Unsupervised machine learning to investigate trajectory patterns of COVID-19 symptoms and physical activity measured via the MyHeart Counts App and smart devices.

Previous studies have associated COVID-19 symptoms severity with levels of physical activity. We therefore investigated longitudinal trajectories of COVID-19 symptoms in a cohort of healthcare workers (HCWs) with non-hospitalised COVID-19 and their real-world physical activity. 121 HCWs with a history of COVID-19 infection who had symptoms monitored through at least two research clinic visits, and via smartphone were examined.

Biological heterogeneity in idiopathic pulmonary arterial hypertension identified through unsupervised transcriptomic profiling of whole blood.

Idiopathic pulmonary arterial hypertension (IPAH) is a rare but fatal disease diagnosed by right heart catheterisation and the exclusion of other forms of pulmonary arterial hypertension, producing a heterogeneous population with varied treatment response. Here we show unsupervised machine learning identification of three major patient subgroups that account for 92% of the cohort, each with unique whole blood transcriptomic and clinical feature signatures. These subgroups are associated with poor, moderate, and good prognosis.

A diagnostic miRNA signature for pulmonary arterial hypertension using a consensus machine learning approach.

Background: Pulmonary arterial hypertension (PAH) is a rare but life shortening disease, the diagnosis of which is often delayed, and requires an invasive right heart catheterisation. Identifying diagnostic biomarkers may improve screening to identify patients at risk of PAH earlier and provide new insights into disease pathogenesis. MicroRNAs are small, non-coding molecules of RNA, previously shown to be dysregulated in PAH, and contribute to the disease process in animal models.

Conformational spectra--probing protein conformational changes.

Stafford [Biophys. J. 17 (1996) MP452] has shown that it is possible, using the analytical ultracentrifuge in sedimentation velocity mode, to calculate the molecular weights of proteins with a precision of approximately 5%, by fitting Gaussian distributions to g(s*) profiles so long as partial specific volume and the radial position of the meniscus are known.

Structure and stability of the alpha-helix: lessons for design.

The alpha-helix is the most abundant secondary structure in proteins. We now have an excellent understanding of the rules for helix formation because of experimental studies of helices in isolated peptides and within proteins, examination of helices in crystal structures, computer modeling and simulations, and theoretical work. Here we discuss structural features that are important for designing peptide helices, including amino acid preferences for interior and terminal positions, side chain interactions, disulfide bonding, metal binding, and phosphorylation.

The CXXC motif at the N terminus of an alpha-helical peptide.

An active site containing a CXXC motif is always found in the thiol-disulphide oxidoreductase superfamily. A survey of crystal structures revealed that the CXXC motif had a very high local propensity (26.3 +/- 6.

A phosphoserine-lysine salt bridge within an alpha-helical peptide, the strongest alpha-helix side-chain interaction measured to date.

Phosphorylation is ubiquitous in control of protein activity, yet its effects on protein structure are poorly understood. Here we investigate the effect of serine phosphorylation in the interior of an alpha-helix when a salt bridge is present between the phosphate group and a positively charged side chain (in this case lysine) at i,i + 4 spacing. The stabilization of the helix is considerable and can overcome the intrinsically low preference of phosphoserine for the interior of the helix.

A copper protein and a cytochrome bind at the same site on bacterial cytochrome c peroxidase.

Pseudoazurin binds at a single site on cytochrome c peroxidase from Paracoccus pantotrophus with a K(d) of 16.4 microM at 25 degrees C, pH 6.0, in an endothermic reaction that is driven by a large entropy change.

The Mycobacterium tuberculosis chaperonin 10 monomer exhibits structural plasticity.

The conditions which favor dissociation of oligomeric Mycobacterium tuberculosis chaperonin 10 and the solution structure of the monomer were studied by analytical ultracentrifugation, size exclusion chromatography, fluorescence, and circular dichroism spectroscopies. At neutral pH and in the absence of divalent cations, the protein is fully monomeric below approximately a 4.7 microM concentration.

Correlation of SEC/MALLS with ultracentrifuge and viscometric data for chitosans.

Attempts have been made to correlate estimates of molecular weight for a group of cationic polysaccharides known as chitosans between the highly popular technique of size-exclusion chromatography coupled to multi-angle laser light scattering, "SEC-MALLS", and the less convenient but more established technique of sedimentation equilibrium in the analytical ultracentrifuge. Four pharmaceutical grade chitosans of various molecular weights and degrees of acetylation (4-30%) were chosen. Better correlation than previous was achieved, although some batch variability was observed.

Mycobacterium tuberculosis chaperonin 10 is secreted in the macrophage phagosome: is secretion due to dissociation and adoption of a partially helical structure at the membrane?

To confirm that Mycobacterium tuberculosis chaperonin 10 (Cpn10) is secreted outside the live bacillus, infected macrophages were examined by electron microscopy. This revealed that the mycobacterial protein accumulates both in the wall of the bacterium and in the matrix of the phagosomes in which ingested mycobacteria survive within infected macrophages. To understand the structural implications underlying this secretion, a structural study of M.

Probing conformation and conformational change in proteins is optimally undertaken in relative mode.

Hydrodynamic bead modelling has been widely used in attempts to assess the 3D conformation of proteins in solution. Initially, simple models employing only a small number of beads were used, with a considerable degree of success. Latterly, high-resolution bead models based upon atomic coordinates have been developed, and much more sophisticated questions can in principle be addressed.

Purification and characterisation of a novel DNA methyltransferase, M.AhdI.

We have cloned the M and S genes of the restriction-modification (R-M) system AhdI and have purified the resulting methyltransferase to homogeneity. M.AhdI is found to form a 170 kDa tetrameric enzyme having a subunit stoichiometry M2S2 (where the M and S subunits are responsible for methylation and DNA sequence specificity, respectively).

Pressure cell assisted solubilization of xyloglucans: tamarind seed polysaccharide and detarium gum.

To improve the solubilization of two water-soluble xyloglucans, tamarind seed polysaccharide and detarium gum, by reducing substantially molecular aggregation, a "pressure cell" heating method was used. Conditions allowing solubilization and chain depolymerization were produced by varying appropriately the pressure, time, and temperature applied. The various MW fractions of solubilized xyloglucans were characterized by capillary viscometry and light scattering techniques in order to extract, with reliability, fundamental macromolecular parameters.

Hydrolysable ATP is a requirement for the correct interaction of molecular chaperonins cpn60 and cpn10.

Over recent years the binding ability of the molecular chaperone cpn60 (GroEL14) and its co-chaperone cpn10 (GroES7) has been reported to occur under an assortment of specific conditions from the use of non-hydrolysable ATP analogues (namely adenosine 5'-[gamma-thio]triphosphate) to requiring hydrolysable ATP for any interaction to occur. We have investigated this further using the molecular hydrodynamic methods (hydrodynamic bead modelling, sedimentation-velocity analytical ultracentrifugation and dynamic light-scattering), allowing the process to be followed under physiologically relevant dilute solution conditions, combined with absorption spectrophotometry to determine GroES7-GroEL14 interaction through the rate inhibition of the cpn60's ATPase activity by GroES7. The results found here indicate that the presence of hydrolysable ATP is required to facilitate correct GroES7 interaction with GroEL14 in solution.

Pressure cell assisted solution characterization of polysaccharides. 1. Guar gum.

To reduce time-dependent aggregation phenomena and achieve true "molecular" solution, the "pressure cell" solubilization method of Vorwerg and co-workers was applied to solutions of guar galactomannans (three samples of different molecular weights), using various heating, time, and pressure profiles. Physicochemical characterization of the guar samples before and after pressure cell treatment included measurements of intrinsic viscosity [eta] by capillary viscometry and M(w) and radius of gyration from size exclusion chromatography coupled to multiangle laser light scattering (SEC/MALLS). Heating the guar solutions (100-160 degrees C) without pressurization produced chain degradation with [eta] and M(w) values being reduced significantly, whereas this effect was reduced substantially for samples subject to initial pressurization ( approximately 5-10 bar).

The heterotrimer of the membrane-peripheral components of transhydrogenase and the alternating-site mechanism of proton translocation.

Transhydrogenase undergoes conformational changes to couple the redox reaction between NAD(H) and NADP(H) to proton translocation across a membrane. The protein comprises three components: dI, which binds NAD(H); dIII, which binds NADP(H); and dII, which spans the membrane. Experiments using isothermal titration calorimetry, analytical ultracentrifugation, and small angle x-ray scattering show that, as in the crystalline state, a mixture of recombinant dI and dIII from Rhodospirillum rubrum transhydrogenase readily forms a dI(2)dIII(1) heterotrimer in solution, but we could find no evidence for the formation of a dI(2)dIII(2) tetramer using these techniques.

Crystal structure of decameric 2-Cys peroxiredoxin from human erythrocytes at 1.7 A resolution.

Background: The peroxiredoxins (Prxs) are an emerging family of multifunctional enzymes that exhibit peroxidase activity in vitro, and in vivo participate in a range of cellular processes known to be sensitive to reactive oxygen species. Thioredoxin peroxidase B (TPx-B), a 2-Cys type II Prx from erythrocytes, promotes potassium efflux and down-regulates apoptosis and the recruitment of monocytes by endothelial tissue.

Results: The crystal structure of human decameric TPx-B purified from erythrocytes has been determined to 1.

Self-interaction of pneumolysin, the pore-forming protein toxin of Streptococcus pneumoniae.

The pathogenically important cholesterol-binding pore-forming bacterial "thiol-activated" toxins (TATs) are commonly believed to be monomeric in solution and to undergo a transition on membrane binding mediated by cholesterol to an oligomeric pore. We present evidence, gained through the application of a number of biochemical and biophysical techniques with associated modelling, that the TAT from Streptococcus pneumoniae, pneumolysin, is in fact able to self-associate in solution to form the same oligomeric structures. The weak interaction leading to solution oligomerization is manifested at low concentrations in a dimeric toxin form.

Probing the stabilizing role of C-terminal residues in trimethylamine dehydrogenase.

In trimethylamine dehydrogenase, a homodimeric iron-sulfur flavoprotein, the C-terminal 17 residues of each subunit (residues 713-729) embrace residues on the other subunit. The role of this unusual mode of interaction at the subunit interface was probed by isolating three mutant forms of trimethylamine dehydrogenase in which the C-terminus of the enzyme was deleted by five residues [delta(725-729], 10 residues [delta(720-729)] and 17 residues [delta(713-729)]. The solution properties and conformational states of the three mutant enzymes were investigated using optical, fluorescence and circular dichroism spectroscopies, ANS binding and a novel and conformationally sensitive hydrodynamic method.

A core-shell model of calcium phosphate nanoclusters stabilized by beta-casein phosphopeptides, derived from sedimentation equilibrium and small-angle X-ray and neutron-scattering measurements.

Calcium phosphate nanoclusters were prepared under standardised conditions using 10 mg ml(-1) of the 25-amino-acid N-terminal tryptic phosphopeptide of bovine beta-casein as a stabilising agent. The Mr determined by sedimentation equilibrium was 197,600+/-13,700 and the apparent radius of gyration determined by X-ray scattering was 2.80+/-0.

Hydrodynamic characterization of chitosans varying in degree of acetylation.

The molecular weights and gross aqueous solution conformation of two chitosans of different degrees of acetylation, 'Sea Cure +210' (11% acetylated) and KN50 (58% acetylated) were characterized by viscometry, analytical ultracentrifugation and dynamic light scattering. The hydrodynamic parameters obtained were used to determine both the molecular weights and the gross solution conformation of the two chitosans. Using the Wales-Van Holde ratio of sedimentation coefficient concentration regression coefficient (ks) to intrinsic viscosity [eta], the Sea Cure +210 chitosan, which is much less acetylated than the KN50, is highly asymmetric in conformation.