scholarly journals A novel mechanism of xylan binding by a lectin-like module from Streptomyces lividans xylanase 10A

2000 ◽  
Vol 350 (3) ◽  
pp. 933-941 ◽  
Author(s):  
Alisdair B. BORASTON ◽  
Peter TOMME ◽  
Emily A. AMANDORON ◽  
Douglas G. KILBURN
Keyword(s):  
Binding Sites ◽  
Association Constant ◽  
Streptomyces Lividans ◽  
Association Constants ◽  
Carbohydrate Binding ◽  
Toxin B ◽  
Ricin Toxin ◽  
Functional Sites ◽  
Directed Mutation ◽  
Single Binding Site

The C-terminal module of xylanase 10A from Streptomyces lividans is a family 13 carbohydrate-binding module (CBM13). CBM13 binds mono- and oligo-saccharides with association constants of ≈ 1×102 M-1−1×103 M-1. It appears to be specific only for pyranose sugars. CBM13 binds insoluble and soluble xylan, holocellulose, pachyman, lichenan, arabinogalactan and laminarin. The association constant for binding to soluble xylan is (6.2±0.6)×103/mol of xylan polymer. Site-directed mutation indicates the involvement of three functional sites on CBM13 in binding to soluble xylan. The sites are similar in sequence, and are predicted to have similar structures, to the α, β and γ sites of ricin toxin B-chain, which is also in family 13. The affinity of a single binding site on CBM13 for soluble xylan is only ≈ (0.5±0.1)×103/mol of xylan. The binding of CBM13 to soluble xylan involves additive and co-operative interactions between the three binding sites. This mechanism of binding has not previously been reported for CBMs binding polysaccharides. CBM13 is the first bacterial module from family 13 to be described in detail.

scholarly journals An H.P.L.C. Study of Cooperative Guest Binding by a Covalently Linked b-Cyclodextrin Dimer

1997 ◽  
Vol 50 (8) ◽  
pp. 857 ◽  
Author(s):  
Anna K. Croft ◽  
Christopher J. Easton ◽  
Stephen F. Lincoln ◽  
Bruce L. May ◽  
John Papageorgiou
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
High Performance ◽  
Association Constant ◽  
Association Constants ◽  
Cooperative Binding ◽  
Cyclodextrin Dimer ◽  
Guest Binding ◽  
Covalently Linked ◽  
Single Binding Site

The complexation of the anions of Methyl Orange (MO¯) (1) and Indomethacin (Ind-) (2) by the β-cyclodextrin dimer (3) has been studied by means of high-performance liquid chromatography. The cyclodextrin annuli are shown to jointly act as a single binding site for complexation of MO¯ (1). Thus the association constants of (3·3±0·3) × 103 and (220±20) × 103 dm3 mol−1 for the 1 : 1 complexes with β-cyclodextrin and the dimer (3), respectively, indicate very strong cooperative binding by the annuli of the linked species. By contrast, the complexation of Ind¯ (2) by the cyclodextrin dimer (3) is characterized by two independent binding sites. This lack of cooperative binding is reflected in the association constant for the 1 : 1 complex in each binding site, which at (1·3±0·1) × 103 dm3 mol−1 is little greater than that of (0·7±0·05) × 103dm3 mol−1 for the complex with β-cyclodextrin.

Identification and glucan-binding properties of a new carbohydrate-binding module family

2001 ◽  
Vol 361 (1) ◽  
pp. 35-40 ◽  
Author(s):  
Alisdair B. BORASTON ◽  
Mazyar GHAFFARI ◽  
R. Antony J. WARREN ◽  
Douglas G. KILBURN
Keyword(s):  
Association Constant ◽  
Association Constants ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Module ◽  
Bacillus Sp ◽  
Binding Properties ◽  
Alkalophilic Bacillus ◽  
Binding Subsites

The C-terminal 191-residue module of Cel5A from the alkalophilic Bacillus sp. 1139 comprises a carbohydrate-binding module (CBM) belonging to a previously unidentified family that we have classified as CBM family 28. This example, called CBM28, bound specifically to cello-oligosaccharides and mixed β-(1,3)(1,4)-glucans (barley β-glucan) with association constants of approximately (1–4)×104 M−1. Its binding to barley β-glucan was remarkably insensitive to pH between 7.0 and 10.9, in keeping with its alkalophilic source. CBM28 bound to cellulose having a significant non-crystalline content with an association constant similar to that for its binding to soluble glucans. CBM17 (CBM family 17) and CBM28 modules naturally occur as tandems. The CBM17/CBM28 tandem from Cel5A bound with apparent co-operativity to barley β-glucan. The association of CBM28 with cello-oligosaccharides was driven enthalpically and marked by the different thermodynamic contribution of three putative binding subsites that accommodate a cellohexaose molecule.

Binding of copper(II) ion to cytochrome c

1981 ◽  
Vol 34 (1) ◽  
pp. 91 ◽  
Author(s):  
MA Augustin ◽  
JK Yandell
Keyword(s):  
Ionic Strength ◽  
Cytochrome C ◽  
Binding Site ◽  
Spectral Data ◽  
Binding Sites ◽  
Association Constant ◽  
Association Constants ◽  
Visible Absorption ◽  
Ph Range ◽  
Horse Cytochrome

Binding of aquacopper(11) ion to horse and tuna ferricytochrome c has been investigated over the pH range 2-9. Between pH 4 and 7 the principal binding site for horse cytochrome has an intrinsic association constant of 1.8 × 104 1. mol-1 and pKa of 6.5�0.6 at 25�C and ionic strength of 0.1. Binding to histidine 33 is consistent with this information, as well as with e.s.r., n.m.r. and visible absorption spectral data. Other sites also bind copper but with association constants at least a factor of ten smaller. At high pH (> 8) further binding sites predominate.

scholarly journals Role of the N-terminal region of phospholipase A2 subunit of β1-bungarotoxin in the toxin-Ca2+ complex-formation

1991 ◽  
Vol 278 (2) ◽  
pp. 481-486 ◽  
Author(s):  
S T Chu ◽  
Y H Chen
Keyword(s):  
Phospholipase A2 ◽  
Metal Ions ◽  
Binding Sites ◽  
Association Constant ◽  
Enzymic Activity ◽  
Association Constants ◽  
High Affinity ◽  
Toxin Molecule ◽  
High Affinity Site

beta 1-Bungarotoxin consists of a phospholipase A2 subunit and a non-phospholipase A2 subunit. Modification of beta 1-bungarotoxin with CNBr resulted in cleavage at Met-6 and Met-8 of its phospholipase A2 subunit. Analysis of the fluorescence data of both the toxin-Ca2+ complex at 300-350 nm and the toxin-Tb3+ complex at 450-650 nm showed the existence of two binding sites for both metal ions on the different domains of the toxin molecule. At pH 7.6 the association constants for the high-affinity and low-affinity sites of the toxin-Ca2+ complex were determined to be 2.79 x 10(3) +/- 0.21 x 10(3) M-1 and 0.47 x 10(3) +/- 0.06 x 10(3) M-1 respectively. For the toxin-Tb3+ complex the association constant for the high-affinity site was 2.95 x 10(3) +/- 0.43 x 10(3) M-1 and that for the low-affinity site was 0.11 x 10(3) +/- 0.03 x 10(3) M-1. Removal of the N-terminal octapeptide of the phospholipase A2 subunit from the toxin molecule caused disintegration of the low-affinity site but did not disrupt the high-affinity site. This might accompany a change in the configuration around His-48 of the phospholipase A2 subunit. Between pH 6 and 8 the binding of metal ions to the high-affinity site increased but that to the low-affinity site did not change with increasing pH. The neurotoxicity and enzymic activity of the toxin were lost on removal of the low-affinity site.

scholarly journals Induction of the Cellular E2F-1 Promoter by the Adenovirus E4-6/7 Protein

2000 ◽  
Vol 74 (5) ◽  
pp. 2084-2093 ◽  
Author(s):  
Joel Schaley ◽  
Robert J. O'Connor ◽  
Laura J. Taylor ◽  
Dafna Bar-Sagi ◽  
Patrick Hearing
Keyword(s):  
Dna Binding ◽  
Binding Site ◽  
Transient Expression ◽  
Binding Sites ◽  
Promoter Region ◽  
Fluorescent Protein ◽  
Protein Accumulation ◽  
Promoter Regions ◽  
Single Binding Site

ABSTRACT The adenovirus type 5 (Ad5) E4-6/7 protein interacts directly with different members of the E2F family and mediates the cooperative and stable binding of E2F to a unique pair of binding sites in the Ad5 E2a promoter region. This induction of E2F DNA binding activity strongly correlates with increased E2a transcription when analyzed using virus infection and transient expression assays. Here we show that while different adenovirus isolates express an E4-6/7 protein that is capable of induction of E2F dimerization and stable DNA binding to the Ad5 E2a promoter region, not all of these viruses carry the inverted E2F binding site targets in their E2a promoter regions. The Ad12 and Ad40 E2a promoter regions bind E2F via a single binding site. However, these promoters bind adenovirus-induced (dimerized) E2F very weakly. The Ad3 E2a promoter region binds E2F very poorly, even via a single binding site. A possible explanation of these results is that the Ad E4-6/7 protein evolved to induce cellular gene expression. Consistent with this notion, we show that infection with different adenovirus isolates induces the binding of E2F to an inverted configuration of binding sites present in the cellular E2F-1 promoter. Transient expression of the E4-6/7 protein alone in uninfected cells is sufficient to induce transactivation of the E2F-1 promoter linked to chloramphenicol acetyltransferase or green fluorescent protein reporter genes. Further, expression of the E4-6/7 protein in the context of adenovirus infection induces E2F-1 protein accumulation. Thus, the induction of E2F binding to the E2F-1 promoter by the E4-6/7 protein observed in vitro correlates with transactivation of E2F-1 promoter activity in vivo. These results suggest that adenovirus has evolved two distinct mechanisms to induce the expression of the E2F-1 gene. The E1A proteins displace repressors of E2F activity (the Rb family members) and thus relieve E2F-1 promoter repression; the E4-6/7 protein complements this function by stably recruiting active E2F to the E2F-1 promoter to transactivate expression.

scholarly journals Two Compound Replication Origins in Saccharomyces cerevisiae Contain Redundant Origin Recognition Complex Binding Sites

2001 ◽  
Vol 21 (8) ◽  
pp. 2790-2801 ◽  
Author(s):  
James F. Theis ◽  
Carol S. Newlon
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Replication ◽  
Binding Site ◽  
Binding Sites ◽  
Origin Recognition Complex ◽  
Replication Origins ◽  
Discrete Site ◽  
Origin Function ◽  
Single Binding Site ◽  
Origin Recognition

ABSTRACT While many of the proteins involved in the initiation of DNA replication are conserved between yeasts and metazoans, the structure of the replication origins themselves has appeared to be different. As typified by ARS1, replication origins inSaccharomyces cerevisiae are <150 bp long and have a simple modular structure, consisting of a single binding site for the origin recognition complex, the replication initiator protein, and one or more accessory sequences. DNA replication initiates from a discrete site. While the important sequences are currently less well defined, metazoan origins appear to be different. These origins are large and appear to be composed of multiple, redundant elements, and replication initiates throughout zones as large as 55 kb. In this report, we characterize two S. cerevisiae replication origins, ARS101 and ARS310, which differ from the paradigm. These origins contain multiple, redundant binding sites for the origin recognition complex. Each binding site must be altered to abolish origin function, while the alteration of a single binding site is sufficient to inactivate ARS1. This redundant structure may be similar to that seen in metazoan origins.

scholarly journals Interaction of rice (Oryza sativa) lectin with N-acetylglucosaminides. Fluorescence studies

1985 ◽  
Vol 229 (3) ◽  
pp. 687-692 ◽  
Author(s):  
F Tabary ◽  
J P Frénoy
Keyword(s):  
Oryza Sativa ◽  
Binding Sites ◽  
Wheat Germ ◽  
Equilibrium Dialysis ◽  
Blue Shift ◽  
Association Constants ◽  
Fluorescence Studies ◽  
Saccharide Binding ◽  
Binding Enthalpy

The interaction of lectin isolated from rice (Oryza sativa) embryos with N-acetylglucosaminides was studied by equilibrium dialysis and fluorescence. Equilibrium dialysis with 4-methylumbelliferyl-(GlcNac)2 showed that rice lectin (Mr 38000) contains four equivalent saccharide-binding sites. Addition of the N-acetylglucosaminides GlcNac, (GlcNac)2 and (GlcNac)3 enhanced the intrinsic fluorescence of rice lectin and this was accompanied by a 10nm blue-shift of its maximum fluorescence with (GlcNac)2 and (GlcNac)3. These changes in intensity allowed determination of the association constants, which increased with the number of saccharide units: at 20 degrees C, Ka = (1.3 +/- 0.1) X 10(3), (5.1 +/- 0.4) X 10(4) and (2.6 +/- 0.1) X 10(5) M−1 for GlcNac, (GlcNac)2 and (GlcNac)3 respectively. The binding enthalpy, delta H0, for the three glucosaminides were very low and ranged from −12.1 to −20.6 kJ X mol-1. The results are compared with those obtained with wheat-germ agglutinin, another GlcNac-specific gramineaous lectin.

scholarly journals Competitive Binding of Novel Cyanine Dye AK3-5 and Europium Coordination Complexes to DNA

2019 ◽  
Keyword(s):  
Dna Binding ◽  
Fluorescence Intensity ◽  
Binding Sites ◽  
Association Constant ◽  
Antitumor Agents ◽  
Coordination Complexes ◽  
Cyanine Dye ◽  
Europium Complexes ◽  
Intensity Decrease ◽  
Dna Binding Sites

The present study was undertaken to assess the applicability of the novel trimethine cyanine dye AK3-5 as a competitive ligand for the antitumor agents, Eu(III) coordination complexes (EC), in the DNA-containing systems, using the displacement assay as an analytical instrument. The analysis of fluorescence spectra revealed a strong association of AK3-5 with nucleic acids, with the strength of interaction being higher for the double stranded DNA, compared to the single-stranded RNA. The binding parameters of the cyanine dye have been determined in terms of the McGhee & von Hippel neighbouring site-exclusion model and a classical Langmuir model. The AK3-5 association constant in the presence of DNA was found to be equal to 5.1×104 M-1, which is consistent to those of the well-known DNA intercalators. In turn, the binding of the cyanine to the RNA was characterized by a significantly lower association constant ( ~ 3.4×103 M-1) indicating either the external or “partially intercalated” binding mode. The addition of the europium complexes to the AK3-5-DNA system was followed by the fluorescence intensity decrease, with a magnitude of this effect being dependent on the EC structure. The observed fluorescence decrease of AK3-5 in the presence of europium complexes V7 and V9 points to the competition between the cyanine dye and antitumor drugs for the DNA binding sites. The dependencies of the AK3-5-DNA fluorescence intensity decrease vs. europium complex concentration were analyzed in terms of the Langmuir adsorption model, giving the values of the drug association constant equal to 5.4×104 M-1and 3.9×105 M-1 for the europium complexes V7 and V9, respectively. A more pronounced decrease of the AK3-5 fluorescence in the presence of V5 and V10 was interpreted in terms of the drug-induced quenching of the dye fluorescence, accompanying the competition between AK3-5 and Eu(III) complexes for the DNA binding sites. Cumulatively, the results presented here strongly suggest that AK3-5 can be effectively used in the nucleic acid studies and in the dye-drug displacement assays.

scholarly journals Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila

2014 ◽  
Author(s):  
Sarah H Carl ◽  
Steven Russell
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Regulatory Networks ◽  
System Development ◽  
Nervous System Development ◽  
Phylogenetic Distance ◽  
Functional Sites ◽  
Sox Proteins ◽  
Alternative Sources ◽  
Group B

Background: Group B Sox proteins are a highly conserved group of transcription factors that act extensively to coordinate nervous system development in higher metazoans while showing both co-expression and functional redundancy across a broad group of taxa. In Drosophila melanogaster, the two group B Sox proteins Dichaete and SoxNeuro show widespread common binding across the genome. While some instances of functional compensation have been observed in Drosophila, the function of common binding and the extent of its evolutionary conservation is not known. Results: We used DamID-seq to examine the genome-wide binding patterns of Dichaete and SoxNeuro in four species of Drosophila. Through a quantitative comparison of Dichaete binding, we evaluated the rate of binding site turnover across the genome as well as at specific functional sites. We also examined the presence of Sox motifs within binding intervals and the correlation between sequence conservation and binding conservation. To determine whether common binding between Dichaete and SoxNeuro is conserved, we performed a detailed analysis of the binding patterns of both factors in two species. Conclusion: We find that, while the regulatory networks driven by Dichaete and SoxNeuro are largely conserved across the drosophilids studied, binding site turnover is widespread and correlated with phylogenetic distance. Nonetheless, binding is preferentially conserved at known cis-regulatory modules and core, independently verified binding sites. We observed the strongest binding conservation at sites that are commonly bound by Dichaete and SoxNeuro, suggesting that these sites are functionally important. Our analysis provides insights into the evolution of group B Sox function, highlighting the specific conservation of shared binding sites and suggesting alternative sources of neofunctionalisation between paralogous family members.

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