Contribution of individual histidines to prion protein copper binding

The prion protein is well-established as a copper binding protein. The N-terminus of the protein contains an octameric repeat region with each of the four repeats containing a histidine. The N-terminus has two additional histidines distal to the repeat region that has been commonly known as the fifth site. While binding of copper by the protein has been extensively studied, the contribution of each histidine to copper binding in the full-length protein has not. Here we used a battery of mutants of the recombinant mouse prion protein to assess copper binding with both isothermal titration calorimetry and cyclic voltammetry. The findings indicate that there is extensive cooperativity between different binding sites in the protein. The two highest-affinity binding events occur at the fifth site and at the octameric repeat region. However, the first binding is that to the octameric repeat region. Subsequent binding events after the two initial binding events have lower affinities within the octameric repeat region.     

铝与钙调蛋白相互作用的荧光光谱研究

本文研究了铝与钙调蛋白相互作用的荧光光谱。实验证明,Al~3与CaM的结合所引起的构象变化与Ca~(2+)与CaM结合所引起的构象变化既有相同之处,也有不同之处。Al~(3+)在CaM分子上的结合有特异性结合与非特异性结合两种情况。其特异性结合位点可能为2—3个。钙调蛋白的非竞争性拮抗剂酸枣仁皂甙A(JuA)可以继续抑制已被Al~(3+)部分抑制的PDE-CaM的活力。     

Analysis of ligand-receptor binding by the difference method

A new method has been proposed for analysis of experimental data on ligand-receptor binding at equilibrium. This method makes it possible to detect heterogeneity of a receptor system in cases where the contribution of the high-affinity site to total binding is rather small and the problem of graphic discrimination of a model cannot be solved unambiguously by other methods. The difference method permits us to exclude experiments on measuring nonspecific binding. A computer program for analysis of ligand-receptor binding has been worked out in which the difference method and traditional methods of binding isotherm analysis are realized. Numerical modeling has shown that the best strategy in experimental data processing is the treatment of total binding isotherms by both the difference method and regression analysis, including the nonspecific binding constant as one of the regression parameters.     

Molecular Forces for the Binding and Condensation of DNA Molecules

Atomic force microscopy has been used to investigate the binding between a double-stranded DNA and bilayers of cationic lipids and zwitterionic lipids in low ionic-strength solutions. The binding of a DNA molecule to freshly cleaved mica surface in solution has also been measured. The binding of DNA molecules to cationic lipid bilayers has a minimal strength of ∼45 pN. On zwitterionic lipid bilayers and mica surface, the minimal binding strength is approximately twice that value. The binding also has a dynamic nature, with only a certain percentage of recorded force curves containing the binding characteristics. Divalent Mg²⁺ ions enhance the binding by increasing that percentage without any effect on the binding strength. We have also observed a long-range attraction between DNA molecules and cationic lipid bilayers with a strength much larger than the minimum force and a range well over 50 nm, possibly related to the driving force responsible for the two-dimensional condensation of DNA.     

Epidermal growth factor and transforming growth factor alpha bind differently to the epidermal growth factor receptor

Epidermal growth factor (EGF) and transforming growth factor alpha (TGF alpha) compete with each other for binding to the EGF receptor. These two growth factors have similar actions, but there are distinguishable differences in their biological activities. It has never been clear how this one receptor can mediate different responses. A monoclonal antibody to the EGF receptor (13A9) has been identified which has only small effects on the binding of EGF to the EGF receptor, but which has very large effects on the binding of TGF alpha to the EGF receptor; 5 micrograms/mL antibody has been shown to totally block 0.87 microM TGF alpha from binding to purified EGF receptor and to lower both the high- and low-affinity binding constants of TGF alpha binding to EGF receptor on A431 cells by about 10-fold. The 13A9 antibody causes a 2.5-fold stimulation of the tyrosine kinase activity of partially purified EGF receptor, compared to a 4.0-fold stimulation of the tyrosine kinase activity by EGF under the same conditions. The data suggest either that the antibody stabilizes a conformation of the EGF receptor which is not favorable for TGF alpha binding or that it blocks a part of the surface of the receptor which is necessary for TGF alpha binding but not EGF binding.     

Optimization of Cross-Linked Lexitropsins

Abstract

In attempts to optimize the cross-linked lexitropsin design, a number of cross-linked dimers composed of two tris(N-methylpyrrolecarboxamide) strands were synthesized and their binding interactions with poly d(A)? poly d(T) and poly d(A-T)?poly d(A-T) were characterized by circular dichroism and ethidium fluorometry. While all alkanediyl-linked dimers showed a similar binding behavior to the homo AT polymer, particularly at low ligand concentrations, the decanediyl linker was found to be the optimal linker permitting the bidentate anti parallel side-by-side binding of the corresponding dimer to the alternating AT polymer. Thus, in comparison with the monomer, the decanediyl-linked dimer has a binding strength enhancement of about 1400 times in the I: I binding mode. Moreover, the hydrophilicity of the linker has a significant effect on the bidentate binding strength. The (3,6)-dioxaoctanediyl-linked dimer has a further binding strength enhancement of 10 times over the decanediyl-linked dimer. Overall, the best optimized dimer has a binding strength enhancement of over 14,000 times in comparison with the monomer in the I: I binding mode. This binding enhancement parallels that observed in the best optimized bisintercalators. Distance-restrained molecular modeling provides support for the experimental results. Dimers of longer linkers can readily accommodate a bidentate anti parallel side-by-side binding mode but those of shorter linkers necessitate marked structural distortions in the bound ligand molecules. It is further observed that the binding strength enhancement to the alternating AT polymer is not always accompanied by the binding specificity improvement. Our analysis suggests that the non-specific appendage-DNA backbone interaction is a key factor that controls the specificity improvement.     

Unusual shapes of absorption isotherms in three-component systems

It has been shown that the shape of Scatchard isotherms upon competitive binding of two ligands to the same binding site in the three-component ligand 1-ligand 2-DNA system depends crucially on the binding constant values. The binding isotherm of ligand 2 in the presence of the competitive ligand 1 turns back (has a bow-like form) when the binding constant of the first ligand is larger than the binding constant of the second one.     

Titanocene anticancer complexes and their binding mode of action to human serum albumin: a computational study

Due to the pivotal role played by human serum albumin (HSA) in the transport and cytotoxicity of titanocene complexes, a docking study has been performed on a selected set of titanocene complexes to aid in the current understanding of the potential mode of action of these titanocenes upon binding HSA. Analysis of the docking results has revealed potential binding at the known drug binding sites in HSA and has provided some explanation for the specificity and subsequent cytotoxicity of these titanocenes. Additionally, a new alternative binding site for these titanocenes has been postulated.     

Binding of spermidine to transfer ribonucleic acid

The binding of spermidine to yeast tRNAPhe and Escherichia coli tRNAGlu2 at low and high ionic strength was studied by equilibrium dialysis. Once corrected for the expected Donnan effect, the binding at low ionic strength obeys the simple relationship of equivalent binding sites, and cooperative binding of spermidine to tRNA could not be detected. At low ionic strength (0.013 M Na+ ion), tRNAPhe (yeast) has 13.9 +/- 2.3 strong spermidine binding sites per molecule with Kd = 1.39 X 10(-6) M and a few weak spermidine binding sites which were inaccessible to experimentation; tRNAGlu2 (E. coli) has 14.8 +/- 1.6 strong spermidine binding sites and 4.0 +/- 0.1 weak spermidine binding sites with Kd = 1.4 X 10(-6) M and Kd = 1.23 X 10(-4) M, respectively. At high ionic strength (0.12 M monovalent cation) and 0.01 M Mg2+, tRNAPhe (yeast) has approximately 13 strong spermidine binding sites with an apparent Kd = 3.4 X 10(-3) M while the dimeric complex tRNAPhe X tRNAGlu2 has 10.4 +/- 1.2 strong spermidine binding sites per monomer with an apparent Kd = 2.0 X 10(-3) M. In the presence of increasing Na+ ion or K+ ion concentration, spermidine binding data do not fit a model for competitive binding to tRNA by monovalent cations. Rather, analysis of binding data by the Debye-Hückel approximation results in a good fit of experimental data, indicating that monovalent cations form a counterion atmosphere about tRNA, thus decreasing electrostatic interactions. On the basis of equilibrium binding analyses, it is proposed that the binding of spermidine to tRNA occurs predominantly by electrostatic forces.     

Influence of Cr(III) and Cr(VI) on the interaction between sparfloxacin and calf thymus DNA

Cr(III) and Cr(VI) have different binding capacity with sparfloxacin, and have different combination modes with calf thymus DNA. Selecting these two different metal ions, the influence of them on the binding constants between sparfloxacin (SPFX) and calf thymus DNA, as well as the related mechanism has been studied by using absorption and fluorescence spectroscopy. The result shows that Cr(III) has weaker binding capacity to SPFX in the SPFX-Cr(III) binary system, but influences the binding between SPFX and DNA obviously in SPFX-DNA-Cr(III) ternary system. However, although Cr(VI) has a stronger binding capacity to SPFX, it has no effect on the binding between SPFX and DNA. Referring to the different modes of Cr(III) and Cr(VI) binding to DNA, the mechanism of the influence of metal ions on the binding between SPFX and DNA has been proposed. SPFX can directly bind to DNA by chelating DNA base sites. If a metal ion at certain concentration binds mainly to DNA bases, it can decrease the binding constants between SPFX and DNA through competing with SPFX. While if a metal ion at certain concentration mainly binds to phosphate groups of DNA, it can increase the binding constants by building a bridge between SPFX and DNA. If a metal ion at certain concentrations binds neither to bases nor phosphate groups in DNA, it will have no effect on the binding constant between SPFX and DNA. Our result supports Palumbo's conclusion that the binding between SPFX and the phosphata groups is the precondition for the combination between SPFX and DNA, which is stabilized through stacking interactions between the condensed rings of SPFX and DNA bases.     

Synthesis and DNA binding studies of a new asymmetric cyanine dye binding in the minor groove of [poly(dA-dT)]2

A new asymmetric cyanine dye has been synthesised and its interaction with different DNA has been investigated. In this dye, BEBO, the structure of the known intercalating cyanine dye BO has been extended with a benzothiazole substituent. The resulting crescent-shape of the molecule is similar to that of the well-known minor groove binder Hoechst 33258. Indeed, comparative studies of BO illustrate a considerable change in binding mode induced by this structural modification. Linear and circular dichroism studies indicate that BEBO binds in the minor groove to [poly (dA-dT)](2), but that the binding to calf thymus DNA is heterogeneous, although still with a significant contribution of minor groove binding. Similar to other DNA binding asymmetric cyanine dyes, BEBO has a large increase in fluorescence intensity upon binding and a relatively large quantum yield when bound. The minor groove binding of BEBO to [poly (dA-dT)](2) affords roughly a 180-fold increase in intensity, which is larger than to that of the commonly used minor groove binding probes DAPI and Hoechst 33258.     

The binding of tyrosinyl-5''-AMP to tyrosyl-tRNA synthetase (E.coli).

The binding between tyrosyl-tRNA synthetase (E.coli) and the alkylanalogue of the aminoacyladenylate, tyrosinyl-5'-AMP, has been investigated by fluorescence titrations and rapid mixing experiments. Tyrosyl-tRNA synthetase has two equivalent and independent binding sites for tyrosinyl-5'-AMP. The intrinsic binding constant is 4 x 10(7)M-1. The binding sites for tRNATyr and tyrosinyl-5'-AMP are independent of each other, the anticooperative mode of tRNA binding being preserved in the presence of tyrosinyl-5-AMP.     

Characterization of the α-cyanocinnamate binding site in rat heart mitochondria and in submitochondrial particles

The effect of pH and substrates on the binding of radiolabelled α-cyanocinnamate to mitochondria and submitochondrial particles has been investigated. It has been found that the binding is strongly influenced by the pH of the medium (it decreases on increasing the pH of the medium). The inhibition of pyruvate oxidation by this inhibitor follows the same pH dependence. The pH affects only the affinity of the α-cyanocinnamate binding site without changing their total number. A similar pH dependence has been found in inside-out submitochondrial particles where the binding sites are directly accessible. The quantitative parameters of the binding of α-cyanocinnamate in submitochondrial particles have been determined. The binding can be prevented or displaced by pyruvate and other substrates of the carrier. The turnover number for pyruvate transport in rat-heart mitochondria has been determined.     

Further studies on the temperature dependence of the binding of testosterone to human pregnancy plasma proteins

The binding of testosterone by pregnancy plasma proteins has been studied by a new equilibrium dialysis system. The temperature dependence on the association constant has been investigated and the enthalpy change ΔH and entropy change ΔS have been calculated.By a computer optimization program, the binding constant of the high affinity testosterone binding protein has been estimated from Scatchard plots. The binding reactions were carried out at 5°, 25° and 37° C. The corresponding values were 3.1.10 1.2.10⁹ and 7.2.10⁸ liter/mole. The resulting enthalpy and entropy changes were ?2.0 kcal/mole and 35.0 cal/(mole.degree) respectively.It can be concluded that the binding of testosterone to the specific binding protein is an exothermic reaction and is stabilized by hydrophobic binding forces.     

The effect of heparin on structural and functional properties of low density lipoproteins

Heparin binding to human low density lipoproteins (LDL) and the effect of heparin on the ability of LDL to bind to the LDL receptor has been investigated. Emphasis has been made on the physiological conditions of temperature, pH and the ionic strength. Intrinsic fluorescence spectroscopy of LDL has been applied to follow heparin binding. Fluorescence anisotropy has been measured to describe the changes in apoB and dansyl-heparin dynamics upon binding. Eu3+-labeled LDL binding to the intact LDL receptor has been monitored by time-resolved fluorescence spectroscopy technique. We have found that heparin binds to LDL under the physiological conditions, probably by Van der Waals interactions and hydrogen bonding. Temperature seems to be the most important factor influencing the interaction. Furthermore, the presence of heparin inhibits LDL binding to the intact LDL receptor that might have consequences on the cholesterol metabolism in vivo.     

Calmodulin binding proteins in rat liver mitochondria

Calmodulin binding proteins have been found in submitochondrial fractions obtained from highly purified rat liver mitochondria. The matrix fraction contains two major calmodulin binding proteins: one, having Mr of 145,000, apparently is carbamoyl-phosphate synthetase. Another has a Mr of 58,000 and has not been associated with enzyme activities. A major calmodulin binding protein of unknown function and having Mr of 32,000 has been found in the Triton X-100 solubilizate of the inner membrane. Minor amounts of two calmodulin binding proteins having Mr of about 37,000 and 56,000 have been found in the outer membrane.     

Kringle-kringle interactions in multimer kringle structures.

The crystal structure of a monoclinic form of human plasminogen kringle 4 (PGK4) has been solved by molecular replacement using the orthorthombic structure as a model and it has been refined by restrained least-squares methods to an R factor of 16.4% at 2.25 A resolution. The X-PLOR structure of kringle 2 of tissue plasminogen activator (t-PAK2) has been refined further using PROFFT (R = 14.5% at 2.38 A resolution). The PGK4 structure has 2 and t-PAK2 has 3 independent molecules in the asymmetric unit. There are 5 different noncrystallographic symmetry "dimers" in PGK4. Three make extensive kringle-kringle interactions related by noncrystallographic 2(1) screw axes without blocking the lysine binding site. Such associations may occur in multikringle structures such as prothrombin, hepatocyte growth factor, plasminogen (PG), and apolipoprotein [a]. The t-PAK2 structure also has noncrystallographic screw symmetry (3(1)) and mimics fibrin binding mode by having lysine of one molecule interacting electrostatically with the lysine binding site of another kringle. This ligand-like binding interaction may be important in kringle-kringle interactions involving non-lysine binding kringles with lysine or pseudo-lysine binding sites. Electrostatic intermolecular interactions involving the lysine binding site are also found in the crystal structures of PGK1 and orthorhombic PGK4. Anions associate with the cationic centers of these and t-PAK2 that appear to be more than occasional components of lysine binding site regions.     

Soluble and membrane-associated human low-affinity adenosine binding protein (adenotin): properties and homology with mammalian and avian stress proteins

A low-affinity adenosine binding protein has recently been distinguished from the adenosine A2 receptor and purified from human placental membranes. Soluble human placental extracts contain an adenosine binding activity that has properties similar to those of the membrane low-affinity adenosine binding protein. The binding protein was purified from soluble human placental extracts 134-fold to 89% purity with a Bmax of 2.5 nmol/mg. It comprises 0.7-0.9% of the soluble protein. The major purified soluble protein has a subunit molecular mass of 98 kDa and a Stokes radius identical with that of the membrane-bound adenosine binding protein. Competition analysis of the soluble protein revealed similar affinities and an identical potency order for displacement of 5'-(N-ethylcarbamoyl)[2,8-3H]adenosine ([3H]NECA) as follows: NECA greater than 2-chloroadenosine greater than adenosine greater than (R)-N6-(2-phenylisopropyl)adenosine. The soluble binding protein was more acidic than the membrane binding protein as revealed by a comparison of the elution properties during ion exchange chromatography. A second form of soluble adenosine binding activity comprised 17% of the major form and had a charge similar to that of the membrane binding protein, a smaller Stokes radius, and a subunit molecular mass of 74 kDa. Carbohydrate composition analysis revealed that the major soluble form has 4.3% carbohydrate by weight as compared to the membrane-associated form, which has 5.5% carbohydrate by weight.(ABSTRACT TRUNCATED AT 250 WORDS)     

Characterization and identification of the hyaluronate binding site from membranes of SV-3T3 cells

Previous research has shown that binding sites for hyaluronate are present on the surfaces of a number of different cell types. To further characterize these binding sites, membranes were prepared from SV-3T3 cells and dissolved in a solution of sodium deoxycholate. Hyaluronate binding activity was detected by mixing the sodium deoxycholate extract with [3H]hyaluronate and then adding an equal volume of saturated (NH4)2SO4, which precipitated the binding protein and any [3H]hyaluronate associated with it, but left free [3H]hyaluronate in solution. Following partial purification by hydroxylapatite chromatography, the binding site was examined by molecular sieve chromatography and by rate-zonal centrifugation, which revealed that it has a Stokes radius of 6.5 nm and a sedimentation coefficient of 4.8 S. From these values, it was possible to calculate that the sodium deoxycholate-solubilized binding site has a frictional coefficient of 1.87 and a molecular weight of 132,000. Since this latter value applies to the complex of both detergent and protein, the binding protein by itself must have a molecular weight lower than 132,000. To determine the molecular weight of the hyaluronate binding site itself, the protein was purified by the sequential application of hydroxylapatite chromatography, molecular sieve chromatography, rate-zonal centrifugation, and finally lectin-affinity chromatography on concanavalin A-agarose. Analysis of the purified material by sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed an 85,000 Mr protein which has been identified as the binding site. This protein was also detected on nitrocellulose blots which had been specifically stained for concanavalin A binding material, suggesting that the binding site is a glycoprotein.     

The binding of calcium to human fibronectin

The binding of calcium to human plasma fibronectin has been measured by equilibrium dialysis at 25° in 0.1 M NaCl 50mM Tris HCL, pH 7.4. Curve fitting of the binding data indicates that fibronectin has two strong calcium binding sites per chain (Mr 220,000), KD = 1.3 mM and approximately 12 weak sites, KD = 2.3 mM. No significant displacement of bound calcium by magnesium was observed at magnesium concentrations up to 1 mM. Calcium binding to a pair of tryptic fragments of fibronectin (Mr ? 160,000 and 180,000) that bind to gelatin has also been investigated. These fragments have a single class of calcium binding sites, with 2.2 sites per chain, KD = 1.1 mM. Negligible calcium binding to tryptic fragments derived from other regions of the fibronectin molecule was observed.