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Centrin-1, a Ca2+ sensor protein of the centrin family is a crucial player for cell division in eukaryotes and plays a key role in the microtubule organising centre. Despite being regarded as a calcium sensor with a matched structure to calmodulin/troponin C, the protein undergoes mild changes in conformation and binds Ca2+ with moderate affinity. We present an in-depth analysis of the Ca2+ sensing by individual EF-hand motifs of centrin-1 and address unsolved questions of the rationales for moderate affinity and conformational transitions of the protein. Employing the more sensitive approach of Trp scanning of individual EF-hand motif, we have undertaken an exhaustive investigation of Ca2+ binding to individual EF-hand motifs, named EF1 to EF4. All four EF-hand motifs of centrin-1 are structural as all of them bind both Ca2+ and Mg2+. EF1 and EF4 are the most flexible sites as they undergo drastic conformational changes following Ca2+ binding, whereas EF3 responds to Ca2+ minimally. On the other hand, EF2 moves towards the protein surface upon binding Ca2+. The independent filling mode of Ca2+ to EF-hand motifs and lack of intermotif communication explain the lack of cooperativity of binding, thus constraining centrin-1 to a moderate affinity binding protein. Thus, centrin-1 is distinct from other calcium sensors such as calmodulin.

The most abundant member of the collagen protein family, collagen I (also known as type I collagen; COL1), is composed of one unique (chain B) and two similar (chain A) polypeptides that self-assemble with one amino acid offset into a heterotrimeric triple helix. Given the offset, chain B can occupy either the leading (BAA), middle (ABA) or trailing (AAB) position of the triple helix, yielding three isomeric biomacromolecules with different protein recognition properties. Despite five decades of intensive research, there is no consensus on the position of chain B in COL1. Here, three triple-helical heterotrimers that each contain a putative von Willebrand factor (VWF) and discoidin domain receptor (DDR) recognition sequence from COL1 were designed with chain B permutated in all three positions. AAB demonstrated a strong preference for both VWF and DDR, and also induced higher levels of cellular DDR phosphorylation. Thus, we resolve this long-standing mystery and show that COL1 adopts an AAB register.

The effect of the ultrasonic treatment on the physicochemical properties, oil-holding capacities, foaming capacities, and TLR2-affinity of the polysaccharides from Pholiota nameko (PNPS), was evaluated. Compared with the protein content of PNPS before ultrasonic treatment, the protein content of PNPS all presented a decrease under different ultrasonic conditions. The viscosity of PNPS showed a decrease when the ultrasonic intensity was strong enough, as well as the molecular weight. The oil-holding capacity and the foaming capacity of PNPS showed a continuous increasing trend with the increase of the ultrasonic treatment time under a set ultrasonic power of 400 W. Further, the ultrasonic operation could induce the decrease of the affinity binding between PNPS and the receptor proteins TLR2. These data confirmed that applying the ultrasonic treatment could obtain PNPS with high carbohydrate contents, low viscosity and low TLR2-affinity under proper ultrasonic condition.

The DNA phosphorothioate modification is a novel physiological variation in bacteria. DndE controls this modification by binding to dsDNA via a mechanism that remains unclear. Structural analysis of the wild-type DndE tetramer suggests that a positively charged region in its center is important for DNA binding. In the present study, we replaced residues G21 and G24 in this region with lysines, which increases the DNA binding affinity but does not affect the DNA degradation phenotype. Structural analysis of the mutant indicates that it forms a new tetrameric conformation and that DndE interacts with DNA as a monomer rather than as a tetramer. A structural model of the DndE-DNA complex, based on its structural homolog P22 Arc repressor, indicates that two flexible loops in DndE are determinants of DNA binding.

Targeted DNA methylation is a technique that aims to methylate cytosines in selected genomic loci. In the most widely used approach a CG-specific DNA methyltransferase (MTase) is fused to a sequence specific DNA binding protein, which binds in the vicinity of the targeted CG site(s). Although the technique has high potential for studying the role of DNA methylation in higher eukaryotes, its usefulness is hampered by insufficient methylation specificity. One of the approaches proposed to suppress methylation at unwanted sites is to use MTase variants with reduced DNA binding affinity. In this work we investigated how methylation specificity of chimeric MTases containing variants of the CG-specific prokaryotic MTase M.SssI fused to zinc finger or dCas9 targeting domains is influenced by mutations affecting catalytic activity and/or DNA binding affinity of the MTase domain. Specificity of targeted DNA methylation was assayed in E. coli harboring a plasmid with the target site. Digestions of the isolated plasmids with methylation sensitive restriction enzymes revealed that specificity of targeted DNA methylation was dependent on the activity but not on the DNA binding affinity of the MTase. These results have implications for the design of strategies of targeted DNA methylation.

Summary Hevin is secreted by astrocytes and its synaptogenic effects are antagonized by the related protein, SPARC. Hevin stabilizes neurexin-neuroligin transsynaptic bridges in vivo. A third protein, membrane-tethered MDGA, blocks these bridges. Here, we reveal the molecular underpinnings of a regulatory network formed by this trio of proteins. The hevin FS-EC structure differs from SPARC, in that the EC domain appears rearranged around a conserved core. The FS domain is structurally conserved and it houses nanomolar affinity binding sites for neurexin and neuroligin. SPARC also binds neurexin and neuroligin, competing with hevin, so its antagonist action is rooted in its shortened N-terminal region. Strikingly, the hevin FS domain competes with MDGA for an overlapping binding site on neuroligin, while the hevin EC domain binds the extracellular matrix protein collagen (like SPARC), so that this trio of proteins can regulate neurexin-neuroligin transsynaptic bridges and also extracellular matrix interactions, impacting synapse formation and ultimately neural circuits.

We present an electrolyte-gated graphene field effect transistor (GFET) nanosensor using aptamer for rapid, highly sensitive and specific detection of a lung cancer biomarker interleukin-6 (IL-6) with enhanced stability. The negatively charged aptamer folds into a compact secondary conformation upon binding with IL-6, thus altering the carrier concentration of graphene and yielding a detectable change in the drain-source current Ids. Aptamer has smaller size than other receptors (e.g. antibodies), making it possible to bring the charged IL-6 more closely to the graphene surface upon affinity binding, thereby enhancing the sensitivity of the detection. Thanks to the higher stability of aptamer over antibodies, which degrade easily with increasing storage time, consistent sensing performance was obtained by our nanosensor over extended-time (>24 h) storage at 25 °C. Additionally, due to the GFET-enabled rapid transduction of the affinity recognition to IL-6, detection of IL-6 can be achieved in several minutes (

VP35 of Ebola viruses (EBOVs) is an attractive potential target because of its multifunction. All-atom molecular dynamics (MD) simulations and Molecular Mechanics Generalized Born surface area (MM/GBSA) energy calculations are performed to investigate the single-walled carbon nanotube (SWCNT) as an inhibitor in wild-type (WT) VP35 as well as in three primary mutants (K248A, I295A, and K248A/I295A) through docking the SWCNT in the first basic patch (FBP) of VP35. The SWCNTs of all the four systems effectively bind to the FBP. Interestingly, the sites and orientations of the SWCNT binding to the I295A mutant and K248A/I295A double mutants change significantly to accommodate the variation of the VP35 conformation. Moreover, the VDW can provide the major forces for affinity binding in all four systems.

Summary Despite high sequence homology among the p53 family members, the regulation of their transactivation potential is based on strikingly different mechanisms. Previous studies revealed that the activity of TAp63α is regulated via an autoinhibitory mechanism that keeps inactive TAp63α in a dimeric conformation. While all p73 isoforms are constitutive tetramers, their basal activity is much lower compared with tetrameric TAp63. We show that the dimeric state of TAp63α not only reduces DNA binding affinity, but also suppresses interaction with the acetyltransferase p300. Exchange of the transactivation domains is sufficient to transfer the regulatory characteristics between p63 and p73. Structure determination of the transactivation domains of p63 and p73 in complex with the p300 Taz2 domain further revealed that, in contrast to p53 and p73, p63 has a single transactivation domain. Sequences essential for stabilizing the closed dimer of TAp63α have evolved into a second transactivation domain in p73 and p53.

It's favorable to alter KRas mutation's location to endomembrane by interfering the binding of PDEδ (the prenyl-binding protein phosphodiesterase delta) to KRas. In the present work, the binding of four inhibitors (Deltarasin, allyl analogue, pyrazolopyridazinone derivative, and Deltazinone 1) to PDEδ is investigated with all-atom Molecular Dynamic (MD) simulations. The binding free energy calculation results reveal that van der Waals (VDW) energy provides the major force for affinity binding. Moreover, the binding energy decomposition indicates that residues R61 and I129 provide important contributions to binding energies in all systems. The conserved hydrogen bonds play crucial roles in anchoring the inhibitors to the exact site for binding. The results for conformational analysis of PDEδ/free and PDEδ/inhibitors systems show that the structures are more stable after the inhibitors' binding to the PDEδ. It is also found that the most unstable system among four complexes is PDEδ/pyrazolopyridazinone derivative system whose α3-helix formed by the residues P113-Q116 disappears. This study may provide valuable information for the design of high potency PDEδ inhibitors. Communicated by Ramaswamy H. Sarma.

Background The successful application of nonviral gene transfer technologies requires both improved understanding and control with respect to intracellular trafficking and release. However, the intracellular space is highly complex and hence well-defined, stable structures are necessary to probe the stages of the delivery pathway. Fluorescent labeling is a regularly used approach to monitor nonviral delivery and release, yet few studies investigate the effects of label incorporation on the structure and activity of gene-containing vehicles. Methods In the present study, the impacts of label incorporation on the assembly and gene transfer capacity of DNA polyplexes were determined through the utilization of a model DNA-polyethylenimine (PEI) delivery system. PEI was fluorescently labeled with the Oregon Green® dye prior to polyplex formation and delivery to CHO-K1 cells. Results The present study provides evidence showing that routine labeling strategies for polyplexes weakened DNA binding affinity, produced large quantities of extracellular structures and significantly increased intracellular polyplex aggregation. Additionally, cellular internalization studies showed that increased labeling fractions led to reductions in polyplex uptake as a result of weakened complexation. Conclusions These results not only provide insight into the assembly of these structures, but also help to identify labeling strategies sufficient to preserve activity at the same time as enabling detailed studies of trafficking and disassembly. Copyright © 2015 John Wiley & Sons, Ltd.

Summary Proteins have evolved to balance efficient binding of desired partners with rejection of unwanted interactions. To investigate the evolution of protein-protein interactions, we selected a random library of pre-stabilized TEM1 β-lactamase against wild-type TEM1 using yeast surface display. Three mutations were sufficient to achieve micromolar affinity binding between the two. The X-ray structure emphasized that the main contribution of the selected mutations was to modify the protein fold, specifically removing the N′-terminal helix, which consequently allowed protein coupling via a β-sheet-mediated interaction resembling amyloid interaction mode. The only selected mutation located at the interaction interface (E58V) is reminiscent of the single mutation commonly causing sickle-cell anemia. Interestingly, the evolved mutations cannot be inserted into the wild-type protein due to reduced thermal stability of the resulting mutant protein. These results reveal a simple mechanism by which undesirable binding is purged by loss of thermal stability.

Post-translational modification of forkhead family transcription factor, FoxO1, is an important regulatory mode for its diverse activities. FoxO1 is acetylated by HAT coactivators and its transcriptional activity is decreased via reduced DNA binding affinity. Here, we report that SET/TAF-Iβ inhibited p300-mediated FoxO1 acetylation in an INHAT domain-dependent manner. SET/TAF-Iβ interacted with FoxO1 and activated transcription of FoxO1 target gene, p21. Moreover, SET/TAF-Iβ inhibited acetylation of FoxO1 and increased p21 transcription induced by oxidative stress. Our results suggest that SET/TAF-Iβ inhibits FoxO1 acetylation and activates its transcriptional activity toward p21.

The HIV-1 Pr55Gag precursor specifically selects genomic RNA (gRNA) from a large variety of cellular and spliced viral RNAs (svRNAs), however the molecular mechanisms of this selective recognition remains poorly understood. To gain better understanding of this process, we analyzed the interactions between Pr55Gag and a large panel of viral RNA (vRNA) fragments encompassing the main packaging signal (Psi) and its flanking regions by fluorescence spectroscopy. We showed that the gRNA harbors a high affinity binding site which is absent from svRNA species, suggesting that this site might be crucial for selecting the HIV-1 genome. Our stoichiometry analysis of protein/RNA complexes revealed that few copies of Pr55Gag specifically associate with the 5′ region of the gRNA. Besides, we found that gRNA dimerization significantly impacts Pr55Gag binding, and we confirmed that the internal loop of stem-loop 1 (SL1) in Psi is crucial for specific interaction with Pr55Gag. Our analysis of gRNA fragments of di...

Systematic Evolution of Ligands by EXponential enrichment (SELEX) is an experimental procedure that allows extraction, from an initially random pool of oligonucleotides, of the oligomers with a desired binding affinity for a given molecular target. The procedure can be used to infer the strongest binders for a given DNA or RNA binding protein, and the highest affinity binding sequences isolated through SELEX can have numerous research, diagnostic and therapeutic applications. Recently, important new modifications of the SELEX protocol have been proposed. In particular, a modification of the standard SELEX procedure allows generating a dataset from which protein-DNA interaction parameters can be determined with unprecedented accuracy. Another variant of SELEX allows investigating interactions of a protein with nucleic-acid fragments derived from the entire genome of an organism. We review here different SELEX-based methods, with particular emphasis on the experimental design and on the applications aimed at inferring protein-DNA interactions. In addition to the experimental issues, we also review relevant methods of data analysis, as well as theoretical modeling of SELEX.

WOS: 000246089000002, PubMed ID: 17222902, The aim of this study is to prepare cholesterol-imprinted polymeric particles. N-Methacryloyl-(L)-tyrosinemethylester (MAT) was chosen as the complexing monomer. In the first step, functional monomer MAT was synthesized by the reaction Of L-tyrosine methylester and methacryloyl chloride and characterized by FTIR and NMR. Then, cholesterol was complexed with MAT in different mol ratios and the cholesterol-imprinted poly(2-hydroxyethyl methacrylate-N-methacrylOyl-(L)-tyrosine methylester) [MIP] particles were synthesized by bulk polymerization. After that, the template molecules (i.e., cholesterol) were removed using chloroform. MIP particles were characterized by elemental analysis, FTIR, SEM, swelling tests and surface area measurements. Cholesterol adsorption experiments were performed in a batch experimental set-up. Adsorption medium was methanol or intestinal mimicking solution. Stigmasterol and estradiol were used as competing molecules in selectivity tests. Obtained results were as follows: swelling ratio of MIP and non-imprinted (NIP) particles were 60.8% and 44.1% in water. With the increase in the amount of MAT in the polymerization medium, incorporation of MAT was increased (16.6-78.0 mu mol/g). SEM photographs showed the surface roughness and porosity. Specific surface area of NIP and MIP particles were found as 19.2 and 31.5 m(2)/g, respectively. Template molecules (i.e., cholesterol) were removed from the polymer structure in the ratio of 76-84% of the initial concentration. Cholesterol adsorption increased with the increase in cholesterol concentration up to 1.5 mg/mL. MIP particles prepared using higher amounts of cholesterol exhibit significantly higher capacity to the NIP particles (i.e., control polymer). MIP particles were 3.09 and 3.60 times selective with respect to the stigmasterol and estradiol, respectively. Reusability of MIP particles was also investigated. MIP particles showed negligible loss in the cholesterol adsorption capacity after five adsorption-desorption cycles with the same adsorbent

WOS: 000243674800014, PubMed ID: 16950507, The aim of this study is to prepare ion-imprinted polymers which can be used for the selective removal of mercury ions [Hg2+] from human serum. N-Methacryloyl-(L)-cysteine (MAC) was chosen as the complexing monomer. In the first step, Hg2+ was complexed with MAC and the Hg2+-imprinted poly(hydroxyethyl methacrylate-N-methacryloyl-(L)-cysteine) (MIP) beads were synthesized by suspension polymerization. After that. the template ions (i.e., Hg2+) were removed using thiourea (0.5%, v/v) in 0.05 M HCl. The specific surface area of the MIP beads was found to be 59.04 m(2)/g with a size range of 63-140 mu m in diameter and the swelling ratio was 91.5%. According to the elemental analysis results, the MIP beads contained 87.0 mu mol MAC/g polymer. The maximum adsorption capacity was 0.45 mg Hg2+/g beads. The applicability of two kinetic models including pseudo-first order and pseudo-second order model was estimated on the basis of comparative analysis of the corresponding rate parameters, equilibrium capacity and correlation coefficients. Results suggest that chemisorption processes could be the rate-limiting step in the adsorption process. The relative selectivity coefficients of MIP beads for Hg2+/Cd2+, Hg2+/Zn2+ were 14.7 and 21.5 times greater than the non-imprinted (NIP) matrix. respectively. The MIP beads could be used many times without decreasing in their adsorption capacities significantly

A photo-controlled version of the engrailed homeodomain (zENG) was created by inserting the homeodomain into a surface loop of a circularly permuted version of the photoactive yellow protein (cPYP). The two proteins fold independently as judged by NMR and fluorescence denaturation measurements. In the dark, the affinity of the zENG domain for its cognate DNA is inhibited >100-fold compared to wild-type zENG. Blue-light irradiation of the hybrid protein leads to enhanced conformational dynamics of the cPYP portion and a two-fold enhancement of the DNA binding affinity of the zENG domain. These results suggest that insertion into a surface loop of cPYP can be a general approach for conferring an initial level of photo-control on a given target protein. Focussed mutation/selection strategies may then be used to enhance the degree of photo-control.

Advances in systematic evolution of ligands by exponential enrichment (SELEX), a selection protocol for aptamers, have resulted in increased applications of DNA and RNA aptamers in developing analytical techniques. We review recent developments in SELEX techniques as well as new aptamer-based bioanalytical applications.

Among a library of 17 bisbenzamidines connected with various linkers, compounds with a flexible pentanediamide (10) or hexanediamide (12) linker were the most potent derivatives against rat Pneumocystis carinii (IC50 values of 3 and 2 nM, respectively) and had the highest selectivity index ratios (GI50 of human tumor cells/IC50 of rat P. carinii cells) of >104. Seven compounds caused 50% growth inhibition (GI50) of tumor cells at concentrations of

The reconstitution of dimeric concanavalin A (ConA) in terms of quaternary association and reactivation, after denaturation in urea, has been investigated using intrinsic fluorescence, 8-anilino-1-naphthalenesulfonate (ANS) binding, far-UV circular dichroism (CD), and an activity assay developed through a combination of affinity binding and the o-phthalaldehyde (OPA) procedure of protein estimation. The equilibrium denaturation of dimeric ConA in urea exhibits a biphasic unfolding pathway involving an intermediate with hydrophobic exposure, and the overall free energy of stabilization for the dimeric protein is obtained as 16.3 kcal mol−1. The time course of reassociation and regain of activity during reconstitution reveals that the reactivation of ConA runs almost parallel to the process of subunit association. The reactivation reaction follows second-order kinetics, with a rate constant (k) of 2.6 × 102 M−1 s−1. These results may provide insight into the relationship between quaternary association and function of legume lectins.

Graphical abstract Procedures for synthesizing α-amino acids on a chip for coordination with transitional metal ions and a His-Tagged protein have been successfully developed as a stable protein microarray. Using the recombinant His-Tagged 3CL-protease (3CLpro) as a model for attachment to chips containing d-/l-Glu, Asp, Orn, Ser via different transitional metal ions, it was found that the Orn chip was the best of affinity binding and stability by which Zn2+ was the best metal ion for affinity while Co2+ was the best metal ion for stability. Thus, this protein microarray can be alternatively used as a high throughput screening method for rapid detection against SARS CoV 3CLpro and/or efficient purification of other Tagged proteins., Procedures for synthesizing α-amino acids on a chip for coordination with transitional metal ions and a His-Tagged protein have been successfully developed as a stable protein microarray. Using the recombinant His-Tagged 3CL-protease (3CLpro) as a model for attachment to chips containing d-/l-Glu, Asp, Orn, Ser via different transitional metal ions, it was found that the Orn chip was the best of affinity binding and stability by which Zn2+ was the best metal ion for affinity while Co2+ was the best metal ion for stability. Thus, this protein microarray can be alternatively used as a high throughput screening method for rapid detection against SARS CoV 3CLpro and/or efficient purification of other Tagged proteins.

The synthesis of new A-C8/C-C2 alkoxyamido-linked pyrrolo[2,1-c][1,4]-benzodiazepine dimers have been described in this report. These dimers exhibit significant DNA-binding ability with moderate anticancer activity.

Several benzo[c]pyrido[2,3,4-kl]acridines bearing different substituents on the A and E rings were synthesized and evaluated for their capacity to bind to DNA and to inhibit DNA topoisomerases. Potent cytotoxic compounds were discovered but no strict correlation with their DNA binding affinity and effects on topoisomerases were observed. DNA is one but not the unique target of these compounds.

The biochemical and molecular characteristics of cytochrome P4501A1 targeted to rat brain mitochondria was studied to determine the generality of the targeting mechanism previously described for mitochondrial cytochrome P450MT2 (P450MT2) from rat liver. In rat brain and C6 glioma cells chronically exposed to β-naphoflavone (BNF), P450MT2 content reached 50 and 95% of the total cellular pool, respectively. P450MT2 from 10 days of BNF-treated rat brain was purified to over 85% purity using hydrophobic chromatography followed by adrenodoxin affinity binding. Purified brain P450MT2 consisted of two distinct molecular species with NH2 termini identical to liver mitochondrial forms. These results confirm the specificity of endoprotease-processing sites. The purified P450MT2 showed a preference for adrenodoxin + adrenodoxin reductase electron donor system and exhibited high erythromycinN-demethylation activity. Brain mitoplasts from 10-day BNF-treated rats and also purified P450MT2 exhibited highN-demethylation activities for a number of neuroactive drugs, including trycyclic anti-depressants, anti-convulsants, and opiates. At 10 days of BNF treatment, the mitochondrial metabolism of these neuroactive drugs represented about 85% of the total tissue activity. These results provide new insights on the role of P450MT2 in modulating the pharmacological potencies of different neuroactive drugs in chronically exposed individuals.

The solution-phase synthesis of two 1000-membered positional scanning libraries of distamycin A analogues is described enlisting acid/base liquid-liquid extractions for isolation and purification of all intermediates and final products. The results of their screening for functional activity (L1210 cytotoxic potency) and DNA binding affinity were compared with those derived from libraries containing the same compound members but prepared in a smaller 10-compound mixture format. The positional scanning libraries, which are substantially less demanding to prepare, allowed the accurate detection of the global observations and the clearly more potent activities, but more subtle discoveries and less distinguishable activities were not detected. This is a natural consequence of testing the larger 100-compound mixtures and the relative insensitivity of the assays to the contribution of any single, uniquely acting compound in the mixture. Thus, the disadvantages associated with the loss of some information contained within the library must be balanced against the advantages of the ease of library synthesis and judged in light of the library screening objectives.

The bis-benzimidazole compound nuclear yellow (NY) belongs to the same chemical family as the DNA binding fluorochromes Hoechst 33258 and Hoechst 33342. Spectroscopic studies of NY alone and in the presence of calf thymus DNA show high DNA binding affinity and behavior similar to the Hoechst fluorochromes above. Mitotic metaphase chromosomes from Balb/c mice stained with NY show C-banding and weak G/Q-banding, both of them disappearing after distamycin A (DA) or methyl green (MG) counterstaining. The same staining of human metaphase chromosomes from lymphocyte cultures, however, reveal only faint G/Q-banding (NY) and a characteristic DA-DAPI-like banding (NY-DA, NY-MG). Image analysis of NY stained human chromosomes, confirms that NY is suitable for studying polymorphisms affecting size in the pericentromeric heterochromatin of pairs 1, 9 and 16, and shows significant enhancement of NY fluorescence induced by DA in DA-DAPI heterochromatin. Our spectroscopic and cytological results show that NY, either alone or counterstained with DA or MG, can be used for DNA cytochemistry and chromosome banding. Possible mechanisms for the banding patterns induced by NY are discussed.

This protocol describes a versatile microfluidic method to generate tethered protein gradients of virtually any user-defined shape on biomimetic hydrogel substrates. It can be applied to test, in a microenvironment of physiologically relevant stiffness, how cells respond to graded biomolecular signals, for example to elucidate how morphogen proteins affect stem cell fate. The method is based on the use of microfluidic flow focusing to rapidly capture in a step-wise manner tagged biomolecules via affinity binding on the gel surface. The entire patterning process can be performed in

Synthesis of pyrrolo[2,1-c][1,4]benzodiazepines via azido reductive cyclization process employing FeCl3–NaI reagent system. This methodology has been extended for the preparation of new nicotinamido-pyrrolobenzodiazepine hybrids linked through piperazino-alkane-oxy spacers that exhibit good DNA binding affinity.

A number of pentamidine-like compounds are known to bind to DNA. DNA could therefore be the molecular target for the anti- P. carinii activity of these compounds. We provide the first evidence demonstrating a correlation between in vitro anti- P. carinii activity and in vitro DNA binding affinity of pentamidine related aromatic dicationic compounds.

Sialic acids are essential components of cell-surface receptors utilized by influenza viruses. To evaluate the recognition of asialic sugar parts of the receptor, three representative strains of human influenza A and B viruses were tested for their binding of a panel of sialyloligosaccharides. The highest affinity binding carbohydrate determinants recognized by the viruses in a context of different core structures were Neu5Ac alpha 2-3Gal for the type B virus, Neu5Ac alpha 2-6 Gal for the H3 subtype virus, and Neu5Ac alpha 2-6Gal beta 1-4GlcNAc for the H1 subtype virus. Penultimate to these determinants parts of the sialyloligosaccharides studied either contributed less significantly to the binding affinity, or interfered with the binding.

A new α-amylase from the extracellular culture of the yeast Lipomyces kononenkoae CBS 5608 has been purified to homogeneity by ammonium sulphate treatment, affinity binding on cross-linked starch, and DEAE–Biogel A chromatography. The enzyme was monomeric, with an apparent Mrof 76 kilodaltons, pI Mfor soluble starch was 0.80 g∙L−1and the kcatwas 622∙s−1. Keywords: α-amylase, glycosylation, intermediate thermal stability, Lipomyces kononenkoae.

The cardiac sarcolemmal Na(+)-Ca2+ exchanger transports Na+ and Ca2+ but is also regulated by Ca2+ at a high affinity binding site. A large intracellular, hydrophilic loop of the exchanger has been suggested to contain the Ca(2+)-binding regulatory domain (Matsuoka S., Nicoll, D. A., Reilly, R. F., Hilgemann, D. W., and Philipson, K. D. (1993) Proc. Natl. Acad. Sci. U. S. A. 90, 3870-3874). To localize the Ca(2+)-binding site(s), we expressed portions of the exchanger loop as fusion proteins and measured binding by 45Ca2+ overlay. The high affinity binding domain is located near the center of the loop and binds Ca2+ in a cooperative manner. K0.5 ranges from 0.3 to 3 microM in the presence of 0.2-5 mM Mg2+. The binding region (amino acids 371-508) has two highly acidic sequences, each characterized by 3 consecutive aspartic acid residues. Ca2+ affinity markedly decreases when these aspartates are mutated. The Ca(2+)-binding region does not contain an EF-hand motif. The mobilities during SDS-polyacrylamide gel electrophoresis of fusion proteins with high Ca2+ affinity differ depending on the presence or absence of Ca2+ in the gel loading buffer. The high affinity Ca(2+)-binding domain is probably responsible for the secondary Ca2+ regulation of the Na(+)-Ca2+ exchanger.

Bax1 has recently been identified as a novel binding partner for the archaeal helicase XPB. We previously characterized Bax1 from Thermoplasma acidophilum as a Mg 2+ -dependent structure-specific endonuclease. Here we directly compare the endonuclease activity of Bax1 alone or in combination with XPB. Using several biochemical and biophysical approaches, we demonstrate regulation of Bax1 endonuclease activity by XPB. Interestingly, incision assays with Bax1 and XPB/Bax1 clearly demonstrate that Bax1 produces different incision patterns depending on the presence or absence of XPB. Using atomic force microscopy (AFM), we directly visualize and compare binding of Bax1 and XPB/Bax1 to different DNA substrates. Our AFM data support enhanced DNA binding affinity of Bax1 in the presence of XPB. Taken together, the DNA incision and binding results suggest that XPB is able to load and position Bax1 on the scissile DNA substrate, thus increasing the DNA substrate range of Bax1.

Photo-controlled DNA-binding proteins promise to be useful tools for probing complex spatiotemporal patterns of gene expression in living organisms. Here we report a novel photoswitchable DNA-binding protein, GCN4(S)Δ25PYP, based on a truncated GCN4-photoactive yellow protein chimera. In contrast to previously reported designed photoswitchable proteins where DNA binding affinity is enhanced upon irradiation, GCN4(S)Δ25PYP dissociates from DNA when irradiated with blue light. In addition, the rate of thermal relaxation to the ground state, part of the PYP photocycle, is enhanced by DNA binding whereas in previous reported constructs it is slowed. The origins of this reversed photoactivity are analyzed in structural terms.

A series of acridin-3,6-diyl dithiourea hydrochloride derivatives (alkyl-AcrDTU) was prepared and tested against sensitive and drug resistant leukemia cell lines for their cytotoxic/cytostatic activity. The products (ethyl-, n-propyl-, n-butyl-, n-pentyl-AcrDTU) showed high DNA binding affinity via intercalation (K = 7.6 − 2.9 × 105 M−1). All derivatives inhibited proliferation of HL-60 cells and its resistant subline HL-60/ADR, unexpectedly the resistant subline was more sensitive than the parental one (IC50 = 3.5 μM, 48-treatment of HL-60/ADR with pentyl-AcrDTU). Cytotoxicity of tested compounds was associated with their DNA-binding properties and the level of intracellular thiols has been changed in the presence of AcrDTU.

Motivation: Discovering cis-regulatory elements in genome sequence remains a challenging issue. Several methods rely on the optimization of some target scoring function. The information content (IC) or relative entropy of the motif has proven to be a good estimator of transcription factor DNA binding affinity. However, these information-based metrics are usually used as a posteriori statistics rather than during the motif search process itself. Results: We introduce here info-gibbs, a Gibbs sampling algorithm that efficiently optimizes the IC or the log-likelihood ratio (LLR) of the motif while keeping computation time low. The method compares well with existing methods like MEME, BioProspector, Gibbs or GAME on both synthetic and biological datasets. Our study shows that motif discovery techniques can be enhanced by directly focusing the search on the motif IC or the motif LLR. Availability: http://rsat.ulb.ac.be/rsat/info-gibbs Contact: defrance@bigre.ulb.ac.be Supplementary information: Supplementary data are available at Bioinformatics online.

Glibenclamide is an antagonist of the ATP-modulated K+ channel in cardiac tissue. This study showed glibenclamide to bind to high (0.2 nM) and low (40 nM) affinity binding sites in canine ventricular membranes. Gpp [NH]p significantly altered the binding characteristics of the low affinity site, while those of the high affinity site were unchanged. This indicates independence of the two sites and suggests the low affinity site may be coupled to a G-binding protein. Although we have identified two [3H]glibenclamide binding sites, the importance of these sites to the cardiac effects of glibenclamide remains to be determined.

A series of saturated heterocyclic analogues of distamycin were prepared and examined. A fluorescent intercalator displacement (FID) assay conducted on p[dA]-p[dT] DNA to obtain C(50) values and a hairpin deoxyoligonucleotide containing an A/T-rich binding site was used to evaluate DNA binding affinity. It is observed that saturated heterocycles greatly reduce the DNA binding relative to distamycin.

Understanding molecular mechanisms that control cell fate in the shoot apical meristem is a fundamental question in plant development. Genetic and molecular studies demonstrate that maize KNOTTED1 (KN1) of the TALE (3-aa acid loop extension) class of homeodomain (HD) proteins is involved in shoot apical meristem function. We show that KN1 interacts with knotted interacting protein (KIP), a BEL1-like TALE HD protein. Interaction between KN1 and KIP is mediated by conserved domains in the N termini of both proteins. The KN1 DNA-binding sequence, TGACAG(G/C)T, was biochemically identified, and in vitro DNA-binding assays show that individually KN1 and the HD of KIP bind specifically to this motif with low affinity. The KN1–KIP complex, however, binds specifically to this DNA-binding motif with high affinity, indicating that the association of KN1 and KIP may function in transcriptional regulation.

Rhizobial Nod factors are lipochitooligosaccharides (LCOs) which are able, at subnanomolar concentrations, to elicit various physiological responses on the roots of host plants. The fact that the Nod factors are active at very low concentrations, and that the biological responses are very sensitive to the Nod factor structure, suggest that they are perceived by specific high affinity receptor(s) on the roots of the host-plant. Bono et al. (1995) have reported the characterisation of a binding site for NodRm factors using tritiated NodRm-IV(Ac, S, C16:2). This binding site was found in a high density fraction of Medicago truncatula root extracts (sedimenting at 3000 x g), and termed NFBS1 (for Nod Factor Binding Site 1). Although this site was specific for LCO structures, its low affinity (Kd = 86 nM), its non-selectivity for Nod factor decorations, and its presence in roots grown under high combined nitrogen conditions, suggest that this binding site is not involved in the early symbiotic events.

The dissociation constants (Kd) of tissue inhibitor of metalloproteinase (TIMP)-1 and TIMP-2 for the active and latent forms of matrix metalloproteinase (MMP)-2 and MMP-9 were evaluated using surface plasmon resonance (SPR) and enzyme inhibition studies. SPR analysis shows biphasic kinetics with high (nM) and low (microM) affinity binding sites of TIMP-2 and TIMP-1 for MMP-2 (72- and 62-kDa species) and MMP-9 (92- and 82-kDa species), respectively. In contrast, binding data of TIMP-2 to an MMP-2 45-kDa active form lacking the C-terminal domain and to an MMP-2 C-terminal domain (CTD) fragment displays monophasic kinetics with Kd values of 315 and 60 nM, respectively. This suggests that the CTD contains the high affinity binding site, whereas the catalytic domain contains the low affinity site. Also, binding of TIMP-2 to pro-MMP-2 is stronger at both the high and low affinity sites than the corresponding binding of TIMP-2 to the MMP-2 62-kDa form demonstrating the importance of the N-terminal prodomain. In addition, the Kd value of TIMP-1 for the MMP-2 62-kDa species is 28. 6 nM at the high affinity site, yet neither the MMP-2 45-kDa species nor the CTD interacts with TIMP-1. Enzyme inhibition studies demonstrate that TIMPs are slow binding inhibitors with monophasic inhibition kinetics. This suggests that a single binding event results in enzyme inhibition. The kinetic parameters for the onset of inhibition are fast (kon approximately 10(5) M-1 s-1) with slow off rates (koff approximately 10(-3) s-1). The inhibition constants (Ki) are in the 10(-7)-10(-9) M range and correlate with the values determined by SPR.

Dexamethasone exerted tissue-specific effects on rat vitamin D receptor levels: upregulation of receptors in intestine, downregulation in kidney, and no effect on receptors in testis, heart, and lung. Scatchard analysis showed selective downregulation of the low affinity receptor site (Kd=0.9 nM) in kidney, thus unmasking a high affinity binding site (Kd=0.05 nM). The single low affinity site in intestine (Kd=0.3-0.7 nM) was upregulated, while the single high affinity site in testis (Kd = 0.07-0.09 nM) was not changed. These results demonstrate the existence of two types of nuclear binding sites in rat kidney and establish that there are similarities between the high affinity binding site in the rat kidney and the single high affinity receptor site in the testis.

Using affinity binding of [125I]-IL-1 alpha and Scatchard analysis, we demonstrate here that exposure of cultured synovial cells (HRSC) to NPX (10(-4) M) for 96 h decreased the binding of IL-1 by 20 to 35%. This effect results from a down-regulation of the IL-1 receptors without change in the apparent binding affinity (kD: 770 pM). Pretreatment of cultures with IL-1 alpha (500 pg/ml) reduced the total binding of [125I]-IL-1 alpha on HRSC by 65%, indicating that IL-1 decreases the expression of its own receptors.

Prostaglandin E 1 has been shown to interact with serum high density lipoproteins (HDL) in a manner resembling the interaction of a ligand with a high affinity binding site. The presence of 10 −12 –10 −10 M prostaglandin E 1 induces a rearrangement of the HDL surface lipids and probably influences the biological functions of the lipoproteins. Fluorescent phospholipid probe High density lipoprotein Prostaglandin E 1

A membrane preparation from Avena sativa root has been found to contain only one low-affinity IAA-binding site having a K d value of 8.4 ×

We have characterized picomolar affinity binding sites for human calcitonin gene-related peptide (CGRP) in rat brain and heart (atria and ventricle) membranes. By saturation analysis, apparent dissociation constant (K D ) values of high affinity sites for [ 125 I]-human CGRP are 9 ∼ 15 pM (brain), 34 pM (ventricle) and 85 pM (atria). Low affinity sites with K D values of about 50 nM are found in rat brain and ventricle, but not in atria. Human and rat CGRP potently inhibited [ 125 I]-human CGRP binding to these high affinity sites with apparent inhibition constant (Ki) values comparable to their K D values. Salmon calcitonin marginally inhibited these binding with Ki values between 0.1 μM and 1 μM. Extremely potent cardiovascular and gastrointestinal actions of CGRP might be mediated through CGRP binding sites with picomolar affinity which are similar to those we characterized in this study.

Steroid radioimmunoassays (RIA) employ antibodies raised against a carrier protein-steroid conjugate. Individual antibodies may recognize the steroid, the protein or the chemical bridge used to Join them together. Use of the same bridge In the tracer results in higher affinity binding of the tracer than the native ligand which in turn results in a loss of sensitivity and precision. We have greatly reduced bridge-binding In a RIA for androstenedione. Conjugates and radioiodinated labels were prepared with either an ester op ether chemical bridge. By using an antibody and the corresponding label with the heterologous bridge very sensitive assays were obtained.

Specific insulin receptors were measured in isolated mouse pancreatic acini. Scatchard analyses revealed a high affinity binding site with a K d of 1.67 nM and a lower affinity site with a K d of 83 nM. Binding of insulin to these receptors was rapid, one-half maximal binding occurring at 2 min and maximal binding at 30 min. Insulin stimulated the uptake of the glucose analogue 2-deoxy-D-glucose; maximum effects were detected at 1.67 μM. Insulin, in contrast, had no direct effects on alpha-aminoisobutyric acid uptake. The finding of high affinity insulin receptors in pancreatic acinar cells supports the hypothesis that insulin may directly regulate specific functions in the exocrine pancreas.