Disorder drives cooperative folding in a multidomain protein

Many human proteins contain intrinsically disordered regions, and disorder in these proteins can be fundamental to their function - for example, facilitating transient but specific binding, promoting allostery, or allowing efficient posttranslational modification. SasG, a multidomain protein implicated in host colonization and biofilm formation in Staphylococcus aureus, provides another example of how disorder can play an important role. Approximately one-half of the domains in the extracellular repetitive region of SasG are intrinsically unfolded in isolation, but these E domains fold in the context of their neighboring folded G5 domains. We have previously shown that the intrinsic disorder of the E domains mediates long-range cooperativity between nonneighboring G5 domains, allowing SasG to form a long, rod-like, mechanically strong structure. Here, we show that the disorder of the E domains coupled with the remarkable stability of the interdomain interface result in cooperative folding kinetics across long distances. Formation of a small structural nucleus at one end of the molecule results in rapid structure formation over a distance of 10 nm, which is likely to be important for the maintenance of the structural integrity of SasG. Moreover, if this normal folding nucleus is disrupted by mutation, the interdomain interface is sufficiently stable to drive the folding of adjacent E and G5 domains along a parallel folding pathway, thus maintaining cooperative folding

Asymmetric phase diagram and dimensional crossover in a system of spin-1/2 dimers under applied hydrostatic pressure

We present the magnetic and structural properties of [Cu(pyrazine)$_{0.5}$(glycine)]ClO$_4$ under applied pressure. As previously reported, at ambient pressure this material consists of quasi-two-dimensional layers of weakly coupled antiferromagnetic dimers which undergo Bose-Einstein condensation of triplet excitations between two magnetic field-induced quantum critical points (QCPs). The molecular building blocks from which the compound is constructed give rise to exchange strengths that are considerably lower than those found in other $S = 1/2$ dimer materials, which allows us to determine the pressure evolution of the entire field-temperature magnetic phase diagram using radio-frequency magnetometry. We find that a distinct phase emerges above the upper field-induced transition at elevated pressures and also show that an additional QCP is induced at zero-field at a critical pressure of $p_{\rm c} = 15.7(5)$ kbar. Pressure-dependent single-crystal X-ray diffraction and density functional theory calculations indicate that this QCP arises primarily from a dimensional crossover driven by an increase in the interdimer interactions between the planes. While the effect of quantum fluctuations on the lower field-induced transition is enhanced with applied pressure, quantum Monte Carlo calculations suggest that this alone cannot explain an unconventional asymmetry that develops in the phase diagram.Comment: Submitted to Phys. Rev.

Asymmetric phase diagram and dimensional crossover in a system of spin-spin- 1/2 dimers under applied hydrostatic pressure

We present the magnetic and structural properties of [Cu(pyrazine)0.5 (glycine)]ClO4 under applied pressure. As previously reported, at ambient pressure this material consists of quasi-two-dimensional layers of weakly coupled antiferromagnetic dimers which undergo Bose-Einstein condensation of triplet excitations between two magnetic field-induced quantum critical points (QCPs). The molecular building blocks from which the compound is constructed give rise to exchange strengths that are considerably lower than those found in other S=1/2 dimer materials, which allows us to determine the pressure evolution of the entire field-temperature magnetic phase diagram using radio-frequency magnetometry. We find that a distinct phase emerges above the upper field-induced transition at elevated pressures and also show that an additional QCP is induced at zero-field at a critical pressure of pc=15.7(5),kbar. Pressure-dependent single-crystal X-ray diffraction and density functional theory calculations indicate that this QCP arises primarily from a dimensional crossover driven by an increase in the interdimer interactions between the planes. While the effect of quantum fluctuations on the lower field-induced transition is enhanced with applied pressure, quantum Monte Carlo calculations suggest that this alone cannot explain an unconventional asymmetry that develops in the phase diagram

Non-collinear spin in electronic structure calculations

Non-collinear spin materials are an exciting class of materials that are of great interest from both a fundamental materials science point of view and also with their possible applications in energy-efficient technological devices. Here we introduce non-collinear magnetism, in particular how to describe the electronic structure of materials with non-collinear magnetically ordered spin structures giving insight as to why it happens. Additionally, the use of electronic structure calculations is ubiquitous in current materials science research, commonly used by both theoretical and experimental researchers; we, therefore, detail how non-collinear magnetism is incorporated into the most commonly used electronic structure method, density functional theory

DNA damage and metabolic activity in the preimplantation embryo

BACKGROUND: Embryos with greater viability have a lower or 'quieter' amino acid metabolism than those which arrest. We have hypothesized this is due to non-viable embryos possessing greater cellular/molecular damage and consuming more nutrients, such as amino acids for repair processes. We have tested this proposition by measuring physical damage to DNA in bovine, porcine and human embryos at the blastocyst stage and relating the data to amino acid profiles during embryo development. METHODS: Amino acid profiles of in vitro-derived porcine and bovine blastocysts were measured by high-performance liquid chromatography and the data related retrospectively to DNA damage in each individual blastomere using a modified alkaline comet assay. Amino acid profiles of spare human embryos on Day 2-3 were related to DNA damage at the blastocyst stage. RESULTS: A positive correlation between amino acid turnover and DNA damage was apparent when each embryo was examined individually; a relationship exhibited by all three species. There was no relationship between DNA damage and embryo grade. CONCLUSIONS: Amino acid profiling of single embryos can provide a non-invasive marker of DNA damage at the blastocyst stage. The data are consistent with the quiet embryo hypothesis with viable embryos (lowest DNA damage) having the lowest amino acid turnover. Moreover, these data support the notion that metabolic profiling, in terms of amino acids, might be used to select single embryos for transfer in clinical IVF

Identification of viable embryos in IVF by non-invasive measurement of amino acid turnover

BACKGROUND: IVF is limited by low success rates and an unacceptably high multiple pregnancy rate. These outcomes would be improved significantly if a single embryo of high viability could be replaced in each treatment cycle, but widespread acceptance of such a policy is hindered by the lack of predictive factors for embryo selection. We have conducted a retrospective clinical study of a novel non-invasive method of embryo selection based on the depletion/appearance of amino acids in the culture medium. METHODS: Fifty-three cycles of IVF treatment using ICSI were studied. Embryos were cultured for 24 h in 4 µl drops of medium containing a physiological mixture of 18 amino acids. The spent medium was analysed for amino acid content by high performance liquid chromatography. RESULTS: The turnover of three amino acids, Asn, Gly and Leu, was significantly correlated with a clinical pregnancy and live birth. These correlations were independent of known predictors, such as female age, basal levels of FSH, embryo cell number and embryo morphological grade. CONCLUSIONS: Non-invasive assay of amino acid turnover has the potential to improve significantly the prospective selection of the most viable embryos, or single embryo, for replacement in an IVF cycle

Disorder drives cooperative folding in a multidomain protein

Many human proteins contain intrinsically disordered regions, and disorder in these proteins can be fundamental to their function - for example, facilitating transient but specific binding, promoting allostery, or allowing efficient posttranslational modification. SasG, a multidomain protein implicated in host colonization and biofilm formation in Staphylococcus aureus, provides another example of how disorder can play an important role. Approximately one-half of the domains in the extracellular repetitive region of SasG are intrinsically unfolded in isolation, but these E domains fold in the context of their neighboring folded G5 domains. We have previously shown that the intrinsic disorder of the E domains mediates long-range cooperativity between nonneighboring G5 domains, allowing SasG to form a long, rod-like, mechanically strong structure. Here, we show that the disorder of the E domains coupled with the remarkable stability of the interdomain interface result in cooperative folding kinetics across long distances. Formation of a small structural nucleus at one end of the molecule results in rapid structure formation over a distance of 10 nm, which is likely to be important for the maintenance of the structural integrity of SasG. Moreover, if this normal folding nucleus is disrupted by mutation, the interdomain interface is sufficiently stable to drive the folding of adjacent E and G5 domains along a parallel folding pathway, thus maintaining cooperative folding