Cardiac adenosine 3':5'-monophosphate. Free and bound forms in the isolated rat atrium.

Adenosine 3':5'-monophosphate (cyclic AMP), a mediator of hormone action in a variety of tissues, has been measured in its free and bound forms in intact cardiac tissue. We have used a rapid high dilution technique which involves tissue homogenization, subcellular fractionation, and separation of bound from free cyclic AMP by Millopore filtration. The precision of this method is dependent upon minimization of binding and dissociation of cyclic AMP that occur during the preparation and handling of tissue homogenates. In each experiment, a tracer of cyclic [3H]AMP prebound to isolated cardiac binding protein was freed of unbound cyclic [3H]AMP by Sephadex gel filtration and added to the tissue just prior to homogenization in cold EDTA buffer. This tracer was therefore treated identically to the sample through all subsequent dilution, fractionation, and filtration procedures, and provided an acurate internal monitor for total cyclic AMP dissociation during the course of the free-bound determination. Each tissue sample was then individually corrected for dissociation. Rapid dilution to produce a 1:1000 homogenate was found to lower endogenous cyclic AMP levels sufficiently to make binding (or rebinding) during the procedure negligible (less than 5%). Spontaneously beating rat right atria (controls) contained 5.96 +/- 0.28 pmol of cyclic AMP/mg of protein (n = 19) of which 41 and 14% were bound to soluble and particulate proteins, respectively. The remaining cyclic AMP was free. Pretreatment of the tissue with 1 muM isoproterenol (30 s at 30 degrees) increased both the bound and free forms of cyclic AMP (n = 8). While free cyclic AMP increased 420% with the catecholamine, the bound forms increased 240% (soluble) and 60% (particulate). Similar results were obtained when atria (n = 6) were treated with the phosphodiesterase inhibitor, methylisobutylxanthine (0.5 mM, 10 min at 30 degrees). When both agents were used together, cyclic AMP bound to soluble proteins was elevated 4-fold over control while free cyclic AMP increased 27-fold (n = 7), indicating saturation of the soluble sites. It could be calculated that less than one-third of these sites are occupied in the unstimulated cell. These sites may represent the R subunit of cyclic AMP-dependent protein kinase. The data suggest that half-maximal binding in vivo occurs at an intracellular free cyclic AMP concentration of about 1 muM.     

Ion channels in icosahedral virus: a comparative analysis of the structures and binding sites at their fivefold axes.

An analysis of the crystallographically determined structures of the icosahedral protein coats of Tomato Bushy Stunt Virus, Southern Bean Mosaic Virus, Satellite Tobacco Necrosis Virus, Human Rhinovirus 14 and Mengovirus around their fivefold axes is presented. Accessibilities surfaces, electrostatic energy profile calculations, ion-protein interaction energy calculations, free energy perturbation methods and comparisons with structures of chelating agents are used in this study. It is concluded that the structures built around the viral fivefold axes would be adequate for ion binding and transport. Relative ion preferences are derived for the binding sites, using free energy perturbation methods, which are consistent with the experimental data when available. In the cases where crystallographic studies determined the existence of ions on the fivefold axes, our results indicate that they would correspond to ions in crystallization or purification buffers. The environment of the fivefold axes are rich in polar residues in all icosahedral viral structures whose atomic coordinates are available, including some that are not being analyzed in detail in this work. The fivefold channel-like structures have most of the basic properties expected for real ion channels including a funnel at the entrance, a polar internal environment with frequent alternation of acidic and basic residues, ion binding sites, the capability to induce ion dehydration and ion transit from the external viral surface to the binding sites.     

Activation of the edema factor of Bacillus anthracis by calmodulin: evidence of an interplay between the EF-calmodulin interaction and calcium binding

Calmodulin (CaM) is a remarkably flexible protein which can bind multiple targets in response to changes in intracellular calcium concentration. It contains four calcium-binding sites, arranged in two globular domains. The calcium affinity of CaM N-terminal domain (N-CaM) is dramatically reduced when the complex with the edema factor (EF) of Bacillus anthracis is formed. Here, an atomic explanation for this reduced affinity is proposed through molecular dynamics simulations and free energy perturbation calculations of the EF-CaM complex starting from different crystallographic models. The simulations show that electrostatic interactions between CaM and EF disfavor the opening of N-CaM domains usually induced by calcium binding. Relative calcium affinities of the N-CaM binding sites are probed by free energy perturbation, and dissociation probabilities are evaluated with locally enhanced sampling simulations. We show that EF impairs calcium binding on N-CaM through a direct conformational restraint on Site 1, by an indirect destabilization of Site 2, and by reducing the cooperativity between the two sites.     

Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation

Relative free energies of binding to the ligand-binding domain of the estrogen receptor have been calculated for a series of 17 hydroxylated polychlorinated biphenyls. Because traditional thermodynamic integration or perturbation approaches are hardly feasible for these numbers of compounds, the one-step perturbation approach is applied and is shown to yield accurate results based on only two 2-ns molecular dynamics simulations of an unphysical, judiciously chosen, reference state. The mean absolute difference between the calculated and experimental binding free energies for the 17 compounds is 3.4 kJ/mol, which illustrates the accuracy of the GROMOS biomolecular force field used. Excluding the three largest ligands from the comparison reduces the deviation to 2.0 kJ/mol (i.e., < k(B)T). Apart from the relative free energy, structural information about the binding mode and binding orientation for every compound can also be extracted from the simulation, showing that a ligand bound to its receptor cannot be represented by a single conformation, but it samples an ensemble of different orientations.     

Site specific point mutation changes specificity: A molecular modeling study by free energy simulations and enzyme kinetics of the thermodynamics in ribonuclease T1 substrate interactions

We have theoretically and experimentally studied the binding of two different ligands to wild-type ribonuclease T₁ (RNT1) and to a mutant of RNT1 with Glu-46 replaced by Gln. The binding of the natural substrate 3′-GMP has been compared with the binding of a fluorescent probe, 2-aminopurine 3′-monophosphate (2AP), and relative free energies of binding of these ligands to the mutant and the wild-type (wt) enzyme have been calculated by free energy perturbation methods. The free energy perturbations predict that the mutant RNT1-Gln-46 binds 2AP better than 3′GMP, in agreement with experiments on dinucleotides. Four free energy perturbations, forming a closed loop, have been performed to allow the detection of systematic errors in the simulation procedure. Because of the larger number of atoms involved, it was necessary to use a much longer simulation time for the change in the protein, i.e., the perturbation from Glu to Gln, than in the perturbation from 3′-GMP to 2AP. Finally the structure of the binding site is analyzed for understanding differences in catalytic speed and binding strength. © 1993 Wiley-Liss, Inc.     

Dimerization of SHBG by gelatin and dithiothreitol. Implications for the measurement of SHBG binding capacity in human serum

In individual serum samples, the sex hormone-binding globulin (SHBG) binding capacity for dihydrotestosterone (DHT) was systematically found to be decreased by 30-60% when either gelatin or dithiothreitol (DTT) was present in the assay buffer. The presence of gelatin in the buffer prevented DTT from further decreasing the SHBG binding capacity of serum samples, suggesting a similar mechanism of action on SHBG for both of these substances. This observation led us to compare the molecular forms of SHBG by high performance liquid chromatography on a TSK G 3000 SW column, in the presence or absence of DTT. When undiluted serum previously incubated with [3H]DHT was chromatographed, only monomeric SHBG could be detected, independently of the presence or absence of DTT in the elution buffer. When the serum was diluted, incubated and chromatographed with buffer devoid of DTT, a dimeric SHBG peak was progressively observed, as a function of the sample dilution. Furthermore, for a given serum dilution, the relative size of the dimeric SHBG peak was also dependent on the steroid concentration present in the sample. By contrast, when serum was diluted, incubated and chromatographed with DTT-supplemented buffer, only the SHBG dimer peak could be detected. These results suggest that in serum, in vitro at least, SHBG is present in its monomeric form. Serum dilution with buffer devoid of DTT or gelatin induces the progressive dimerization of the protein, resulting in a progressive decrease of its apparent binding capacity. This could explain the great discrepancies of SHBG levels as reported in the literature. Because serum dilution with buffer supplemented with DTT or gelatin induces the complete dimerization of SHBG, independently of the sample dilution, we suggest that these substances be routinely used for the measurement of SHBG binding capacity. The SHBG binding capacity obtained in these latter conditions reflects however half the binding capacity of undiluted serum.     

Ionophore-induced disassembly of blood platelet microtubules: effect of cyclic AMP and indomethacin

Cytoplasmic calcium levels are believed to be important in blood platelet activation. Upon activation, the discrete marginal microtubule band, which maintains the discoid shape of non-activated platelets, becomes disrupted. Present studies demonstrate that the extent of assembly of the marginal microtubule band is related to cytoplasmic calcium levels. The divalent cationophore, A23187, causes platelet aggregation, secretion, and contraction by promoting calcium transport from intraplatelet storage sites into the cytoplasm. A23187 caused disassembly of platelet microtubules. Quantitation of electron micrographs revealed that numbers of microtubules were reduced by approximately 80% after A23187 treatment. Secondly, assembled microtubules in homogenates of platelets, in which microtubules were stabilized prior to homogenization, were decreased in favor of free tubulin in A23187-treated platelets. Thirdly, A23187 increased 14C-colchicine binding by intact platelets; this also indicated a shift in the microtubule subunit equilibrium to favor free, colchicine-binding tubulin subunits. In control experiments, A23187 did not affect the stability of platelet tubulin, the colchicine binding reaction, or the total tubulin content of platelets. Stimulation of colchicine binding depended on A23187 concentration (0.05-0.5 microM) and did not require extracellular calcium. A23187-stimulation of colchicine binding was blocked by dibutyryl cyclic AMP (0.80 mM) and/or 3-isobutyl-1-methylxanthine (50 microM) and by indomethacin (10 microM). Cyclic AMP or indomethacin also interferes with A23187-induced platelet activation, but indomethacin is not likely to completely inhibit the perturbation of intraplatelet calcium gradients by A23187. It is suggested that A23187-induced microtubule disassembly may be an indirect effect of calcium on microtubules.     

Accounting for Ligand Conformational Restriction in Calculations of Protein-Ligand Binding Affinities

The conformation adopted by a ligand on binding to a receptor may differ from its lowest-energy conformation in solution. In addition, the bound ligand is more conformationally restricted, which is associated with a configurational entropy loss. The free energy change due to these effects is often neglected or treated crudely in current models for predicting binding affinity. We present a method for estimating this contribution, based on perturbation theory using the quasi-harmonic model of Karplus and Kushick as a reference system. The consistency of the method is checked for small model systems. Subsequently we use the method, along with an estimate for the enthalpic contribution due to ligand-receptor interactions, to calculate relative binding affinities. The AMBER force field and generalized Born implicit solvent model is used. Binding affinities were estimated for a test set of 233 protein-ligand complexes for which crystal structures and measured binding affinities are available. In most cases, the ligand conformation in the bound state was significantly different from the most favorable conformation in solution. In general, the correlation between measured and calculated ligand binding affinities including the free energy change due to ligand conformational change is comparable to or slightly better than that obtained by using an empirically-trained docking score. Both entropic and enthalpic contributions to this free energy change are significant.     

Statistical thermodynamic analysis of peptide and protein insertion into lipid membranes.

A statistical thermodynamic approach is used to analyze the various contributions to the free energy change associated with the insertion of proteins and protein fragments into lipid bilayers. The partition coefficient that determines the equilibrium distribution of proteins between the membrane and the solution is expressed as the ratio between the partition functions of the protein in the two phases. It is shown that when all of the relevant degrees of freedom (i.e., those that change their character upon insertion into the membrane) can be treated classically, the partition coefficient is fully determined by the ratio of the configurational integrals and thus does not involve any mass-dependent factors, a conclusion that is also valid for related processes such as protein adsorption on a membrane surface or substrate binding to proteins. The partition coefficient, and hence the transfer free energy, depend only on the potential energy of the protein in the membrane. Expressing this potential as a sum of a "static" term, corresponding to the equilibrium (minimal free energy) configuration of the protein in the membrane, and a "dynamical" term representing fluctuations around the equilibrium configuration, we show that the static term contains the "solvation" and "lipid perturbation" contributions to the transfer free energy. The dynamical term is responsible for the "immobilization" free energy, reflecting the loss of translational and rotational entropy of the protein upon incorporation into the membrane. Based on a recent molecular theory of lipid-protein interactions, the lipid perturbation and immobilization contributions are then expressed in terms of the elastic deformation free energy resulting from the perturbation of the lipid environment by the foreign (protein) inclusion. The model is formulated for cylindrically shaped proteins, and numerical estimates are given for the insertion of an alpha-helical peptide into a lipid bilayer. The immobilization free energy is shown to be considerably smaller than in previous estimates of this quantity, and the origin of the difference is discussed in detail.     

Virtual screening using molecular simulations

Effective virtual screening relies on our ability to make accurate prediction of protein-ligand binding, which remains a great challenge. In this work, utilizing the molecular-mechanics Poisson-Boltzmann (or Generalized Born) surface area approach, we have evaluated the binding affinity of a set of 156 ligands to seven families of proteins, trypsin β, thrombin α, cyclin-dependent kinase (CDK), cAMP-dependent kinase (PKA), urokinase-type plasminogen activator, β-glucosidase A, and coagulation factor Xa. The effect of protein dielectric constant in the implicit-solvent model on the binding free energy calculation is shown to be important. The statistical correlations between the binding energy calculated from the implicit-solvent approach and experimental free energy are in the range of 0.56-0.79 across all the families. This performance is better than that of typical docking programs especially given that the latter is directly trained using known binding data whereas the molecular mechanics is based on general physical parameters. Estimation of entropic contribution remains the barrier to accurate free energy calculation. We show that the traditional rigid rotor harmonic oscillator approximation is unable to improve the binding free energy prediction. Inclusion of conformational restriction seems to be promising but requires further investigation. On the other hand, our preliminary study suggests that implicit-solvent based alchemical perturbation, which offers explicit sampling of configuration entropy, can be a viable approach to significantly improve the prediction of binding free energy. Overall, the molecular mechanics approach has the potential for medium to high-throughput computational drug discovery.     

A competitive enzyme-linked ligand sorbent assay (ELLSA) for quantitation of folates

An enzyme-linked ligand sorbent assay (ELLSA) for quantitation of folates is described. The method involves the following steps: (a) folate complexed to bovine serum albumin is adsorbed onto microtiter plates; (b) added folates compete with immobilized folate for binding to added biotinylated folate-binding protein; (c) biotinylated folate-binding protein bound to immobilized folate is detected after binding of avidin-alkaline phosphatase. The specificity of ELLSA is similar to that of conventional radioisotope dilution methods, and the sensitivity is high (lower limit of detection 20 fmol/sample). Quantitation of folates in erythrocyte lysates from 43 persons was performed by ELLSA. The results correlated fairly well with those obtained by the conventional radioisotope dilution method.     

Determination of insulin antibodies.

Insulin antibodies were determined as percentage binding of 125I-insulin in the sera of normal persons and of diabetic subjects treated and untreated with insulin. The effect of the dilution of the serum, circulating insulin and extraction of free and total insulin was evaluated. The determination of insulin antibodies in samples at a final dilution of 1:10 clearly discriminated between insulin-treated and untreated subjects. In insulin-treated subjects, the determination of insulin antibodies in samples at a final dilution of 1:100 gave false-negative results in 28 per cent. However, the determination of insulin antibodies at a final dilution of 1:100 discriminated between insulin-resistant and non-resistant diabetic subjects. Extraction of total insulin at pH 3.0 using 0.1 N HCl increased the percentage of 125I-insulin binding significantly. Extraction of free insulin by charcoal from the samples did not increase the binding of 125I-insulin. The injection of crystalline insulin 4 hours prior to withdrawing the samples did not decrease binding of 125I-insulin.     

New capabilities in determining the binding parameters for ligand-receptor interaction

A new method for determining the binding parameters of ligand-receptor interaction is suggested. The method is based on the application of the so-called coordinate of dilution, suggested by us earlier. We demonstrated that it is possible to determine the binding characteristics of ligand-receptor interaction using either the measurement of the concentration of the ligand-receptor complex at a state of equilibrium or the concentration of free receptors at different dilutions of the studying ligand-receptor mixture. The method also allows the determination of the concentration of the ligand in a pre-existing ligand-receptor mixture without preliminary separation of the interacting counterparts. For this reason the suggested method could be especially useful when the studying very labile receptors for which purification from the corresponding ligand is very difficult or impossible.     

Competitive binding assays for riboflavin and riboflavin-binding protein

A competitive binding procedure that can be used to determine either riboflavin or riboflavin-binding protein has been developed. Riboflavin-binding protein from chicken egg white binds tightly to DEAE-cellulose while free riboflavin does not. Stock [2-¹⁴C]riboflavin solutions, diluted with varying amounts of a standard unlabeled riboflavin solution or an unknown sample, are mixed with aporiboflavin-binding protein and washed through small DEAE-cellulose columns. The protein-bound riboflavin is batch eluted into scintillation vials, counted, and the unknown samples compared to a standard curve. This is a simple, rapid method for assaying riboflavin by isotope dilution. By a slight modification of the incubation conditions of this procedure, the degree of saturation and amount of riboflavin-binding protein can be determined. Data from both assays can be represented by linear plots in which slopes or intercepts correspond to unknown values. The principles presented here have been extended to the assay of biotin and avidin and should apply to other vitamins and vitamin-binding proteins.     

The problem of prozone in serum antibody titration and its mathematical interpretation

The question of the mechanism of "prozone" creation was considered from the point of view of the concentrations of free and semi-blocked bivalent antibodies in the mixture of these antibodies with monovalent antigen. Using the so called "coordinates of dilution", suggested by the author earlier, it was possible to calculate the relationships between the concentrations of either free or semi-blocked bivalent antibodies and the dilution of the antigen-antibody mixture. It was shown that dilution of antigen-antibody mixture leads to an increase of the concentration of free bivalent antibodies and simultaneous sharp decrease of the concentration of semi-blocked antibodies. It is suggested, that such a relationship is quite enough for the creation of prozone effect in reactions, when only bivalent antibodies are active and semi-blocked antibodies compete with free antibodies, providing inhibition of the reaction.     

Free Energy Perturbations in Ribonuclease T1 Substrate Binding. A Study of the Influence of Simulation Length,Internal Degrees of Freedom and Structure in Free Energy Perturbations

Abstract

We have studied the reliability of free energy perturbation calculations with respect to simulation protocol and simulation length in a real biological system, the binding of two different ligands to wildtype Ribonuclease T ₁ (RNT1) and to a mutant of RNT1 with Glu-46 replaced by Gln (RNT1-Gln46). The binding of the natural substrate 3′ GMP has been compared with the binding of a fluorescent probe, 2-aminopurine 3′ mono phosphate (2AP3′MP). These simulations predict that the mutant binds 2AP3′MP better than 3′GMP. Four complete free energy perturbations were performed that form a closed loop of four free energy differences, which should sum up to zero. This could be used as a tool for searching for systematic errors that are not detected by standard forward ? backward perturbations. The perturbation between 2AP3′MP and 3′GMP is quite straightforward and similar to what has been done by other groups. The perturbation between Glu46 and Gln46 is much more complex, involving as many as twelve atoms and a change of charge. This perturbation needs much longer simulation time, 500-600 ps, than used in free energy perturbations before. The increased simulation time is needed both to reach an equilibrium and to include several phases of fluctuations of the observed parameters in the production run. The extremely long simulation time is not such a severe problem as much of the work might be done on several different machines in parallel and cheap workstations are excellent for these calculations. Problems may also occur with values of the coupling parameter Λ close to 0 or 1, due to the high mobility of atoms as well as insertion/deletion in a previously unoccupied space involved in the perturbation.     

Relative binding free energy calculations of inhibitors to two mutants (Glu46----Ala/Gln) of ribonuclease T1 using molecular dynamics/free energy perturbation approaches.

We present free energy perturbation calculations on the complexes of Glu46----Ala46 (E46A) and Glu46----Gln46 (E46Q) mutants of ribonuclease T1 (RNaseT1) with inhibitors 2'-guanosine monophosphate (GMP) and 2'-adenosine monophosphate (AMP) by a thermodynamic perturbation method implemented with molecular dynamics (MD). Using the available crystal structure of the RNaseT1-GMP complex, the structures of E46A-GMP and E46Q-GMP were model built and equilibrated with MD simulations. The structures of E46A-AMP and E46Q-AMP were obtained as a final structure of the GMP----AMP perturbation calculation respectively. The calculated difference in the free energy of binding (delta delta Gbind) was 0.31 kcal/mol for the E46A system and -1.04 kcal/mol for the E46Q system. The resultant free energies are much smaller than the experimental and calculated value of approximately 3 kcal/mol for the native RNaseT1, which suggests that both mutants have greater relative adenine affinities than native RNaseT1. Especially E46Q is calculated to have a larger affinity for adenine than guanine, as we suggested previously from the calculation on the native RNaseT1. Thus, the molecular dynamics/free energy perturbation method may be helpful in protein engineering, directed toward increasing or changing the substrate specificity of enzymes.     

A simple and convenient approach for evaluation of the parameters of ligand-receptor interaction. Receptor blocking index and its application

A new approach for determination of the parameters for ligand-receptor interaction, which is based on so-called dilution coordinates, was developed earlier. Equations that allow evaluation of not only the affinity of ligand-receptor interaction but also of the amount of free (or occupied by corresponding ligand) receptors were suggested. The most important advantage of this approach as compared with well-known methods is the ability to determine the binding parameters for ligand-receptor interaction even for the cases in which ligand and receptor are already present in a mixture and separation of counterparts from each other is technically difficult or even impossible. Due to this reason, the proposed approach can be especially useful for studying interactions between highly-labile biological receptors and corresponding ligands as found in vivo. In the present paper I continue to consider how to determine the binding parameters for a given ligand-receptor interaction if the value of receptor blocking index is determined experimentally.     

The removal of exogenous thiols from proteins by centrifugal column chromatography

Centrifugal column chromatography was shown to provide a rapid, efficient, and useful means of separation of various low molecular weight thiols from proteins. The single chromatographic step procedure employed standard 5 ml plastic syringes containing Sephadex G-25 as the bed matrix and required less than 5 min to produce average dilutions of 5000-, 980-, and 25-fold, respectively, from 5 to 200 mM initial concentrations of 2-mercaptoethanol, dithiothreitol, and reduced glutathione in the sample as measured by titration with 5,5'-dithiobis-(2-nitrobenzoic acid). Dihydrofolate reductase solutions of 0.07-0.08 mM were separated from 50 mM 2-mercaptoethanol, dithiothreitol, or reduced glutathione with a minimum 16,500-fold dilution of the thiol after centrifugal chromatography on two consecutive columns. Thymidylate synthase solutions of 0.06 mM were effectively separated from 50 mM 2-mercaptoethanol or dithiothreitol with a minimum average 5900-fold dilution of the thiol after consecutive column chromatography. There was no change in either the physical or chemical properties of the enzyme throughout the course of the experiments as determined by activity, active site sulfhydryl group titration, and binding assays. Recoveries of protein obtained in the load fraction were usually in excess of 70% of the protein loaded with virtually no dilution from the initial concentration. This method was developed in order to facilitate the study of the active site sulfhydryl groups in enzymes.