scholarly journals Steady State and Multifrequency Phase Fluorometry Studies of Binding Site Flexibility in Related Antibodies†

2004 ◽  
Vol 108 (39) ◽  
pp. 7871-7877 ◽  
Author(s):  
Gopi S. Mohan ◽  
Philip T. Chiu ◽  
Cathrine A. Southern ◽  
Patricia B. O'Hara
Keyword(s):  
Steady State ◽  
Binding Site ◽  
Phase Fluorometry

RAP1 is required for BAS1/BAS2- and GCN4-dependent transcription of the yeast HIS4 gene

1991 ◽  
Vol 11 (7) ◽  
pp. 3642-3651 ◽  
Author(s):  
C Devlin ◽  
K Tice-Baldwin ◽  
D Shore ◽  
K T Arndt
Keyword(s):  
Steady State ◽  
Binding Site ◽  
Binding Sites ◽  
Binding Activity ◽  
Micrococcal Nuclease ◽  
Mrna Levels ◽  
High Affinity ◽  
Steady State Levels

The major in vitro binding activity to the Saccharomyces cerevisiae HIS4 promoter is due to the RAP1 protein. In the absence of GCN4, BAS1, and BAS2, the RAP1 protein binds to the HIS4 promoter in vivo but cannot efficiently stimulate HIS4 transcription. RAP1, which binds adjacently to BAS2 on the HIS4 promoter, is required for BAS1/BAS2-dependent activation of HIS4 basal-level transcription. In addition, the RAP1-binding site overlaps with the single high-affinity HIS4 GCN4-binding site. Even though RAP1 and GCN4 bind competitively in vitro, RAP1 is required in vivo for (i) the normal steady-state levels of GCN4-dependent HIS4 transcription under nonstarvation conditions and (ii) the rapid increase in GCN4-dependent steady-state HIS4 mRNA levels following amino acid starvation. The presence of the RAP1-binding site in the HIS4 promoter causes a dramatic increase in the micrococcal nuclease sensitivity of two adjacent regions within HIS4 chromatin: one region contains the high-affinity GCN4-binding site, and the other region contains the BAS1- and BAS2-binding sites. These results suggest that RAP1 functions at HIS4 by increasing the accessibility of GCN4, BAS1, and BAS2 to their respective binding sites when these sites are present within chromatin.

scholarly journals EPO receptor circuits for primary erythroblast survival

Blood ◽  
2008 ◽  
Vol 111 (11) ◽  
pp. 5390-5399 ◽  
Author(s):  
Pradeep Sathyanarayana ◽  
Arvind Dev ◽  
Jing Fang ◽  
Estelle Houde ◽  
Olga Bogacheva ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Steady State ◽  
Binding Site ◽  
Ectopic Expression ◽  
Wild Type ◽  
Survival Factor ◽  
Survival Gene ◽  
Primary Bone ◽  
Primary Bone Marrow ◽  
Stimulation Of

Abstract EPO functions primarily as an erythroblast survival factor, and its antiapoptotic actions have been proposed to involve predominantly PI3-kinase and BCL-X pathways. Presently, the nature of EPO-regulated survival genes has been investigated through transcriptome analyses of highly responsive, primary bone marrow erythroblasts. Two proapoptotic factors, Bim and FoxO3a, were rapidly repressed not only via the wild-type EPOR, but also by PY-deficient knocked-in EPOR alleles. In parallel, Pim1 and Pim3 kinases and Irs2 were induced. For this survival gene set, induction failed via a PY-null EPOR-HM allele, but was restored upon reconstitution of a PY343 STAT5–binding site within a related EPOR-H allele. Notably, EPOR-HM supports erythropoiesis at steady state but not during anemia, while EPOR-H exhibits near wild-type EPOR activities. EPOR-H and the wild-type EPOR (but not EPOR-HM) also markedly stimulated the expression of Trb3 pseudokinase, and intracellular serpin, Serpina-3G. For SERPINA-3G and TRB3, ectopic expression in EPO-dependent progenitors furthermore significantly inhibited apoptosis due to cytokine withdrawal. BCL-XL and BCL2 also were studied, but in highly responsive KitposCD71highTer119neg erythroblasts, neither was EPO modulated. EPOR survival circuits therefore include the repression of Bim plus FoxO3a, and EPOR/PY343/STAT5-dependent stimulation of Pim1, Pim3, Irs2 plus Serpina-3G, and Trb3 as new antiapoptotic effectors.

scholarly journals Interactions between inhibitors of dihydrofolate reductase

1989 ◽  
Vol 258 (2) ◽  
pp. 335-342 ◽  
Author(s):  
K Bowden ◽  
A D Hall ◽  
B Birdsall ◽  
J Feeney ◽  
G C K Roberts
Keyword(s):  
Steady State ◽  
Binding Site ◽  
Dihydrofolate Reductase ◽  
Binding Sites ◽  
High Field ◽  
Ph Dependence ◽  
Histidine Residue ◽  
Adenine Ring ◽  
Steady State Kinetics ◽  
Pka Value

The binding of substrates and inhibitors to dihydrofolate reductase was studied by steady-state kinetics and high-field 1H-n.m.r. spectroscopy. A series of 5-substituted 2,4-diaminopyrimidines were examined and were found to be ‘tightly binding’ inhibitors of the enzyme (Ki less than 10(-9) M). Studies on the binding of 4-substituted benzenesulphonamides and benzenesulphonic acids also established the existence of a ‘sulphonamide-binding site’ on the enzyme. Subsequent n.m.r. experiments showed that there are two binding sites for the sulphonamides on the enzyme, one of which overlaps the coenzyme (NADPH) adenine-ring-binding site. An examination of the pH-dependence of the binding of sulphonamides to the enzyme indicated the influence of an ionizable group on the enzyme that was not directly involved in the sulphonamide binding. The change in pKa value from 6.7 to 7.2 observed on sulphonamide binding suggests the involvement of a histidine residue, which could be histidine-28.

Using lithium to probe sequential cation interactions with GAT1

2012 ◽  
Vol 302 (11) ◽  
pp. C1661-C1675 ◽  
Author(s):  
Anne-Kristine Meinild ◽  
Ian C. Forster
Keyword(s):  
Steady State ◽  
Binding Site ◽  
Voltage Dependence ◽  
Cation Binding ◽  
Experimental Conditions ◽  
Net Charge ◽  
Cation Binding Site ◽  
Voltage Dependent ◽  
Experimental Findings ◽  
Kinetics Of

Li+ interacts with the Na+/Cl−-dependent GABA transporter, GAT1, under two conditions: in the absence of Na+ it induces a voltage-dependent leak current; in the presence of Na+ and GABA, Li+ stimulates GABA-induced steady-state currents. The amino acids directly involved in the interaction with the Na+ and Li+ ions at the so-called “ Na2” binding site have been identified, but how Li+ affects the kinetics of GABA cotransport has not been fully explored. We expressed GAT1 in Xenopus oocytes and applied the two-electrode voltage clamp and 22Na uptake assays to determine coupling ratios and steady-state and presteady-state kinetics under experimental conditions in which extracellular Na+ was partially substituted by Li+. Three novel findings are: 1) Li+ reduced the coupling ratio between Na+ and net charge translocated during GABA cotransport; 2) Li+ increased the apparent Na+ affinity without changing its voltage dependence; 3) Li+ altered the voltage dependence of presteady-state relaxations in the absence of GABA. We propose an ordered binding scheme for cotransport in which either a Na+ or Li+ ion can bind at the putative first cation binding site ( Na2). This is followed by the cooperative binding of the second Na+ ion at the second cation binding site ( Na1) and then binding of GABA. With Li+ bound to Na2, the second Na+ ion binds more readily GAT1, and despite a lower apparent GABA affinity, the translocation rate of the fully loaded carrier is not reduced. Numerical simulations using a nonrapid equilibrium model fully recapitulated our experimental findings.

scholarly journals The Tarantula Venom Peptide Eo1a Binds to the Domain II S3-S4 Extracellular Loop of Voltage-Gated Sodium Channel NaV1.8 to Enhance Activation

2022 ◽  
Vol 12 ◽  
Author(s):  
Jennifer R. Deuis ◽  
Lotten Ragnarsson ◽  
Samuel D. Robinson ◽  
Zoltan Dekan ◽  
Lerena Chan ◽  
...  
Keyword(s):  
Steady State ◽  
Binding Site ◽  
Rational Design ◽  
Voltage Dependence ◽  
Fast Inactivation ◽  
Extracellular Loop ◽  
Peak Current ◽  
Future Studies ◽  
Voltage Gated ◽  
Functional Characterisation

Venoms from cone snails and arachnids are a rich source of peptide modulators of voltage-gated sodium (NaV) channels, however relatively few venom-derived peptides with activity at the mammalian NaV1.8 subtype have been isolated. Here, we describe the discovery and functional characterisation of β-theraphotoxin-Eo1a, a peptide from the venom of the Tanzanian black and olive baboon tarantula Encyocratella olivacea that modulates NaV1.8. Eo1a is a 37-residue peptide that increases NaV1.8 peak current (EC50 894 ± 146 nM) and causes a large hyperpolarising shift in both the voltage-dependence of activation (ΔV50–20.5 ± 1.2 mV) and steady-state fast inactivation (ΔV50–15.5 ± 1.8 mV). At a concentration of 10 μM, Eo1a has varying effects on the peak current and channel gating of NaV1.1–NaV1.7, although its activity is most pronounced at NaV1.8. Investigations into the binding site of Eo1a using NaV1.7/NaV1.8 chimeras revealed a critical contribution of the DII S3-S4 extracellular loop of NaV1.8 to toxin activity. Results from this work may form the basis for future studies that lead to the rational design of spider venom-derived peptides with improved potency and selectivity at NaV1.8.

scholarly journals Serine acetyltransferase of Escherichia coli: substrate specificity and feedback control by cysteine

2003 ◽  
Vol 375 (3) ◽  
pp. 745-752 ◽  
Author(s):  
V. John HINDSON
Keyword(s):  
Escherichia Coli ◽  
Steady State ◽  
Reaction Mechanism ◽  
Binding Site ◽  
Ternary Complex ◽  
Random Order ◽  
Hydroxyl Group ◽  
Acyl Donor ◽  
Complex Reaction ◽  
Serine Acetyltransferase

Although SAT (serine acetyltransferase) of Escherichia coli, which catalyses the first step in cysteine synthesis, proceeds via a random-order ternary complex reaction mechanism [Hindson and Shaw (2003) Biochemistry 42, 3113–3119], it has been suggested that the nearly identical enzyme from Salmonella typhimurium might involve an acetyl-enzyme intermediate [Leu and Cook (1994) Protein Peptide Lett. 1, 157–162]. In this study the alternative acetyl acceptor threonine and the alternative acyl donor, propionyl-CoA were used to further investigate the reaction mechanism of SAT from E. coli. Steady-state kinetic data and dead-end inhibition studies were again diagnostic of a random-order ternary complex reaction mechanism for alternative substrates. Since earlier kinetic studies with SAT from S. typhimurium suggested that cysteine competes with acetyl-CoA for binding, rather than serine with which it is isostructural, the specificity of the serine-binding pocket was assessed with three substrate mimics; β-hydroxypropionic acid, glycine and ethanolamine. The data show that SAT interacts productively with the amino and hydroxymethyl moieties of serine, whereas the carboxyl group provides an essential contribution to binding strongly, supporting a view that cysteine will interact productively at the serine-binding site. Furthermore, since the hydroxymethyl contact region of the serine-binding site appears able to accommodate the methylene and acetyl moeties of threonine and O-acetyl-serine respectively, the site is unlikely to provide obligatory short-range contacts with the hydroxyl group of serine, a prerequisite for exclusion of cysteine. Such a proposal is supported by the results of micro-calorimetric studies which show that cysteine competes with serine for binding to SAT rather than with CoA. It follows that tight binding of cysteine at the serine-binding site near the catalytic centre may be the effector of a substantial reduction in the affinity of SAT for CoA, yielding the observed pattern of steady-state inhibition and the mechanism by which cysteine mediates effective end-product control of its synthesis.

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