6π Josephson Effect in Majorana Box Devices.

We study Majorana devices featuring a competition between superconductivity and multichannel Kondo physics. Our proposal extends previous work on single-channel Kondo systems to a topologically nontrivial setting of a non-Fermi liquid type, where topological superconductor wires (with gap Δ) represent leads tunnel coupled to a Coulomb-blockaded Majorana box. On the box, a spin degree of freedom with Kondo temperature T_{K} is nonlocally defined in terms of Majorana states. For Δ≫T_{K}, the destruction of Kondo screening by superconductivity implies a 4π-periodic Josephson current-phase relation. Using a strong-coupling analysis in the opposite regime Δ≪T_{K}, we find a 6π-periodic Josephson relation for three leads, with critical current I_{c}≈eΔ^{2}/ℏT_{K}, corresponding to the transfer of fractionalized charges e^{*}=2e/3.

Topological filters and high-pass/low-pass devices for solitons in inhomogeneous networks.

We show that, by inserting suitable finite networks at a site of a chain, it is possible to realize filters and high-pass/low-pass devices for solitons propagating along the chain. The results are presented in the framework of coupled optical waveguides; possible applications to different contexts, such as photonic lattices and Bose-Einstein condensates in optical networks are also discussed. Our results provide a first step in the control of the soliton dynamics through the network topology.

Proton hyperfine resonance assignments in trimethylphosphine ligated ferrimyoglobin using saturation transfer spectroscopy.

1H-NMR saturation transfer spectroscopy and nuclear Overhauser effect (NOE) have been utilized to assign several heme resonances in the low-spin trimethyl phosphine complex of sperm whale metmyoglobin. The two methods permit the location of the heme methyl resonances and the heme 2-vinyl group resonances. A qualitative comparison involving the methyl shift pattern in metMbN3, metMbCN, imidazole metMb and trimethyl phosphine metMb shows a reverse methyl shift between pyrrole I and pyrrole IV. The different hyperfine shift pattern for metMbPMe3 is suggested to arise from: (i) a possible reorientation of the proximal histidine plane; (ii) different heme protein contacts in the different ligated proteins, and (iii) a small contribution from high-spin character. The 2-vinyl group is formed in the cis plane orientation.

31P chemical shifts as structural probes for heme environments. 31P-NMR study of the binding of trimethyl phosphine to various hemoglobins and myoglobins.

A 31P-NMR study of trimethyl phosphine bound to the heme iron(II) atom in natural myoglobins, hemoglobins and synthetic porphyrin iron(II) shows that the iron-bound trimethylphosphine 31P chemical shifts are sensitive to the presence of globin:separated NMR signals can be observed for 31PMe3 bound to the hemes of the alpha and beta chains. On the basis of previous hemoprotein studies, the markedly high field resonance observed with one of the two PMe3-rabbit subunits is consistent with a specific role of the distal histidine (E7) in rabbit alpha-subunit.

Phosphines as a new structural probe of hemoglobin. 1H-NMR evidence for perturbations in the beta heme pocket induced by a thiol reagent.

Binding of trimethylphosphine to myoglobins and hemoglobins from a variety of sources has been examined by 1H-nuclear magnetic resonance. The hemoglobins exhibit two resonances at high field (approx. -3.5 ppm) which have been assigned to PMe3 bound to alpha or to beta subunits. Perturbations in the beta heme pocket induced by a thiol reagent have been detected both in 1H and 31P spectra.

Sequence-specific 1H n.m.r. assignments and determination of the three-dimensional structure of reduced Escherichia coli glutaredoxin.

The determination of the nuclear magnetic resonance structure of reduced E. coli glutaredoxin in aqueous solution is described. Based on nearly complete, sequence-specific resonance assignments, 813 nuclear Overhauser effect distance constraints and 191 dihedral angle constraints were employed as the input for the structure calculations, for which the distance geometry program DIANA was used followed by simulated annealing with the program X-PLOR. The molecular architecture of reduced glutaredoxin is made up of three helices and four-stranded beta-sheet. The first strand of the beta-sheet (residues 2 to 7) runs parallel to the second strand (32 to 37) and antiparallel to the third strand (61 to 64), and the sheet is extended in an antiparallel fashion with a fourth strand (67 to 69). The first helix with residues 13 to 28 and the last helix (71 to 83) run parallel to each other on one side of the beta-sheet, with their direction opposite to that of the two parallel beta-strands, and the helix formed by residues 44 to 53 fills space available due to the twist of the beta-sheet and the reduced length of the last two beta-strands. The active site Cys11-Pro-Tyr-Cys14 is located after the first beta-strand and occupies the latter part of the loop connecting this strand with the first helix.

Solution structure of drosomycin, the first inducible antifungal protein from insects.

Drosomycin is the first antifungal protein characterized recently among the broad family of inducible peptides and proteins produced by insects to respond to bacterial or septic injuries. It is a small protein of 44 amino acid residues extracted from Drosophila melanogaster that exhibits a potent activity against filamentous fungi. Its three-dimensional structure in aqueous solution was determined using 1H 2D NMR. This structure, involving an alpha-helix and a twisted three-stranded beta-sheet, is stabilized by three disulfide bridges. The corresponding Cysteine Stabilized alpha beta (CS alpha beta) motif, which was found in other defense proteins such as the antibacterial insect defensin A, short- and long-chain scorpion toxins, as well as in plant thionins and potent antifungal plant defensins, appears as remarkably persistent along evolution.

NMR structure of oxidized Escherichia coli glutaredoxin: comparison with reduced E. coli glutaredoxin and functionally related proteins.

The determination of the NMR structure of oxidized Escherichia coli glutaredoxin in aqueous solution is described, and comparisons of this structure with that of reduced E. coli glutaredoxin and the related proteins E. coli thioredoxin and T4 glutaredoxin are presented. Based on nearly complete sequence-specific 1H-NMR assignments, 804 nuclear Overhauser enhancement distance constraints and 74 dihedral angle constraints were obtained as the input for the structure calculations, for which the distance geometry program DIANA was used followed by simulated annealing with the program X-PLOR. The molecular architecture of oxidized glutaredoxin is made up of three helices and a four-stranded beta-sheet. The three-dimensional structures of oxidized and the recently described reduced glutaredoxin are very similar. Quantitative analysis of the exchange rates of 34 slowly exchanging amide protons from corresponding series of two-dimensional [15N,1H]-correlated spectra of oxidized and reduced glutaredoxin showed close agreement, indicating almost identical hydrogen-bonding patterns. Nonetheless, differences in local dynamics involving residues near the active site and the C-terminal alpha-helix were clearly manifested. Comparison of the structure of E. coli glutaredoxin with those of T4 glutaredoxin and E. coli thioredoxin showed that all three proteins have a similar overall polypeptide fold. An area of the protein surface at the active site containing Arg 8, Cys 11, Pro 12, Tyr 13, Ile 38, Thr 58, Val 59, Pro 60, Gly 71, Tyr 72, and Thr 73 is proposed as a possible site for interaction with other proteins, in particular ribonucleotide reductase. It was found that this area corresponds to previously proposed interaction sites in T4 glutaredoxin and E. coli thioredoxin. The solvent-accessible surface area at the active site of E. coli glutaredoxin showed a general trend to increase upon reduction. Only the sulfhydryl group of Cys 11 is exposed to the solvent, whereas that of Cys 14 is buried and solvent inaccessible.

Solution structure and lipid binding of a nonspecific lipid transfer protein extracted from maize seeds.

The three-dimensional solution structure of a nonspecific lipid transfer protein extracted from maize seeds determined by 1H NMR spectroscopy is described. This cationic protein consists of 93 amino acid residues. Its structure was determined from 1,091 NOE-derived distance restraints, including 929 interresidue connectivities and 197 dihedral restraints (phi, psi, chi 1) derived from NOEs and 3J coupling constants. The global fold involving four helical fragments connected by three loops and a C-terminal tail without regular secondary structures is stabilized by four disulfide bridges. The most striking feature of this structure is the existence of an internal hydrophobic cavity running through the whole molecule. The global fold of this protein, very similar to that of a previously described lipid transfer protein extracted from wheat seeds (Gincel E et al., 1994, Eur J Biochem 226:413-422) constitutes a new architecture for alpha-class proteins. 1H NMR and fluorescence studies show that this protein forms well-defined complexes in aqueous solution with lysophosphatidylcholine. Dissociation constants, Kd, of 1.9 +/- 0.6 x 10(-6) M and > 10(-3) M were obtained with lyso-C16 and -C12, respectively. A structure model for a lipid-protein complex is proposed in which the aliphatic chain of the phospholipid is inserted in the internal cavity and the polar head interacts with the charged side chains located at one end of this cavity. Our model for the lipid-protein complex is qualitatively very similar to the recently published crystal structure (Shin DH et al., 1995, Structure 3:189-199).

1H NMR and fluorescence studies of the complexation of DMPG by wheat non-specific lipid transfer protein. Global fold of the complex.

Plant non-specific lipid transfer proteins (LTPs) are proteins which transfer lipids between membranes in vitro and are believed to be involved in the transport of cutin monomers to the cuticle layer in vivo or in the plant defence against phytopathogens. The complexation of DMPG, a diacyl phospholipid, by wheat ns-LTP, a protein extracted from wheat seeds, was followed by 1H NMR and fluorescence spectroscopy. The global fold of the protein was calculated using the DIANA software package from a list of 968 distance constraints. The internal cavity volume, a feature common to all known ns-LTP structures, was estimated to be 750 A3 using the 'CAVITE' program. This model of the complex was obtained by inserting a lipid molecule in the cavity and was energy minimized. The study showed that the protein fold described for the free form was only weakly affected by the insertion of the bulky lipid. Observation of some intermolecular NOEs between the protein and the lipid glycerol moiety revealed that the cavity entrance was located between residues His35 and Arg44. The resulting solution structure was compared to the crystal structure of the maize ns-LTP/palmitate complex.

A novel composite 90 degrees pulse sequence which provides distortionless NMR spectra and suppresses without destroying the water magnetization.

A novel 90 degrees composite pulse sequence which allows one to record 1D and 2D NMR spectra without disturbing the water magnetization is described. A home-written program was used to optimize the pulse angles for which the pulse sequence response fitted best the desired excitation profile, producing a neat and distortionless spectrum with a broad null excitation at the carrier frequency. The resulting pulse sequence was first evaluated using the simulation program "PENCIL" and then tested on two protein samples. A 3.5 degrees phase shift of the last pulse was required to cancel correctly the water signal. The pulse scheme was appended to a NOESY pulse sequence. Inspection of the water cross section revealed interactions between water and some protons of drosomycine, a small insect antifungal protein.

Secondary structure in solution of the hydrophobic protein of soybean (HPS) as revealed by 1H NMR.

COSY, TOCSY and NOESY experiments have been used to assign sequentially the 1H 500 MHz NMR spectra of the Hydrophobic Protein of Soybean (HPS). Spin systems identification combined with sequential assignment allowed to identify the proton resonances of this 80 residues protein. Analysis of medium range connectivities showed that its secondary structure involved four helical fragments similarly located as in the structure deduced from X-ray diffraction. This work set the basis for a further fine comparison between the crystal and the solution structures and a dynamical study of HPS in solution. In addition, search of secondary structure similarities showed that the global folding of HPS should be rather similar to that found for non specific Lipid Transfer Proteins (ns-LTP) from vegetal origin. Distributions of the helical fragments along the primary sequences of these two classes of proteins were compared.