Characterisation of FAD-family folds using a machine learning approach

Flavin adenine dinucleotide (FAD) and its derivatives play a crucial role in biological processes. They are major organic cofactors and electron carriers in both enzymatic activities and biochemical pathways. We have analysed the relationships between sequence and structure of FAD-containing proteins using a machine learning approach. Decision trees were generated using the C4.5 algorithm as a means of automatically generating rules from biological databases (TOPS, CATH and PDB). These rules were then used as background knowledge for an ILP system to characterise the four different classes of FAD-family folds classified in Dym and Eisenberg (2001). These FAD-family folds are: glutathione reductase (GR), ferredoxin reductase (FR), p-cresol methylhydroxylase (PCMH) and pyruvate oxidase (PO). Each FADfamily was characterised by a set of rules. The “knowledge patterns” generated from this approach are a set of rules containing conserved sequence motifs, secondary structure sequence elements and folding information. Every rule was then verified using statistical evaluation on the measured significance of each rule. We show that this machine learning approach is capable of learning and discovering interesting patterns from large biological databases and can generate “knowledge patterns” that characterise the FADcontaining proteins, and at the same time classify these proteins into four different families

Anomalous Pressure Dependence of Kadowaki-Woods ratio and Crystal Field Effects in Mixed-valence YbInCu4

The mixed-valence (MV) compound YbInCu4 was investigated by electrical resistivity and ac specific heat at low temperatures and high pressures. At atmospheric pressure, its Kadowaki-Woods (KW) ratio, A/\gamma ^2, is 16 times smaller than the universal value R_{KW}(=1.0 x 10^-5 \mu \Omega cm mol^2 K^2 mJ^-2), but sharply increases to 16.5R_{KW} at 27 kbar. The pressure-induced change in the KW ratio and deviation from R_{KW} are analyzed in terms of the change in f-orbital degeneracy N and carrier density n. This analysis is further supported by a dramatic change in residual resistivity \rho_0 near 25 kbar, where \rho_0 jumps by a factor of 7.Comment: 4pages, 3figure

Presure-Induced Superconducting State of Antiferromagnetic CaFe2_2As2_2

The antiferromagnet CaFe$_2$As$_2$ does not become superconducting when subject to ideal hydrostatic pressure conditions, where crystallographic and magnetic states also are well defined. By measuring electrical resistivity and magnetic susceptibility under quasi-hydrostatic pressure, however, we find that a substantial volume fraction of the sample is superconducting in a narrow pressure range where collapsed tetragonal and orthorhombic structures coexist. At higher pressures, the collapsed tetragonal structure is stabilized, with the boundary between this structure and the phase of coexisting structures strongly dependent on pressure history. Fluctuations in magnetic degrees of freedom in the phase of coexisting structures appear to be important for superconductivity.Comment: revised (6 pages, 5 figures) - includes additional experimental result

Pressure dependence of upper critical fields in FeSe single crystals

We investigate the pressure dependence of the upper critical fields ({\mu}$_0$$H$$_{c2}$) for FeSe single crystals with pressure up to 2.57 GPa. The superconducting (SC) properties show a disparate behavior across a critical pressure where the pressure-induced antiferromagnetic phase coexists with superconductivity. The magnetoresistance for $H//ab$ and $H//c$ is very different: for $H//c$, magnetic field induces and enhances a hump in the resistivity close to the $T_c$ for pressures higher than 1.2 GPa, while it is absent for $H//ab$. Since the measured {\mu}$_0$$H$$_{c2}$ for FeSe samples is smaller than the orbital limited upper critical field ($H$$^{orb}$$_{c2}$) estimated by the Werthamer Helfand and Hohenberg (WHH) model, the Maki parameter ({\alpha}) related to Pauli spin-paramagnetic effects is additionally considered to describe the temperature dependence of {\mu}$_0$$H$$_{c2}$($T$). Interestingly, the {\alpha} value is hardly affected by pressure for $H//ab$, while it strongly increases with pressure for $H//c$. The pressure evolution of the {\mu}$_0$$H$$_{c2}$(0)s for the FeSe single crystals is found to be almost similar to that of $T_c$($P$), suggesting that the pressure-induced magnetic order adversely affects the upper critical fields as well as the SC transition temperature.Comment: 23 pages, 6 figures, 1 tabl

Effect of magnetic order on the superfluid response of single-crystal ErNi2_{2}B2_{2}C: A penetration depth study

We report measurements of the in-plane magnetic penetration depth $\Delta \lambda$(T) in single crystals of ErNi$_{2}$B$_{2}$C down to $\sim$0.1 K using a tunnel-diode based, self-inductive technique at 21 MHz. We observe four features: (1) a slight dip in $\Delta \lambda$(T) at the N$\acute{e}$el temperature $T_{N}$ = 6.0 K, (2) a peak at $T_{WFM}$ = 2.3 K, where a weak ferromagnetic component sets in, (3) another maximum at 0.45 K, and (4) a final broad drop down to 0.1 K. Converting to superfluid density $\rho_{s}$, we see that the antiferromagnetic order at 6 K only slightly depresses superconductivity. We seek to explain some of the above features in the context of antiferromagnetic superconductors, where competition between the antiferromagnetic molecular field and spin fluctuation scattering determines increased or decreased pairbreaking. Superfluid density data show only a slight decrease in pair density in the vicinity of the 2.3 K feature, thus supporting other evidences against bulk ferromagnetism in this temperature range.Comment: 15 pages, 5 figure

Addressing the Requirements of High‐Sensitivity Single‐Molecule Imaging of Low‐Copy‐Number Proteins in Bacteria

Single‐molecule fluorescence super‐resolution imaging and tracking provide nanometer‐scale information about subcellular protein positions and dynamics. These single‐molecule imaging experiments can be very powerful, but they are best suited to high‐copy number proteins where many measurements can be made sequentially in each cell. We describe artifacts associated with the challenge of imaging a protein expressed in only a few copies per cell. We image live Bacillus subtilis in a fluorescence microscope, and demonstrate that under standard single‐molecule imaging conditions, unlabeled B. subtilis cells display punctate red fluorescent spots indistinguishable from the few PAmCherry fluorescent protein single molecules under investigation. All Bacillus species investigated were strongly affected by this artifact, whereas we did not find a significant number of these background sources in two other species we investigated, Enterococcus faecalis and Escherichia coli. With single‐molecule resolution, we characterize the number, spatial distribution, and intensities of these impurity spots.Bright spots: A single‐molecule‐like fluorescent background signal is reported in Bacillus subtilis cells, and the density and fluorescence intensity of these spots are quantified in several Bacillus species and other Gram‐negative and Gram‐positive organisms.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/144710/1/cphc201600035_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/144710/2/cphc201600035.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/144710/3/cphc201600035-sup-0001-misc_information.pd