Search

Results demonstrate that a six base long single-stranded DNA serves as the binding site for the fission yeast N-terminal domain protection telomeres protein (Pot1pN), which consists of amino acid residues 1-185. Furthermore, multiple Pot1pN proteins can cooperatively bind to long telomeric double-stranded DNA.

Results point out that nitric oxide binding to ferric and ferrous cytochromes, during the course of their function as a nitric oxide carrier, follows cooperativity and a dimer to monomer equilibrium. Data indicate that the binding affinity of the ferrous form is lower than those of myoglobins, hemoglobins, and pentacoordinate heme models, while ferric form binding is comparable to ferric myoglobins and hemoglobins.

The conformational change in the 12S subunit of transcarboxylase is triggered by substrate binding and involves an increase in alpha-helix with varying number of MM-CoA ligands bound per 12S hexamer. Results indicate that the -COO- group on MM-CoA ligand mediates the cooperative conformational change in 12S.

Results point out that all luteovirid P1-P2 pseudoknots assume folded structures maximizing cooperativity and complementarity of L1-S2 and L2-S1 loop-stem interactions involved in the stabilization of the pseudoknotted conformation relative to those of partially folded and inactive stem-loop structures.

BK channels (Slo1) are widely distributed K+ channels that control [Ca.sup.2+]-dependent processes and cellular excitability. Their activation by intracellular [Ca.sup.2+] ([Ca.sup.2+.sub.i]) is highly cooperative, with Hill coefficients of typically 2-5. To investigate the cooperativity contributed by each of the four [alpha] subunits that form the BK channel, we studied single channels comprised of mixtures of functional subunits and subunits with a mutation to disrupt a key site (Ca-bowl) required for activation by low concentrations of [Ca.sup.2+.sub.i]. As the number of functional subunits increased, we found a stepwise increase in the Hill coefficient of 0.3-0.8 per functional subunit and a stepwise decrease in the [Ca.sup.2+.sub.i] required for half activation ([K.sub.d]). These results show directly that BK channels can open with 0, 1, 2, 3, or 4 functional Ca-bowls, and that each subunit with a functional Ca-bowl contributes a stepwise increase to both the cooperativity of activation and the apparent [Ca.sup.2+] affinity. A model with 0-4 high-affinity allosteric activators and four low-affinity allosteric activators was examined. In this model, [Ca.sup.2+] bindings were independent of one another and the cooperativity arose from the joint action of the allosteric activators on the open-closed equilibrium. Although this model described well the major features of the experimental data, some differences between the observed and predicted results indicated that additional factors not included in the model also contribute to the cooperativity.

The cation selectivity of Na,K- and gastric H,K-ATPase is determined by three residues in the TM4 transmembrane segment but can not be reproduced by the mutants for these residues . Instead, the TM3-TM4 ectodomain establishes the cation selectivity.

The coadsorption properties of carbon monoxide and oxygen on gold clusters reveals that instead of competitive coadsorption, cooperative coadsorption with an increase in the adsorption of both is observed. Furthermore, the coadsorption causes new peaks in the mass spectrum, which may be due to the carbon dioxide released.

The ternary complex model, consisting of a superantigen interacting with a major histocompatibility complex and T cell receptor, reveals a positive and negarive cooperativity and a marked increase in the temperature dependent binding kinetics due to the cooperative interaction of the individual protein components in the complex.

Research demonstrates the dicalcium state of the calbindin mutants P43G and P43M substantially differs and are not due to the flexible linker region of the protein as previously believed. Further, substituting lanthanide ion for calcium does not lead to any marked change in the mobility of the native protein.

A series of podands based on two or three hydrogen bonding 'arms' situated in mutually ortho, meta, or para relationships about an aryl core have been prepared, and their affinities for simple inorganic anions were measured. Of the two-arm hosts the meta compound and to a lesser extent the ortho host exhibit a cooperative anion binding effect. The two arms function essentially independently in the para derivative. The mutually meta three-arm host shows dramatically enhanced cooperative binding. Conformational changes within the meta two-arm host result in significantly enhanced electrochemical anion sensing compared with the more conformationally rigid three-arm host.

Results show 23S rRNA fragments containing hairpin 92 and helix 90 elements catalyze high affinity binding of both ATP and RNA to Escherichia coli DbpA protein. Data indicate an allosteric cooperativity in the binding of larger RNA substrates and ATP to the protein, which requires 23S rRNA:helix 89 helix.

Results demonstrate that the 11beta-hydrosteroid dehydrogenase type 1 from human liver is active as a dimeric enzyme and exhibits cooperative kinetics for glucocorticoid 11-oxoreduction. The enzyme also shows remarkable adaptation to low and high substrate concentrations in response to plasma glucocorticoid concentration and also mediates its activation.

The specificity of cohesin-dockerin interactions are analyzed using mutants of the dockerin domains of endoglucanases CelD and CipA. Data indicate that the mutagenesis occurs in one segment and the mutations do not cause large changes in the binding affinity. The cohesin-dockerin binding is mostly by hydrophobic interactions.

Reverse isothermal microcalorimetric titration data indicate that the di- and trivalent carbohydrate analogues of lectins exhibit two functional binding epitopes. The data show that the microscopic enthalpies of the binding are similar, suggesting negative Hill coefficients for the analogues binding to concanavalin A.

Isothermal titration microcalorimetric analyses reveal that di-, tri-, and tetravalent carbohydrate analogues exhibit negative binding cooperativity in their bindinng to two lectins. The curvilinear Hill plots indicate that the multivalent analogues bind with decreasing affinity to the carbohydrate epitopes of the analogues.

Research demonstrates that the human erythrocyte sugar transporter is a cooperative tetramer exhibiting two subunits for sugar uptake and two subunits for sugar exit as revealed by labeled cytochalasin B binding studies.

Site-directed mutagenesis of R67 dihydrofolate reductase reveals that the enzyme possesses a 'hot spot' binding surface, which binds both folate and NADPH ligands, during catalysis. Data indicate that the enzyme exhibits an endo conformer for cooperative binding of ligands, which suggests primitivity of the enzyme.

Results demonstrate that arabinose regulon is negatively controlled by AraR protein, which represses ara promoters in vivo upon L-arabinose depletion. Data further indicate that metabolic operon and transport gene promoters are prone for catabolite repression suggesting that promoters enforce a tight and flexible control of ara regulon in Bacillus subtilis.

This review elucidates the structural and functional aspects of the virulence factors in gram-positive bacteria exemplified by Streptococcus pneumoniae. The polysaccharide capsule and proteins are virulence factors and potential vaccine candidates as well. They exhibit highly alpha-helical domains and coil structure and aid in the adherence of pneumococcus to host cells.

Isothermal titration calorimetry analysis of the D-peptide inhibitor binding to the N-terminal hydrophobic pocket of HIV-1 gp41 protein reveals that the inhibitor binds to a transiently exposed perfusion intermediate protein surface. Data indicate that no cooperative interactions among the three binding sites of the protein and the binding is enthalpically driven.

Research demonstrates that the hydrophobic and bulky benzo(a)pyreneDE residues mediate the mechanism of TATA binding protein binding different from prebending. Data also indicate that RNA transcription efficiency of the TATA binding protein promoters is also influenced by the bulky residues leading to a reduced gene expression.

Results demonstrate that phosphofructokinase from Escherichia coli exhibits unique binding and catalytic properties with different substrates. The enzyme is inhibited by ATP and reveals cooperativity with sugar phosphates and nucleotide phosphoryl donors, with mutagenesis, and with altered substrate affinity.

Research describes the structure of the extracelular loop of human cholecystokinin-A receptor and its molecular contact with the C-terminal octapeptide of cholecystokinin. Results demonstrate unique molecular interactions involved in the binding process of the receptor and the octapeptide.

Research examines the role of oligomerization of the R1 subunit and its interaction with purine substrates, the deoxynucleoside triphosphate allosteric effectors, and the dimeric R2 subunit of the ribonucleotide reductases using a 16 species model. Data reveal that neither the allosteric site nor the active site exhibits nucleotide specificity.

Results show that the regulatory proteins KorB and TrbA of the plasmid RK2 exhibit up to a 10-fold cooperativity in the repression of the promoter trbBp. Data indicate that the C-terminal domain of the proteins mediate the cooperativity, which is brought about by the interaction between these proteins.

Results demonstrate that the BvgA response regulator's high-affinity and lower affinity binding to filamentous hemagglutinin promoter is cooperative in nature in Bordetella pertussis. Data further reveal that for full promoter activity, both primary and secondary binding sites are essential and the secondary binding region exhibits restricted DNA sequence specificity.

Results show that the conformational behavior of the rat mitochondrial rhodanese presequence peptide, during its binding to small and large unilamellar phospholipid vesicles, is similar with respect to helix formation thermodynamics as determined by varying helix content.

This article reviews cyclic nucleotide-gated ion channels in terms of the subfamilies, their functional similarities, and their activation. Data show that the channels are very sensitive to cyclic nucleotide concentration changes and they coassemble producing channels with specificity for either cAMP or cGMP. Physical models are presented.

Research describes alterations in the structure of human normal adult hemoglobin by site-directed mutagenesis. Data from three such mutant hemoglobins reveal that the mutants possess a new hydrogen bond in the alpha1beta1 subunit interface that lowers their oxygen affinity. The recombinant hemoglobins alternate between R quaternary to T quaternary structure.

Results demonstrate that yeast calmodulin exhibits high cooperative binding of calcium leading to the rearrangement of the four alpha-helices, exposition of the hydrophobic surface, and conformational change of the beta-sheet of the protein.

Research demonstrates that the membrane-bound annexin I molecules laterally aggregate in a monlayer exposing their hydrophobic interaction site, which then directly interacts with the secondary membrane causing membrane aggregation.

The crystal structure of a c-Cbl-UbcH7-ZAP70 peptide ternary complex reveals the rigid coupling between the peptide binding and the ubiquitin-conjugating enzyme binding domains. Results further show that RING domain of the c-Cbl proto-oncogene aids in positioning the substrate and the enzyme for ubiquitin transfer.

Results show that spectroscopic and calorimetric characteristics of single-chain Fv fragment of the F11 ferritin antibody suggest that it is a functional protein in a partial structured state. Data further indicate that isolated V(sub)L domain binds human ferritin but with lesser affinity than the parent F11 antibody.

Results show that calcium vector protein exhibit two EF-hand motifs having binding affinity for calcium ions. Domain analysis of the active sites reveal that the tertiary structure to be similar to other calcium-binding domains and show a stepwise calcium binding.

Results show that inhibition of S-adenosylmethionine synthetase is inhibited by imidodiphosphate and diimidotriphosphate. The inhibition by the latter is governed by the presence or absence of S-adenosylmethionine, in its presence, it acts as a slow binding inhibitor and in its absence a competitive inhibitor.

Results show zinc or cobalt stabilize the native form of both wild type and mutant carbonic anhydrase II (CAII). The high metal specificity of CAII is mediated by the hydrophobic cluster orienting histidine residues in optimal position stabilizing the bound metal.

The binding of aminoglycoside antibiotics with the 5'-untranslated region of thymidylate synthase (TS) messenger RNA has been studied. TS catalyze the reductive methylation of 2'-deoxyuridine 5'-monophosphate to form thymidine 5'-monophosphate. Results show the aminoglycosides bind in a specific and saturable fashion with dissociation constants of approximately 1 microM to a TS mRNA site 1 construct. The binding site for the aminoglycosides is in the CC bubble region.

Research was conducted to understand the activity regulation of kinesin protein in microtubules. The data indicate that the light chain form of the protein interacts with the heavy chain form in rendering kinesin inactive.

The preparation and properties of aqueous micelles derived from n-hexadecylphosphoryladenosine (C16-AMP), n-hexadecylphosphorylcytidine (C16-CMP) and n-hexadecylphosphoryluridine (C16-UMP) have been studied. Ultraviolet (UV) ultracentrifugation along with UV absorption and circular dichroism spectroscopic analysis have been undertaken. Results show the aggregation of the micelles is not affected by the chemical nature of the base. It was also observed that the complementary base binding is not more visible nor faster than binding in liposomes.

Frontal analysis continuous capillary electrophoresis was used in studying the binding of beta-lactoglobulins to sodium polystyrenesulfonate. This analytical method hastens the collection of protein-polyelectrolyte binding data in a rapid and reproducible manner. The obtained data were plotted on a modified Scatchard plot and the intrinsic binding constant was measured as a function of pH at an ionic strength of 0.05 M. Results indicate the binding of beta-lactoglobulin is very much dependent on the pH value. Binding takes place when the protein has a negative net charge and similar to the sign of the polyelectrolyte.

The incorporation of sucrose to dipalmitoylphosphatidylcholine (DPPC) thin films has been investigated using a combination of quartz-crystal microbalance and Fourier transform infrared reflection-absorption spectroscopies. The former is a powerful method in measuring the mass of thin films on a nanogram scale. Results indicate that sucrose molecules are strongly incorporated in fully hydrated DPPC thin films but weakly in partially hydrated films. The sucrose molecules can be squeezed out easily by lateral pressure in partially hydrated films.

Research was conducted to examine the process involving the creation of a discrete RSC-nucleosome complex, its transformation into an activated state via adenosine triphosphate analysis and the subsequent release of a revised nucleosome. The complex features a full complement of histones and is susceptible to endo- and exo-nucleases. Results revealed the existence of three states of nucleosomal configuration.

An investigation tested the applicability of the lattice-fluid hydrogen-bonding (LFHB) equation-of-state model, which incorporates the Veytsman statistics, to the cooperativity, cyclic associate formation and intramolecular-hydrogen bonding problems. Results demonstrated that the LFHB model can be used to consistently characterize self-association, cross-association, cyclic associate formation, intramolecular hydrogen bonding and hydrogen bond cooperativity, under the condition that bonds of varying strengths are considered as different types of hydrogen bonds.

Antithrombin, a plasma serpin, is relatively inactive as an inhibitor of the coagulation proteases until it binds to the heparan side chains that line the microvasculature. The binding specifically occurs to a core pentasaccharide present both in the heparans and in their therapeutic derivative heparin. The accompanying conformational change of antithrombin is revealed in a 2.9-[Angstrom] structure of a dimer of latent and active antithrombins, each in complex with the high-affinity pentasaccharide. Inhibitory activation results from a shift in the main sheet of the molecule from a partially six-stranded to a five-stranded form, with extrusion of the reactive center loop to give a more exposed orientation. There is a tilting and elongation of helix D with the formation of a 2-turn helix P between the C and D helices. Concomitant conformational changes at the heparin binding site explain both the initial tight binding of antithrombin to the heparans and the subsequent release of the antithrombin-protease complex into the circulation. The pentasaccharide binds by hydrogen bonding of its sulfates and carboxylates to Arg-129 and Lys-125 in the D-helix, to Arg-46 and Arg-47 in the A-helix, to Lys-114 and Glu-113 in the P-helix, and to Lys-11 and Arg-13 in a cleft formed by the amino terminus. This clear definition of the binding site will provide a structural basis for developing heparin analogues that are more specific toward their intended target antithrombin and therefore less likely to exhibit side effects.

Experiments focused on the thermodynamic coupling between repressor self assembly and DNA binding found that an unfavorable contribution to interaction cooperativity is transmitted by the DNA. The coupling, however, is mediated by the protein. Sedimentation equilibrium analysis and fluorescence spectroscopy data of phage operators binding to free represor dimers indicate that structural transitions in both macromolecules moderate the effect of self-association.

A study followed a binding site numbering convention developed in previous research in domain E of cyclodextrin glycosyltransferase to determine the function of several tryptophan residues in the granular starch binding domain (SBD) of Aspergillus niger glucoamylase I. Findings show that the binding site 2 of SBD has a significantly higher affinity for the ligand than site. It appears that site 1 acts as the initial recognition site while site 2 is more involved in pre[paring the substrate for catalysis.

The importance of multiple steroidogenic factor 1 binding elements in the human steroidogenic acute regulatory protein gene 5'-flanking region in cyclic AMP responsiveness and maximal promoter activity was analyzed. It was shown that the proximal promoter of the human StAR gene contains three SF-1-controlled elements that must be intact for maximal promoter activity and cAMP responsiveness.