Bioinspired structural transition of synthetic polymers through biomolecular ligand binding

The bioinspired structural transition of thermoresponsive poly(N-isopropylacrylamide) was demonstrated by specific ligand binding of artificially evolved peptides to the polymer.

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Computational Biology Tools for Identifying Specific Ligand Binding Residues for Novel Agrochemical and Drug Design

Current Protein and Peptide Science ◽

10.2174/1389203716666150505234923 ◽

2015 ◽

Vol 16 (8) ◽

pp. 701-717 ◽

Cited By ~ 4

Author(s):

Izabella Pena Neshich ◽

Leticia Nishimura ◽

Fabio de Moraes ◽

Jose Salim ◽

Fabian Villalta-Romero ◽

...

Keyword(s):

Drug Design ◽

Computational Biology ◽

Ligand Binding ◽

Binding Residues ◽

Specific Ligand

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Broadly distributed nucleophilic reactivity of proteins coordinated with specific ligand binding activity

Journal of Molecular Recognition ◽

10.1002/jmr.734 ◽

2005 ◽

Vol 18 (4) ◽

pp. 295-306 ◽

Cited By ~ 15

Author(s):

Yasuhiro Nishiyama ◽

Yukie Mitsuda ◽

Hiroaki Taguchi ◽

Stephanie Planque ◽

Mariko Hara ◽

...

Keyword(s):

Ligand Binding ◽

Binding Activity ◽

Nucleophilic Reactivity ◽

Ligand Binding Activity ◽

Specific Ligand

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Mechanism of ligand binding – PDZ domain taken as example

Bio-Algorithms and Med-Systems ◽

10.1515/bams-2017-0022 ◽

2017 ◽

Vol 13 (4) ◽

Author(s):

Dawid Dułak ◽

Mateusz Banach ◽

Zdzisław Wiśniowski ◽

Leszek Konieczny ◽

Irena Roterman

Keyword(s):

Crystal Structure ◽

Ligand Binding ◽

Ion Channel ◽

Pdz Domain ◽

Traditional Model ◽

Beta Sheet ◽

Hydrophobic Core ◽

Beta Strand ◽

Model Based ◽

Specific Ligand

AbstractThe mechanism of specific ligand binding by proteins is discussed using the PDZ domain complexing the pentapeptide. This process is critical for clustering the membrane ion channel. The traditional model based on the Beta-sheet extension by complexed pentapeptide is interpreted as a hydrophobic core extension supported by additional Beta-strand generated by complexed pentapeptide. The explanation is based on the fuzzy oil drop model applied to the crystal structure of PDZ-pentapeptide.

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Selection in vitro of single-stranded DNA molecules that fold into specific ligand-binding structures

Nature ◽

10.1038/355850a0 ◽

1992 ◽

Vol 355 (6363) ◽

pp. 850-852 ◽

Cited By ~ 502

Author(s):

Andrew D. Ellington ◽

Jack W. Szostak

Keyword(s):

Ligand Binding ◽

Dna Molecules ◽

Single Stranded Dna ◽

Specific Ligand

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Introduction of Bisecting GlcNAc into Integrin α5β1Reduces Ligand Binding and Down-regulates Cell Adhesion and Cell Migration

Journal of Biological Chemistry ◽

10.1074/jbc.m311627200 ◽

2004 ◽

Vol 279 (19) ◽

pp. 19747-19754 ◽

Cited By ~ 122

Author(s):

Tomoya Isaji ◽

Jianguo Gu ◽

Ryoko Nishiuchi ◽

Yanyang Zhao ◽

Motoko Takahashi ◽

...

Keyword(s):

Cell Adhesion ◽

Ligand Binding ◽

Cell Matrix ◽

Lung Colonization ◽

Focal Adhesion Kinase Phosphorylation ◽

And Migration ◽

Kinase Phosphorylation ◽

Cell Matrix Adhesion ◽

Specific Ligand ◽

Bisecting Glcnac

The enzyme β1,4-N-acetylglucosaminyltransferase III (GnT-III) catalyzes the addition of a bisecting GlcNAc residue to glycoproteins, resulting in a modulation in biological function. Our previous studies showed that the transfection of the GnT-III gene into B16 melanoma cells results in a suppression of invasive ability and lung colonization. The suppression has been postulated to be due to an increased level of E-cadherin expression on the cell surface, which in turn leads to the up-regulation of cell-cell adhesion. In this study, we report on the effects of overexpression of GnT-III on cell-matrix adhesion. The overexpression of GnT-III, but not that of an enzymatic inactive GnT-III (D323A), inhibits cell spreading and migration on fibronectin, a specific ligand for integrin α5β1, and the focal adhesion kinase phosphorylation. E4-PHA lectin blot analyses showed that the levels of bisecting GlcNAc structures on the integrin α5subunit as well as α2and α3subunits immunoprecipitated from GnT-III transfectants were substantially increased. In addition, the affinity of the binding of integrin α5β1to fibronectin was significantly reduced by the introduction of the bisecting GlcNAc, to the α5subunit. These findings suggest that the modification ofN-glycan of integrin by GnT-III inhibits its ligand binding ability, subsequently leading to the down-regulation of integrin-mediated signaling.

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Detecting Specific Ligand Binding to Nucleic Acids: A Test for Ultrasoft Laser Mass Spectrometry

Zeitschrift für Physikalische Chemie ◽

10.1524/zpch.2007.221.5.689 ◽

2007 ◽

Vol 221 (5) ◽

pp. 689-704 ◽

Cited By ~ 6

Author(s):

N. Morgner ◽

H. D. Barth ◽

T. L. Schmidt ◽

A. Heckel ◽

U. Scheffer ◽

...

Keyword(s):

Mass Spectrometry ◽

Nucleic Acids ◽

Ligand Binding ◽

Laser Mass Spectrometry ◽

Specific Ligand

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Specific Ligand Binding Attributable to Individual Epitopes of Gonococcal Transferrin Binding Protein A

Infection and Immunity ◽

10.1128/iai.70.2.732-740.2002 ◽

2002 ◽

Vol 70 (2) ◽

pp. 732-740 ◽

Cited By ~ 22

Author(s):

Heather P. Masri ◽

Cynthia Nau Cornelissen

Keyword(s):

Ligand Binding ◽

Fusion Proteins ◽

Iron Uptake ◽

Solid Phase ◽

Protein A ◽

Dot Blot ◽

Affinity Tags ◽

Amino Terminal ◽

Dot Blot Assay ◽

Specific Ligand

ABSTRACT The gonococcal transferrin receptor complex comprises two iron-regulated proteins, TbpA and TbpB. TbpA is essential for transferrin-iron uptake and is a TonB-dependent integral outer membrane protein. TbpB is thought to increase the efficiency of iron uptake from transferrin and is lipid modified and surface exposed. To evaluate the structure-function relationships in one of the components of the receptor, TbpA, we created constructs that fused individual putative loops of TbpA with amino-terminal affinity tags. The recombinant proteins were then overexpressed in Escherichia coli, and the fusions were recovered predominately from inclusion bodies. Inclusion body proteins were solubilized, and the epitope fusions were renatured by slow dialysis. To assess transferrin binding capabilities, the constructs were tested in a solid-phase dot blot assay followed by confirmatory quantitative chemiluminescent enzyme-linked immunosorbent assays. The constructs with only loop 5 and with loops 4 and 5 demonstrated dose-dependent specific ligand binding in spite of being out of the context of the intact receptor. The immunogenicities of individual TbpA-specific epitopes were investigated by generating rabbit polyclonal antisera against the fusion proteins. Most of the fusion proteins were immunogenic under these conditions, and the resulting sera recognized full-length TbpA in immunoblots. These results suggest that individual epitopes of TbpA are both immunogenic and functional with respect to ligand binding capabilities, and the vaccine implications of these findings are discussed.

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