1.Agonist binding by the β2-adrenergic receptor: an effect of receptor conformation on ligand association-dissociation characteristics.
Plazinska A1, Plazinski W, Jozwiak K. Eur Biophys J. 2015 Apr;44(3):149-63. doi: 10.1007/s00249-015-1010-4. Epub 2015 Mar 1.
The β2-adrenergic receptor (β2-AR), a G protein-coupled receptor (GPCR), is a physiologically important transmembrane protein that is a target for drugs used for treatment of asthma and cardiovascular diseases. Study of the first steps of ligand recognition and the molecular basis of ligand binding to the orthosteric site is essential for understanding the pharmacological properties of the receptor. In this work we investigated the characteristic features of the agonist association-dissociation process to and from the different conformational forms of β2-AR by use of advanced molecular modeling techniques. The investigation was focused on estimating the free energy profiles (FEPs) corresponding to the process of a full agonist ((R,R)-fenoterol) and an inverse agonist (carazolol) binding and unbinding to and from β2-AR. The two different conformational forms of β2-AR, i.e. active β2-AR-PDB: 3P0G and inactive β2-AR-PDB: 2RH1 were included in this stage of the study.
2.[Simultaneous determination of nine beta-blockers in porcine tissues by ultra-fast liquid chromatography coupled with quadrupole/linear ion trap mass spectrometry].
Zhang H, Xu H, Gao J, Liang C, Xu B, Geng J, Wang F, Zhang X, Cheng G. Se Pu. 2014 Jun;32(6):573-81.
A highly sensitive method using ultra-fast liquid chromatography coupled with quadrupole/linear ion trap mass spectrometry (UFLC-Q/Trap MS) was developed to simultaneously screen and confirm nine beta-blockers (BBs) in porcine tissues (porcine muscle, liver and kidney). The method was used for trace determination of atenolol, pindolol, acebutolol, metoprolol, carazolol, labetalol, bisoprolol, propranolol and penbutolol. The homogenized tissues were hydrolyzed by beta-glucuronidase/aryl sulfatase and extracted with acetonitrile, followed by continuous purification procedures of disperse solid phase extraction (d-SPE) with diatomaceous earth and BondElut cartridge. The ultra-fast chromatographic separation was conducted on a Kinetex C18-XB column (150 mm x 2.1 mm, 2.6 microm) using 0.1% (v/v) formic acid aqueous solution and methanol as mobile phases in gradient elution. The optimized ion transitions were mployed in the mixed-mode of scheduled multiple reaction monitoring (sMRM) -information dependent acquisition (IDA)-enhanced product ion (EPI) scan.
3.Renewable sorbent material for solid phase extraction with direct coupling of sequential injection analysis-bead injection to liquid chromatography-electrospray ionization tandem mass spectrometry.
Boonjob W1, Sklenářová H, Barron L, Solich P, Smith N. Anal Bioanal Chem. 2015 Jul;407(19):5719-28. doi: 10.1007/s00216-015-8752-9. Epub 2015 May 14.
The use of small scale renewable sorbent material for automated solid phase extraction of multi-residue pharmaceuticals in environmental samples exploiting the sequential injection analysis-bead injection with direct coupling to liquid chromatography-electrospray ionization tandem mass spectrometry (SIA-BI-μSPE-LC-ESI-MS/MS) is presented to determine beta-blockers, namely atenolol, sotalol, pindolol, acebutolol, timolol, metoprolol, labetalol, carazolol, propranolol and betaxolol. These compounds yielded the same product ions, therefore were affected in terms of quantification when flow injection analysis-mass spectrometry (FIA-MS) was used. Thus, analytes and matrix present in the sample travel together into the ionization source which can seriously affect the ionization efficiency and analyte signals due to monitoring over a short time period. Graphical abstract A two-dimensional analysis involving a time dimension (retention time) and an m/z dimension (fragmentation ion) is promising for the various sample types.
4.DIRECT-ID: An automated method to identify and quantify conformational variations-application to β2 -adrenergic GPCR.
Lakkaraju SK1, Lemkul JA1, Huang J1, MacKerell AD Jr1. J Comput Chem. 2016 Feb 5;37(4):416-25. doi: 10.1002/jcc.24231. Epub 2015 Nov 12.
The conformational dynamics of a macromolecule can be modulated by a number of factors, including changes in environment, ligand binding, and interactions with other macromolecules, among others. We present a method that quantifies the differences in macromolecular conformational dynamics and automatically extracts the structural features responsible for these changes. Given a set of molecular dynamics (MD) simulations of a macromolecule, the norms of the differences in covariance matrices are calculated for each pair of trajectories. A matrix of these norms thus quantifies the differences in conformational dynamics across the set of simulations. For each pair of trajectories, covariance difference matrices are parsed to extract structural elements that undergo changes in conformational properties. As a demonstration of its applicability to biomacromolecular systems, the method, referred to as DIRECT-ID, was used to identify relevant ligand-modulated structural variations in the β2 -adrenergic (β2 AR) G-protein coupled receptor.