinformatics/btm404 Larkin, 2007, Clustal W and Clustal X version 2.0, Bioinformatics, 23, 2947, 10.1093/bioinformatics/btm404 Cheng, 2007, DOMAC: an accurate, hybrid protein domain prediction server, Nucleic Acids Research, 35, 354, 10.1093/nar/gkm390 Cheng, 2005, SCRATCH: a protein structure and structural feature prediction server, Nucleic Acids Research, 33, 72, 10.1093/nar/gki396 Krogh, 2001, Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes, J Mol Biol, 305, 567, 10.1006/jmbi.2000.4315 Hirokawa, 1998, SOSUI: classification and secondary structure prediction system for membrane proteins, Bioinformatics, 144, 378, 10.1093/bioinformatics/14.4.378 Gaabor, 1998, Principles Governing Amino Acid Composition of Integral Membrane Proteins Application to Topology Prediction, J Mol Biol, 283, 489, 10.1006/jmbi.1998.2107 Hofmann, 1993, TMbase - A database of membrane spanning proteins segments, Biol Chem Hoppe-Seyler, 374, 166 Cserzo, 1994, Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: Application of the Dense Alignment Surface (DAS) method, J Mol Biol, 243, 388 Claros, 1994, TopPred II: an improved software for membrane protein structure predictions, Comput Appl Biosci, 10, 685 Cai, 2003, SVM-Prot: Web-Based Support Vector Machine Software for Functional Classification of a Protein from Its Primary Sequence, Nucleic Acids Res, 31, 3692, 10.1093/nar/gkg600 Cai, 2005, Prediction of Functional Class of the SARS Coronavirus Proteins by a Statistical Learning Method, Proteome Res, 4, 1855, 10.1021/pr050110a Sahoo, 2008, Functional assignment to JEV proteins using SVM, Bioinformation, 3, 1, 10.6026/97320630003001 Ganesh, 2009, Homology Modeling and Functional Analysis of LPG2 Protein of Leishmania Strains, J Proteomics Bioinform, 2, 32, 10.4172/jpb.1000059 Hendlich, 1997, LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins, J Mol Graph Model, 15, 359, 10.1016/S1093-3263(98)00002-3 Puntervoll, 2003, ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins, Nucleic Acids Res, 31, 3625, 10.1093/nar/gkg545 Venkatachalam, 2003, LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites, J Mol Graph Model, 21, 289, 10.1016/S1093-3263(02)00164-X Ganesh, 2009, Structural Modeling, Evolution and Ligand Interaction of KMP11 Protein of Different Leishmania Strains, J Comput Sci Syst Biol, 2, 147, 10.4172/jcsb.1000026 Suhre, 2004, ElNémo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement, Nucleic Acids Res, 32, 610, 10.1093/nar/gkh368 Holm, 2008, Searching protein structure databases with DaliLitev.3, Bioinformatics, 24, 2780, 10.1093/bioinformatics/btn507 Heinz, 1988, 136 Binmore, 2007, 190 Chang, 2003, Proteolytic cleavage of the EMR2 receptor requires both the extracellular stalk and the GPS motif, FEBS Lett, 547, 145, 10.1016/S0014-5793(03)00695-1 Charlesworth, 2009, The genetics of inbreeding depression, Nature Reviews Genetics, 10, 783, 10.1038/nrg2664 Rong-Rong, 1997, cDNA Cloning of the Basement Membrane Chondroitin Sulfate Proteoglycan Core Protein, Bamacan: A Five Domain Structure Including Coiled-Coil Motifs Couchman, J Cell Biol, 136, 433, 10.1083/jcb.136.2.433 Zhenqiang, 2008, The Crystal and Molecular Structures of a Cathepsin K: Chondroitin Sulfate Complex, J Mol Biol, 383, 78, 10.1016/j.jmb.2008.07.038 Selvaraj, 2008, Modeling of human CCR5 as Target for HIV-I and Virtual Screening with Marine Therapeutic compounds, Bioinformation, 3, 89, 10.6026/97320630003089