Multidimensional umbrella sampling and replica‐exchange molecular dynamics simulations for structure prediction of transmembrane helix dimers

Structural information of a transmembrane (TM) helix dimer is useful in understanding molecular mechanisms of important biological phenomena such as signal transduction across the cell membrane. Here, we describe an umbrella sampling (US) scheme for predicting the structure of a TM helix dimer in implicit membrane using the interhelical crossing angle and the TM–TM relative rotation angles as the reaction coordinates. This scheme conducts an efficient conformational search on TM–TM contact interfaces, and its robustness is tested by predicting the structures of glycophorin A (GpA) and receptor tyrosine kinase EphA1 (EphA1) TM dimers. The nuclear magnetic resonance (NMR) structures of both proteins correspond to the global free‐energy minimum states in their free‐energy landscapes. In addition, using the landscape of GpA as a reference, we also examine the protocols of temperature replica‐exchange molecular dynamics (REMD) simulations for structure prediction of TM helix dimers in implicit membrane. A wide temperature range in REMD simulations, for example, 250–1000 K, is required to efficiently obtain a free‐energy landscape consistent with the US simulations. The interhelical crossing angle and the TM–TM relative rotation angles can be used as reaction coordinates in multidimensional US and be good measures for conformational sampling of REMD simulations. © 2013 Wiley Periodicals, Inc.     

95Mo magic angle spinning NMR at high field: improved measurements and structural analysis of the quadrupole interaction in monomolybdates and isopolymolybdates

In this study, 95Mo quadrupole couplings in various molydbates were measured easily and accurately with magic angle spinning (MAS) NMR under a directing field of 19.6 T. The resonance frequency of 54 MHz was sufficiently high to remove acoustic ringing artifacts, and the spectra could be analyzed in the usual terms of chemical shift and quadrupolar line shapes. For monomolybdates and molybdite, the quadrupole coupling dominated the NMR response, and the quadrupole parameters could be measured with better accuracy than in previous lower field studies. Moreover, despite the low symmetry of the molybdenum coordination, the usefulness of such measurements to probe molybdenum environments was established by ab initio density functional theory (DFT) calculations of the electric field gradient from known structures. The experimental NMR data correlated perfectly with the refined structures. In isopolymolybdates, the resonances were shapeless and DFT calculations were impossible because of the large and low symmetry unit cells. Nevertheless, empirical but clear NMR signatures were obtained from the spinning sidebands analysis or the MQMAS spectra. This was possible for the first time thanks to the improved baseline and sensitivity at high fields. With the generalization of NMR spectrometers operating above 17 T, it was predicted that 95Mo MAS NMR could evolve as a routine characterization tool for ill-defined structures such as supported molybdates in catalysis.     

Comparison of methods for particulate phase mercury analysis: sampling and analysis

Accurate and reliable sampling and analysis of mercury forms is an overriding aim of any atmospheric monitoring effort which seeks to understand the fate and transport of the metal in the environment. Although a fraction of the total mercury forms found in the atmosphere, particulate phase mercury, Hg(p), is believed to play a prominent role in both wet and dry deposition to the terrestrial and aquatic environments. Currently, microwave acid extraction and thermoreductive methodologies for analysis of Hg(p) samples are widely used. We report on the potential for the use of a thermoreductive method for Hg(p) analysis to evaluate and optimize it for use in routine monitoring networks. Pre-baked quartz filters can be placed in particulate samplers with well-characterized size cuts, such as dichotomous samplers and microoriface impactors. The thermoreductive methodology facilitates rapid analysis after sample collection. It requires no chemical extraction thereby eliminating the potential for contamination and generation of hazardous waste. Our results indicate that, on average, the thermoreductive method yields 30% lower values for fine fraction Hg(p) when compared with microwave acid digestion. This may be due to matrix interferents that reduce the collection efficiency of mercury onto gold preconcentration traps. Results for total particulate mercury samples indicate that on average the thermoreductive method yields 56% lower values for the coarse fraction when compared with microwave acid digestion.Experiments were also conducted in Detroit, MI, USA to investigate whether elevated reactive gaseous mercury (Hg(2+)(g)) in an urban environment can lead to an artifact during the collection of filters for Hg(p) analysis. Our results indicate a significantly higher amount of Hg(p) collected onto a filter using the conventional methodology as compared to a filter collected downstream of KCl-coated annular denuders in the absence of Hg(2+)(g). These results point to the presence of Hg(2+)(g) as an artifact during Hg(p) measurement. These results indicate that a denuder must be utilized upstream of a filter for Hg(p) collection to prevent significant Hg(2+)(g) artifact formation.     

Comparison of the spin exchange interactions in PbCu2(PO4)2 and SrCu2(PO4)2 on the basis of spin dimer analysis

The spin exchange interactions of PbCu₂(PO₄)₂ were examined by performing the spin dimer analysis based on the extended Hückel tight-binding method, and were compared with those of SrCu₂(PO₄)₂. The two strongest Cu–O⋯O–Cu super–superexchange interactions, J₁ (with Cu⋯Cu = 5.868 Å) and J₂ (with Cu⋯Cu = 5.184 Å), are strong and lead to a linear-four-spin-cluster model for both PbCu₂(PO₄)₂ and SrCu₂(PO₄)₂. Adjacent linear-four-spin-clusters interact substantially in SrCu₂(PO₄)₂, but weakly in PbCu₂(PO₄)₂. The difference in the magnetization behaviors of the two compounds was examined by calculating the magnetic excitation energies of the linear-four-spin-cluster model.     

Comparison of ultrasonic assisted digestion with traditional methods for alpha/beta analysis

An ever-increasing priority of many customers in the radiochemistry field is the turn-around time of sample analysis. While modern instrumentation provides acceptable detection limits with relatively short count times, the sample preparation step remains the time-consuming step in radiochemical analysis. We have developed fast sample preparation techniques for gross alpha/beta analysis based on ultrasonically assisted digestion as part of a mobile radiological analytical laboratory program in place at Los Alamos National Laboratory (LANL).     

An automated system for the analysis of G protein-coupled receptor transmembrane binding pockets: alignment, receptor-based pharmacophores, and their application

G protein-coupled receptors (GPCRs) share a common architecture consisting of seven transmembrane (TM) domains. Various lines of evidence suggest that this fold provides a generic binding pocket within the TM region for hosting agonists, antagonists, and allosteric modulators. Here, a comprehensive and automated method allowing fast analysis and comparison of these putative binding pockets across the entire GPCR family is presented. The method relies on a robust alignment algorithm based on conservation indices, focusing on pharmacophore-like relationships between amino acids. Analysis of conservation patterns across the GPCR family and alignment to the rhodopsin X-ray structure allows the extraction of the amino acids lining the TM binding pocket in a so-called ligand binding pocket vector (LPV). In a second step, LPVs are translated to simple 3D receptor pharmacophore models, where each amino acid is represented by a single spherical pharmacophore feature and all atomic detail is omitted. Applications of the method include the assessment of selectivity issues, support of mutagenesis studies, and the derivation of rules for focused screening to identify chemical starting points in early drug discovery projects. Because of the coarseness of this 3D receptor pharmacophore model, however, meaningful scoring and ranking procedures of large sets of molecules are not justified. The LPV analysis of the trace amine-associated receptor family and its experimental validation is discussed as an example. The value of the 3D receptor model is demonstrated for a class C GPCR family, the metabotropic glutamate receptors.     

Comparison of ab initio and density functional methods for vibrational analysis of TeCl4

Vibrational analysis of tellurium tetrachloride, TeCl₄, was performed with Hartree–Fock (HF), MP2, and generalized gradient approximation density functional theory (DFT) methods supplemented with polarized double-zeta split valence (DZVP) basis sets and relativistic effective core potentials (RECP) of Hay and Wadt. The molecular geometry is best reproduced at the HF and MP2/RECP+DZVP [polarized Hay and Wadt RECP for Te and 6–31G(d) basis set for Cl] levels of theory. The DFT methods gave rise to poorer results, especially those using Becke's 1988 exchange functional. Generally, the vibrational frequencies calculated by the MP2 and B3-type DFT methods with the all electron and RECP+DZVP basis sets as well as at the HF/RECP level were in satisfactory accord with the experimental data. The agreement was good enough to assist the assignment of the measured vibrational spectra. The best agreement with the experimental vibrational frequencies was achieved with the scaled HF/RECP force field. Consistent results were obtained for the unobserved A₂ (ν₄) fundamental, where the results of the best methods were within 4 cm⁻¹. The best force fields were obtained with the following methods: Becke3–Lee–Yang–Parr and Becke3–Perdew/all electron basis, MP2 and Becke3-Perdew/RECP+DZVP, and HF/RECP. The methods using RECPs are advantageous for large-scale computations. The RECP basis set effectively compensates the errors of the HF method for TeCl₄; however, it provides poor results with correlated methods. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 308–318, 1998     

Comparison of HPLC and multivariate regression methods for hydrocortisone and lidocaine analysis of pharmaceutical preparations

A reverse-phase high-performance liquid chromatographic (HPLC) method to determine hydrocortisone acetate, hydrocortisone hemisuccinate and lidocaine is described in this paper. The separation was made in a LichrCART C(18) column using a methanol-NaH(2)PO(4)/Na(2)HPO(4) (0.1 mol L(-1)) (pH=4.5) buffer solution as a mobile phase in isocratic mode (60:40 (v/v)). The mobile phase flow rate and the sample volume injected were 1 mL min(-1) and 20 micro L, respectively. The detection was made with a diode-array detector measuring at the maximum for each compound. Quantification limits ranging from 0.18 to 0.84 micro g L(-1) were obtained when the peak area was measured. The method was applied in pharmaceutical formulations that were compared with those obtained by through multivariate regression spectrophotometry and micellar capillary electrophoresis (MEKC). HPLC results are in accordance with the results obtained by MEKC. The spectrophotometric method was suitable only for synthetic samples.     

Comparison of extraction and derivatization methods for fatty acid analysis in solid environmental matrixes

This study involved comparison of different extraction and derivatization methods for determining FAs in soil and in four highly organic matrixes (cattle manure, pig slurry, compost, and vermicompost), by application of a multifactor categorical design. Although some studies have been carried out regarding the application of FA analysis to highly organic matrixes, comparison and verification are still required to test which methods of extraction and derivatization of FAs function best for these matrixes. We compared three extraction methods (one in which the same extraction mixture as used in the Folch method was employed, a modification of the Bligh and Dyer method, and a microwave-assisted extraction) and two derivatization procedures (alkaline methanolysis and derivatization with trimethylsulfonium hydroxide (TMSH)). The highest yields of FAs belonging to different structural classes, and of individual FAs used as microbial biomarkers were obtained by application of the same extraction mixture as in the Folch method and use of TMSH as derivatization agent. These methods also involved a significant reduction in the complexity and time involved in sample preparation.     

An IARC Manual series aimed at assisting cancer epidemiology and prevention. "Environmental carcinogens: selected methods of analysis"

Since 1975, the IARC has been preparing a series of volumes entitled "Environmental Carcinogens: Selected Methods of Analysis" (IARC Manual series) of which the purposes are to assist analysts, epidemiologists and regulatory authorities in planning or performing exposure measurements that are truly comparable between different studies. The Manual series provides expert information within each volume on multi-media sampling, methods of analyses and some background of epidemiology, metabolism, use/occurrence for a group of known or suspect carcinogens. So far, eleven volumes have been published or are in preparation on the following subjects: N-nitrosamines, vinyl chloride, PAH, aromatic amines, mycotoxins, N-nitroso compounds, volatile halogenated hydrocarbons, metals, passive smoking, benzene and alkylated benzenes, dioxins, PCDFs and PCBs. The presentation will discuss needs and priorities for use of analytical chemistry in estimating exposures of apparently greatest relevance to cancer causation, i.e. the approach to developing this series. Indications from epidemiology, evaluations of carcinogenic risk to humans, and recent developments in total exposure assessment are that new methods and matrices need more emphasis, e.g. as with biochemical dosimetry, exhaled breath, and in indoor air.     

Comparison and evaluation of some available methods for the analysis of lanthanide induced shift data

Some available methods for the analysis of lanthanide induced shift data have been examined. These methods are compared and evaluated using the data gathered from substituted phenyl tert-butyl carbinols.     

Comparison of three methods for fractionation and enrichment of low molecular weight proteins for SELDI-TOF-MS differential analysis

In most diseases, the clinical need for serum/plasma markers has never been so crucial, not only for diagnosis, but also for the selection of the most efficient therapies, as well as exclusion of ineffective or toxic treatment. Due to the high sample complexity, prefractionation is essential for exploring the deep proteome and finding specific markers.In this study, three different sample preparation methods (i.e., highly abundant protein precipitation, restricted access materials (RAM) combined with IMAC chromatography and peptide ligand affinity beads) were investigated in order to select the best fractionation step for further differential proteomic experiments focusing on the LMW proteome (MW inferior to 40,000 Da). Indeed, the aim was not to cover the entire plasma/serum proteome, but to enrich potentially interesting tissue leakage proteins. These three methods were evaluated on their reproducibility, on the SELDI-TOF-MS peptide/protein peaks generated after fractionation and on the information supplied.The studied methods appeared to give complementary information and presented good reproducibility (below 20%). Peptide ligand affinity beads were found to provide efficient depletion of HMW proteins and peak enrichment in protein/peptide profiles.     

"Up" versus "down" alignment and hydration structures of solutes at the air/water interface revealed by heterodyne-detected electronic sum frequency generation with classical molecular dynamics simulation

We unambiguously demonstrate the "up" versus "down" alignment of a pair of prototypical solute molecules adsorbed at the air/water interface for the first time using heterodyne-detected electronic sum frequency generation spectroscopy. This molecular alignment is also reproduced by classical molecular dynamics (MD) simulation theoretically. Furthermore, the MD simulation indicates distinctly different interface-specific hydration structures around the two solute molecules, which dictate the molecular alignment at the interface. It is concluded that the hydrophilicity difference between the terminal functional groups of the solute governs the molecular orientation and surrounding hydration structures at the interface.     

1H-13C/1H-15N heteronuclear dipolar recoupling by R-symmetry sequences under fast magic angle spinning for dynamics analysis of biological and organic solids

Fast magic angle spinning (MAS) NMR spectroscopy is becoming increasingly important in structural and dynamics studies of biological systems and inorganic materials. Superior spectral resolution due to the efficient averaging of the dipolar couplings can be attained at MAS frequencies of 40 kHz and higher with appropriate decoupling techniques, while proton detection gives rise to significant sensitivity gains, therefore making fast MAS conditions advantageous across the board compared with the conventional slow- and moderate-MAS approaches. At the same time, many of the dipolar recoupling approaches that currently constitute the basis for structural and dynamics studies of solid materials and that are designed for MAS frequencies of 20 kHz and below, fail above 30 kHz. In this report, we present an approach for (1)H-(13)C/(1)H-(15)N heteronuclear dipolar recoupling under fast MAS conditions using R-type symmetry sequences, which is suitable even for fully protonated systems. A series of rotor-synchronized R-type symmetry pulse schemes are explored for the determination of structure and dynamics in biological and organic systems. The investigations of the performance of the various RN(n)(v)-symmetry sequences at the MAS frequency of 40 kHz experimentally and by numerical simulations on [U-(13)C,(15)N]-alanine and [U-(13)C,(15)N]-N-acetyl-valine, revealed excellent performance for sequences with high symmetry number ratio (N/2n > 2.5). Further applications of this approach are presented for two proteins, sparsely (13)C/uniformly (15)N-enriched CAP-Gly domain of dynactin and U-(13)C,(15)N-Tyr enriched C-terminal domain of HIV-1 CA protein. Two-dimensional (2D) and 3D R16(3)(2)-based DIPSHIFT experiments carried out at the MAS frequency of 40 kHz, yielded site-specific (1)H-(13)C/(1)H-(15)N heteronuclear dipolar coupling constants for CAP-Gly and CTD CA, reporting on the dynamic behavior of these proteins on time scales of nano- to microseconds. The R-symmetry-based dipolar recoupling under fast MAS is expected to find numerous applications in studies of protein assemblies and organic solids by MAS NMR spectroscopy.     

Comparison of solid-phase microextraction and purge-and-trap methods for the analysis of the volatile fraction of butter

The volatile fraction of butter stored at three different temperatures was investigated to monitor quality during commercial shelf-life (90 days). Two different extraction techniques were compared: dynamic headspace (purge-and-trap), and static headspace (solid-phase microextraction, SPME). As expected, the dynamic extraction provided a generally higher amount of volatile compounds than that obtained by SPME, but, with reference to individual compounds, SPME seemed to provide better extraction for volatiles having a higher molecular mass. Despite the different performances, both methods were able to detect volatiles useful for evaluating changes during storage.     

Comparison of microemulsion electrokinetic chromatography and micellar electrokinetic chromatography methods for the analysis of phenolic compounds

In this study, microemulsion electrokinetic chromatography (MEEKC) and micellar electrokinetic chromatography (MEKC) were compared for their abilities to separate and detect thirteen phenolic compounds (syringic acid, p-coumaric acid, vanillic acid, caffeic acid, gallic acid, 3,4-dihydroxybenzoic acid, 4-hydroxybenzoic acid, (+)-catechin, (-)-epigallocatechin, (-)-epicatechin gallate, (-)-epigallocatechin gallate, (-)-epicatechin, and (-)-gallocatechin), and two other ingredients (caffeine and theophylline) in teas and grapes. Separation of phenolic compounds was improved by changing the SDS concentration for MEEKC, but the SDS concentration rarely affected the resolution for MEKC. Organic modifier (acetonitrile or methanol) was found to markedly influence the resolution and selectivity for both MEEKC and MEKC systems. In addition, a higher voltage and a higher column temperature improved the separation efficiency without any noticeable reduction in resolution for MEEKC whereas they caused a poor resolution for the MEKC system. Although separations with baseline resolution were achieved by the optimized MEEKC and MEKC methods, the separation selectivity resulting from the proposed MEEKC method was completely different from that of MEKC.     

Comparison of three post-column reaction methods for the analysis of bromate and nitrite in drinking water

Three post-column ion chromatographic methods (i.e., a sodium bromide–sodium nitrite method, an o-dianisidine method, and a potassium iodide–ammonium heptamolybdate method) were compared for bromate and nitrite analysis. Also, the effect of direct mixing of the reagents without ion suppressors for the sodium bromide–sodium nitrite method and the potassium iodide–ammonium heptamolybdate method was investigated. For the analysis of bromate, the three methods showed similar method detection limits (0.17–0.24 μg/l) with pneumatic reagent delivery systems. Direct reagent mixing achieved comparable detection limits to the suppressor configuration. The three methods are also compatible with conductivity detection. When used in combination with conductivity detection, this compatibility allows simultaneous analysis of bromate, nitrite, and other common ions in drinking water, such as bromide. It was found that the o-dianisidine method achieves μg/l-level detection of nitrite and bromate with a simpler configuration than the potassium iodide–ammonium heptamolybdate method, while the sodium bromide–sodium nitrite method was not sufficiently sensitive for nitrite analysis at the μg/l level.     

Comparison of QuEChERS sample preparation methods for the analysis of pesticide residues in fruits and vegetables

This article describes the comparison of different versions of an easy, rapid and low-cost sample preparation approach for the determination of pesticide residues in fruits and vegetables by concurrent use of gas and liquid chromatography (GC and LC) coupled to mass spectrometry (MS) for detection. The sample preparation approach is known as QuEChERS, which stands for “quick, easy, cheap, effective, rugged and safe”. The three compared versions were based on the original unbuffered method, which was first published in 2003, and two interlaboratory validated versions: AOAC Official Method 2007.01, which uses acetate buffering, and European Committee for Standardization (CEN) Standard Method EN 15662, which calls for citrate buffering. LC–MS/MS and GC–MS analyses using each method were tested from 50 to 1000 ng/g in apple–blueberry sauce, peas and limes spiked with 32 representative pesticides. As expected, the results were excellent (overall average of 98% recoveries with 10% RSD) using all 3 versions, except the unbuffered method gave somewhat lower recoveries for the few pH-dependent pesticides. The different methods worked equally well for all matrices tested with equivalent amounts of matrix co-extractives measured, matrix effects on quantification and chemical noise from matrix in the chromatographic backgrounds. The acetate-buffered version gave higher and more consistent recoveries for pymetrozine than the other versions in all 3 matrices and for thiabendazole in limes. None of the versions consistently worked well for chlorothalonil, folpet or tolylfluanid in peas, but the acetate-buffered method gave better results for screening of those pesticides. Also, due to the recent shortage in acetonitrile (MeCN), ethyl acetate (EtOAc) was evaluated as a substitute solvent in the acetate-buffered QuEChERS version, but it generally led to less clean extracts and lower recoveries of pymetrozine, thiabendazole, acephate, methamidophos, omethoate and dimethoate. In summary, the acetate-buffered version of QuEChERS using MeCN exhibited advantages compared to the other tested methods in the study.     

Comparison of metal analysis in sediments using EDXRF and ICP-OES with the HCl and Tessie extraction methods

The work presents an investigation on metal availability in sediments during 13 months using the dispersive-energy X-ray fluorescence (EDXRF) and atomic emission spectrometry with induced argon plasma (ICP-OES) techniques and single extraction (0.1 mol l⁻¹ HCl) and Tessie’s sequential speciation methods. The EDXRF technique could yield essentially the same profile as ICP-OES for the seasonal variation of metals in sediments, but in a more practical way. The sequential extraction procedure (SEP) was more efficient in metal dissolution than single extraction. The Pb, Ni, Al, Cr, and Fe elements were less efficiently extracted with single extraction in relation to sequential extraction. For Co both methodologies were equivalent, but for Cu and Mn the extraction was higher with single extraction. Single extraction does not mobilize Pb, Ni, Al, Cr, and Fe adsorbed on oxides and bound to organic matter. However for Cu and Mn, not only extracted these metals from the four fractions, but it also dissolved part of the fifth fraction (residual). Principal Component Analysis discriminated seasonal variations in the content of several metals, mainly Fe, Co, Ni, and Zn. The mobility of metallic ions in the sediments is conditioned to the seasonal flow of organic and inorganic material coming from the river or by the erosion of adjacent soils.