Inhomogeneous magnetization in dipolar ferromagnetic liquids

At high densities fluids of strongly dipolar spherical particles exhibit spontaneous long-ranged orientational order. Typically, due to demagnetization effects induced by the long range of the dipolar interactions, the magnetization structure is spatially inhomogeneous and depends on the shape of the sample. We determine this structure for a cubic sample by the free minimization of an appropriate microscopic density functional using simulated annealing. We find a vortex structure resembling four domains separated by four domain walls whose thickness increases proportional to the system size L. There are indications that for large L the whole configuration scales with the system size. Near the axis of the mainly planar vortex structure the direction of the magnetization escapes into the third dimension or, at higher temperatures, the absolute value of the magnetization is strongly reduced. Thus the orientational order is characterized by two point defects at the top and the bottom of the sample, respectively. The equilibrium structure in an external field and the transition to a homogeneous magnetization for strong fields are analyzed, too.Comment: 17 postscript figures included, submitted to Phys. Rev.

Phase separation in the two-dimensional electron liquid in MOSFETs

We show that the existence of an intermediate phase between the Fermi liquid and the Wigner crystal phases is a generic property of the two-dimensional pure electron liqd in MOSFET's at zero temperature. The physical reason for the existence of these phases is a partial separation of the uniform phases. We discuss properties of these phases and a possible explanation of experimental results on transport properties of low density electron gas in Si MOSFET's. We also argue that in certain range of parameters the partial phase separation corresponds to a supersolid phas e discussed in [AndreevLifshitz].Comment: 11 pages, 3 figure

Crystal Structure of Human Protein N-Terminal Glutamine Amidohydrolase, an Initial Component of the N-End Rule Pathway

The N-end rule states that half-life of protein is determined by their N-terminal amino acid residue. N-terminal glutamine amidohydrolase (Ntaq) converts N-terminal glutamine to glutamate by eliminating the amine group and plays an essential role in the N-end rule pathway for protein degradation. Here, we report the crystal structure of human Ntaq1 bound with the N-terminus of a symmetry-related Ntaq1 molecule at 1.5 Å resolution. The structure reveals a monomeric globular protein with alpha-beta-alpha three-layer sandwich architecture. The catalytic triad located in the active site, Cys-His-Asp, is highly conserved among Ntaq family and transglutaminases from diverse organisms. The N-terminus of a symmetry-related Ntaq1 molecule bound in the substrate binding cleft and the active site suggest possible substrate binding mode of hNtaq1. Based on our crystal structure of hNtaq1 and docking study with all the tripeptides with N-terminal glutamine, we propose how the peptide backbone recognition patch of hNtaq1 forms nonspecific interactions with N-terminal peptides of substrate proteins. Upon binding of a substrate with N-terminal glutamine, active site catalytic triad mediates the deamination of the N-terminal residue to glutamate by a mechanism analogous to that of cysteine proteases

Overview of the crystal structure of hNtaq1.

<p>(A) Overall structure of hNtaq1. α-helices, β-strands, and loops are colored in orange, cyan, and white, respectively. The representative amino acid residues in the active site are shown as stick model (carbon, oxygen, nitrogen, and sulfur in yellow, red, blue, and gold color, respectively). (B) Stereo view of the crystallographic contact of hNtaq1 with a symmetry-related molecule. hNtaq1 and symmetry-related molecules are represented as green, cyan, and magenta cartoon, respectively. Unit cell is shown with green line and electron density map is shown as gray cloud. (C) Sequence alignment of hNtaq1 with Ntaq proteins from <i>Mus musculus</i>, <i>Caenorhabditis elegans</i>, protein-glutaminase from <i>Chryseobacterium proteolyticum</i>, secreted effector protein SseI from <i>Sallonella typhimurium</i>, and periplasmic protease LapG from <i>Legionella pneumophila</i>. Residues of the catalytic triad are represented by red asterisk below the amino acid sequences. Completely conserved, identical, moderately conserved residues are highlighted with red, green, and yellow shaded boxes, respectively. The secondary structure of hNtaq1 is shown on top of the sequence alignment. α-helix, β-sheet, and connecting region are represented by red spiral, blue arrow, and black line, respectively. Structural comparison of hNtaq1 with protein-glutaminase from <i>C. proteolyticum</i> (D), secreted effector protein SseI from <i>S. typhimurium</i> (E), and periplasmic protease LapG from <i>L. peumophila</i> (F). The catalytic triads are shown as stick models and main chains of hNtaq1, protein-glutaminase, SseI, and LapG are represented with ribbon diagram in green, magenta, orange, and blue, respectively.</p

Docking study and suggested binding pose of N-terminal glutamine peptide in hNtaq1.

<p>(A) Tripeptides docking study of hNtaq1. Categorized by features of its second residue, the backbone of Ala, Gly, Ile, Leu, Met, Pro, Val tripeptides are colored in yellow, the backbone of Cys, Asn, Gln, Ser, Thr tripetides are colored in green, the His, Lys, Arg tripeptides are colored in blue, the Phe, Trp, Tyr tripeptides are colored in black, and the Asp, Glu tripeptides are colored in orange. (B) The nearest tripeptide in docking study. The substrate-mimicking peptide is shown as green and predicted docking tripeptide Gln-Tyr-Pro is colored in magenta. (C) Binding mode of refined Ser1Gln hNtaq1 mutant on electron density map of hNtaq1. Carbon in substrate-mimicking peptide, catalytic triad, β-strands, loops, and Ser1Gln mutant are colored in green, yellow, cyan, white, and blue, respectively. Oxygen, nitrogen, and sulfur are represented as red, blue, and gold, respectively. Two water molecules are shown as red sphere and electron density map is represented as gray mesh contoured at 2.0 σ.</p

Active site and electrostatic potential surface charge of hNtaq1.

<p>(A) Substrate binding cleft of hNtaq1. Carbon in the substrate-mimicking peptide, catalytic triad, α-helices, β-strands, and loops are colored in green, yellow, orange, cyan, and white, respectively. Oxygen, nitrogen, and sulfur atoms are represented as red, blue, and gold, respectively. Two water molecules are shown as red sphere and labeled as W1 and W2. (B) Electron density map from an <i>Fo</i>–<i>Fc</i> omit map calculated without the bound substrate-mimicking peptide. Positive electron density are shown as a green mesh contoured at 2.0 σ, in a stereo view. (C) Electrostatic potential surface and substrate binding cleft region of hNtaq1. Negatively and positively charged surfaces are represented as red and blue shade, respectively. Residues interacting with the substrate-mimicking peptide molecule are labeled.</p

Statistics for data collection, phasing, and model refinement.

a<p>Data collected at the Sector 23-ID-D of the Advanced Photon Source.</p>b<p>Numbers in parentheses indicate the highest resolution shell of 20.</p>c<p><i>R_merge</i> = Σ_h Σ_i |<i>I</i>(<i>h</i>)_i–<<i>I</i>(<i>h</i>)>|/Σ_h Σ_i<i>I</i>(<i>h</i>)_i, where <i>I</i>(<i>h</i>) is the observed intensity of reflection h, and <<i>I</i>(<i>h</i>)> is the average intensity obtained from multiple measurements.</p>d<p>Figure of merit = <|Σ P(α)e^iα/Σ P(α)|>, where α is the phase angle and P(α) is the phase probability distribution.</p>e<p><i>R_work</i> = Σ | |<i>F_o</i>|–|<i>F_c</i>| |/Σ |<i>F_o</i>|, where |<i>F_o</i>| is the observed structure factor amplitude and |<i>F_c</i>| is the calculated structure factor amplitude.</p>f<p><i>R_free</i> = R-factor based on 5.0% of the data excluded from refinement.</p><p>Statistics for data collection, phasing, and model refinement.</p

Proposed catalytic mechanism of hNtaq1.

<p>Proposed catalytic mechanism of hNtaq1.</p