Monitoring copopulated conformational states during protein folding events using electrospray ionization-ion mobility spectrometry-mass spectrometry

The precise mechanism of protein folding remains elusive and there is a deficiency of biophysical techniques that are capable of monitoring the individual behavior of copopulated protein conformers during the folding process. Herein, an ion mobility spectrometry (IMS) device integrated with electrospray ionization mass spectrometry (ESI-MS) has been used to successfully separate and analyze protein conformers differing in cross section and/or charge state. In an initial test, an ensemble of folded and partially folded conformers of the protein cytochrome c was separated. A detailed study undertaken on the amyloidogenic protein beta(2)-microglobulin (beta(2)m), which forms fibrils by protein unfolding followed by self-aggregation and is responsible for the disease dialysis-related amyloidosis, has generated important insights into its folding landscape. Initially, a systematic titration of beta(2)m over the pH range 2 to 7 using ESI-IMS-MS allowed individual conformers to be monitored and quantified throughout the acid denaturation process. Furthermore, a comparison of wild-type beta(2)m with single and double amino acid variants with a range of folding stabilities and propensities for amyloid fibril formation has provided illuminating evidence of the role of different conformers in protein stability and amyloidogenic aggregation. The ESI-IMS-MS data presented here not only demonstrate an important and informative further dimension to ESI-MS, but also illustrate the potential of the ESI-IMS-MS technique for unravelling protein folding enigmas in general and studying protein misfolding diseases in particular.     

Ciliation and lamellae in crystalline polymers

Molecular cilia, the uncrystallized portions of chains already partly attached to polymer crystals, exert a profound influence on the course of polymeric crystallization with ultimate responsibility for the divergence of adjacent lamellae which leads to spherulitic growth. Their effective size and pressure have been measured, in α-polypropylene, from electron microscopic measurements of the separation and maximum curvature of lamellae in row structures. That cilia exist and extend the effective region occupied by a lamella beyond the geometrical confines of its fold surfaces is important for crystallization theory and may well have implications for the connection of lamellae into networks and for gelation.     

Darobactin B Stabilises a Lateral-Closed Conformation of the BAM Complex in E. coli Cells

The β-barrel assembly machinery (BAM complex) is essential for outer membrane protein (OMP) folding in Gram-negative bacteria, and represents a promising antimicrobial target. Several conformational states of BAM have been reported, but all have been obtained under conditions which lack the unique features and complexity of the outer membrane (OM). Here, we use Pulsed Electron-Electron Double Resonance (PELDOR, or DEER) spectroscopy distance measurements to interrogate the conformational ensemble of the BAM complex in E. coli cells. We show that BAM adopts a broad ensemble of conformations in the OM, while in the presence of the antibiotic darobactin B (DAR-B), BAM′s conformational equilibrium shifts to a restricted ensemble consistent with the lateral closed state. Our in-cell PELDOR findings are supported by new cryoEM structures of BAM in the presence and absence of DAR-B. This work demonstrates the utility of PELDOR to map conformational changes in BAM within its native cellular environment.     

Markov Chain Sampling Methods for Dirichlet Process Mixture Models

Abstract

This article reviews Markov chain methods for sampling from the posterior distribution of a Dirichlet process mixture model and presents two new classes of methods. One new approach is to make Metropolis—Hastings updates of the indicators specifying which mixture component is associated with each observation, perhaps supplemented with a partial form of Gibbs sampling. The other new approach extends Gibbs sampling for these indicators by using a set of auxiliary parameters. These methods are simple to implement and are more efficient than previous ways of handling general Dirichlet process mixture models with non-conjugate priors.     

Enhanced fusion-evaporation cross sections in neutron-rich 132Sn on 64Ni

Evaporation residue cross sections have been measured with neutron-rich radioactive 132Sn beams on 64Ni in the vicinity of the Coulomb barrier. The average beam intensity was 2 x 10(4) particles per second and the smallest cross section measured was less than 5 mb. Large sub-barrier fusion enhancement was observed. Coupled-channel calculations taking into account inelastic excitation significantly underpredict the measured cross sections below the barrier. The presence of several neutron transfer channels with large positive Q values suggests that multinucleon transfer may play an important role in enhancing the fusion of 132Sn and 64Ni.     

Precise mass measurement of a double-stranded 500 base-pair (309 kDa) polymerase chain reaction product by negative ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry

Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS) has been used to determine the mass of a double-stranded 500 base-pair (bp) polymerase chain reaction (PCR) product with an average theoretical mass of the blunt-ended (i.e. unadenylated) species of 308 859.35 Da. The PCR product was generated from the linearized bacteriophage Lambda genome which is a double-stranded template. Utilization of ethanol precipitation in tandem with a rapid microdialysis step to purify and desalt the PCR product was crucial to obtain a precise mass measurement. The PCR product (0.8 pmol/μL) was electrosprayed from a solution containing 75% acetonitrile, 25 mM piperidine, and 25 mM imidazole and was infused at a rate of 200 nL/min. The average molecular mass and the corresponding precision were determined using the charge-states ranging from 172 to 235 net negative charges. The experimental mass and corresponding precision (reported as the 95% confidence interval of the mean) was 309 406 +/- 27 Da (87 ppm). The mass accuracy was compromised due to the fact that the PCR generates multiple products when using Taq polymerase due to the non-template directed 3'-adenylation. This results in a mixture of three PCR products with nearly identical mass (i.e. blunt-ended, mono-adenylated and di-adenylated) with unknown relative abundances that were not resolved in the spectrum. Thus, the experimental mass will be a weighted average of the three species which, under our experimental conditions, reflects a nearly equal concentration of the mono- and di-adenylated species. This report demonstrates that precise mass measurements of PCR products up to 309 kDa (500 bp) can be routinely obtained by ESI-FTICR requiring low femtomole amounts. Copyright 1999 John Wiley & Sons, Ltd.     

Lifetime of the 3.854 MeV state in 13C by the recoil-distance method

The lifetime of the 3.85 MeV state in ¹³C has been remeasured by the recoil-distance method using the ¹²C(d, p)¹³C reaction. The value of the mean life determined is τ = 13.0 ± 0.4 ps. This result is compared to previous measurements, both by the Doppler-shift attenuation method and the recoil-distance method.     

In situ vinylindole synthesis. Diels-alder reactions with maleimides to give tetrahydrocarbazoles

Tetrahydrocarbazoles have been prepared in one-flask syntheses from indoles, ketones or aldehydes, and maleimides, with acid catalysis. The reactions involve a condensation of the indole with the ketone or aldehyde, followed by an in situ trapping of the vinylindole in a Diels-Alder addition with a maleimide. Isomerization of the double bond into the indole nucleus gave the tetrahydrocarbazoles which were isolated ( 6, 9 , and 10 ). Variation of the indole, carbonyl compound, and maleimide has been explored. The predominant stereochemistry of the tetrahydro ring in the products is all-cis, although a second stereoisomer has been isolated. Two regioisomers were generated from all unsymmetrical 2-alkanones, except 2-butanone, which gave the single isomer 9a . Aromatization of tetrahydrocarbazoles 6 to carbazoles 7 was accomplished with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone.     

Controlled/living radical polymerization of isoprene and butadiene in emulsion

A process for RAFT-controlled radical polymerization in emulsion [36] has been applied to the polymerizations of isoprene and of butadiene in emulsion systems, with the goal of producing latex particles containing block copolymers of acrylic acid (stabilizer and starting polymer), styrene (second polymer) and isoprene or butadiene (third polymer). The microstructure of the polymer chains was examined using dual-detection size-exclusion chromatography, and the nanostructure of the materials was investigated by differential scanning calorimetry and solid-state nuclear magnetic resonance. Reactions were always slow (although faster than the corresponding processes in solution), and exhibited limited reinitiation by isoprene when in emulsion. The materials containing isoprene exhibit a nanostructure with a phase separation into high-T_g polystyrene-rich domains and low-T_g polyisoprene-rich domains, revealed by DSC and NMR. This has the potential to lead to barrier materials with novel physical properties.