scholarly journals Multiple Tyrosine Residues Contribute to GABA Binding in the GABAC Receptor Binding Pocket

2012 ◽  
Vol 3 (3) ◽  
pp. 186-192 ◽  
Author(s):  
Sarah C. R. Lummis ◽  
Neil J. Harrison ◽  
Jinti Wang ◽  
Jamie A. Ashby ◽  
Katherine S. Millen ◽  
...  
Keyword(s):  
Receptor Binding ◽  
Binding Pocket ◽  
Tyrosine Residues ◽  
Gabac Receptor ◽  
Gaba Binding

A Comprehensive Ligand Based Mapping of the σ2 Receptor Binding Pocket

2013 ◽  
Vol 10 (1) ◽  
pp. 98-121 ◽  
Author(s):  
Derek Rhoades ◽  
David Kinder ◽  
Tarek Mahfouz
Keyword(s):  
Receptor Binding ◽  
Binding Pocket

scholarly journals GPI- and transmembrane-anchored influenza hemagglutinin differ in structure and receptor binding activity

1993 ◽  
Vol 122 (6) ◽  
pp. 1253-1265 ◽  
Author(s):  
GW Kemble ◽  
YI Henis ◽  
JM White
Keyword(s):  
Cell Surface ◽  
Receptor Binding ◽  
Conformational Changes ◽  
Binding Pocket ◽  
Binding Activity ◽  
Great Distance ◽  
Fusion Peptides ◽  
Wild Type ◽  
Influenza Hemagglutinin ◽  
Receptor Binding Activity

We investigated the influence of a glycosylphosphatidylinositol (GPI) anchor on the ectodomain of the influenza hemagglutinin (HA) by replacing the wild type (wt) transmembrane and cytoplasmic domains with a GPI lipid anchor. GPI-anchored HA (GPI-HA) was transported to the cell surface with equal efficiency and at the same rate as wt-HA. Like wt-HA, cell surface GPI-HA, and its ectodomain released with the enzyme PI-phospholipase C (PI-PLC), were 9S trimers. Compared to wt-HA, the GPI-HA ectodomain underwent additional terminal oligosaccharide modifications; some of these occurred near the receptor binding pocket and completely inhibited the ability of GPI-HA to bind erythrocytes. Growth of GPI-HA-expressing cells in the presence of the mannosidase I inhibitor deoxymannojirimycin (dMM) abrogated the differences in carbohydrate modification and restored the ability of GPI-HA to bind erythrocytes. The ectodomain of GPI-HA produced from cells grown in the presence or absence of dMM underwent characteristic low pH-induced conformational changes (it released its fusion peptides and became hydrophobic and proteinase sensitive) but at 0.2 and 0.4 pH units higher than wt-HA, respectively. These results demonstrate that although GPI-HA forms a stable trimer with characteristics of the wt, its structure is altered such that its receptor binding activity is abolished. Our results show that transmembrane and GPI-anchored forms of the same ectodomain can exhibit functionally important differences in structure at a great distance from the bilayer.

Synthetic site-directed ligands

1989 ◽  
Vol 323 (1217) ◽  
pp. 495-509 ◽  
Keyword(s):  
Binding Site ◽  
Conformational Changes ◽  
Opioid Peptides ◽  
Binding Pocket ◽  
Tyrosine Residues ◽  
Chemotactic Peptides ◽  
Binding Cavity ◽  
False Floor ◽  
Type Site ◽  
Main Cavity

Complexes of nucleotides, peptides and arom atic hapten-like compounds with immunoglobulin fragments were studied by X-ray analysis. Alter tri- or hexanucleotides of deoxythymidylate were diffused into triclinic crystals of a Fab (BV04- 01) with specificity for single-stranded DNA, extensive changes were detected throughout the structure of the protein. The Fab co-crystallized with a tri- or pentanucleotide in a different space group (monoclinic), an observation sometimes correlated with alterations in the structure of the ‘native’ protein. Structural analyses of the co-crystals are in progress for direct comparisons with the unliganded Fab. In crystals of a human (Meg) Bence-Jones dimer, synthetic opioid peptides, chemotactic peptides or dinitrophenyl (DNP) derivatives could be diffused into a large conical binding cavity. The conformations of both the ligand and the protein were usually altered during the binding process. At the base of the cavity tyrosine residues could be displaced like trap-doors to permit entry of some opioid peptides and DNP compounds into a deep binding pocket. In co-crystals of the dimer and bis(DNP)lysine, two ligand molecules were bound in tandem, one in the main cavity and the second in the deep pocket. One ligand adopted an extended conformation, with the ε-DNP ring near the floor of the main cavity and the α-DNP group in solvent outside the binding site. There were no significant conformational changes in the protein. In contrast, the second ligand was very compact, with both DNP rings immersed in the deep pocket, and the binding site was expanded to accommodate the oversized ligand. Peptides designed to be specific for the main cavity were incrementally constructed from minimal binding units by M. Geysen, G. Trippick, S. Rodda and their colleagues. A pentapeptide optimized for binding by this method was diffused into a crystal of the dimer and found by Fourier difference analysis to lodge exclusively in the main cavity as predicted. Binding regions in the BV04-01 Fab and the Meg dimer were markedly different in size and shape. The Fab had a groove-type site, in which a layer of sidechains acted like a false floor over regions analogous to the cavity and deep pocket of the Bence-Jones dimer.

scholarly journals Substitution in position 222 of haemagglutinin of pandemic influenza A (H1N1) viruses isolated from pigs in Poland

2015 ◽  
Vol 59 (4) ◽  
pp. 451-456
Author(s):  
Andrzej Kowalczyk ◽  
Kinga Urbaniak ◽  
Iwona Markowska-Daniel ◽  
Zygmunt Pejsak
Keyword(s):  
Genetic Diversity ◽  
Amino Acids ◽  
Receptor Binding ◽  
Pandemic Influenza ◽  
Influenza A ◽  
Binding Pocket ◽  
Mild Case ◽  
Clinical Specimens ◽  
Influenza A H1n1 ◽  
Viral Isolates

Abstract The aim of the study was to monitor genetic diversity and antigenic changes in the genome of influenza A(H1N1)pdm09 viral isolates detected during the post-pandemic period in Poland. Clinical specimens obtained from three suspected cases of influenza were analysed by sequencing. Among the differences identified in amino acids sequences, nine substitutions were located within the antigenic HA1 sites and in five residues forming receptor-binding pocket. The HA(D222G) mutation was shown in the isolate Swine/Poland/134312/12 obtained from a mild case of the disease. It must be emphasized that, in general, clinically mild cases are caused by the viruses in which that specific mutation, i.e. haemagglutinin (D222G), does not occur.

scholarly journals Identification of a Receptor-Binding Pocket on the Envelope Protein of Friend Murine Leukemia Virus

1999 ◽  
Vol 73 (5) ◽  
pp. 3758-3763 ◽  
Author(s):  
Robert A. Davey ◽  
Yi Zuo ◽  
James M. Cunningham
Keyword(s):  
Receptor Binding ◽  
Envelope Protein ◽  
Murine Leukemia Virus ◽  
Leukemia Virus ◽  
Binding Pocket ◽  
Fusion Pore ◽  
Detectable Effect ◽  
Virus Envelope ◽  
Receptor Binding Site ◽  
Murine Leukemia

ABSTRACT Based on previous structural and functional studies, a potential receptor-binding site composed of residues that form a pocket at one end of the two long antiparallel helices in the receptor-binding domain of Friend 57 murine leukemia virus envelope protein (RBD) has been proposed. To test this hypothesis, directed substitutions for residues in the pocket were introduced and consequences for infection and for receptor binding were measured. Receptor binding was measured initially by a sensitive assay based on coexpression of receptor and RBD inXenopus oocytes, and the findings were confirmed by using purified proteins. Three residues that are critical for both binding and infection (S84, D86, and W102), with side chains that extend into the pocket, were identified. Moreover, when mCAT-1 was overexpressed, the infectivity of Fr57-MLV carrying pocket substitutions was partially restored. Substitutions for 18 adjacent residues and 11 other previously unexamined surface-exposed residues outside of the RBD pocket had no detectable effect on function. Taken together, these findings support a model in which the RBD pocket interacts directly with mCAT-1 (likely residues, Y235 and E237) and multiple receptor-envelope complexes are required to form the fusion pore.

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