Anomalous binding of MgADP to myosin of skeletal muscle

Binding of adenosine diphosphate to skeletal muscle myosin was studied using a range of concentrations from 0 to 2 mM. Up to 0.2 mM adenosine diphosphate two equivalent and independent nucleotide binding sites were detected, characterized by the single association constant of 5 x 10(4)M(-1). At greater adenosine diphosphate concentrations a decreasing binding capacity was noticed, bound nucleotide being essentially approximately 0.1 mol/mol at a 1-2mM adenosine diphosphate concentration. We tentatively propose that nucleotides act indirectly on myosin by promoting the perturbation of the solvent, which is supported by the fact that polyphosphates are known powerful kosmotropes.     

Structural energetics of MgADP binding to the isolated beta subunit of F1-ATPase from thermophilic Bacillus PS3

The energetics of binding of MgADP to the isolated beta subunit of F(1)-ATPase from thermophilic Bacillus (Tbeta) was characterized by high-precision isothermal titration calorimetry. The reaction was enthalpically driven, with a DeltaCp of -36cal(molK)(-1). To gain insight into the molecular basis of this small DeltaCp, we analyzed the changes in accessible surface areas (DeltaASA) between the structures of empty and MgADP-filled beta subunits, extracted from the crystal structure of bovine heart F(1). Consistent with the experimental DeltaCp, the DeltaASA was small (-775A(2)). We used a reported surface area model developed for protein reactions to calculate DeltaCp and DeltaH from DeltaASA, obtaining good agreement with the experimental values. Conversely, using the same model, a DeltaASA of -770A(2) was estimated from experimental DeltaCp and DeltaH for the Tbeta-MgADP complex. Our structural-energetic study indicates that on MgADP binding the isolated Tbeta subunit exhibits intrinsic structural changes similar to those observed in F(1).     

ATP-induced dissociation of rabbit skeletal actomyosin subfragment 1. Characterization of an isomerization of the ternary acto-S1-ATP complex

The adenosine 5'-O-(3-thiotriphosphate) (ATP gamma S) induced dissociation of actomyosin subfragment 1 (S1) has been investigated by monitoring the light scattering changes that occur on dissociation. We have shown that ATP gamma S dissociates acto-S1 by a mechanism similar to that of ATP but at a rate 10 times slower. The maximum rate of dissociation is limited by an isomerization of the ternary actin-S1-nucleotide complex, which has a rate of 500 s-1 for ATP gamma S and an estimated rate of 5000 s-1 for ATP (20 degrees C, 0.1 M KCl, pH 7.0). The activation energy for the isomerization is the same for ATP and ATP gamma S, and both show a break in the Arrhenius plot at 5 degrees C. The reaction between acto-S1 and ATP was also followed by the fluorescence of a pyrene group covalently attached to Cys-374. We show that the fluorescence of the pyrene group reports the isomerization step and not actin dissociation. The characterization of this isomerization is discussed in relation to force-generating models of the actomyosin cross-bridge cycle.     

Calcium regulation of calmodulin binding to and dissociation from the myo1c regulatory domain

Myo1c is an unconventional myosin involved in cell signaling and membrane dynamics. Calcium binding to the regulatory-domain-associated calmodulin affects myo1c motor properties, but the kinetic details of this regulation are not fully understood. We performed actin gliding assays, ATPase measurements, fluorescence spectroscopy, and stopped-flow kinetics to determine the biochemical parameters that define the calmodulin-regulatory-domain interaction. We found calcium moderately increases the actin-activated ATPase activity and completely inhibits actin gliding. Addition of exogenous calmodulin in the presence of calcium fully restores the actin gliding rate. A fluorescently labeled calmodulin mutant (N111C) binds to recombinant peptides containing the myo1c IQ motifs at a diffusion-limited rate in the presence and absence of calcium. Measurements of calmodulin dissociation from the IQ motifs in the absence of calcium show that the calmodulin bound to the IQ motif adjacent to the motor domain (IQ1) has the slowest dissociation rate (0.0007 s-1), and the IQ motif adjacent to the tail domain (IQ3) has the fastest dissociation rate (0.5 s-1). When the complex is equilibrated with calcium, calmodulin dissociates most rapidly from IQ1 (60 s-1). However, this increased rate of dissociation is limited by a slow calcium-induced conformational change (3 s-1). Fluorescence anisotropy decay of fluorescently labeled N111C bound to myo1c did not depend appreciably on Ca2+. Our data suggest that the calmodulin bound to the IQ motif adjacent to the motor domain is rapidly exchangeable in the presence of calcium and is responsible for regulation of myo1c ATPase and motile activity.     

The limiting rate of the ATP-mediated dissociation of actin from rabbit skeletal muscle myosin subfragment 1

The ATP-induced dissociation of actoS1 has been studied at temperatures between −10°C and +30°C in a stopped-flow apparatus using ethylene glycol as antifreeze. At temperatures at and below 0°C the observed rate of the dissociation of actin shows a hyperbolic dependence on ATP concentration. This is interpreted in terms of a rapid binding of ATP followed by an isomerisation of the ternary complex which results in actin dissociation. Ethylene glycol weakens ATP binding but the rate of the isomerisation is unaffected. The second order rate constant for the dissociation shows a break in the Arrhenius plot.     

Ribosome binding to and dissociation from translocation sites of the endoplasmic reticulum membrane

We have addressed how ribosome-nascent chain complexes (RNCs), associated with the signal recognition particle (SRP), can be targeted to Sec61 translocation channels of the endoplasmic reticulum (ER) membrane when all binding sites are occupied by nontranslating ribosomes. These competing ribosomes are known to be bound with high affinity to tetramers of the Sec61 complex. We found that the membrane binding of RNC-SRP complexes does not require or cause the dissociation of prebound nontranslating ribosomes, a process that is extremely slow. SRP and its receptor target RNCs to a free population of Sec61 complex, which associates with nontranslating ribosomes only weakly and is conformationally different from the population of ribosome-bound Sec61 complex. Taking into account recent structural data, we propose a model in which SRP and its receptor target RNCs to a Sec61 subpopulation of monomeric or dimeric state. This could explain how RNC-SRP complexes can overcome the competition by nontranslating ribosomes.     

Stability constants of Mg2+ and Cd2+ complexes of adenine nucleotides and thionucleotides and rate constants for formation and dissociation of MgATP and MgADP

Stability constants for the Mg2+ and Cd2+ complexes of ATP, ADP, ATP alpha S, ATP beta S, and ADP alpha S have been determined at 30 degrees C and mu = 0.1 M by 31P NMR. Besides being of the utmost importance for determining species distributions for enzymatic studies, these constants allow an estimation of the preference of Cd2+ for sulfur vs. oxygen coordination in phosphorothioate complexes. Stability constants for Mg2+ complexes decreases when sulfur replaces oxygen (log K: ADP, 4.11; ADP alpha S, 3.66; ATP, 4.70; ATP alpha S, 4.47; ATP beta S, 4.04) because of (a) a statistical factor resulting from the loss of one potential phosphate oxygen ligand and (b) either an alteration in the charge distribution between oxygen and sulfur or destabilization of the chelate ring structure by loss of an internal hydrogen bond between an oxygen of coordinated phosphate and metal-bound water. Cd2+ complexes with sulfur-substituted nucleotides are more stable than those without sulfur (log K: ADP, 3.58; ADP alpha S, 4.95; ATP, 4.36; ATP alpha S, 4.42; ATP beta S, 5.44) because of the preferential binding of Cd2+ to sulfur rather than oxygen, which we estimate to be approximately 60 in CdADP alpha S and CdATP beta S. The proportion of tridentate coordination is estimated to be 50-60% in MgATP and MgATP beta S, approximately 27% in MgATP alpha S, approximately 16% in CdATP or CdATP beta S, but approximately 75% in CdATP alpha S. By analysis of the data of Jaffe and Cohn [Jaffe, E. K., & Cohn, M. (1979) J. Biol. Chem. 254, 10839], we conclude that the preference for oxygen over sulfur coordination to ATP beta S is 31 000 for Mg2+, 3100-3900 for Ca2+, and 158-193 for Mn2+. Proton NMR demonstrates that bidentate Cd2+ complexes form intramolecular chelates with the N-7 of adenine while Mg2+ nucleotides and the tridenate CdATP alpha S do not. An analysis of the 31P NMR line widths shows that the rate constants for dissociation of MgADP and MgATP are both 7000 s-1 while the association rate constants are 7 X 10(7) and 4 X 10(8) M-1 s-1, respectively. The observed dependence of the line width on nucleotide concentration is best explained by a base-stacking model at nucleotide concentrations above 5 mM.     

Properties of the MgATP and MgADP binding sites on the Fe protein of nitrogenase from Azotobacter vinelandii

Flow dialysis was used to study the binding of MgATP and MgADP to the nitrogenase proteins of Azotobacter vinelandii. Both reduced and oxidized Av2 bind two molecules of MgADP, with the following dissociation constants: reduced Av2, K1 = 0.091 +/- 0.021 mM and K2 = 0.044 +/- 0.009 mM; oxidized Av2, K1 = 0.024 +/- 0.015 mM and K2 = 0.039 +/- 0.022 mM. Binding of MgADP to reduced Av2 shows positive co-operativity. Oxidized Av2 binds two molecules of MgATP with dissociation constants K1 = 0.049 +/- 0.016 mM and K2 = 0.18 +/- 0.05 mM. Binding data of MgATP to reduced Av2 can be fitted by assuming one binding site, but a better fit was obtained by assuming two binding sites on the protein with negative co-operativity and with dissociation constants K1 = 0.22 +/- 0.03 mM and K2 = 1.71 +/- 0.50 mM. It was found that results concerning the number of binding sites and the dissociation constants of MgATP-Av2 and MgADP-Av2 complexes depend to a great extent on the specific activity of the Av2 preparation used, and that it is difficult to correct binding data for inactive protein. No binding of MgADP to Av1 could be demonstrated. Binding studies of MgADP to a mixture of Av1 and Av2 showed that Av1 did not affect the binding of MgADP to either oxidized or reduced Av2. Inhibition studies were performed to investigate the interaction of MgATP and MgADP binding to oxidized and reduced Av2. All the experimental data can be explained by the minimum hypothesis, i.e. the presence of two adenine nucleotide binding sites on Av2. MgATP and MgADP compete for these two binding sites on the Fe protein.     

GABA, depressants and chloride ions affect the rate of dissociation of 35S-t-butylbicyclophosphorothionate binding

The dissociation of 35S-TBPS was studied from binding sites of rat cerebral cortex. Monophasic dissociation plots became polyphasic and accelerated in the presence of micromolar concentrations of GABA suggesting the involvement of low (or super-low) affinity GABA receptors. The presence of the depressants etazolate, R(-)MPPB and ethanol resulted in similarly accelerated dissociation patterns. In contrast, the convulsants S(+)MPPB and pentamethylenetetrazol did not significantly affect the dissociation of TBPS. Dissociation initiated by dilution was not affected either by an excess of picrotoxin or by varying the equilibrium occupancy of the TBPS sites. These findings rule out the possibility of a kinetic cooperativity for the binding of convulsants. The removal of chloride ions also enhanced the rate of TBPS dissociation. Kinetic heterogeneity of the TBPS binding sites can be interpreted with allosteric interactions mediated by various sites at the GABA receptor complex coupled to different states of the chloride ionophore.     

Dynamics of myo1c (myosin-ibeta ) lipid binding and dissociation

Myosin-I is the single-headed member of the myosin superfamily that associates with lipid membranes. Biochemical experiments have shown that myosin-I membrane binding is the result of electrostatic interactions between the basic tail domain and acidic phospholipids. To better understand the dynamics of myosin-I membrane association, we measured the rates of association and dissociation of a recombinant myo1c tail domain (which includes three IQ domains and bound calmodulins) to and from large unilamellar vesicles using fluorescence resonance energy transfer. The apparent second-order rate constant for lipid-tail association in the absence of calcium is fast with nearly every lipid-tail collision resulting in binding. The rate of binding is decreased in the presence of calcium. Time courses of myo1c-tail dissociation are best fit by two exponential rates: a fast component that has a rate that depends on the ratio of acidic phospholipid to myo1c-tail (phosphatidylserine (PS)/tail) and a slow component that predominates at high PS/tail ratios. The dissociation rate of the slow component is slower than the myo1c ATPase rate, suggesting that myo1c is able to stay associated with the lipid membrane during multiple catalytic cycles of the motor. Calcium significantly increases the lifetimes of the membrane-bound state, resulting in dissociation rates 0.001 s(-1).     

On-chip non-equilibrium dissociation curves and dissociation rate constants as methods to assess specificity of oligonucleotide probes

Nucleic acid hybridization serves as backbone for many high-throughput systems for detection, expression analysis, comparative genomics and re-sequencing. Specificity of hybridization between probes and intended targets is always critical. Approaches to ensure and evaluate specificity include use of mismatch probes, obtaining dissociation curves rather than single temperature hybridizations, and comparative hybridizations. In this study, we quantify effects of mismatch type and position on intensity of hybridization signals and provide a new approach based on dissociation rate constants to evaluate specificity of hybridized signals in complex target mixtures. Using an extensive set of 18mer oligonucleotide probes on an in situ synthesized biochip platform, we demonstrate that mismatches in the center of the probe are more discriminating than mismatches toward the extremities of the probe and mismatches toward the attached end are less discriminating than those toward the loose end. The observed destabilizing effect of a mismatch type agreed in general with predictions using the nearest neighbor model. Use of a new parameter, specific dissociation temperature (T_d-w, temperature of maximum specific dissociation rate constant), obtained from probe–target duplex dissociation profiles considerably improved the evaluation of specificity. These results have broad implications for hybridization data obtained from complex mixtures of nucleic acids.     

Evaluation of dissociation constants from competition binding experiments based on the relative binding ratio

Methods probing protein–DNA associations include direct binding titrations and competition binding experiments. For the latter, we present here a simple procedure allowing the quantitative evaluation of dissociation constants. We show that the ratio between the fraction of a DNA probe bound to protein in the absence of competitor and that in the presence of competitor is, at large competitor concentrations, a linear function of the competitor concentration, and we derive equations allowing the dissociation constant for the protein–competitor complex to be evaluated from the slope. We show further that a self-competition experiment, where the DNA probe and competitor are chemically the same species, can be used as a complement to a direct titration to determine the fraction of protein that is correctly folded for specific DNA binding. Thus, such a combination of direct and self-competition titration can be used as a check of the conformational purity of DNA binding proteins.     

The dissociation of 1-N6-ethenoadenosine diphosphate from regulated actomyosin subfragment 1

The effective rate of dissociation of 1-N6-ethenoadenosine diphosphate (epsilon ADP) from the regulated actin X subfragment 1 X epsilon ADP complex of rabbit skeletal muscle is approximately 10-15 times smaller in the absence of calcium ion compared to the presence of calcium ion. The decrease in fluorescence emission with dissociation of the bound epsilon ADP fitted two exponential terms. The evidence is consistent with a kinetic scheme in which two first-order transitions precede the dissociation step: (Formula: see text) where D is epsilon ADP, A is regulated actin, M is subfragment 1, the asterisks refer to the degree of fluorescence enhancement, and AM(D) is a collision complex in equilibrium with free epsilon ADP. Both rate constants k-2 and k-1 were reduced approximately 15-fold in the absence of calcium ion. The rate constants for the dissociation of epsilon ATP, epsilon ADP X Pi, formed in the enzyme cycle, and epsilon ADP are all reduced in the absence of calcium ion; consequently, the primary effect in calcium regulation of the actin-subfragment 1 ATPase is on the rate constant of a transition (or transitions) between actomyosin-nucleoside phosphate complexes.     

The specific binding of small molecule isoprenoids to rhoGDP dissociation inhibitor (rhoGDI)

The activities of small G-proteins are in part regulated by their interactions with GDI proteins. This binding is thought to be dependent on the C-terminal isoprenoid modification (geranylgeranyl or farnesyl) of these proteins. G-proteins are generally isoprenylated/methylated at their C-terminal cysteine residues. A quantitative fluorescence assay is reported here to evaluate the specificity of binding of rhoGDI. A rhodamine-labeled geranylgeranylated/methylated cysteine derivative is used to measure its binding to rhoGDI. Saturable binding in the low micromolar range is found with various geranylgeranylated/farnesylated analogues. Interestingly, the carboxymethylated derivatives bound significantly better than their free acid counterparts, suggesting that the state of methylation of the analogues is important for binding. The binding is also selective with respect to isoprenoid. Analogues containing hydrophobic modifications other than geranylgeranyl or farnesyl do not bind with significant affinities. These data demonstrate a substantial degree of specificity in the binding of isoprenoids to a protein important in signal transduction.     

The beta and cytoplasmic actins are differentially thermostabilized by MgADP; gamma actin binds MgADP more strongly.

Using the technique of thermal denaturation in a temperature gradient followed by two-dimensional gel electrophoresis of the fractions, the thermostabilities of the cytoplasmic actins have been investigated. Addition of 5 mM MgADP (but not NADH or CaCl₂) to stripped, radiolabeled leukocyte lysate thermostabilizies the actins by about 16°C relative to stripped lysate alone, producing a slightly stronger stabilization in γ actin. This result will allow preparative fractionation of β and γ actins and additional biochemical characterization of their differences.     

Dimer dissociation is essential for interleukin-8 (IL-8) binding to CXCR1 receptor

Chemokines play a fundamental role in trafficking of immune cells and in host defense against infection. The role of chemokines in the recruitment process is highly regulated spatially and temporally and involves interactions with G protein-coupled receptors and cell surface glycosaminoglycans. The dynamic equilibrium between chemokine monomers and dimers, both free in solution and in cell surface-bound forms, regulates different components of recruitment such as chemotaxis and receptor signaling. The binding and activity of the chemokine interleukin-8 (IL-8) for its receptors, previously studied using "trapped" non-associating monomers and non-dissociating dimers, show that the monomer has a native-like function but support conflicting roles for the dimer. We have measured the binding of native IL-8 to the CXCR1 N-domain, using isothermal titration calorimetry and sedimentation equilibrium techniques. The N-domain constitutes a critical binding site, and IL-8 binding affinity to the receptor N-domain is in the same concentration range as the IL-8 monomerdimer equilibrium. We observed that only the IL-8 monomer, and not the dimer, is competent in binding the receptor N-domain. Based on our results, we propose that IL-8 dimerization functions as a negative regulator for the receptor function and as a positive regulator for binding to glycosaminoglycans and that both play a role in the neutrophil recruitment process.