The repetitive structure of DNA clamps: An overlooked protein tandem repeat

Structured tandem repeats proteins (STRPs) are a specific kind of tandem repeat proteins characterized by a modular and repetitive three-dimensional structure arrangement. The majority of STRPs adopt solenoid structures, but with the increasing availability of experimental structures and high-quality predicted structural models, more STRP folds can be characterized. Here, we describe “Box repeats”, an overlooked STRP fold present in the DNA sliding clamp processivity factors, which has eluded classification although structural data has been available since the late 1990s. Each Box repeat is a β⍺βββ module of about 60 residues, which forms a class V “beads-on-a-string” type STRP. The number of repeats present in processivity factors is organism dependent. Monomers of PCNA proteins in both Archaea and Eukarya have 4 repeats, while the monomers of bacterial beta-sliding clamps have 6 repeats. This new repeat fold has been added to the RepeatsDB database, which now provides structural annotation for 66 Box repeat proteins belonging to different organisms, including viruses

Quantum Dot as Spin Filter and Spin Memory

We consider a quantum dot in the Coulomb blockade regime weakly coupled to current leads and show that in the presence of a magnetic field the dot acts as an efficient spin-filter (at the single-spin level) which produces a spin-polarized current. Conversely, if the leads are fully spin-polarized the up or down state of the spin on the dot results in a large sequential or small cotunneling current, and thus, together with ESR techniques, the setup can be operated as a single-spin memory.Comment: 4 pages, 3 figures, REVTe

Ground state properties of ferromagnetic metal/conjugated polymer interfaces

We theoretically investigate the ground state properties of ferromagnetic metal/conjugated polymer interfaces. The work is partially motivated by recent experiments in which injection of spin polarized electrons from ferromagnetic contacts into thin films of conjugated polymers was reported. We use a one-dimensional nondegenerate Su-Schrieffer-Heeger (SSH) Hamiltonian to describe the conjugated polymer and one-dimensional tight-binding models to describe the ferromagnetic metal. We consider both a model for a conventional ferromagnetic metal, in which there are no explicit structural degrees of freedom, and a model for a half-metallic ferromagnetic colossal magnetoresistance (CMR) oxide which has explicit structural degrees of freedom. The Fermi energy of the magnetic metallic contact is adjusted to control the degree of electron transfer into the polymer. We investigate electron charge and spin transfer from the ferromagnetic metal to the organic polymer, and structural relaxation near the interface. Bipolarons are the lowest energy charge state in the bulk polymer for the nondegenerate SSH model Hamiltonian. As a result electrons (or holes) transferred into the bulk of the polymer form spinless bipolarons. However, there can be spin density in the polymer localized near the interface.Comment: 7 figure

Ultrasensitive immuno-detection using viral nanoparticles with modular assembly using genetically-directed biotinylation

We report a novel, modular approach to immuno-detection based on antibody recognition and PCR read-out that employs antibody-conjugated bacteriophage, easily-manipulated nonpathogenic viruses, as affinity agents. Our platform employs phage genetically tagged for in vivo biotinylation during phage maturation that can easily be linked, through avidin, to any biotinylatable affinity agent, including full-length antibodies, peptides, lectins or aptamers. The presence of analyte is reported with high sensitivity through real-time PCR. This approach avoids the need to clone antibody-encoding DNA fragments, allows the use of full-length, high affinity antibodies and, by having DNA reporters naturally encapsulated inside the bacteriophage, greatly reduces nonspecific binding of DNA. We validate the efficacy of this new approach through the detection of VEGF (Vascular Endothelial Growth Factor), a known angiogenic cancer biomarker protein, at attomolar concentrations in bronchoalveolar lavage (BAL) fluid

Resistance effects due to magnetic guiding orbits

The Hall and magnetoresistance of a two dimensional electron gas subjected to a magnetic field barrier parallel to the current direction is studied as function of the applied perpendicular magnetic field. The recent experimental results of Nogaret {\em et al.} [Phys. Rev. Lett. {\bf 84}, 2231 (2000)] for the magneto- and Hall resistance are explained using a semi-classical theory based on the Landauer-B\"{u}ttiker formula. The observed positive magnetoresistance peak is explained as due to a competition between a decrease of the number of conducting channels as a result of the growing magnetic field, from the fringe field of the ferromagnetic stripe as it becomes magnetized, and the disappearance of snake orbits and the subsequent appearance of cycloidlike orbits.Comment: 7 pages, 7 figure

Domain shuffling of a highly mutable ligand-binding fold drives adhesin generation across the bacterial kingdom

\ua9 2023 The Authors. Proteins: Structure, Function, and Bioinformatics published by Wiley Periodicals LLC. Bacterial fibrillar adhesins are specialized extracellular polypeptides that promote the attachment of bacteria to the surfaces of other cells or materials. Adhesin-mediated interactions are critical for the establishment and persistence of stable bacterial populations within diverse environmental niches and are important determinants of virulence. The fibronectin (Fn)-binding fibrillar adhesin CshA, and its paralogue CshB, play important roles in host colonization by the oral commensal and opportunistic pathogen Streptococcus gordonii. As paralogues are often catalysts for functional diversification, we have probed the early stages of structural and functional divergence in Csh proteins by determining the X-ray crystal structure of the CshB adhesive domain NR2 and characterizing its Fn-binding properties in vitro. Despite sharing a common fold, CshB_NR2 displays an ~1.7-fold reduction in Fn-binding affinity relative to CshA_NR2. This correlates with reduced electrostatic charge in the Fn-binding cleft. Complementary bioinformatic studies reveal that homologues of CshA/B_NR2 domains are widely distributed in both Gram-positive and Gram-negative bacteria, where they are found housed within functionally cryptic multi-domain polypeptides. Our findings are consistent with the classification of Csh adhesins and their relatives as members of the recently defined polymer adhesin domain (PAD) family of bacterial proteins

Virtual karyotyping with SNP microarrays reduces uncertainty in the diagnosis of renal epithelial tumors

<p>Abstract</p> <p>Background</p> <p>Renal epithelial tumors are morphologically, biologically, and clinically heterogeneous. Different morphologic subtypes require specific management due to markedly different prognosis and response to therapy. Each common subtype has characteristic chromosomal gains and losses, including some with prognostic value. However, copy number information has not been readily accessible for clinical purposes and thus has not been routinely used in the diagnostic evaluation of these tumors. This information can be useful for classification of tumors with complex or challenging morphology. 'Virtual karyotypes' generated using SNP arrays can readily detect characteristic chromosomal lesions in paraffin embedded renal tumors and can be used to correctly categorize the common subtypes with performance characteristics that are amenable for routine clinical use.</p> <p>Methods</p> <p>To investigate the use of virtual karyotypes for diagnostically challenging renal epithelial tumors, we evaluated 25 archived renal neoplasms where sub-classification could not be definitively rendered based on morphology and other ancillary studies. We generated virtual karyotypes with the Affymetrix 10 K 2.0 mapping array platform and identified the presence of genomic lesions across all 22 autosomes.</p> <p>Results</p> <p>In 91% of challenging cases the virtual karyotype unambiguously detected the presence or absence of chromosomal aberrations characteristic of one of the common subtypes of renal epithelial tumors, while immunohistochemistry and fluorescent in situ hybridization had no or limited utility in the diagnosis of these tumors.</p> <p>Conclusion</p> <p>These results show that virtual karyotypes generated by SNP arrays can be used as a practical ancillary study for the classification of renal epithelial tumors with complex or ambiguous morphology.</p

Co-ordination between Rashba spin-orbital interaction and space charge effect and enhanced spin injection into semiconductors

We consider the effect of the Rashba spin-orbital interaction and space charge in a ferromagnet-insulator/semiconductor/insulator-ferromagnet junction where the spin current is severely affected by the doping, band structure and charge screening in the semiconductor. In diffusion region, if the the resistance of the tunneling barriers is comparable to the semiconductor resistance, the magnetoresistance of this junction can be greatly enhanced under appropriate doping by the co-ordination between the Rashba effect and screened Coulomb interaction in the nonequilibrium transport processes within Hartree approximation.Comment: 4 pages, 3 figure

Diffuse transport and spin accumulation in a Rashba two-dimensional electron gas

The Rashba Hamiltonian describes the splitting of the conduction band as a result of spin-orbit coupling in the presence of an asymmetric confinement potential and is commonly used to model the electronic structure of confined narrow-gap semiconductors. Due to the mixing of spin states some care has to be exercised in the calculation of transport properties. We derive the diffusive conductance tensor for a disordered two-dimensional electron gas with spin-orbit interaction and show that the applied bias induces a spin accumulation, but that the electric current is not spin-polarized.Comment: REVTeX4 format, 5 page