蛋白受体结合筛选-气质联用法测定动物组织中的氯霉素残留

建立了动物组织中氯霉素残留的蛋白受体结合筛选和GC MS分析方法。受体结合生物筛选的筛选限为0.1μg kg,假阴性率为零,其它常用抗生素的交叉反应率均<0.1%。筛选阳性样本经液液分配萃取、C18SPE固相萃取净化后衍生进行GC MS的NCI选择离子监测分析。其定量检出限为0 1μg kg,样品添加水平0 1～10μg kg时,回收率为76 2%～103 5%,相对标准偏差为7 5%～10 6%。     

Development and validation of a high‐performance liquid chromatography method for the quantification of talazoparib in rat plasma: Application to plasma protein binding studies

A sensitive and selective RP‐HPLC method has been developed and validated for the quantification of a highly potent poly ADP ribose polymerase inhibitor talazoparib (TZP) in rat plasma. Chromatographic separation was performed with isocratic elution method. Absorbance for TZP was measured with a UV detector (SPD‐20A UV–vis) at a λ_max of 227 nm. Protein precipitation was used to extract the drug from plasma samples using methanol–acetonitrile (65:35) as the precipitating solvent. The method proved to be sensitive and reproducible over a 100–2000 ng/mL linearity range with a lower limit of quantification (LLQC) of 100 ng/mL. TZP recovery was found to be >85%. Following analytical method development and validation, it was successfully employed to determine the plasma protein binding of TZP. TZP has a high level of protein binding in rat plasma (95.76 ± 0.38%) as determined by dialysis method.     

An application of fast protein liquid chromatography (FPLC) in the purification of retinol binding protein from rat serum

Summary Retinol Binding Protein (RBP) is the specific plasma protein for the transport of retinol from liver to peripheral tissues. It is a single polypeptide chain of approximately 21 KDa, and circulates as a 11 molar complex with transthyretin (TTR). The relative low concentration in plasma (40–50 g/ml and its chromatographic behaviour on ionic exchangers render the purification of rat RBP particularly laborious. In this paper we report a simple and semi-automatic method for the preparative purification to homogeneity of rat serum RBP. The method includes: (1) Selective removal of albumin by affinity chromatography on a Blue Sepharose column; (2) Chromatography on a Mono Q strong anion exchange column; (3) Dissociation of the RBP-TTR complex by 3 M urea; (4) Concentration, desalting and freeze drying. The purified RBP has been used for the production in rabbit of antirat RBP specific antibodies for studies on nutritional control of RBP synthesis and metabolism.     

An automated method for predicting the positions of hydrogen-bonding atoms in binding sites

Hydrogen bonds are the most specific, and therefore predictable of the intermolecular interactions involved in ligand–protein binding. Given the structure of a molecule, it is possible to estimate the positions at which complementary hydrogen-bonding atoms could be found. Crystal-survey data are used in the design of a program, HBMAP, that generates a hydrogen-bond map for any given ligand, which contains all the feasible positions at which a complementary atom could be found. On superposition of ligands, the overlapping regions of their maps represent positions of receptor atoms to which each molecule can bind. The certainty of these positions is increased by the incorporation of a larger number and diversity of molecules. In this work, superposition is achieved using the program HBMATCH, which uses simulated annealing to generate the correspondence between points from the hydrogen-bonding maps of the two molecules. Equivalent matches are distinguished on the basis of their steric similarity. The strategy is tested on a number of ligands for which ligand–protein complexes have been solved crystallographically, which allows validation of the techniques. The receptor atom positions of thermolysin are successfully predicted when the correct superposition is obtained.     

Enantioseparation of N‐acetyl‐glutamine enantiomers by LC–MS/MS and its application to a plasma protein binding study

A novel chiral method was developed and validated to determine N‐acetyl‐glutamine (NAG) enantiomers by liquid chromatography–tandem mass spectrometry (LC–MS/MS). Enantioseparation was achieved on a Chiralpak QD‐AX column (150 × 4.6 mm i.d., 5 μm) using methanol–water (50 mm ammonium formate, pH 4.3; 70:30, v/v) at a flow rate of 500 μL/min. The detection was operated with an electrospray ionization source interface in positive mode. The ion transition for NAG enantiomers was m/z 189.0 → 130.0. The retention time of N‐acetyl‐l ‐glutamine and N‐acetyl‐d ‐glutamine were 15.2 and 17.0 min, respectively. Calibration curves were linear over the range of 0.02–20 μg/mL with r > 0.99. The deviation of accuracy and the coefficient of variation of within‐run and between‐run precision were within 10% for both enantiomers, except for the lower limit of quantification (20 ng/mL), where they deviated <15%. The recovery was >88% and no obvious matrix effect was observed. This method was successfully applied to investigate the plasma protein binding of NAG enantiomers in rats. The results showed that the plasma protein binding of NAG enantiomers was stereoselective. The assay method also exhibited good application prospects for the clinical monitoring of free drugs in plasma.     

Coarse-graining of protein structures for the normal mode studies

The coarse-grained structural model such as Gaussian network has played a vital role in the normal mode studies for understanding protein dynamics related to biological functions. However, for the large proteins, the Gaussian network model is computationally unfavorable for diagonalization of Hessian (stiffness) matrix for the normal mode studies. In this article, we provide the coarse-graining method, referred to as "dynamic model condensation," which enables the further coarse-graining of protein structures consisting of small number of residues. It is shown that the coarser-grained structures reconstructed by dynamic model condensation exhibit the dynamic characteristics, such as low-frequency normal modes, qualitatively comparable to original structures. This sheds light on that dynamic model condensation and may enable one to study the large protein dynamics for gaining insight into biological functions of proteins.     

Simultaneous determination of imperatorin and its metabolites in vitro and in vivo by a GC‐MS method: application to a bioavailability and protein binding ability study in rat plasma

In this study, a simple and sensitive gas chromatography–mass spectrometry method was developed for the study of bioavailability and protein binding and the metabolism of imperatorin in rat. The results showed that the pharmacokinetics of imperatorin after intravenous and oral administration in rats exhibited linear characteristics. The absolute bioavailability of imperatorin was calculated as ~3.85, ~33.51 and ~34.76% for 6.25, 12.5 and 25 mg/kg, respectively. The low bioavailability of imperatorin may be attributed to the poor absorption or extensive metabolism. The phase I metabolites of imperatorin formed in vitro by rat liver microsomes were studied, and two metabolites were isolated and identified as xanthotoxol and heraclenin. Following oral administration of imperatorin, one metabolite (heraclenin) was detected in rat plasma, and two potential metabolites (xanthotoxol and heraclenin) were detected in rat urine. However, none of potential metabolites was detected in rat feces and bile. The results showed that the metabolites of imperatorin were excreted by kidney, and heraclenin was associated with an active component. Demethylation and oxygenization were the main metabolic pathways. In vitro plasma protein binding of imperatorin was 90.1 and 92.6% for the spiked rat plasma concentrations of 1.0 and 50.0 µg/mL, respectively, indicating that imperatorin showed slow distribution into the intra‐ and extracellular space. Copyright © 2013 John Wiley & Sons, Ltd.     

An efficient use of the WATERGATE W5 sequence for observing a ligand binding with a protein receptor

An efficient pulse sequence for observing a ligand binding with a receptor has been developed by incorporating the WATERGATE W5 sequence. In the conventional water ligand observed via gradient spectroscopy (WaterLOGSY) techniques, the water resonance is selectively excited using, e.g. the double-pulsed field gradient spin-echo (DPFGSE) sequence at the initial portion of pulse sequence. In the current version, the modified WATERGATE W5 sequence is incorporated at the initial portion of the pulse sequence, and the resonance at the water frequency can be selectively reserved by the modified WATERGATE W5 sequence. The efficiency of ligand-observed NMR screening techniques has been demonstrated using the human serum albumin (HSA)-tryptophan complex.     

A HMM-based method to predict the transmembrane regions of beta-barrel membrane proteins

A novel method is developed to model and predict the transmembrane regions of beta-barrel membrane proteins. It is based on a Hidden Markov model (HMM) with architecture obeying those proteins' construction principles. The HMM is trained and tested on a non-redundant set of 11 beta-barrel membrane proteins known to date at atomic resolution with a jack-knife procedure. As a result, the method correctly locates 97% of 172 transmembrane beta-strands. Out of the 11 proteins, the barrel size for ten proteins and the overall topology for seven proteins are correctly predicted. Additionally, it successfully assigns the entire topology for two new beta-barrel membrane proteins that have no significant sequence homology to the 11 proteins. Predicted topology for two candidates for beta-barrel structure of the outer mitochondrial membrane is also presented in the paper.     

Generic approach to the method development of intact protein separations using hydrophobic interaction chromatography

We describe a liquid chromatography method development approach for the separation of intact proteins using hydrophobic interaction chromatography. First, protein retention was determined as function of the salt concentration by isocratic measurements and modeled using linear regression. The error between measured and predicted retention factors was studied while varying gradient time (between 15 and 120 min) and gradient starting conditions, and ranged between 2 and 15%. To reduce the time needed to develop optimized gradient methods for hydrophobic interaction chromatography separations, retention‐time estimations were also assessed based on two gradient scouting runs, resulting in significantly improved retention‐time predictions (average error < 2.5%) when varying gradient time. When starting the scouting gradient at lower salt concentrations (stronger eluent), retention time prediction became inaccurate in contrast to predictions based on isocratic runs. Application of three scouting runs and a nonlinear model, incorporating the effects of gradient duration and mobile‐phase composition at the start of the gradient, provides accurate results (improved fitting compared to the linear solvent‐strength model) with an average error of 1.0% and maximum deviation of –8.3%. Finally, gradient scouting runs and retention‐time modeling have been applied for the optimization of a critical‐pair protein isoform separation encountered in a biotechnological sample.     

An alternative to the “Star Path” enhancement of the ADMA linear scaling method for protein modeling

With the aim of improving the performance of macromolecular quantum chemistry conformation analysis and reaction path following methods, the Adjustable Density Matrix Assembler (ADMA) method has already been combined with some faster although less accurate density matrix extrapolation methods, such as the Löwdin‐Inverse‐Löwdin (LIL) extrapolation along a potential energy surface, and a strategically arranged back‐and‐forth switching between these methods has been proven to be advantageous. Here, an alternative approach is proposed and investigated, based on several actual test calculations, where the “inexpensive” LIL density matrix extrapolation steps are replaced by only somewhat more expensive, but still ADMA‐based calculations, where in the “rough‐search stage,” only interactions of shorter distances within the macromolecule are considered. It is shown that this approach is viable, as an alternative to the “Star Path” method including both ADMA and LIL steps. © 2017 Wiley Periodicals, Inc.