Faculty Opinions recommendation of L1-mediated branching is regulated by two ezrin-radixin-moesin (ERM)-binding sites, the RSLE region and a novel juxtamembrane ERM-binding region.

2005 ◽  
Author(s):  
Christopher Stipp
Keyword(s):  
Binding Sites ◽  
Binding Region

scholarly journals First Characterization of an Archaeal GTP-Dependent Phosphoenolpyruvate Carboxykinase from the Hyperthermophilic Archaeon Thermococcus kodakaraensis KOD1

2004 ◽  
Vol 186 (14) ◽  
pp. 4620-4627 ◽  
Author(s):  
Wakao Fukuda ◽  
Toshiaki Fukui ◽  
Haruyuki Atomi ◽  
Tadayuki Imanaka
Keyword(s):  
Binding Sites ◽  
Phosphoenolpyruvate Carboxykinase ◽  
Cation Binding ◽  
Activity Levels ◽  
Binding Region ◽  
Hyperthermophilic Archaeon ◽  
Dependent Activity ◽  
Additional Role

ABSTRACT Phosphoenolpyruvate carboxykinase (PCK), which catalyzes the nucleotide-dependent, reversible decarboxylation of oxaloacetate to yield phosphoenolpyruvate and CO2, is one of the important enzymes in the interconversion between C3 and C4 metabolites. This study focused on the first characterization of the enzymatic properties and expression profile of an archaeal PCK from the hyperthermophilic archaeon Thermococcus kodakaraensis (Pck Tk ). Pck Tk showed 30 to 35% identities to GTP-dependent PCKs from mammals and bacteria but was located in a branch distinct from that of the classical enzymes in the phylogenetic tree, together with other archaeal homologs from Pyrococcus and Sulfolobus spp. Several catalytically important regions and residues, found in all known PCKs irrespective of their nucleotide specificities, were conserved in Pck Tk . However, the predicted GTP-binding region was unique compared to those in other GTP-dependent PCKs. The recombinant Pck Tk actually exhibited GTP-dependent activity and was suggested to possess dual cation-binding sites specific for Mn2+ and Mg2+. The enzyme preferred phosphoenolpyruvate formation from oxaloacetate, since the Km value for oxaloacetate was much lower than that for phosphoenolpyruvate. The transcription and activity levels in T. kodakaraensis were higher under gluconeogenic conditions than under glycolytic conditions. These results agreed with the role of Pck Tk in providing phosphoenolpyruvate from oxaloacetate as the first step of gluconeogenesis in this hyperthermophilic archaeon. Additionally, under gluconeogenic conditions, we observed higher expression levels of Pck Tk on pyruvate than on amino acids, implying that it plays an additional role in the recycling of excess phosphoenolpyruvate produced from pyruvate, replacing the function of the anaplerotic phosphoenolpyruvate carboxylase that is missing from this archaeon.

The Kringle V-Protease Domain Is a Fibrinogen Binding Region within Apo(a)

2001 ◽  
Vol 86 (11) ◽  
pp. 1229-1237 ◽  
Author(s):  
Song Xue ◽  
Edwin Madison ◽  
Lindsey Miles
Keyword(s):  
Binding Sites ◽  
Protease Domain ◽  
Binding Region ◽  
Molecular Weights ◽  
Fibrinogen Binding ◽  
Liver Cdna Library ◽  
Interaction Treatment ◽  
Dose Dependent Fashion ◽  
Affinity Interaction ◽  
Dose Dependent

SummaryLp(a) binds directly to fibrin and competes for the interaction of plasminogen with this substrate. This competition may play a role in the proatherothrombogenic consequences of high Lp(a) levels. Previous studies by us and others showed that apo(a) Kringle IV-10 competes for the interaction of Lp(a) with plasmin-treated fibrinogen. However, kringle IV-10 cannot account for the entire high affinity interaction of Lp(a) with fibrinogen. Therefore, we tested the hypothesis that the apo(a) kringle V protease-like domain (KV-PD) could interact with plasmin-treated fibrinogen. We cloned the apo(a) KV-PD region from a human liver cDNA library. Fusion apo(a) KV-PD was expressed in COS 7 cells and purified from the conditioned media. Western blotting of the apo(a) KV-PD protein revealed two bands migrating with apparent molecular weights of 45K and 48K. When fusion apo(a) KV-PD was treated with O-glycosidase and neuraminidase, the higher molecular weight band disappeared suggesting that the apo(a) KV-PD was O-glycosylated. Apo(a) KV-PD bound to plasmin-treated fibrinogen in a dose-dependent fashion. An EC50 of 3.9 ± 0.2 μM was determined for this interaction. Treatment of the apo(a) KV-PD with O-glycosidase did not significantly affect its ability to bind to plasmin-treated fibrinogen. In addition, apo(a) KV-PD competed for the binding of 125I-Lp(a) to plasmin-treated fibrinogen. An IC50 of 7.90 ± 0.95 μM was obtained. Our data suggest that the KV-PD of apo(a) shares binding sites on plasmin-treated fibrinogen with Lp(a) and also may participate in the interaction of the Lp(a) particle with plasmin-treated fibrinogen.

scholarly journals Cytomegalovirus Basic Phosphoprotein (pUL32) Binds to Capsids In Vitro through Its Amino One-Third

2001 ◽  
Vol 75 (15) ◽  
pp. 6865-6873 ◽  
Author(s):  
Michael K. Baxter ◽  
Wade Gibson
Keyword(s):  
Molecular Structure ◽  
Binding Sites ◽  
Sequence Conservation ◽  
Binding Region ◽  
Present Evidence ◽  
Tegument Proteins ◽  
Infected Cells ◽  
Human Cmv

ABSTRACT The cytomegalovirus (CMV) basic phosphoprotein (BPP) is a component of the tegument. It remains with the nucleocapsid fraction under conditions that remove most other tegument proteins from the virion, suggesting a direct and perhaps tight interaction with the capsid. As a step toward localizing this protein within the molecular structure of the virion and understanding its function during infection, we have investigated the BPP-capsid interaction. In this report we present evidence that the BPP interacts selectively, through its amino one-third, with CMV capsids. Radiolabeled simian CMV (SCMV) BPP, synthesized in vitro, bound to SCMV B-capsids, and C-capsids to a lesser extent, following incubation with either isolated capsids or lysates of infected cells. Human CMV (HCMV) BPP (pUL32) also bound to SCMV capsids, and SCMV BPP likewise bound to HCMV capsids, indicating that the sequence(s) involved is conserved between the two proteins. Analysis of SCMV BPP truncation mutants localized the capsid-binding region to the amino one-third of the molecule—the portion of BPP showing the greatest sequence conservation between the SCMV and HCMV homologs. This general approach may have utility in studying the interactions of other proteins with conformation-dependent binding sites.

scholarly journals Clathrin assembly involves a light chain-binding region.

1987 ◽  
Vol 105 (5) ◽  
pp. 2011-2019 ◽  
Author(s):  
G S Blank ◽  
F M Brodsky
Keyword(s):  
Monoclonal Antibodies ◽  
Binding Site ◽  
Heavy Chain ◽  
Light Chain ◽  
Intermediate Filament ◽  
Binding Sites ◽  
Light Chains ◽  
Binding Region ◽  
Intermediate Filament Proteins ◽  
Interaction Site

Two regions on the clathrin heavy chain that are involved in triskelion interactions during assembly have been localized on the triskelion structure. These regions were previously identified with anti-heavy chain monoclonal antibodies X19 and X35, which disrupt clathrin assembly (Blank, G. S., and F. M. Brodsky, 1986, EMBO (Eur. Mol. Biol. Organ.) J., 5:2087-2095). Antibody-binding sites were determined based on their reactivity with truncated triskelions, and were mapped to an 8-kD region in the middle of the proximal portion of the triskelion arm (X19) and a 6-kD region at the triskelion elbow (X35). The elbow site implicated in triskelion assembly was also shown to be included within a heavy chain region involved in binding the light chains and to constitute part of the light chain-binding site. We postulate that this region of the heavy chain binds to the interaction site identified on the light chains that has homology to intermediate filament proteins (Brodsky, F. M., C. J. Galloway, G. S. Blank, A. P. Jackson, H.-F. Seow, K. Drickamer, and P. Parham, 1987, Nature (Lond.), 326:203-205). These findings suggest the existence of a heavy chain site, near the triskelion elbow, which is involved in both intramolecular and intermolecular interactions during clathrin assembly.

scholarly journals Mutational Scanning and Affinity Cleavage Analysis of UhpA-Binding Sites in the Escherichia coli uhpT Promoter

2002 ◽  
Vol 184 (10) ◽  
pp. 2682-2691 ◽  
Author(s):  
Igor N. Olekhnovich ◽  
Robert J. Kadner
Keyword(s):  
Escherichia Coli ◽  
Binding Sites ◽  
Promoter Activity ◽  
Consensus Sequence ◽  
Response Regulators ◽  
Binding Region ◽  
Nucleotide Substitutions ◽  
Iron Chelate ◽  
Affinity Cleavage

ABSTRACT UhpA, a member of the NarL family of response regulators, activates transcription of the Escherichia coli uhpT gene for the sugar phosphate transporter UhpT in response to extracellular glucose-6-phosphate. UhpA binds with different affinities to adjacent regions in the uhpT promoter, termed the strong-binding (S) region from −80 to −50 and the weak-binding (W) region from −50 to −32. Transcription activation by UhpA is stimulated by the catabolite gene activator protein (CAP)-cyclic AMP complex and depends on the C-terminal domains of the RNA polymerase RpoA and RpoD subunits. Because single-base substitutions in the UhpA-binding region had little effect on promoter activity, nucleotide substitutions in successive 4-bp blocks throughout this region were examined for their effects on promoter activation and UhpA binding. Changes in three of four blocks within the W region substantially impaired the ability of UhpA to bind to this region, to drive expression of a uhpT-lacZ reporter, and to support UhpA-dependent in vitro transcription. These W region variant promoters were strongly stimulated by CAP. Changes in several parts of the S region impaired UhpA binding to both the S and W regions and decreased promoter activity in vivo and in vitro. Thus, binding of UhpA to the W region is crucial for UhpA-dependent activation and depends on occupancy of the S region. None of these substitutions eliminated promoter function. The orientation of UhpA-binding sites was assessed by the affinity cleavage method. The iron chelate FeBABE [iron (S)-1-(p-bromoacetamidobenzyl) EDTA] was covalently attached to engineered cysteine residues near the DNA-binding region in UhpA. Hydroxyl radicals generated by the iron chelate attached at position 187 resulted in DNA strand cleavages in two clusters of sites located in the middle of the S and W regions. These results are consistent with the binding of two dimers of UhpA. Each dimer binds to an inverted repeat of monomer-binding sites with the consensus sequence CCTGRR, where R is A or G, and each is separated by 6 bp. It is likely that members of the NarL family bind to dyad targets, in contrast to the binding of OmpR family response regulators to direct-repeat targets.

scholarly journals Design of novel CV-N variants: Modulation of binding dynamics through distal mutations

2020 ◽  
Author(s):  
I. Can Kazan ◽  
Prerna Sharma ◽  
Andrey Bobkov ◽  
Raimund Fromme ◽  
Giovanna Ghirlanda ◽  
...  
Keyword(s):  
Binding Affinity ◽  
Binding Sites ◽  
Computational Method ◽  
Experimental Characterization ◽  
Dynamic Coupling ◽  
Binding Region ◽  
Novel Approach ◽  
Allosteric Sites ◽  
Docking Tool

AbstractWe develop a computational approach to identify distal residues that allosterically modulate the dynamics of binding sites by combining dynamic coupling with statistical analysis of co-evolution. Putative mutants of these predicted allosteric sites are subjected to Adaptive BP-Dock docking tool for binding analysis. Here, we apply this method to a small lectin, Cyanovirin-N (CV-N), that selectively binds to dimannose. Our computational method points out mutations on I34, that is 16Å away from binding site can modulate binding. Experimental characterization of I34 mutants confirms that I34Y increases affinity towards dimannose, while I34K completely abolish binding. The increased affinity is not due to changes in the binding region, which are conserved in the crystal structure. However, ITC analysis reveals an opposite contribution of TΔS (negative in WT, and positive in I34Y) and suggests that modulation of dynamics (i.e., dynamic allostery) is responsible for the change in binding affinity. Our results point to a novel approach to identify and substitute distal sites, guiding the mutational landscape in glycan-binding proteins to improve binding affinity.

scholarly journals Importin β contains a COOH-terminal nucleoporin binding region important for nuclear transport

2003 ◽  
Vol 162 (3) ◽  
pp. 391-401 ◽  
Author(s):  
Janna Bednenko ◽  
Gino Cingolani ◽  
Larry Gerace
Keyword(s):  
Nuclear Pore Complex ◽  
Nuclear Import ◽  
Binding Sites ◽  
Nuclear Transport ◽  
Terminal Region ◽  
Nuclear Pore ◽  
Binding Region ◽  
Similar Extent ◽  
Importin Α ◽  
Import Receptor

Proteins containing a classical NLS are transported into the nucleus by the import receptor importin β, which binds to cargoes via the adaptor importin α. The import complex is translocated through the nuclear pore complex by interactions of importin β with a series of nucleoporins. Previous studies have defined a nucleoporin binding region in the NH2-terminal half of importin β. Here we report the identification of a second nucleoporin binding region in its COOH-terminal half. Although the affinity of the COOH-terminal region for nucleoporins is dramatically weaker than that of the NH2-terminal region, sets of mutations that perturb the nucleoporin binding of either region reduce the nuclear import activity of importin β to a similar extent (∼50%). An importin β mutant with a combination of mutations in the NH2- and COOH-terminal regions is completely inactive for nuclear import. Thus, importin β possesses two nucleoporin binding sites, both of which are important for its nuclear import function.

scholarly journals Water-mediated conformational preselection mechanism in substrate binding cooperativity to protein kinase A

2018 ◽  
Vol 115 (15) ◽  
pp. 3852-3857 ◽  
Author(s):  
Piotr Setny ◽  
Marta D. Wiśniewska
Keyword(s):  
Protein Kinase ◽  
Protein Kinase A ◽  
Binding Sites ◽  
Substrate Binding ◽  
Binding Region ◽  
Allosteric Coupling ◽  
Single Water Molecule ◽  
Allosteric Pathway ◽  
Significant Attention ◽  
Kinase A

Substrate binding cooperativity in protein kinase A (PKA) seems to involve allosteric coupling between the two binding sites. It received significant attention, but its molecular basis still remains not entirely clear. Based on long molecular dynamics of PKA and its complexes, we characterized an allosteric pathway that links ATP binding to the redistribution of states adopted by a protein substrate positioning segment in favor of those that warrant correct binding. We demonstrate that the cooperativity mechanism critically depends on the presence of water in two distinct, buried hydration sites. One holds just a single water molecule, which acts as a switchable hydrogen bond bridge along the allosteric pathway. The second, filled with partially disordered solvent, is essential for providing a smooth free energy landscape underlying conformational transitions of the peptide binding region. Our findings remain in agreement with experimental data, also concerning the cooperativity abolishing effect of the Y204A mutation, and indicate a plausible molecular mechanism contributing to experimentally observed binding cooperativity of the two substrates.

Sign in / Sign up

Export Citation Format

Share Document