Sizing large proteins and protein complexes by electrospray ionization mass spectrometry and ion mobility

Mass spectrometry (MS) and ion mobility with electrospray ionization (ESI) have the capability to measure and detect large noncovalent protein-ligand and protein-protein complexes. Using an ion mobility method of gas-phase electrophoretic mobility molecular analysis (GEMMA), protein particles representing a range of sizes can be separated by their electrophoretic mobility in air. Highly charged particles produced from a protein complex solution using electrospray can be manipulated to produce singly charged ions, which can be separated and quantified by their electrophoretic mobility. Results from ESI-GEMMA analysis from our laboratory and others were compared with other experimental and theoretically determined parameters, such as molecular mass and cryoelectron microscopy and X-ray crystal structure dimensions. There is a strong correlation between the electrophoretic mobility diameter determined from GEMMA analysis and the molecular mass for protein complexes up to 12 MDa, including the 93 kDa enolase dimer, the 480 kDa ferritin 24-mer complex, the 4.6 MDa cowpea chlorotic mottle virus (CCMV), and the 9 MDa MVP-vault assembly. ESI-GEMMA is used to differentiate a number of similarly sized vault complexes that are composed of different N-terminal protein tags on the MVP subunit. The average effective density of the proteins and protein complexes studied was 0.6 g/cm(3). Moreover, there is evidence that proteins and protein complexes collapse or become more compact in the gas phase in the absence of water.     

Do intramolecular halogen bonds exist? Ab initio calculations and crystal structures’ evidences

Cl···O intramolecular contacts are analysed here. Hence the Cambridge Structural Database (CSD) search was performed to find five-membered Cl–C=C–C=O pseudo-rings closed through Cl···O intramolecular contacts. Such rings were analysed and it was found that some of Cl···O distances are smaller than the corresponding sum of van der Waals radii. Additionally ab initio MP2/6-311++G(d,p) calculations and AIM analyses were carried out here on 3-chloropropenal and its fluoro derivatives to deepen the nature of intramolecular Cl···O interactions, some of findings may indicate that they are attractive and stabilizing ones. This paper is dedicated to Prof. T. M. Krygowski on the occasion of his 70th birthday     

Comparative Evaluation of CE and HPLC for Determination of Cotinine in Human Urine

Two rapid and popular methods—capillary electrophoresis (CE) and high-performance liquid chromatography (HPLC) have been compared for analysis of cotinine in human urine. Cotinine was analyzed in less than 7 min, with detection limits of 5 and 3.2 ng mL⁻¹ for CE and HPLC, respectively. The performance of the methods was evaluated in terms of sensitivity, specificity, precision, accuracy, and limits of detection and quantification. Calibration plots were linear in the range 50–4,000 ng mL⁻¹, at least, and mean recoveries were satisfactory for both techniques. The methods were successfully used for quantification of cotinine in urine.     

Sparsely substituted chlorins as core constructs in chlorophyll analogue chemistry. I. Synthesis

Five routes to stable chlorins bearing 0 or 1 meso substituents have been investigated, among which reaction of a 9-bromo-1-formyldipyrromethane and 2,3,4,5-tetrahydro-1,3,3-trimethyldipyrrin proved most effective. Application of this route afforded metallochlorins [Cu(II), Zn(II), and Pd(II)] including the chlorin lacking any β-pyrrole and meso substituents.     

Sparsely substituted chlorins as core constructs in chlorophyll analogue chemistry. II. Derivatization

Stable chlorins bearing few or no substituents have been subjected to a variety of reactions including demetalation, magnesium insertion, oxochlorin formation, and bromination followed by Suzuki coupling. The kinetics of deuteration also have been determined for two oxochlorins and a series of chlorins bearing 0, 1, 2, or 3 meso-aryl substituents.     

Pattern formation in nonextensive thermodynamics: selection criterion based on the Renyi entropy production

We analyze a system of two different types of Brownian particles confined in a cubic box with periodic boundary conditions. Particles of different types annihilate when they come into close contact. The annihilation rate is matched by the birth rate, thus the total number of each kind of particles is conserved. When in a stationary state, the system is divided by an interface into two subregions, each occupied by one type of particles. All possible stationary states correspond to the Laplacian eigenfunctions. We show that the system evolves towards those stationary distributions of particles which minimize the Renyi entropy production. In all cases, the Renyi entropy production decreases monotonically during the evolution despite the fact that the topology and geometry of the interface exhibit abrupt and violent changes.     

An analysis of the electrostatic interaction between nucleic acid bases

Results from several commonly used approximate methods of evaluating electrostatic interactions have been compared to the rigorous, nonexpanded electrostatic energies at both uncorrelated and correlated levels of theory. We examined a number of energy profiles for both hydrogen bonded and stacked configurations of the nucleic acid base pairs. We found that the penetration effects play an extremely important role and the expanded electrostatic energies are significantly underestimated with respect to the ab initio values. Apart from the inability to reproduce the magnitudes of the ab initio electrostatic energy, there are other problems with the available approximate electrostatic models. For example, the distributed multipole analysis, one of the most advanced methods, is extremely sensitive to the basis set and level of theory used to evaluate the multipole moments. Detailed ab initio results are provided that other researchers could use to test their approximate models.     

Infrared and Raman Spectroscopy of Methylcyanodiacetylene (CH3C5N)

A spectroscopic study combining IR absorption and Raman scattering is presented for methylcyanodiacetylene (CH₃C₅N). Gas‐phase, cryogenic matrix‐isolated, and pure solid‐phase substance was analyzed. Out of 16 normal vibrational modes, 14 were directly observed. The analysis of the spectra was assisted by quantum chemical calculations of vibrational frequencies, IR absorption intensities, and Raman scattering activities at density functional theory and ab initio levels. Previous assignments of gas‐phase IR absorption bands were revisited and extended.