Binding pose and affinity prediction in the 2016 D3R Grand Challenge 2 using the Wilma-SIE method

The Farnesoid X receptor (FXR) exhibits significant backbone movement in response to the binding of various ligands and can be a challenge for pose prediction algorithms. As part of the D3R Grand Challenge 2, we tested Wilma-SIE, a rigid-protein docking method, on a set of 36 FXR ligands for which the crystal structures had originally been blinded. These ligands covered several classes of compounds. To overcome the rigid protein limitations of the method, we used an ensemble of publicly available structures for FXR from the PDB. The use of the ensemble allowed Wilma-SIE to predict poses with average and median RMSDs of 2.3 and 1.4 Å, respectively. It was quite clear, however, that had we used a single structure for the receptor the success rate would have been much lower. The most successful predictions were obtained on chemical classes for which one or more crystal structures of the receptor bound to a molecule of the same class was available. In the absence of a crystal structure for the class, observing a consensus binding mode for the ligands of the class using one or more receptor structures of other classes seemed to be indicative of a reasonable pose prediction. Affinity prediction proved to be more challenging with generally poor correlation with experimental IC50s (Kendall tau?~?0.3). Even when the 36 crystal structures were used the accuracy of the predicted affinities was not appreciably improved. A possible cause of difficulty is the internal energy strain arising from conformational differences in the receptor across complexes, which may need to be properly estimated and incorporated into the SIE scoring function.     

Hydration forces between silica surfaces: experimental data and predictions from different theories

Silica is a very interesting system that has been thoroughly studied in the last decades. One of the most outstanding characteristics of silica suspensions is their stability in solutions at high salt concentrations. In addition to that, measurements of direct-interaction forces between silica surfaces, obtained by different authors by means of surface force apparatus or atomic force microscope (AFM), reveal the existence of a strong repulsive interaction at short distances (below 2 nm) that decays exponentially. These results cannot be explained in terms of the classical Derjaguin, Landau, Verwey, and Overbeek (DLVO) theory, which only considers two types of forces: the electrical double-layer repulsion and the London-van der Waals attraction. Although there is a controversy about the origin of the short-range repulsive force, the existence of a structured layer of water molecules at the silica surface is the most accepted explanation for it. The overlap of structured water layers of different surfaces leads to repulsive forces, which are known as hydration forces. This assumption is based on the very hydrophilic nature of silica. Different theories have been developed in order to reproduce the exponentially decaying behavior (as a function of the separation distance) of the hydration forces. Different mechanisms for the formation of the structured water layer around the silica surfaces are considered by each theory. By the aid of an AFM and the colloid probe technique, the interaction forces between silica surfaces have been measured directly at different pH values and salt concentrations. The results confirm the presence of the short-range repulsion at any experimental condition (even at high salt concentration). A comparison between the experimental data and theoretical fits obtained from different theories has been performed in order to elucidate the nature of this non-DLVO repulsive force.     

Improved sensitivity for quantification of proteins using triply charged cleavable isotope-coded affinity tag peptides

Isotope-coded affinity tag (ICAT) methods, in conjunction with capillary liquid chromatography/tandem mass spectrometry (LC/MS/MS), represent a promising approach for accurate protein quantification. However, sensitivity remains a challenge for the quantification of low-copy proteins in complex biological matrices. Here we investigated the electrospray ionization (ESI) and collision-activated dissociation (CAD) behavior of peptides derivatized with the cleavable ICAT (cICAT) reagent. For cICAT-peptides that were either synthesized or obtained by digestion of model proteins, the cICAT moiety showed a tendency toward protonation under positive ESI, producing relatively intense triply charged cICAT-peptide ions ([IP+3H]3+). [IP+3H]3+ exhibited significantly higher CAD reactivity than did the doubly charged cICAT-peptide ([IP+2H]2+), and produced a greater abundance of fragments at lower collision energies. Fragmentation spectra of [IP+3H]3+ showed variable intensities of doubly charged y and b ions, and the amount of sequence information obtained was dependent on the position of the cICAT-labeled cysteine residue in the peptide sequence. However, the absolute abundances of major fragments of [IP+3H]3+ were much higher than for [IP+2H]2+. Although the efficiency of identification of cICAT-peptides was compromised by their charge distribution toward the triply charged state and by the unique CAD behavior of the [IP+3H]3+ ions, it was found that the triply charged ions provided higher sensitivity than [IP+2H]2+ for quantification using multiple reaction monitoring (MRM). ESI and CAD conditions for MRM of [IP+3H]3+ were optimized, and, for all cICAT-peptides studied, MRM using [IP+3H]3+ as precursors showed 2- to 8-fold higher sensitivity than obtained using [IP+2H]2+, without compromising quantitative accuracy. Using this approach, the time course of tyrosine aminotransferase induction by methylprednisolone was monitored in rat livers. A remarkably better signal-to-noise ratio was observed by using [IP+3H]3+ for quantification compared to [IP+2H]2+.     

Conformational changes of protein adsorbed on tailored flat substrates with different chemistries

Changes in the bioactivity of a protein after being adsorbed on a material surface may result from conformational changes of the protein. Unfortunately, however, direct evidence of such conformational changes of proteins adsorbed on a flat material surface is sparse so far. This is because probing the conformation of an adsorbed protein on material surfaces, especially flat ones, remains a challenge due to considerable experimental difficulties. In this study, the surface-enhanced Raman scattering (SERS) technique is used to characterize the conformational changes of a protein (lysozyme) adsorbed on tailored flat gold substrates with different chemistries. Two such substrates are formed by self-assembly of octadecanethiol and thiolated PEG on gold chips (Au-C18 and Au-PEG). Preliminary results reveal that, compared to the hydrophobic Au-C18 surface, the hydrophilic Au-PEG surface has much smaller effect on the conformation of lysozyme in aqueous solution, which thereby keeps its high bioactivity. The conformational changes of lysozyme adsorbed on material surfaces with different chemistries are well correlated with changes in its bioactivity.     

Improved proton affinity measurements for proline and modified prolines using triple quadrupole and ion trap mass spectrometers

Proton affinity (PA) of compounds such as proline, cis-3-methylproline, cis-3-ethylproline, cis-3-isopropylproline and cis-3-isopentanylproline was determined by kinetic method with amines as the reference bases. The effective temperatures determined using ion trap and triple quadrupole mass spectrometers were found to be significantly different. In the case of the triple quadrupole instruments, the effective temperature depends significantly on the collision energy. The influence of the apparent basicity (GBapp) on the effective temperature may be used to estimate the difference in protonation entropy (DeltaDeltaS degrees) between the sample and reference compounds. In case of the ion trap mass spectrometer, the variation of the effective temperature as a function of the excitation amplitude is small, so it is difficult to account for the contribution of the entropy effects to the proton affinity value. A better estimation of the PA and DeltaDeltaS degrees values for the investigated molecules is obtained by combining the GBapp and Teff data pairs that are obtained from both the mass spectrometers.     

Lifetime predictions of EPR materials using the Wear-out approach

The Wear-out approach for lifetime prediction, based on cumulative damage concepts, is applied to several ethylene propylene rubber (EPR) cable insulation materials. EPR materials typically follow “induction-time” behavior in which their material properties change very slowly until just before failure, precluding the use of such time-dependent properties to predict failure. In the Wear-out approach, a material that has been aged at its ambient aging temperature T_a or at a low accelerated aging temperature is subsequently aged at a higher “Wear-out” temperature T_w in order to cause the material to reach its “failure” condition. In the simplest case, which involves the same chemical processes underlying degradation at T_a and T_w, a linear relationship is predicted between the time spent at T_a and the time required at T_w to complete the degradation. Data consistent with this expectation are presented for one of the EPR insulation materials. When the degradation chemistry at the two temperatures is different, a linear relationship between the time spent at T_a and the time required at T_w to complete the degradation is not generally expected. Even so, the Wear-out results for a second EPR material, which has evidence of changing chemistry, are reasonably linear and therefore useful from a predictive point-of-view. The Wear-out approach can therefore be used to transform non-predictive time-dependent material property results into predictive lifetime estimates. As a final example, the Wear-out approach is applied to an EPR insulation that had been aged in a nuclear power plant environment (∼51 °C) for times up to 23 years to show its likely viability for the hundreds of years predicted at this aging temperature from accelerated aging tests on EPR insulation materials.     

Study on the degeneracy of antisense peptides using affinity chromatography

The degeneracy of antisense peptides was studied by high-performance affinity chromatography. A model sense peptide (AAAA) and its antisense peptides (CGGG, GGGG, RGGG, SGGG) were designed and synthesized according to the degeneracy of genetic codes. An affinity column with AAAA as the ligand was prepared. The affinity chromatographic behaviors of antisense peptides on the column were evaluated. The results indicated that model antisense peptides have clear retention on the immobilized AAAA affinity column. RGGG showed the strongest affinity interaction. Similar result was obtained from another experiment that Arg-substituted antisense peptide of fusion peptide (1-11) of influenza virus A was also shown the highest affinity binding to immobilized fusion peptide.     

Electrostatic component of binding energy: Interpreting predictions from poisson–boltzmann equation and modeling protocols

Macromolecular interactions are essential for understanding numerous biological processes and are typically characterized by the binding free energy. Important component of the binding free energy is the electrostatics, which is frequently modeled via the solutions of the Poisson–Boltzmann Equations (PBE). However, numerous works have shown that the electrostatic component (ΔΔG_elec) of binding free energy is very sensitive to the parameters used and modeling protocol. This prompted some researchers to question the robustness of PBE in predicting ΔΔG_elec. We argue that the sensitivity of the absolute ΔΔG_elec calculated with PBE using different input parameters and definitions does not indicate PBE deficiency, rather this is what should be expected. We show how the apparent sensitivity should be interpreted in terms of the underlying changes in several numerous and physical parameters. We demonstrate that PBE approach is robust within each considered force field (CHARMM‐27, AMBER‐94, and OPLS‐AA) once the corresponding structures are energy minimized. This observation holds despite of using two different molecular surface definitions, pointing again that PBE delivers consistent results within particular force field. The fact that PBE delivered ΔΔG_elec values may differ if calculated with different modeling protocols is not a deficiency of PBE, but natural results of the differences of the force field parameters and potential functions for energy minimization. In addition, while the absolute ΔΔG_elec values calculated with different force field differ, their ordering remains practically the same allowing for consistent ranking despite of the force field used. © 2016 Wiley Periodicals, Inc.     

Enrichment and analysis of phosphopeptides under different experimental conditions using titanium dioxide affinity chromatography and mass spectrometry

Titanium dioxide metal oxide affinity chromatography (TiO₂‐MOAC) is widely regarded as being more selective than immobilized metal‐ion affinity chromatography (IMAC) for phosphopeptide enrichment. However, the widespread application of TiO₂‐MOAC to biological samples is hampered by conflicting reports as to which experimental conditions are optimal. We have evaluated the performance of TiO₂‐MOAC under a wide range of loading and elution conditions. Loading and stringent washing of peptides with strongly acidic solutions ensured highly selective enrichment for phosphopeptides, with minimal carryover of non‐phosphorylated peptides. Contrary to previous reports, the addition of glycolic acid to the loading solution was found to reduce specificity towards phosphopeptides. Base elution in ammonium hydroxide or ammonium phosphate provided optimal specificity and recovery of phosphorylated peptides. In contrast, elution with phosphoric acid gave incomplete recovery of phosphopeptides, whereas inclusion of 2,5‐dihydroxybenzoic acid in the eluant introduced a bias against the recovery of multiply phosphorylated peptides. TiO₂‐MOAC was also found to be intolerant of many reagents commonly used as phosphatase inhibitors during protein purification. However, TiO₂‐MOAC showed higher specificity than immobilized gallium (Ga³⁺), immobilized iron (Fe³⁺), or zirconium dioxide (ZrO₂) affinity chromatography for phosphopeptide enrichment. Matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS) was more effective in detecting larger, multiply phosphorylated peptides than liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI‐MS/MS), which was more efficient for smaller, singly phosphorylated peptides. Copyright © 2009 Crown in the right of Canada. Published by John Wiley & Sons, Ltd.     

Comparing different protocols of temperature selection in the parallel tempering method

Parallel tempering Monte Carlo simulations have been applied to a variety of systems presenting rugged free-energy landscapes. Despite this, its efficiency depends strongly on the temperature set. With this query in mind, we present a comparative study among different temperature selection schemes in three lattice-gas models. We focus our attention in the constant entropy method (CEM), proposed by Sabo et al. In the CEM, the temperature is chosen by the fixed difference of entropy between adjacent replicas. We consider a method to determine the entropy which avoids numerical integrations of the specific heat and other thermodynamic quantities. Different analyses for first- and second-order phase transitions have been undertaken, revealing that the CEM may be an useful criterion for selecting the temperatures in the parallel tempering.     

Improved extraction and clean-up of imidazolinone herbicides from soil solutions using different solid-phase sorbents

Extraction and quantification of herbicide residues from soil are important in understanding the behaviour of persistent herbicides. This research investigated extraction and clean-up methods for imidazolinone herbicides from soil and soil amended with organic material. A series of solvent mixes, pH conditions and sorbents was tested. Across three imidazolinone herbicides: imazapyr, imazethapyr and imazaquin, 0.5 M NaOH extraction gave greater than 90% recovery from soil samples; however, 0.5 M NaOH:MeOH (80:20) resulted in higher recovery for imazaquin, but not for the other two herbicides. Of the sorbents tested, the use of chromatographic mode sequencing using C₁₈ and SCX sorbents provided consistent high (>85%) recovery of all three herbicides from soil and separation of the herbicides from other soil components by high performance liquid chromatography (HPLC). These two methods will allow high recovery of these imidazolinone herbicides from soil and have the ability to detect these herbicides without interference from other soil components.     

Description of heterogeneity of the sorbent surface on the basis of adsorption kinetic data

The kinetics of adsorption of Rb⁺ and Cs⁺ ions on different non-polarized and polarized active carbons at temperatures of 25, 35, 45, and 65 °C was investigated. The obtained results were processed using the equations of the pseudo-first- and pseudo-second-order models. The pseudo-second-order model better describes the adsorption of alkaline metal ions on the carbons studied. The kinetic dependences of three types reflecting heterogeneity of the sorbent surface were revealed on the basis of the theoretical analysis of sorption systems.     

Syntheses of polyfunctionalized resveratrol derivatives using Wittig and Heck protocols

Improved protocols for Wittig reaction and palladium-catalyzed Heck coupling give expedient access to a series of unprecedented polyfunctionalized artificial-resveratrol derivatives. In the modified Wittig protocol, trimethylsilyl was used as a highly valuable protective group of the phenolic functions of starting aromatic materials. A clean O-alkylation of hydroxylated stilbenes with ethylene carbonate was also conducted. Thus, Wittig reaction followed by hydroxyethylation take place one-pot with only carbon dioxide as waste. Additionally, a palladium-catalyzed Heck coupling strategy was developed by using ferrocenyl phosphane ligands, and multi-functionalized hydroxylated stilbenes were obtained without the need of any protection/deprotection sequence. Up to six functional groups are introduced by these procedures, which limit the number of reactions steps, the waste toxicity, and the use of costly reagents.     

High-throughput profiling of the mitochondrial proteome using affinity fractionation and automation

Recent studies have demonstrated the need for complementing cellular genomic information with specific information on expressed proteins, or proteomics, since the correlation between the two is poor. Typically, proteomic information is gathered by analyzing samples on two-dimensional gels with the subsequent identification of specific proteins of interest by using trypsin digestion and mass spectrometry in a process termed peptide mass fingerprinting. These procedures have, as a rule, been labor-intensive and manual, and therefore of low throughput. The development of automated proteomic technology for processing large numbers of samples simultaneously has made the concept of profiling entire proteomes feasible at last. In this study, we report the initiation of the (eventual) complete profile of the rat mitochondrial proteome by using high-throughput automated equipment in combination with a novel fractionation technique using minispin affinity columns. Using these technologies, approximately one hundred proteins could be identified in several days. In addition, separate profiles of calcium binding proteins, glycoproteins, and hydrophobic or membrane proteins could be generated. Because mitochondrial dysfunction has been implicated in numerous diseases, such as cancer, Alzheimer's disease and diabetes, it is probable that the identification of the majority of mitochondrial proteins will be a beneficial tool for developing drug and diagnostic targets for associated diseases.     

Universal system for liquid stationary phase classification on the basis of thermodynamical data

Summary Equations modifying Rohrschneider's relationship between I and thermodynamical characteristics values are derived. Polarity in chromatography is discussed as a possibility of stationary phases or absorbents to enter into intermolecular interactions and is determined on the basis of the partial molar free energies of solution (G) of six test substances. A simple method for the calculation of stationary phase polarity in terms of G from retention indices and McReynolds constants is given. Equations are presented for the calculation of stationary phase selectivity utilizing G data tabulated for selected test substances. The thermodynamical basis of selecting a reference phase for a unified system expressing the selectivity of stationary phases which can also be applied for adsorbents is suggested. The energy equivalent to an index unit, G_i.u., is discussed.     

Second-order and higher-order multivariate calibration methods applied to non-multilinear data using different algorithms

We discuss and evaluate the current state of second-order and higher-order multivariate calibration methods devoted to the determination of compounds in non-multilinear data systems. We examine possible causes of multilinearity deviations:

(1)

a non-linear relationship between signal and analyte concentration;

(2)

a signal for a given sample that is non-multilinear; and,

(3)

component profiles that are not constant across the different samples.

We discuss the advantages and the limitations of the algorithms available to cope with these different situations.The review covers relevant analytical problems found in samples of environmental and biological interest, highlighting some significant examples, and evaluating the advantages and the limitations of the different algorithms available.     

Calorimetric study of the copolymers on basis perfluorinated germanium hydrides with different structures

The temperature dependences of heat capacity of copolymers on the basis of perfluorinated germanium hydrides have been measured using an adiabatic vacuum calorimeter over the temperature range from 6 K to the final temperature of their stability for the first time. Thus, the physical transformations were detected and their thermodynamic characteristics were estimated. The experimental results were used to calculate the standard thermodynamic functions, namely heat capacity, enthalpy, entropy and Gibbs function over the range from T → 0 to the final temperature stability of copolymers. The standard entropy of formation of the under study copolymers at T = 298.15 K was calculated. The obtained results were compared with corresponding data for hyperbranching perfluor polyphenylenegermaniums with other structures. Some conclusions about dependences of the thermodynamic polymers properties versus their structures were made.     

Exploring the effects of cooperative interactions on affinity using a pinwheel sensor system

A series of three pinwheel sensors were constructed with 1, 2, and 3 binding sites. Binding of Zn⁺² and Cd⁺² was monitored by fluorescence over a range of temperatures. The data demonstrate that cooperative interactions generally increase the effective affinity of the sensor. This effect is more pronounced in systems which have lower inherent affinity for the analyte.