Search results for "Binding selectivity"

2019

The DNA-binding of the natural benzophenanthridine alkaloid chelerythrine (CHE) has been assessed by combining molecular modeling and optical absorption spectroscopy. Specifically, both double-helical (B-DNA) and G-quadruplex sequences—representative of different topologies and possessing biological relevance, such as telomeric or regulatory sequences—have been considered. An original multiscale protocol, making use of molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations, allowed us to compare the theoretical and experimental circular dichroism spectra of the different DNA topologies, readily providing atomic-level details of the CHE–DNA binding…

The size of aryl linker between two polyaza-cyclophane moieties controls the binding selectivity to ds-RNA vs ds-DNA

2013

Aryl-linked (pyridine- vs. phenanthroline-) bis-polyaza pyridinophane scorpiands PYPOD and PHENPOD strongly bind to the double stranded DNA and RNA, whereby very intriguing RNA over DNA selectivity is finely tuned by aryl-linker length and aromatic surface. Moreover, PYPOD and PHENPOD dimer formation at high compound/polynucleotide ratios is highly sensitive to the fine interplay between the steric and binding properties of compound-dimers and the DNA minor groove/RNA major groove. That is demonstrated by significantly different induced CD spectra, which allow spectroscopic differentiation between various DNA/RNA secondary structures. A significantly higher (micromolar) antiproliferative ef…

Comparison of quantum dot-binding protein tags: Affinity determination by ultracentrifugation and FRET

2013

Abstract Background Hybrid complexes of proteins and colloidal semiconductor nanocrystals (quantum dots, QDs) are of increasing interest in various fields of biochemistry and biomedicine, for instance for biolabeling or drug transport. The usefulness of protein–QD complexes for such applications is dependent on the binding specificity and strength of the components. Often the binding properties of these components are difficult and time consuming to assess. Methods In this work we characterized the interaction between recombinant light harvesting chlorophyll a / b complex (LHCII) and CdTe/CdSe/ZnS QDs by using ultracentrifugation and fluorescence resonance energy transfer (FRET) assay exper…

Identification of a positively evolving putative binding region with increased variability in posttranslational motifs in zonadhesin MAM domain 2.

2005

Positive selection has been shown to be pervasive in sex-related proteins of many metazoan taxa. However, we are only beginning to understand molecular evolutionary processes on the lineage to humans. To elucidate the evolution of proteins involved in human reproduction, we studied the sequence evolution of MAM domains of the sperm-ligand zonadhesin in respect to single amino acid sites, solvent accessibility, and posttranslational modification. GenBank-data were supplemented by new cDNA-sequences of a representative non-human primate panel. Solvent accessibility predictions identified a probably exposed fragment of 30 amino acids belonging to MAM domain 2 (i.e., MAM domain 3 in mouse). The…

Carbohydrate binding specificity and purification by biospecific affinity chromatography of Ascidiamalaca traust. Hemagglutinins

1982

The carbohydrate specificities of Ascidia malaca serum hemagglutinins were determined by hemagglutination inhibition tests. Analysis of agglutinins against rabbit and human A, B, O erythrocytes suggests that the size of the combining site corresponds to a disaccharide with a specificity for saccharides containing a D-galacto configuration (D-melibiose, D-raffinose, D-galactose, alpha-lactose, lactulose, L-arabinose). No anomeric specificity was observed with oligosaccharides. Hydroxyl groups probably involved in hydrogen-bond formation with agglutinin binding site, were identified as carbons C2, C4, C5 and C6 of D-galactose. Absorption experiments showed that two distinct agglutinins with s…

Addressing selectivity criteria in binding equilibria

2012

Abstract Chemical systems, in particular those involving biological and environmental backgrounds, develop through selective processes which are determined by multiple equilibria. Several methods that have been developed to assess thermodynamic selectivity in binding equilibria, including the analysis of selectivity coefficients, the use of calculated species distribution diagrams, selectivity diagrams, and conditional stability constants, are reviewed in this paper with reference to examples mainly related to chemical systems of biological and/or environmental concern. Also the concept of binding affinity has been dealt with, since binding selectivity in equilibrium systems relates to the …

Reaction of dirhodium and diruthenium paddlewheel tetraacetate complexes with nucleophilic protein sites: A computational study

2022

Abstract The biomolecular affinity of three paddlewheel dinuclear complexes Rh2(µ-O2CCH3)4(H2O)2, Ru2(µ-O2CCH3)4(H2O)Cl, [Ru2(µ-O2CCH3)4(H2O)2]+ for the binding at cancer-specific protein targets was determined by means of DFT approaches. Thermodynamics of axial ligand substitution reaction by models of suitable protein sites was investigated in order to assess the binding selectivity displayed by the paddlewheel complexes. Both Rh2(µ-O2CCH3)4(H2O)2 and Ru2(µ-O2CCH3)4(H2O)Cl resulted to react favorably with most of the examined models of the protein side chains, with higher exergodicity demonstrated in the reaction of Arg, Cys, His, Lys, Sec, thus showing a limited selectivity. On the other…

alpha 11beta 1 integrin recognizes the GFOGER sequence in interstitial collagens.

2002

The integrins alpha(1)beta(1), alpha(2)beta(1), alpha(10)beta(1), and alpha(11)beta(1) are referred to as a collagen receptor subgroup of the integrin family. Recently, both alpha(1)beta(1) and alpha(2)beta(1) integrins have been shown to recognize triple-helical GFOGER (where single letter amino acid nomenclature is used, O = hydroxyproline) or GFOGER-like motifs found in collagens, despite their distinct binding specificity for various collagen subtypes. In the present study we have investigated the mechanism whereby the latest member in the integrin family, alpha(11)beta(1), recognizes collagens using C2C12 cells transfected with alpha(11) cDNA and the bacterially expressed recombinant a…

2NH and 3OH are crucial structural requirements in sphingomyelin for sticholysin II binding and pore formation in bilayer membranes.

2013

AbstractSticholysin II (StnII) is a pore-forming toxin from the sea anemone Stichodactyla heliantus which belongs to the large actinoporin family. The toxin binds to sphingomyelin (SM) containing membranes, and shows high binding specificity for this lipid. In this study, we have examined the role of the hydrogen bonding groups of the SM long-chain base (i.e., the 2NH and the 3OH) for StnII recognition. We prepared methylated SM-analogs which had reduced hydrogen bonding capability from 2NH and 3OH. Both surface plasmon resonance experiments, and isothermal titration calorimetry measurements indicated that StnII failed to bind to bilayers containing methylated SM-analogs, whereas clear bind…

Selective recognition of aromatic hydrocarbons by endo-functionalized molecular tubes via C/N-H⋅⋅⋅π interactions

2018

Abstract Molecular recognition of aromatic hydrocarbons by four endo -functionalized molecular tubes has been studied by 1 H NMR spectroscopy, computational methods, and single crystal X-ray crystallography. The binding selectivity is rationalized by invoking shape complementarity and dipole alignment. The non-covalent interactions are proved to predominantly be C/N-H⋅⋅⋅ π interactions.