Practical aspects of (1)H transverse paramagnetic relaxation enhancement measurements on macromolecules

The use of (1)H transverse paramagnetic relaxation enhancement (PRE) has seen a resurgence in recent years as method for providing long-range distance information for structural studies and as a probe of large amplitude motions and lowly populated transient intermediates in macromolecular association. In this paper we discuss various practical aspects pertaining to accurate measurement of PRE (1)H transverse relaxation rates (Gamma(2)). We first show that accurate Gamma(2) rates can be obtained from a two time-point measurement without requiring any fitting procedures or complicated error estimations, and no additional accuracy is achieved from multiple time-point measurements recorded in the same experiment time. Optimal setting of the two time-points that minimize experimental errors is also discussed. Next we show that the simplistic single time-point measurement that has been commonly used in the literature, can substantially underestimate the true value of Gamma(2), unless a relatively long repetition delay is employed. We then examine the field dependence of Gamma(2), and show that Gamma(2) exhibits only a very weak field dependence at high magnetic fields typically employed in macromolecular studies. The theoretical basis for this observation is discussed. Finally, we investigate the impact of contamination of the paramagnetic sample by trace amounts (5%) of the corresponding diamagnetic species on the accuracy of Gamma(2) measurements. Errors in Gamma(2) introduced by such diamagnetic contamination are potentially sizeable, but can be significantly reduced by using a relatively short time interval for the two time-point Gamma(2) measurement.     

Time-Resolved Crystallography at X-ray Free Electron Lasers and Synchrotron Light Sources

Serial femtosecond crystallography with biological macromolecules is a rapidly developing method tailored to the immense brilliance of the emerging free electron lasers for hard X-rays (X-ray FELs). Recently, the first successful time-resolved serial femtosecond crystallographic experiment at near atomic resolution was conducted at the Linac Coherent Light Source. The X-ray FEL-based experiments will trigger new developments not only at the X-ray FELs, but also at existing synchrotron light sources. This review will attempt to summarize some of the most important experiments to date and give a brief outlook on what to expect.     

Photoionization and Pyrolysis of a 1,4‐Azaborinine: Retro‐Hydroboration in the Cation and Identification of Novel Organoboron Ring Systems

The photoionization and dissociative photoionization of 1,4‐di‐tert‐butyl‐1,4‐azaborinine by means of synchrotron radiation and threshold photoelectron photoion coincidence spectroscopy is reported. The ionization energy of the compound was determined to be 7.89 eV. Several low‐lying electronically excited states in the cation were identified. The various pathways for dissociative photoionization were modeled by statistical theory, and appearance energies AE_0K were obtained. The loss of isobutene in a retro‐hydroboration reaction is the dominant pathway, which proceeds with a reverse barrier. Pyrolysis of the parent compound in a chemical reactor leads to the generation of several yet unobserved boron compounds. The ionization energies of the C₄H₆BN isomers 1,2‐ and 1,4‐dihydro‐1,4‐azaborinine and the C₃H₆BN isomer 1,2‐dihydro‐1,3‐azaborole were determined from threshold photoelectron spectra.     

Total Synthesis of the Anti‐inflammatory and Pro‐resolving Lipid Mediator MaR1n−3 DPA Utilizing an sp3–sp3 Negishi Cross‐Coupling Reaction

The first total synthesis of the lipid mediator MaR1_{n?3 DPA} ( 5 ) has been achieved in 12 % overall yield over 11 steps. The stereoselective preparation of 5 was based on a Pd‐catalyzed sp³–sp³ Negishi cross‐coupling reaction and a stereocontrolled Evans–Nagao acetate aldol reaction. LC‐MS/MS results with synthetic material matched the biologically produced 5 . This novel lipid mediator displayed potent pro‐resolving properties stimulating macrophage efferocytosis of apoptotic neutrophils.     

Improving Site‐Directed RNA Editing In Vitro and in Cell Culture by Chemical Modification of the GuideRNA

Adenosine‐to‐inosine deamination can be re‐addressed to user‐defined mRNAs by applying phosphothioate/2′‐methoxy‐modified guideRNAs. Dense chemical modification of the guideRNA clearly improves performance of the covalent conjugates inside the living cell. Furthermore, careful positioning of a few modifications controls editing selectivity in vitro and was exploited for the challenging repair of the Factor 5 Leiden missense mutation.     

Characterizing Methyl‐Bearing Side Chain Contacts and Dynamics Mediating Amyloid β Protofibril Interactions Using 13Cmethyl‐DEST and Lifetime Line Broadening

Many details pertaining to the formation and interactions of protein aggregates associated with neurodegenerative diseases are invisible to conventional biophysical techniques. We recently introduced ¹⁵N dark‐state exchange saturation transfer (DEST) and ¹⁵N lifetime line‐broadening to study solution backbone dynamics and position‐specific binding probabilities for amyloid β (Aβ) monomers in exchange with large (2–80 MDa) protofibrillar Aβ aggregates. Here we use ¹³C_methyl DEST and lifetime line‐broadening to probe the interactions and dynamics of methyl‐bearing side chains in the Aβ‐protofibril‐bound state. We show that all methyl groups of Aβ40 populate direct‐contact bound states with a very fast effective transverse relaxation rate, indicative of side‐chain‐mediated direct binding to the protofibril surface. The data are consistent with position‐specific enhancements of ¹³C_methyl‐${R{{{\rm tethered}\hfill \atop 2\hfill}}}$ values in tethered states, providing further insights into the structural ensemble of the protofibril‐bound state.     

Effective Control of the Electron-donating Ability of Phosphines by using Phosphazenyl and Phosphoniumylidyl Substituents

Phosphoniumylidyl and phosphazenyl groups are effective substituents to increase the electron-donating ability of tertiary phosphines. However, the influence of structural variations among those substituents on the electronic properties of the phosphines is little explored. Herein, we show that protonation of the ylidic carbon atom of phosphoniumylidyl phosphines increases the Tolman electronic parameter (TEP) by ΔTEP = 16.0–18.8 cm^–1. Furthermore, phosphazenyl phosphines were synthesized with isopropyl groups (NP{iPr}₃) and tetramethylguanidino groups (NP{tmg}₃) at the phosphonium center. Determination of their TEP values reveals a remarkable low substituent parameter of χ = –18.5 cm^–1 for the NP(tmg)₃ group. In addition, we prepared the corresponding gold(I) complexes and determined their solid-state structures using single-crystal X-ray diffraction studies to analyze the steric profile of the new phosphine ligands.     

Synthesis of Small‐Molecule Fluorescent Probes for the In Vitro Imaging of Calcium‐Activated Potassium Channel KCa3.1

Small‐molecule probes for the in vitro imaging of K_Ca3.1 channel‐expressing cells were developed. Senicapoc, showing high affinity and selectivity for the K_Ca3.1 channels, was chosen as the targeting component. BODIPY dyes 15 – 20 were synthesized and connected by a Cu^I‐catalyzed azide–alkyne [3+2]cycloaddition with propargyl ether senicapoc derivative 8 , yielding fluorescently labeled ligands 21 – 26 . The dimethylpyrrole‐based imaging probes 25 and 26 allow staining of K_Ca3.1 channels in NSCLC cells. The specificity was shown by removing the punctate staining pattern by pre‐incubation with senicapoc. The density of K_Ca3.1 channels detected with 25 and by immunostaining was identical. The punctate structure of the labeled channels could also be observed in living cells. Molecular modeling showed binding of the senicapoc‐targeting component towards the binding site within the ion channel and orientation of the linker with the dye along the inner surface of the ion channel.     

Improvements for ground-based remote sensing of atmospheric aerosol properties by additional polarimetric measurements

We discuss the improvements in the aerosol properties characterization resulting from the additional multi-wavelength polarization measurements measured by a new CIMEL polarized sun/sky-photometer, CE318-DP. In order to process direct-sun, sky and polarization measurements in a wide spectral range (340–1640 nm), we developed new calibration methods and strategies, e.g. using the Langley plot method to calibrate both direct-sun irradiance and sky radiance, as well as combining laboratory facilities with a vicarious method to calibrate the polarized sky measurements. For studying the impact of new polarimetric measurements on the retrievals of aerosol properties, we have processed an extensive record of field measurements using an updated Dubovik and King retrieval algorithm [Dubovik O, Sinyuk A, Lapyonok T, Holben BN, Mishchenko MI, et al. Application of spheroid models to account for aerosol particle nonsphericity in remote sensing of desert dust. J Geophys Res 2006;111:D11208.]. A preliminary analysis shows that adding polarization in the inversion can reduce possible errors (notably for about 30% of our field cases) in the fine mode size distribution, real part of refractive index and particle shape parameter retrievals, especially for small particles.     

Predicted binding rate of new cephalosporin antibiotics by a 3D-QSAR method: a new approach

Abstract  

Antibiotics are chemotherapeutic agents with activity against microorganisms, for example bacteria, fungi, or protozoa, used for the treatment of many types of diseases. Binding of antibiotics to serum proteins in human plasma is a major determinant of their pharmacodynamic and pharmacokinetic behavior and, consequently, can affect their systemic distribution in the body. Here, the predicted binding rates of ceftazidime and 13 other pharmacological agents classified as antibiotics to plasma proteins (percentage fraction bound; PFB) were evaluated by use of 3D-QSAR models. We attempted to establish the contribution of hydrogen bond donor/acceptor and hydrophobic properties supplied by electrostatic fields to the PFB. Significant cross-validated correlation q ² (0.5–0.7) and the fitted correlation r ² (0.7–0.97) coefficients revealed that these models have reasonable power to predict the design 19 new antibiotics using ceftazidime as template, these compounds being our suggestion for further studies.