Constructing ensembles of flexible fragments in native proteins by iterative stochastic elimination is relevant to protein-protein interfaces

We investigate the extent to which ensembles of flexible fragments (FF), generated by our loop conformational search method, include conformations that are near experimental and reflect conformational changes that these FFs undergo when binary protein-protein complexes are formed. Twenty-eight FFs, which are located in protein-protein interfaces and have different conformations in the bound structure (BS) and unbound structure (UbS) were extracted. The conformational space of these fragments in the BS and UbS was explored with our method which is based on the iterative stochastic elimination (ISE) algorithm. Conformational search of BSs generated bound ensembles and conformational search of UbSs produced unbound ensembles. ISE samples conformations near experimental (less than 1.05 A root mean square deviation, RMSD) for 51 out of the 56 examined fragments in the bound and unbound ensembles. In 14 out of the 28 unbound fragments, it also samples conformations within 1.05 A from the BS in the unbound ensemble. Sampling the bound conformation in the unbound ensemble demonstrates the potential biological relevance of the predicted ensemble. The 10 lowest energy conformations are the best choice for docking experiments, compared with any other 10 conformations of the ensembles. We conclude that generating conformational ensembles for FFs with ISE is relevant to FF conformations in the UbS and BS. Forming ensembles of the isolated proteins with our method prior to docking represents more comprehensively their inherent flexibility and is expected to improve docking experiments compared with results obtained by docking only UbSs.     

Measurement of plasma unbound unconjugated bilirubin

A method is described for measuring the unconjugated fraction of the unbound bilirubin concentration in plasma by combining the peroxidase method for determining unbound bilirubin with a diazo method for measuring conjugated and unconjugated bilirubin. The accuracy of the unbound bilirubin determination is improved by decreasing sample dilution, eliminating interference by conjugated bilirubin, monitoring changes in bilirubin concentration using diazo derivatives, and correcting for rate-limiting dissociation of bilirubin from albumin. The unbound unconjugated bilirubin concentration by the combined method in plasma from 20 jaundiced newborns was significantly greater than and poorly correlated with the unbound bilirubin determined by the existing peroxidase method (r = 0.7), possibly due to differences in sample dilution between the methods. The unbound unconjugated bilirubin was an unpredictable fraction of the unbound bilirubin in plasma samples from patients with similar total bilirubin concentrations but varying levels of conjugated bilirubin. A bilirubin-binding competitor was readily detected at a sample dilution typically used for the combined test but not at the dilution used for the existing peroxidase method. The combined method is ideally suited to measuring unbound unconjugated bilirubin in jaundiced human newborns or animal models of kernicterus.     

Modeling flux of free and protein-bound radioisotopes into the pulmonary interstitium

Several groups of investigators are using external detection of radiolabeled protein to study the flux of protein from plasma into the pulmonary interstitium. A basic assumption for these studies has been that the unbound (free) tracer concentration is small and insignificant. The purpose of this study is to evaluate how free tracer influences the determination of normalized slope index. A five-compartment model for the lung was used with transport equations for both unbound and bound nuclide flux. Parameters of the unbound and bound transport equations were varied to evaluate the sensitivity of normalized slope index to each parameter. The model was also compared with published protein flux data to investigate the validity of the transport model. Application of the model to external scan data provides a sensitive method for evaluating the flux of bound and unbound tracers into the pulmonary interstitium. We conclude that because the distribution volume for unbound tracer is large with respect to protein distribution volume, even a small amount of unbound tracer (2-5%) can create large errors in the determination of normalized slope index.     

Development and validation of a method to determine the unbound paclitaxel fraction in human plasma

Paclitaxel is pharmaceutically formulated in a mixture of Cremophor EL and ethanol (1:1, v/v). The unbound fraction of the anticancer drug paclitaxel in plasma is dependent on both plasma protein binding and entrapment in Cremophor EL micelles. We have developed a simple and reproducible method for the quantification of the unbound paclitaxel fraction in human plasma. Human plasma was spiked with [3H]paclitaxel and [14C]glucose (unbound reference) and incubated at 37 degrees C for 30 min. Plasma ultrafiltrate was prepared by a micropartition system (MPS-1) and collected in a sample cup containing 100 microl of plasma to prevent the loss of paclitaxel due to adsorption. The radionuclides were separated after combustion of the biological samples using a sample oxidizer and the radioactivity was determined by liquid scintillation counting. The unbound fraction of paclitaxel was calculated by dividing the ratios of 3H and 14C in plasma ultrafiltrate and in plasma. The method was thoroughly validated using human plasma spiked with pharmacologically relevant concentrations of paclitaxel (10-1000 ng/ml) and Cremophor EL (0.25-2.0%). The method was precise, with a within-day precision ranging from 3.9 to 11.0% and a between-day precision ranging from 5.8 to 13.1%. In patient plasma with low serum albumin values containing 1% of Cremophor EL, the unbound fraction appeared to be significantly higher than that in plasma with normal albumin values. The determination of the unbound fraction of paclitaxel proved to be stable during a 10-week storage at -20 degrees C. Furthermore, the assay was applicable in patient samples. This assay can be used to determine the unbound fraction of paclitaxel in plasma. Moreover, its design should allow the determination of the unbound concentrations of other hydrophobic drugs.     

Accurate, rapid measurement of the fraction of unbound estradiol and progesterone in small volumes of undiluted serum at 37 degrees C by miniature steady-state gel filtration

A method is described for the accurate, rapid measurement of the unbound fractions of estradiol and of progesterone in small volumes of plasma or serum at 37 degrees C by a miniature method of steady-state gel filtration. There is minimal perturbation of the equilibrium between bound and free hormone and no derived kinetic parameters are required. The method has been used to measure the unbound fraction of progesterone in plasma from women during the second and third trimesters of pregnancy and of estradiol in sera of developing female rats.     

Considerations for using fluorescence polarization in the screening of G protein-coupled receptors

Fluorescence polarization must be classified as a unique detection method relative to other intensity-based methods because both bound and unbound tracer is measured. Other fluorescence techniques require either physical removal of unbound tracer or a means for distinguishing only bound tracer. The presence of unbound tracer in the detection volume has profound consequences on how assay performance is gauged. The intent here is to provide tools for accurate assay performance assessment and to discuss some of the practical considerations necessary for understanding the advantages and limitations of the technology. An emphasis is placed on applications using G protein-coupled receptors.     

Clinical use of unbound plasma cortisol as calculated from total cortisol and corticosteroid-binding globulin

A method to calculate unbound cortisol from total cortisol (measured by competitive protein binding) and CBG (measured by radial immunodiffusion) based on the binding equilibrium has been evaluated. The calculated results (y) correlate well with those (x) obtained by centrifugal ultrafiltration at 37 degrees C (y = 1.04 x - 2.11 ng/ml; r = 0.975; n = 150). The concentration of CBG is similar in normal men (37.7 +/- 3.5 (SD) micrograms/ml; n = 12) and women (39.5 +/- 3.7 (SD) micrograms/ml; n = 7) and shows no diurnal variation, but marked diurnal variation is observed for total cortisol (193.7 +/- 35.0 (SD) ng/ml at 08.00 h vs 43.2 +/- 23.3 (SD) ng/ml at 22.00 h; n = 19) and particularly for unbound cortisol (16.5 +/- 5.6 (SD) ng/ml at 08.00 h vs 2.3 +/- 1.8 (SD) ng/ml at 22.00 h; n = 19). The concentration of CBG (89.1 +/- 11.2 (SD) micrograms/ml) and of total cortisol (395.6 +/- 103.3 (SD) ng/ml at 08.00 h; 110.3 +/- 16.6 (SD) ng/ml at 22.00 h) are clearly elevated in estrogen treated women (n = 11) but unbound cortisol levels (17.2 +/- 7.7 (SD) ng/ml at 08.00 h; 2.5 +/- 0.5 (SD) ng/ml at 22.00 h) are similar to the control group. The concentration of CBG is significantly decreased in patients with Cushing's syndrome (33.2 +/- 5.6 micrograms/ml; n = 17) and unbound cortisol is relatively more elevated than total cortisol in these patients. In adrenal insufficiently CBG is normal, but total and unbound cortisol are markedly decreased. There is a significant decrease of CBG in hyperthyroidism (35.7 +/- 5.5 micrograms/ml; n = 22), in cirrhosis (32.0 +/- 8.0 micrograms/ml; n = 14) and in renal disease and a significant increase in patients treated with antiepileptic drugs (47.5 +/- 6.3 micrograms/ml; n = 14), but total and unbound cortisol are normal in all these conditions. We conclude that unbound cortisol can be calculated in a simple and reliable way from total cortisol and CBG and permits a better evaluation of adrenal function, particularly in patients with altered CBG concentrations.     

Colorimetric method for estimating polylysine and polyarginine

A rapid and sensitive method is described for estimating polylysine and polyarginine. The method involves the stoichiometric precipitation of these polyamino acids by excess of the anionic dye methyl orange, followed by spectrophotometric determination of unbound dye. 10 μg or less of polylysine or polyarginine can thus be estimated. The effects of various salts on the estimation are described.     

A Sterol-binding assay for potato glycoalkaloids

A method is described for quantitative analysis of potato glycoalkaloids based on their ability to complex with free sterols in alcoholic solution, the amount of unbound sterol being inversely proportional to the amount of alkaloid present. Since the alkaloid-sterol complex is soluble, unbound sterol is estimated by GLC.     

Automated docking of peptides and proteins by using a genetic algorithm combined with a tabu search.

A genetic algorithm (GA) combined with a tabu search (TA) has been applied as a minimization method to rake the appropriate associated sites for some biomolecular systems. In our docking procedure, surface complementarity and energetic complementarity of a ligand with its receptor have been considered separately in a two-stage docking method. The first stage was to find a set of potential associated sites mainly based on surface complementarity using a genetic algorithm combined with a tabu search. This step corresponds with the process of finding the potential binding sites where pharmacophores will bind. In the second stage, several hundreds of GA minimization steps were performed for each associated site derived from the first stage mainly based on the energetic complementarity. After calculations for both of the two stages, we can offer several solutions of associated sites for every complex. In this paper, seven biomolecular systems, including five bound complexes and two unbound complexes, were chosen from the Protein Data Bank (PDB) to test our method. The calculated results were very encouraging-the hybrid minimization algorithm successfully reaches the correct solutions near the best binded modes for these protein complexes. The docking results not only predict the bound complexes very well, but also get a relatively accurate complexed conformation for unbound systems. For the five bound complexes, the results show that surface complementarity is enough to find the precise binding modes, the top solution from the tabu list generally corresponds to the correct binding mode. For the two unbound complexes, due to the conformational changes upon binding, it seems more difficult to get their correct binding conformations. The predicted results show that the correct binding mode also corresponds to a relatively large surface complementarity score. In these two test cases, the correct solution can be found in the top several solutions from the tabu list. For unbound complexes, the interaction energy from energetic complementarity is very important, it can be used to filter these solutions from the surface complementarity. After the evaluation of the energetic complementarity, the conformations and orientations close to the crystallographically determined structures are resolved. In most cases, the smallest root mean square distance (r.m.s.d.) from the GA combined with TA solutions is in a relatively small region. Our program of automatic docking is really a universal one among the procedures used for the theoretical study of molecular recognition.     

Identification of ligand binding sites of proteins using the Gaussian Network Model

The nonlocal nature of the protein-ligand binding problem is investigated via the Gaussian Network Model with which the residues lying along interaction pathways in a protein and the residues at the binding site are predicted. The predictions of the binding site residues are verified by using several benchmark systems where the topology of the unbound protein and the bound protein-ligand complex are known. Predictions are made on the unbound protein. Agreement of results with the bound complexes indicates that the information for binding resides in the unbound protein. Cliques that consist of three or more residues that are far apart along the primary structure but are in contact in the folded structure are shown to be important determinants of the binding problem. Comparison with known structures shows that the predictive capability of the method is significant.     

SymmRef: a flexible refinement method for symmetric multimers

Symmetric protein complexes are abundant in the living cell. Predicting their atomic structure can shed light on the mechanism of many important biological processes. Symmetric docking methods aim to predict the structure of these complexes given the unbound structure of a single monomer, or its model. Symmetry constraints reduce the search-space of these methods and make the prediction easier compared to asymmetric protein-protein docking. However, the challenge of modeling the conformational changes that the monomer might undergo is a major obstacle. In this article, we present SymmRef, a novel method for refinement and reranking of symmetric docking solutions. The method models backbone and side-chain movements and optimizes the rigid-body orientations of the monomers. The backbone movements are modeled by normal modes minimization and the conformations of the side-chains are modeled by selecting optimal rotamers. Since solved structures of symmetric multimers show asymmetric side-chain conformations, we do not use symmetry constraints in the side-chain optimization procedure. The refined models are re-ranked according to an energy score. We tested the method on a benchmark of unbound docking challenges. The results show that the method significantly improves the accuracy and the ranking of symmetric rigid docking solutions. SymmRef is available for download at http:// bioinfo3d.cs.tau.ac.il/SymmRef/download.html.     

Prediction of DNA-binding protein based on statistical and geometric features and support vector machines

Background

Previous studies on protein-DNA interaction mostly focused on the bound structure of DNA-binding proteins but few paid enough attention to the unbound structures. As more new proteins are discovered, it is useful and imperative to develop algorithms for the functional prediction of unbound proteins. In our work, we apply an alpha shape model to represent the surface structure of the protein-DNA complex and extract useful statistical and geometric features, and use structural alignment and support vector machines for the prediction of unbound DNA-binding proteins.

Results

The performance of our method is evaluated by discriminating a set of 104 DNA-binding proteins from 401 non-DNA-binding proteins. In the same test, the proposed method outperforms the other method using conditional probability. The results achieved by our proposed method for; precision, 83.33%; accuracy, 86.53%; and MCC, 0.5368 demonstrate its good performance.

Conclusions

In this study we develop an effective method for the prediction of protein-DNA interactions based on statistical and geometric features and support vector machines. Our results show that interface surface features play an important role in protein-DNA interaction. Our technique is able to predict unbound DNA-binding protein and discriminatory DNA-binding proteins from proteins that bind with other molecules.

     

Enantioselective analysis of unbound tramadol, O-desmethyltramadol and N-desmethyltramadol in plasma by ultrafiltration and LC-MS/MS: application to clinical pharmacokinetics

This study describes the enantioselective analysis of unbound and total concentrations of tramadol and its main metabolites O-desmethyltramadol (M1) and N-desmethyltramadol (M2) in human plasma. Sample preparation was preceded by an ultrafiltration step to separate the unbound drug. Both the ultrafiltrate and plasma samples were submitted to liquid/liquid extraction with methyl t-butyl ether. Separation was performed on a Chiralpak(?) AD column and tandem mass spectrometry consisting of an electrospray ionization source, positive ion mode and multiple reaction monitoring was used as the detection system. Linearity was observed in the following ranges: 0.2-600 and 0.5-250 ng/mL for analysis of total and unbound concentrations of the tramadol enantiomers, respectively, and 0.1-300 and 0.25-125 ng/mL for total and unbound concentrations of the M1 and M2 enantiomers, respectively. The lower limits of quantitation were 0.2 and 0.5 ng/mL for analysis of total and unbound concentration of each tramadol enantiomer, respectively, and 0.1 and 0.25 ng/mL for total and unbound concentrations of M1 and M2 enantiomers, respectively. Intra- and interassay reproducibility and inaccuracy did not exceed 15%. Clinical application of the method to patients with neuropathic pain showed plasma accumulation of (+)-tramadol and (+)-M2 after a single oral dose of racemic tramadol. Fractions unbound of tramadol, M1 or M2 were not enantioselective in the patients investigated.     

Determination of unbound ticagrelor and its active metabolite (AR-C124910XX) in human plasma by equilibrium dialysis and LC-MS/MS

Ticagrelor is the first direct acting reversibly binding oral platelet P2Y(12) receptor antagonist. The parent molecule and the main metabolite (AR-C124910XX) are both able to block adenosine diphosphate-induced receptor signaling with similar potency. Drug binding to plasma proteins reduces free drug available for pharmacologic activity. Therefore, assessing unbound drug is important for interpretation of pharmacokinetic/pharmacodynamic findings. This paper describes the development and validation of an equilibrium dialysis/LC-MS/MS method for measuring unbound ticagrelor and AR-C124910XX in human plasma. Plasma samples (200μl) were dialysed against phosphate buffered saline (37 °C, 24h) in 96-well dialysis plates to separate unbound analytes. Drug-protein binding alterations during dialysis were minimized by maintaining physiologic conditions (pH 7.4, 37 °C). Ticagrelor and AR-C124910XX were quantified in dialysates (unbound fraction), retentates and plasma (total concentration) using liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) methods. Calibration curves were established for the retentate and plasma (total concentration) in the ranges 5-5000 ng/ml (ticagrelor) and 2.5-2500 ng/ml (AR-C124910XX), and for the dialysate in the range 0.25-100 ng/ml (both analytes). Both ticagrelor and AR-C124910XX were highly protein bound (>99.8%), i.e. unbound fraction <0.2%. Yet, the methodology was successfully applied to determine unbound concentrations of ticagrelor and AR-C124910XX in clinical samples.     

Simultaneous measurement of unbound testosterone and estradiol fractions in undiluted plasma at 37 degrees C by steady-state gel filtration

A method is described for the simultaneous measurement of percent unbound testosterone (T) and estradiol (E₂) using steady-state gel filtration (SSGF), a technique which maintains physiological conditions of pH, temperature and plasma constituents, thus avoiding alterations in the original equilibria. Combined with specific assays of their total plasma levels it probably yields a closer estimate of the true circulating unbound (biologically-active) concentration of T and E₂ than previous methods. Its main application lies in the study of sex-hormone disorders which may result in an imbalance between unbound T and E₂ concentrations. Results of percent unbound are: normal men - T, 1.71 ± 0.29 (SD); E₂, 1.79 ± 0.32: normal women - T, 1.02 ± 0.17; E₂, 1.49 ± 0.35: hirsute women - T, 1.68 ± 0.52; E₂, 1.55 ± 0.29; women on estrogens - T, 0.67 ± 0.06; E₂, 1.02 ± 0.13. As predicted from earlier studies in hirsute females the fall in SHBG level is associated with a significant rise in percent unbound T, but no rise in percent unbound E₂.