NMR structure of C-terminally tagged gramicidin channels

A biotin group was covalently attached to the C terminus of gramicidin A (gA) through a linker arm comprising a glycine residue with either one (gAXB) or two caproyl groups (gAXXB). High-resolution two-dimensional NMR spectroscopy was used to determine the structure of these modified gA analogues and [Lys(16)]gramicidin A (gA-Lys) in sodium dodecyl-d(25) sulphate micelles. Gated gA ion channels based on linking a receptor group to these gA analogues have been used recently as a component in a sensing device. The conformations of the gA backbones and amino acid side chains of lysinated gA and biotinylated gA in detergent micelles were found to be almost identical to that of native gA, i.e. that of an N-terminal to N-terminal (head to head) dimer formed by two right-handed, single-stranded beta(6.3) helices. The biotin tail of the gAXB and gAXXB and the lysine extremity of gA-Lys appeared to lie outside the micelle. Thus it appears that the covalent attachment of functional groups to the C terminus of gA does not disrupt the peptide's helical configuration. Further, single channel measurements of all three gA analogues showed that functioning ion channels were preserved within a membrane environment. (C) 1999 Elsevier Science B.V. All rights reserved.

The Heisenberg antiferromagnet on an anisotropic triangular lattice: linear spin-wave theory

We consider the effect of quantum spin fluctuations on the ground-state properties of the Heisenberg antiferromagnet on an anisotropic triangular lattice using linear spin-wave (LSW) theory. This model should describe the magnetic properties of the insulating phase of the kappa-(BEDT-TTF)(2)X family of superconducting molecular crystals. The ground-state energy, the staggered magnetization, magnon excitation spectra, and spin-wave velocities are computed as functions of the ratio of the antiferromagnetic exchange between the second and first neighbours, J(2)/J(1). We find that near J(2)/J(1) = 0.5, i.e., in the region where the classical spin configuration changes from a Neel-ordered phase to a spiral phase, the staggered magnetization vanishes, suggesting the possibility of a quantum disordered state. in this region, the quantum correction to the magnetization is large but finite. This is in contrast to the case for the frustrated Heisenberg model on a square lattice, for which the quantum correction diverges logarithmically at the transition from the Neel to the collinear phase. For large J(2)/J(1), the model becomes a set of chains with frustrated interchain coupling. For J(2) > 4J(1), the quantum correction to the magnetization, within LSW theory, becomes comparable to the classical magnetization, suggesting the possibility of a quantum disordered state. We show that, in this regime, the quantum fluctuations are much larger than for a set of weakly coupled chains with non-frustrated interchain coupling.

Phase diagram for a class of spin-1/2 Heisenberg models interpolating between the square-lattice, the triangular-lattice, and the linear-chain limits

We study the spin-1/2 Heisenberg models on an anisotropic two-dimensional lattice which interpolates between the square lattice at one end, a set of decoupled spin chains on the other end, and the triangular-lattice Heisenberg model in between. By series expansions around two different dimer ground states and around various commensurate and incommensurate magnetically ordered states, we establish the phase diagram for this model of a frustrated antiferromagnet. We find a particularly rich phase diagram due to the interplay of magnetic frustration, quantum fluctuations, and varying dimensionality. There is a large region of the usual two-sublattice Neel phase, a three-sublattice phase for the triangular-lattice model, a region of incommensurate magnetic order around the triangular-lattice model, and regions in parameter space where there is no magnetic order. We find that the incommensurate ordering wave vector is in general altered from its classical value by quantum fluctuations. The regime of weakly coupled chains is particularly interesting and appears to be nearly critical. [S0163-1829(99)10421-1].

Phase diagram of a Heisenberg spin-Peierls model with quantum phonons

Using a new version of the density-matrix renormalization group we determine the phase diagram of a model of an antiferromagnetic Heisenberg spin chain where the spins interact with quantum phonons. A quantum phase transition from a gapless spin-fluid state to a gapped dimerized phase occurs at a nonzero value of the spin-phonon coupling. The transition is in the same universality class as that of a frustrated spin chain, to which the model maps in the diabatic limit. We argue that realistic modeling of known spin-Peierls materials should include the effects of quantum phonons.

Human and murine cytomegalovirus evasion of cytotoxic T lymphocyte and natural killer cell-mediated immune responses

Herpesviruses, such as human and murine cytomegalovirus, possess an impressive array of genes believed to assist in virus survival against the host immune response. In this review, we cover the rapidly growing area of cytomegalovirus evasion of cellular immunity, specifically cytotoxic T lymphocytes and natural killer cells. The proposed mechanisms of action of viral proteins involved in blocking peptide presentation to CD8(+) T cells, namely, interference with peptide generation, inhibition of peptide assembly with class I MHC and retention/destabilization of class I MHC complexes, are described. In addition, recent evidence implicating the viral class I MHC-like proteins as inhibitors of natural killer cell-mediated clearance is reviewed, (C) 1998 Academic Press.

Solution structure of a defensin-like peptide from platypus venom

Three defensin-like peptides (DLPs) were isolated from platypus venom and sequenced. One of these peptides, DLP-1, was synthesized chemically and its three-dimensional structure was determined using NMR spectroscopy. The main structural elements of this 42-residue peptide were an anti-parallel beta-sheet comprising residues 15-18 and 37-40 and a small 3(10) helix spanning residues 10-12. The overall three-dimensional fold is similar to that of beta-defensin-12, and similar to the sodium-channel neurotoxin ShI (Stichodactyla helianthus neurotoxin I). However, the side chains known to be functionally important in beta-defensin-12 and ShI are not conserved in DLP-1, suggesting that it has a different biological function. Consistent with this contention, we showed that DLP-1 possesses no anti-microbial properties and has no observable activity on rat dorsal-root-ganglion sodium-channel currents.

Ontogenetic changes in the retinal photoreceptor mosaic in a fish, the black bream, Acanthopagrus butcheri

The morphological development of the photoreceptor mosaic was followed by light and electron microscopy in a specific region of dorsal retina of the black bream, Acanthopagrus butcheri (Sparidae, Teleostei), from hatching to eight weeks of age. The retina was differentiated when the larvae reached a total length of 3 mm (3-5 days posthatch). Single cones, arranged in tightly packed rows, were the only morphologically distinct type of photoreceptor present until the larvae were 6 mm (day 15) in standard length (SL). At this time, the rad nuclei had become differentiated and the ellipsoids of selected cones began to form subsurface cisternae along neighbouring cone membranes. In this way, double, triple, quadruple, and occasionally photoreceptor chains of up to 10 cones were formed. At 8 mm SL, there was little apparent order in the photoreceptor mosaic. However, concomitant with subsequent growth, quadruple and other multiple cone receptors disappeared, with the exception of the triple cones, which gradually reduced in both number and retinal coverage to be restricted to central retina by 15 mm SL (days 40-55). Following this stage, the arrangement of double and single cones peripheral to the region of triple cones in dorsal retina was transformed into the adult pattern of a regular mosaic of four double cones surrounding a single cone. These results demonstrate that an established photoreceptor mosaic of rows of single cones can be reorganised to form a regular square mosaic composed of single and double cones. J. Comp. Neural. 412:203-217, 1999. (C) 1999 Wiley-Liss, Inc.

NMR studies of the low-density lipoprotein receptor-binding peptide of apolipoprotein E bound to dodecylphosphocholine micelles

Circular dichroism and NMR spectroscopy have been used to determine the structure of the low-density lipoprotein (LDL) receptor-binding peptide, comprising residues 130-152, of the human apolipoprotein E. This peptide has little persistent three-dimensional structure in solution, but when bound to micelles of dodecylphosphocholine (DPC) it adopts a predominantly alpha-helical structure. The three-dimensional structure of the DPC-bound peptide has been determined by using H-1-NMR spectroscopy: the structure derived from NOE-based distance constraints and restrained molecular dynamics is largely helical. The derived phi and psi angle order parameters show that the helical structure is well defined but with some flexibility that causes the structures not to be superimposable over the full peptide length. Deuterium exchange experiments suggest that many peptide amide groups are readily accessible to the solvent, but those associated with hydrophobic residues exchange more slowly, and this helix is thus likely to be positioned on the surface of the DPC micelles. In this conformation the peptide has one hydrophobic face and two that are rich in basic amino acid side chains. The solvent-exposed face of the peptide contains residues previously shown to be involved in binding to the LDL receptor.

Solution of a two-leg spin ladder system

A model for a spin-1/2 ladder system with two legs is introduced. It is demonstrated that this model is solvable via the Bethe ansatz method for arbitrary values of the rung coupling J. This is achieved by a suitable mapping from the Hubbard model with appropriate twisted boundary conditions. We determine that a phase transition between gapped and gapless spin excitations occurs at the critical value J(c) = 1/2 of the rung coupling.

Functional analysis, using in vitro mutagenesis, of amino acids located in the phenylalanine hydroxylase active site

The 3-dimensionaI structure determination of rat phenylalanine hydroxylase (PAH) has identified potentially important amino acids lining the active site cleft with the majority of these having hydrophobic side-chains including several with aromatic side chains. Here we have analyzed the effect on rat PAH enzyme kinetics of in vitro mutagenesis of a number of these amino acids lining the PAH active site. Mutation of F299, Y324, F331, and Y343 caused a significant decrease in enzyme activity but no change in the K-m for substrate or cofactor. me conclude that these aromatic residues are essential for activity but are not significantly involved in binding of the substrate or cofactor. in contrast the PAH mutant, S349T, showed an 18-fold increase in K-m for phenylalanine, showing the first functional evidence that this residue was binding at or near the phenylalanine binding site. This confirms the recently published model for the binding of phenylalanine to the PAH active site that postulated S349 interacts with the amino group on the main chain of the phenylalanine molecule. This result differs with that found for the equivalent mutation (S395T), in the closely related tyrosine hydroxylase, which had no effect on substrate K-m, showing that while the architecture of the two active sites are very similar the amino acids that bind to the respective substrates are different. (C) 2000 Academic Press.

Quantum spin ladder systems associated with su(2 vertical bar 2)

Two integrable quantum spin ladder systems will be introduced associated with the fundamental su(2 \2) solution of the Yang-Baxter equation. The first model is a generalized quantum Ising system with Ising rung interactions. In the second model the addition of extra interactions allows us to impose Heisenberg rung interactions without violating integrability. The existence of a Bethe ansatz solution for both models allows us to investigate the elementary excitations for antiferromagnetic rung couplings. We find that the first model does not show a gap whilst in the second case there is a gap for all positive values of the rung coupling.

Algebraic Bethe ansatz for integrable one-dimensional extended Hubbard models with open boundary conditions

Nine classes of integrable open boundary conditions, further extending the one-dimensional U-q (gl (212)) extended Hubbard model, have been constructed previously by means of the boundary Z(2)-graded quantum inverse scattering method. The boundary systems are now solved by using the algebraic Bethe ansatz method, and the Bethe ansatz equations are obtained for all nine cases.

Homomeric ring assemblies of eukaryotic Sm proteins have affinity for both RNA and DNA - Crystal structure of an oligomeric complex of yeast SmF

Sm and Sm-like proteins are key components of small ribonucleoproteins involved in many RNA and DNA processing pathways. In eukaryotes, these complexes contain seven unique Sm or Sm-like (Lsm) proteins assembled as hetero-heptameric rings, whereas in Archaea and bacteria six or seven-membered rings are made from only a single polypeptide chain. Here we show that single Sm and Lsm proteins from yeast also have the capacity to assemble into homo-oligomeric rings. Formation of homo-oligomers by the spliceosomal small nuclear ribonucleoprotein components SmE and SmF preclude hetero-interactions vital to formation of functional small nuclear RNP complexes in vivo. To better understand these unusual complexes, we have determined the crystal structure of the homomeric assembly of the spliceosomal protein SmF. Like its archaeal/bacterial homologs, the SmF complex forms a homomeric ring but in an entirely novel arrangement whereby two heptameric rings form a co-axially stacked dimer via interactions mediated by the variable loops of the individual SmF protein chains. Furthermore, we demonstrate that the homomeric assemblies of yeast Sm and Lsm proteins are capable of binding not only to oligo(U) RNA but, in the case of SmF, also to oligo(dT) single-stranded DNA.

Flexibility revealed by the 1.85 angstrom crystal structure of the beta sliding-clamp subunit of Escherichia coli DNA polymerase III

The beta subunit of the Escherichia coli replicative DNA polymerase III holoenzyme is the sliding clamp that interacts with the alpha (polymerase) subunit to maintain the high processivity of the enzyme. The beta protein is a ring-shaped dimer of 40.6 kDa subunits whose structure has previously been determined at a resolution of 2.5 Angstrom [Kong et al. (1992), Cell, 69, 425-437]. Here, the construction of a new plasmid that directs overproduction of beta to very high levels and a simple procedure for large-scale purification of the protein are described. Crystals grown under slightly modified conditions diffracted to beyond 1.9 Angstrom at 100 K at a synchrotron source. The structure of the beta dimer solved at 1.85 Angstrom resolution shows some differences from that reported previously. In particular, it was possible at this resolution to identify residues that differed in position between the two subunits in the unit cell; side chains of these and some other residues were found to occupy alternate conformations. This suggests that these residues are likely to be relatively mobile in solution. Some implications of this flexibility for the function of beta are discussed.

NMR characterization of blends of poly(hydroxybutyrate-co-hydroxyvalerate) with poly(vinyl acetate)

The extent of mixing in blends of poly(hydroxybutyrate-co-hydroxyvalerate) (PHBV) (27% HV) and poly(vinyl acetate) (PVAc) has been measured using a number of different techniques, principally solid-state NMR. Differential scanning calorimetry DSC measurements indicated effective mixing of the polymer chains on a scale of several nanometres. The results of H-1 T-1 and H-1 T-1rho. measurements confirm intimate mixing of the chains. A change on blending in the H-1 T-1rho, and the H-1 NMR line width of the signal from the protons of PVAc was consistent with an increase in the amplitude and frequency of motion of this component. The PVAc chains reside within the inter-lamellar space, as confirmed by spin diffusion measurements after H-1 T-1rho preparation. (C) 2003 Society of Chemical Industry.