What is the structure of the RecA-DNA filament?

The bacterial RecA protein has been a model system for understanding how a protein can catalyze homologous genetic recombination. RecA-like proteins have now been characterized from many organisms, from bacteriophage to humans. Some of the RecA-like proteins, including human RAD51, appear to function as helical filaments formed on DNA. However, we currently have high resolution structures of inactive forms of the protein, and low resolution structures of the active complexes formed by RecA-like proteins on DNA in the presence of ATP or ATP analogs. Within a crystal of the E. coli RecA protein, a helical polymer exists, and it has been widely assumed that this polymer is quite similar to the active helical filament formed on DNA. Recent developments have suggested that this may not be the case.     

Supramolecular chemistry: What is the commercialisation plan?

Opportunities for commercialisation along with personal views are provided in this essay.     

What is the mechanism of soap film entrainment?

Classical Frankel's law describes the formation of soap films and their evolution upon pulling, a model situation of film dynamics in foams (formation, rheology, and destabilization). With the purpose of relating film pulling to foam dynamics, we have built a new setup able to give an instantaneous measurement of film thickness, thus allowing us to determine film thickness profile during pulling. We found that only the lower part of the film is of uniform thickness and follows Frankel's law, provided the entrainment velocity is small. We show that this is due to confinement effects: there is not enough surfactant in the bulk to fully cover the newly created surfaces which results in immobile film surfaces. At large velocities, surfaces become mobile and then Frankel's law breaks down, leading to a faster drainage and thus to a nonstationary thickness at the bottom of the film. These findings should help in understanding the large dispersion of previous experimental data reported during the last 40 years and clarifying the pulling phenomenon of thin liquid films.     

What is the acidity of a plutonium solution?

The determination of the pH of a plutonium solution has traditionally depended on an electrode or a titration in the presence of a complexing agent. A new approach uses the equilibrium distribution of the Pu oxidation states to estimate the hydrogen ion concentration. The method is used to estimate the equilibrium constant of the first hydrolysis reaction of tetravalent plutonium.     

What is the unperturbed state in polymer solutions?

We report theoretical results about amphiphilic random copolymers in a quasi‐ideal conformation with an overall size very close to that of the analogue homopolymers. We found that a few states may coexist with about the same free energy and a similar radius of gyration, but with different intramolecular conformations. We also argue that, in most cases, amphiphilic copolymers may never achieve the unperturbed Θ state, defined thermodynamically by a vanishing second virial coefficient. Thus, we suggest that such copolymers usually show neither an unperturbed conformation nor an unperturbed state from the thermodynamic viewpoint. We also briefly discuss star homopolymers, which show a depression of the Θ temperature with respect to linear chains and a significant, though finite, Θ swelling, as well as linear chains in the Θ state and in the melt. The main general conclusion is that interactions between chain segments do not cancel each other and are non‐negligible. Accordingly, we suggest that the word "unperturbed" be used only with reference to solution thermodynamics and not for the chain size or conformation.     

What is dietary fiber?

Dietary fiber consists of the remnants of the edible plant cell, polysaccharides, lignin, and associated substances resistant to digestion (hydrolysis) by human alimentary enzymes. This physiological definition has been translated into a chemical method (AOAC Method 985.29), which has recently been shown to miss substances of 10, 11, and 12 degrees of polymerization. It also fails to precipitate some hydrolysis-resistant oligosaccharides which contain many physiological properties expected in dietary fiber, such as inulin and oligofructose, indigestible dextrin (Fibersol-2), galactooligosaccharides and the synthetic polymer polydextrose. The Executive Board of the American Association of Cereal Chemists has appointed a committee to explore the possibility of expanding the definition or chemical methodology for dietary fiber to accommodate components that are not hydrolyzed by human alimentary enzymes, yet have the physiological attributes normally associated with dietary fiber. However, the present review suggests that the current definition is sufficient, along with new methodology, to detect recently discovered components of the dietary fiber complex.     

What is Conservation Science?

‘Conservation science’ or ‘cultural heritage research’ is defined through a discussion of research needs, training and employment patterns world-wide, and trends in published work. Parallels with mainstream polymer science are drawn throughout. Some aspects are discussed in more detail: traditional paint composites; studies in modern, synthetic, paint composites; the relevance of accelerated ageing to a range of polymer types.     

What exactly is uncertainty?

Uncertainty is defined in VIM3 as a ‘parameter’ but that, in my view, is a mistake that detracts from the clarity of the concept. Trying to overcome the resulting difficulties while retaining ‘parameter’ has brought about progressive amendments to the definition, and an increasing list of footnotes that have failed to resolve the issue. Surely the uncertainty of a result is the density function (or mass function) that best describes the probability of possible values of the measurand.     

What is the initiation step of the Grubbs-Hoveyda olefin metathesis catalyst?

Density function theory calculations reveal that the Grubbs-Hoveyda olefin metathesis pre-catalyst is activated by the formation of a complex in which the incoming alkene substrate and outgoing alkoxy ligand are both clearly associated with the ruthenium centre. The computed energies for reaction are in good agreement with the experimental values, reported here.     

Native Mass Spectrometry: What is in the Name?

Electrospray ionization mass spectrometry (ESI-MS) is nowadays one of the cornerstones of biomolecular mass spectrometry and proteomics. Advances in sample preparation and mass analyzers have enabled researchers to extract much more information from biological samples than just the molecular weight. In particular, relevant for structural biology, noncovalent protein–protein and protein–ligand complexes can now also be analyzed by MS. For these types of analyses, assemblies need to be retained in their native quaternary state in the gas phase. This initial small niche of biomolecular mass spectrometry, nowadays often referred to as “native MS,” has come to maturation over the last two decades, with dozens of laboratories using it to study mostly protein assemblies, but also DNA and RNA-protein assemblies, with the goal to define structure–function relationships. In this perspective, we describe the origins of and (re)define the term native MS, portraying in detail what we meant by “native MS,” when the term was coined and also describing what it does (according to us) not entail. Additionally, we describe a few examples highlighting what native MS is, showing its successes to date while illustrating the wide scope this technology has in solving complex biological questions.

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What is the time scale for α-helix nucleation?

Helix formation is an elementary process in protein folding, influencing both the rate and mechanism of the global folding reaction. Yet, because helix formation is less cooperative than protein folding, the kinetics are often multiexponential, and the observed relaxation times are not straightforwardly related to the microscopic rates for helix nucleation and elongation. Recent ultrafast spectroscopic measurements on the peptide Ac-WAAAH(+)-NH(2) were best fit by two relaxation modes on the ～0.1-1 ns time scale, (1) apparently much faster than had previously been experimentally inferred for helix nucleation. Here, we use replica-exchange molecular dynamics simulations with an optimized all-atom protein force field (Amber ff03w) and an accurate water model (TIP4P/2005) to study the kinetics of helix formation in this peptide. We calculate temperature-dependent microscopic rate coefficients from the simulations by treating the dynamics between helical states as a Markov process using a recently developed formalism. The fluorescence relaxation curves obtained from simulated temperature jumps are in excellent agreement with the experimentally determined results. We find that the kinetics are multiphasic but can be approximated well by a double-exponential function. The major processes contributing to the relaxation are the shrinking of helical states at the C-terminal end and a faster re-equilibration among coil states. Despite the fast observed relaxation, the helix nucleation time is estimated from our model to be 20-70 ns at 300 K, with a dependence on temperature well described by Arrhenius kinetics.     

What is the effective charge of TGA-stabilized CdTe nanocolloids?

The surface charge of semiconductor nanoparticles, Q, is an important parameter which determines their electrokinetic behavior, stability in water and polar solvents, functions of optical and electronic devices, self-assembly properties, and interactions with cell membranes. We have developed a simple method for quantitative determination of Q in their native aqueous environment. The method does not require the knowledge of exact atomic structure or make assumptions about effects of drying on charge distribution. The method is based on titration of nanoparticle dispersion with a solution of oppositely charged polyelectrolyte. The point of complete neutralization is recognized as an inflection point on the dependence of fluorescence intensity on the amount of polyelectrolyte added. Thioglycolic acid-stabilized CdTe nanoparticles 2 nm in diameter were found to carry an average Q from -2.6 to -5.5 for pH 7.5 to 10, respectively. This charge is found to be smaller than that calculated theoretically for an analogous structure (i.e., Q = -8), presumably due to adsorption of Cd(2+) ions on the stabilizer shell and on Te atoms with unsaturated valence located on the side planes of CdTe tetrahedrons.     

What is the flow activation volume of entangled polymer melts?

We evaluate the flow activation volume in polymer melts of isotactic polypropylene and atactic polystyrene with step-shear experiments at different melt temperatures. The melt is initially sheared with constant shear rate until the attainment of a melt state with nearly constant viscosity. Perturbations to this experiment, involving shear steps in short-time intervals with decreasing rates, are induced next. Measurements of the shear stress value at each shear rate step allow the evaluation of an experimental (apparent) flow activation volume. The true flow activation volume is evaluated by extrapolating the experimental data to infinite shear stress values. The value obtained is larger than the physical volume of the chain and agrees with the volume of a tube confining chains with a molecular weight between M _n and M _w. Besides supporting the validity of tube model, experiments based on this protocol may be used on model polymer samples, in composites with nanoparticles and in polymer blends to access the validity of mechanisms considered by flow models.     

What is the future of electrophoresis in large-scale genomic sequencing?

Although a finished human genome reference sequence is now available, the ability to sequence large, complex genomes remains critically important for researchers in the biological sciences, and in particular, continued human genomic sequence determination will ultimately help to realize the promise of medical care tailored to an individual's unique genetic identity. Many new technologies are being developed to decrease the costs and to dramatically increase the data acquisition rate of such sequencing projects. These new sequencing approaches include Sanger reaction-based technologies that have electrophoresis as the final separation step as well as those that use completely novel, nonelectrophoretic methods to generate sequence data. In this review, we discuss the various advances in sequencing technologies and evaluate the current limitations of novel methods that currently preclude their complete acceptance in large-scale sequencing projects. Our primary goal is to analyze and predict the continuing role of electrophoresis in large-scale DNA sequencing, both in the near and longer term.     

What is the best definition of a liquid cluster at the molecular scale?

We investigate the ability of different cluster definitions to serve as a good reaction coordinate in molecular simulations of nucleation. In particular, the most commonly used Stillinger criterion [J. Chem. Phys. 38, 1486 (1963)] is compared with the cluster definition introduced by ten Wolde and Frenkel [J. Chem. Phys. 109, 9901 (1998)]. The accuracy of these two different cluster definitions is tested by using molecular dynamics to study the vapor-liquid nucleation of Lennard-Jones argon as a model system. We are able to compare the size of the critical cluster identified by each cluster definition with a completely model-independent value provided by the nucleation theorem, aided by a recently introduced method that accurately extracts the location of the transition state directly from the kinetics. It is found that the Stillinger definition strongly overestimates the size of small molecular clusters by up to a factor of 2. A simple change of the Stillinger radius is unable to rectify this deficiency. On the contrary, the ten Wolde-Frenkel definition, while being only slightly more elaborate than a simple Stillinger criterion, is remarkably successful in identifying the correct molecular excess of the small clusters if the parameters are chosen adequately. The method described here can also be generalized to identify a proper reaction coordinate in other activated processes.     

What is the smallest saturated acyclic alkane that cannot be made?

Saturated acyclic alkanes may show a high degree of strain if they have many branches close to each other. We report calculations which indicate how strained a molecule may become before it falls apart rapidly at room temperature and so allow us to identify the simplest alkane which cannot be made.     

To What Extent is FAIMS Beneficial in the Analysis of Proteins?

High field asymmetric waveform ion mobility spectrometry (FAIMS), also known as differential ion mobility spectrometry, is emerging as a tool for biomolecular analysis. In this article, the benefits and limitations of FAIMS for protein analysis are discussed. The principles and mechanisms of FAIMS separation of ions are described, and the differences between FAIMS and conventional ion mobility spectrometry are detailed. Protein analysis is considered from both the top-down (intact proteins) and the bottom-up (proteolytic peptides) perspective. The roles of FAIMS in the analysis of complex mixtures of multiple intact proteins and in the analysis of multiple conformers of a single protein are assessed. Similarly, the application of FAIMS in proteomics and targeted analysis of peptides are considered.

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