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The Journal of Biological Chemistry May 1981A binding protein from liver which binds reversibly to yeast mannan depending on the presence or absence of calcium has been purified to near homogeneity by affinity...
A binding protein from liver which binds reversibly to yeast mannan depending on the presence or absence of calcium has been purified to near homogeneity by affinity chromatography. The binding of the isolated protein to 125I-mannan is proportional to protein concentration and is apparently an unsaturable process. The Scatchard plot of the binding is a curvilinear, indicating the presence of a high affinity binding site with a dissociation constant of 1.62 X 10(-8) M. Evidence is presented to show that the protein recognizes and binds mannose and N-acetylglucosamine residues almost indiscriminately at the same binding site. Physical and chemical studies suggest the intact binding protein with an approximate molecular weight of 194,000 to be composed of six identical subunits. The protein is characterized as a glycine-rich protein. The apparent ubiquitous distribution of mannan-binding protein in mammalian liver is consistent with the proposal that the binding protein is the cellular receptor mediating the hepatic uptake of glycoproteins terminated with mannose and/or N-acetylglucosamine residues.
Topics: Amino Acids; Animals; Binding, Competitive; Carrier Proteins; Collectins; Electrophoresis, Polyacrylamide Gel; Hydrogen-Ion Concentration; Kinetics; Liver; Mannans; Polysaccharides; Rats; Saccharomyces cerevisiae
PubMed: 7012150
DOI: No ID Found -
Acta Crystallographica. Section D,... Jan 2023Periplasmic binding proteins (PBPs) are a class of proteins that participate in the cellular transport of various ligands. They have been used as model systems to study...
Periplasmic binding proteins (PBPs) are a class of proteins that participate in the cellular transport of various ligands. They have been used as model systems to study mechanisms in protein evolution, such as duplication, recombination and domain swapping. It has been suggested that PBPs evolved from precursors half their size. Here, the crystal structures of two permuted halves of a modern ribose-binding protein (RBP) from Thermotoga maritima are reported. The overexpressed proteins are well folded and show a monomer-dimer equilibrium in solution. Their crystal structures show partially noncanonical PBP-like fold type I conformations with structural deviations from modern RBPs. One of the half variants forms a dimer via segment swapping, suggesting a high degree of malleability. The structural findings on these permuted halves support the evolutionary hypothesis that PBPs arose via a duplication event of a flavodoxin-like protein and further support a domain-swapping step that might have occurred during the evolution of the PBP-like fold, a process that is necessary to generate the characteristic motion of PBPs essential to perform their functions.
Topics: Carrier Proteins; Ribose; Proteins; Periplasmic Binding Proteins; Molecular Conformation; Bacterial Proteins
PubMed: 36601806
DOI: 10.1107/S205979832201186X -
Nature Structural & Molecular Biology Jul 2018Dynamic protein interaction networks such as DNA double-strand break (DSB) signaling are modulated by post-translational modifications. The DNA repair factor 53BP1 is a...
Dynamic protein interaction networks such as DNA double-strand break (DSB) signaling are modulated by post-translational modifications. The DNA repair factor 53BP1 is a rare example of a protein whose post-translational modification-binding function can be switched on and off. 53BP1 is recruited to DSBs by recognizing histone lysine methylation within chromatin, an activity directly inhibited by the 53BP1-binding protein TIRR. X-ray crystal structures of TIRR and a designer protein bound to 53BP1 now reveal a unique regulatory mechanism in which an intricate binding area centered on an essential TIRR arginine residue blocks the methylated-chromatin-binding surface of 53BP1. A 53BP1 separation-of-function mutation that abolishes TIRR-mediated regulation in cells renders 53BP1 hyperactive in response to DSBs, highlighting the key inhibitory function of TIRR. This 53BP1 inhibition is relieved by TIRR-interacting RNA molecules, providing proof-of-principle of RNA-triggered 53BP1 recruitment to DSBs.
Topics: Amino Acid Substitution; Binding Sites; Carrier Proteins; Crystallography, X-Ray; DNA Breaks, Double-Stranded; DNA Repair; Histones; Humans; Models, Molecular; Mutagenesis, Site-Directed; Protein Binding; Protein Engineering; Protein Interaction Maps; Protein Processing, Post-Translational; Pyrophosphatases; RNA-Binding Proteins; Tumor Suppressor p53-Binding Protein 1
PubMed: 29967538
DOI: 10.1038/s41594-018-0083-z -
Current Opinion in Lipidology Feb 2002
Topics: Adipocytes; Animals; Arteriosclerosis; Carrier Proteins; Drosophila Proteins; Fatty Acid-Binding Protein 7; Fatty Acid-Binding Proteins; Humans; Lipids; Macrophages; Mice; Muscle Proteins; Neoplasm Proteins; Nerve Tissue Proteins; Receptors, Cytoplasmic and Nuclear; Signal Transduction; Transcription Factors; Tumor Suppressor Proteins
PubMed: 11790967
DOI: 10.1097/00041433-200202000-00013 -
FEBS Letters Aug 2003Periplasmic binding proteins from Gram-negative bacteria possess a common architecture, comprised of two domains linked by a hinge region, a fold which they share with...
Periplasmic binding proteins from Gram-negative bacteria possess a common architecture, comprised of two domains linked by a hinge region, a fold which they share with the neurotransmitter-binding domains of ionotropic glutamate receptors (GluRs). Glutamine-binding protein (GlnBP) is one such protein, whose crystal structure has been solved in both open and closed forms. Multi-nanosecond molecular dynamics simulations have been used to explore motions about the hinge region and how they are altered by ligand binding. Glutamine binding is seen to significantly reduce inter-domain motions about the hinge region. Essential dynamics analysis of inter-domain motion revealed the presence of both hinge-bending and twisting motions, as has been reported for a related sugar-binding protein. Significantly, the influence of the ligand on GlnBP dynamics is similar to that previously observed in simulations of rat glutamate receptor (GluR2) ligand-binding domain. The essential dynamics analysis of GlnBP also revealed a third class of motion which suggests a mechanism for signal transmission in GluRs.
Topics: Binding Sites; Carrier Proteins; Computer Simulation; Escherichia coli; Glutamine; Hydrogen Bonding; Ligands; Models, Molecular; Protein Binding; Protein Conformation; Protein Structure, Tertiary
PubMed: 12935905
DOI: 10.1016/s0014-5793(03)00866-4 -
The Biochemical Journal Apr 1999Expression of epidermal-type fatty acid-binding protein (E-FABP) and S100A7 has previously been shown to be elevated in psoriatic skin, a disease characterized by...
Expression of epidermal-type fatty acid-binding protein (E-FABP) and S100A7 has previously been shown to be elevated in psoriatic skin, a disease characterized by abnormal keratinocyte differentiation. However, no causal relationship between the up-regulation of these proteins and the disease has been shown. E-FABP is thought to be involved in cytosolic fatty acid (FA) transport, whereas the role of S100A7 is still unknown. In this report, we show by overlay assays that E-FABP, immobilized on nitrocellulose, is able to capture S100A7 from cytosolic psoriatic protein extracts and vice versa, suggesting the formation of a complex between the two proteins. Using purified E-FABP and S100A7, the complex can be reconstituted only in presence of EDTA. Moreover, we show that increased EDTA concentrations in psoriatic cytosolic protein extracts enhance complex formation. Partial complex disruption was obtained by the addition of physiological concentrations of Zn2+ (0.1 mM), whereas Ca2+ at 5 mM and Mg2+ at 30 mM had no effect. On the other hand, high Ca2+ concentrations (30 mM) resulted in partial complex disruption. Oleic acid-binding properties were observed for free E-FABP and the complex E-FABP-S100A7, but not for free S100A7. By using confocal microscopy we show that S100A7 and E-FABP are co-localized in the cytoplasm of differentiating keratinocytes from lesional psoriatic skin. These data indicate that formation of the E-FABP-S100A7 complex and its FA-binding function might be regulated at least by bivalent cations.
Topics: Calcium-Binding Proteins; Carrier Proteins; Cells, Cultured; Chromatography, Gel; Cytosol; Electrophoresis, Polyacrylamide Gel; Epidermis; Fatty Acid-Binding Protein 7; Fatty Acid-Binding Proteins; Humans; Isoelectric Point; Keratinocytes; Myelin P2 Protein; Neoplasm Proteins; Oleic Acid; Protein Binding; Psoriasis; S100 Calcium Binding Protein A7; S100 Proteins; Tumor Suppressor Proteins
PubMed: 10191275
DOI: No ID Found -
TheScientificWorldJournal Sep 2003Rab GTPases, proteins belonging to the Ras-like small GTP-binding protein superfamily, have emerged as master regulators of cellular membrane transport. Rab11 GTPase, a... (Review)
Review
Rab GTPases, proteins belonging to the Ras-like small GTP-binding protein superfamily, have emerged as master regulators of cellular membrane transport. Rab11 GTPase, a member of the Rab protein family, plays a role in regulating various cellular functions, including plasma membrane recycling, phagocytosis, and cytokinesis. Rab11 acts by forming mutually exclusive complexes with Rab11-family binding proteins, known as FIPs. Rab11-FIP complexes serve a role of "targeting complexes" by recruiting various membrane traffic factors to cellular membranes. Recent studies have identified several Rab11-FIP complex-binding proteins that regulate distinct membrane traffic pathways.
Topics: Adaptor Proteins, Signal Transducing; Amino Acid Sequence; Animals; Carrier Proteins; Cell Membrane; Endocytosis; Humans; Membrane Proteins; Mitochondrial Proteins; Molecular Sequence Data; Protein Transport; rab GTP-Binding Proteins
PubMed: 14532427
DOI: 10.1100/tsw.2003.69 -
Journal of Bacteriology Mar 1980A binding protein for branched-chain amino acids was purified to a homogeneous state from shock fluid of Pseudomonas aeruginosa PML14. It was a monomeric protein with an...
A binding protein for branched-chain amino acids was purified to a homogeneous state from shock fluid of Pseudomonas aeruginosa PML14. It was a monomeric protein with an apparent molecular weight of 4.3 x 10(4) or 4.0 x 10(4) by sodium dodecyl sulfate-polyacrylamide gel electrophoresis or gel filtration, respectively. The isoelectric point was determined to be pH 4.1 by electrofocusing. Amino acid analysis of the protein showed that aspartic acid, glutamic acid, glycine, and alanine were major components and that the protein contained only one residue each of tryptophan and cysteine per molecule. The binding protein contained no sugar. The binding activity of the protein was specific for the branched-chain amino acids. The protein also bound alanine and threonine with lower affinity. The dissociation constants of this protein for leucine, isoleucine, and valine were found to be 0.4, 0.3, and 0.5 microM, respectively. Mutants defective in the production of the binding protein were identified among the mutants deficient in a transport system for branched-chain amino acids (LIV-I). The revertants from these mutants to LIV-I-positive phenotype simultaneously recovered normal levels of the binding protein. These findings suggest strongly the association of the binding protein with the LIV-I transport system.
Topics: Bacterial Proteins; Biological Transport, Active; Carrier Proteins; Isoelectric Point; Leucine; Molecular Weight; Pseudomonas aeruginosa
PubMed: 6767701
DOI: 10.1128/jb.141.3.1055-1063.1980 -
The Journal of Biological Chemistry Aug 1993Small-angle x-ray scattering and computer modeling have been used to study the effects of ligand binding to the leucine/isoleucine/valine-binding protein, an initial...
Small-angle x-ray scattering and computer modeling have been used to study the effects of ligand binding to the leucine/isoleucine/valine-binding protein, an initial component of the high-affinity active transport system for branched-chain aliphatic amino acids in Escherichia coli. Measurements were made with no ligand present and with either L-leucine or L-valine present. Upon binding of either leucine or valine, there is a decrease in the radius of gyration, from 23.2 +/- 0.2 to 22.2 +/- 0.2 A, and in the maximum particle dimension, from 82 +/- 3 to 73 +/- 3 A. The x-ray structure of the unbound form has been determined and gives a radius of gyration and a maximum dimension consistent with the values found for the solution structure in this study (Sack, J. S., Saper, M. A., and Quiocho, F. A. (1989) J. Mol. Biol. 206, 171-191). The reduction in the radius of gyration and maximum dimension upon ligand binding can be accounted for by a substrate-induced cleft closure in a combined "hinge-twist" motion. Modeling of the substrate-bound state was done by comparison of this protein with another periplasmic binding protein (L-arabinose-binding protein), which possesses a similar two-lobe structure and for which the x-ray structure is known in its ligand-bound form.
Topics: Bacterial Proteins; Carrier Proteins; Escherichia coli Proteins; Leucine; Ligands; Models, Molecular; Valine; X-Ray Diffraction
PubMed: 8344909
DOI: No ID Found -
The Journal of Biological Chemistry Mar 1985Human liver fatty acid binding protein (L-FABP) cDNA clones were identified in a liver cDNA library. The two longest clones were completely sequenced. The nucleotide... (Comparative Study)
Comparative Study
Human liver fatty acid binding protein (L-FABP) cDNA clones were identified in a liver cDNA library. The two longest clones were completely sequenced. The nucleotide sequence predicts a protein of 127 amino acid residues. Identity of the clones was confirmed by limited amino acid sequence analysis of purified human L-FABP peptides and Edman degradation of radiolabeled in vitro translated FABP. Statistical analysis of the amino acid and mRNA sequences of human L-FABP, rat L-FABP, rat intestinal (I-) FABP, and mouse 422 protein indicates that the human and rat L-FABPs are highly homologous and that L-FABP and I-FABP diverged a long time ago (approximately 650-690 million years ago), although they are more closely related to each other than either of them is to 422 protein. Secondary structure predictions from the primary sequence of human and rat L-FABP reveal a region (residues 12-30) that might be the putative fatty acid binding domain of the two L-FABPs. Knowledge of the primary amino acid sequence of L-FABP and possible functional domains will be pivotal in further defining and understanding the mechanism of ligand binding and transfer by this protein.
Topics: Amino Acid Sequence; Animals; Base Sequence; Carrier Proteins; Cattle; DNA; Fatty Acid-Binding Protein 7; Fatty Acid-Binding Proteins; Humans; Liver; Mice; Neoplasm Proteins; Nerve Tissue Proteins; Protein Conformation; Rabbits; Rats; Tumor Suppressor Proteins
PubMed: 3838309
DOI: No ID Found