A method for distance determination in proteins using a designed metal ion binding site and site-directed spin labeling: evaluation with T4 lysozyme.

The use of molecular genetics to introduce both a metal ion binding site and a nitroxide spin label into the same protein opens the use of paramagnetic metalnitroxyl interactions to estimate intramolecular distances in a wide variety of proteins. In this report, a His-Xaa3-His metal ion binding motif was introduced at the N terminus of the long interdomain helix of T4 lysozyme (Lys-65 --> His/Gln-69 --> His) of three mutants, each containing a single nitroxide-labeled cysteine residue at position 71, 76, or 80. The results show that Cu(II)-induced relaxation effects on the nitroxide can be quantitatively analyzed in terms of interspin distance in the range of 10-25 A using Redfield theory, as first suggested by Leigh [Leigh, J.S. (1970) J. Chem. Phys. 52, 2608-2612]. Of particular interest is the observation that distances can be determined both under rigid lattice conditions in frozen solution and in the presence of motion of the spins at room temperature under physiological conditions. The method should be particularly attractive for investigating structure in membrane proteins that are difficult to crystallize. In the accompanying paper, the technique is applied to a polytopic membrane protein, lactose permease.

Distance determination in proteins using designed metal ion binding sites and site-directed spin labeling: application to the lactose permease of Escherichia coli.

As shown in the accompanying paper, the magnetic dipolar interaction between site-directed metal-nitroxide pairs can be exploited to measure distances in T4 lysozyme, a protein of known structure. To evaluate this potentially powerful method for general use, particularly with membrane proteins that are difficult to crystallize, both a paramagnetic metal ion binding site and a nitroxide side chain were introduced at selected positions in the lactose permease of Escherichia coli, a paradigm for polytopic membrane proteins. Thus, three individual cysteine residues were introduced into putative helix IV of a lactose permease mutant devoid of native cysteine residues containing a high-affinity divalent metal ion binding site in the form of six contiguous histidine residues in the periplasmic loop between helices III and IV. In addition, the construct contained a biotin acceptor domain in the middle cytoplasmic loop to facilitate purification. After purification and spin labeling, electron paramagnetic resonance spectra were obtained with the purified proteins in the absence and presence of Cu(II). The results demonstrate that positions 103, 111, and 121 are 8, 14, and > 23 A from the metal binding site. These data are consistent with an alpha-helical conformation of transmembrane domain IV of the permease. Application of the technique to determine helix packing in lactose permease is discussed.

Preparation and properties of nido-carborane-specific monoclonal antibodies for potential use in boron neutron capture therapy for cancer.

As the first step of a research program aimed at developing a bispecific monoclonal antibody system for the delivery of boron-rich molecules to tumor cells for boron neutron capture therapy, monoclonal antibodies (mAbs) were produced against an anionic nido-carborane derivative, 4-[7,8-dicarbadodecahydroundecaborat(-1)-7-yl]butanoic acid. Two IgG subclass mAbs, designated HAW101 and HAW102, were identified that specifically bound the anionic nido-carborane hapten, as well as a variety of other anionic nido-carborane cage derivatives. By using surface plasmon resonance technology, the affinity constants of HAW101 and HAW102 were determined to be 1.9 x 10(9) and 6.8 x 10(8) M-1, respectively. A diverse array of 7-substituted and 7,8-disubstituted anionic nido-carborane derivatives reacted with the mAb HAW101 in competition ELISA, whereas anionic closo-polyhedral boranes showed negligible binding, suggesting a role for the open nido-carborane cage structure. These results suggest that mAbs such as HAW101, which bind anionic nido-carboranes, are useful in the development of bispecific mAbs for specific targeting and enhanced boron delivery to tumor sites.

Applications of EPR with an Emphasis on Tau Fibril Structure

Substances containing unpaired electrons have been studied by electron paramagnetic resonance (EPR) for nearly 70 years. With continual development and enhancement of EPR techniques, questions have arisen regarding optimum method selection for a given sample based on its properties. In this work, radiation defects, natural lattice defects, solid organic radicals, radicals in solution, and spin-labeled proteins were analyzed using CW, pulse, and rapid scan EPR to compare methods. Studies of solid BDPA, EOe in quartz, Ns0 in diamond, and a-Si:H, showed that rapid scan could overcome many obstacles presented by other techniques, cementing rapid scan as an effective alternative to CW and pulse methods. Relaxation times of six nitroxide radicals were characterized from 0.25-34 GHz, guiding synthesis of improved nitroxides for in vivo imaging experiments. Processes contributing to T1 of DPPH in polystyrene were found through variable temperature measurements at X- and Q-band, resolving previously-reported discrepancies in relaxation properties and providing new insight into this commonly-used standard. In the history of EPR, the study of proteins is relatively new. Double electron-electron resonance (DEER) has emerged as a powerful technique for the study of amyloid fibrils, a class of protein aggregates implicated in a number of neurodegenerative disorders. Microtubule-associated protein tau forms fibrils linked to Alzheimerfs disease through seeded conversion of monomer. Self-assembly is mediated by the microtubule binding repeats in tau, and there are either three or four repeats present depending on the isoform. DEER was used to show that filaments of 3R and 4R tau are conformationally distinct and that 4R fibrils adopt a heterogeneous mixture of conformations. Populations of 4R fibril conformations, which were independently validated using a model system, can be modulated by introduction of mutations to the primary sequence or by varying fibril growth conditions. These findings provided unprecedented insights into the seed selection of tau monomers and established conformational compatibility as an important driving force in tau fibril propagation. Lastly, DEER acquisition was improved through addition of paramagnetic metal to spin-labeled protein, decreasing collection time, and through use of a novel spin label with increased T2, thereby lengthening the available acquisition window.

Emergence of half-metallicity in suspended NiO chains: Ab initio electronic structure and quantum transport calculations

Contrary to the antiferromagnetic and insulating character of bulk NiO, one-dimensional chains of this material can become half metallic due to the lower coordination of their atoms. Here we present ab initio electronic structure and quantum transport calculations of ideal infinitely long NiO chains and of more realistic short ones suspended between Ni electrodes. While infinite chains are insulating, short suspended chains are half-metallic minority-spin conductors that displays very large magnetoresistance and a spin-valve behavior controlled by a single atom.

Electronic structure and transport properties of atomic NiO spinvalves

Ab initio quantum transport calculations show that short NiO chains suspended in Ni nanocontacts present a very strong spin-polarization of the conductance.The generalized gradient approximation we use here predicts a similar polarization of the conductance as the one previously computed with non-local exchange, confirming the robustness of the result. Their use as nanoscopic spinvalves is proposed.

Graphene single-electron transistor as a spin sensor for magnetic adsorbates

We study single-electron transport through a graphene quantum dot with magnetic adsorbates. We focus on the relation between the spin order of the adsorbates and the linear conductance of the device. The electronic structure of the graphene dot with magnetic adsorbates is modeled through numerical diagonalization of a tight-binding model with an exchange potential. We consider several mechanisms by which the adsorbate magnetic state can influence transport in a single-electron transistor: tuning the addition energy, changing the tunneling rate, and in the case of spin-polarized electrodes, through magnetoresistive effects. Whereas the first mechanism is always present, the others require that the electrode has to have either an energy- or spin-dependent density of states. We find that graphene dots are optimal systems to detect the spin state of a few magnetic centers.

A highly resistive layer within the crust of X-ray pulsars limits their spin periods

The lack of isolated X-ray pulsars with spin periods longer than 12 s raises the question of where the population of evolved high-magnetic-field neutron stars has gone. Unlike canonical radiopulsars, X-ray pulsars are not subject to physical limits to the emission mechanism nor observational biases against the detection of sources with longer periods. Here we show that a highly resistive layer in the innermost part of the crust of neutron stars naturally limits the spin period to a maximum value of about 10–20 s. This highly resistive layer is expected if the inner crust is amorphous and heterogeneous in nuclear charge, possibly owing to the existence of a nuclear ‘pasta’ phase. Our findings suggest that the maximum period of isolated X-ray pulsars may be the first observational evidence for an amorphous inner crust, whose properties can be further constrained by future X-ray timing missions combined with more detailed models.

Population synthesis of isolated neutron stars with magneto-rotational evolution

We revisit the population synthesis of isolated radio-pulsars incorporating recent advances on the evolution of the magnetic field and the angle between the magnetic and rotational axes from new simulations of the magneto-thermal evolution and magnetosphere models, respectively. An interesting novelty in our approach is that we do not assume the existence of a death line. We discuss regions in parameter space that are more consistent with the observational data. In particular, we find that any broad distribution of birth spin periods with P0 ≲ 0.5 s can fit the data, and that if the alignment angle is allowed to vary consistently with the torque model, realistic magnetospheric models are favoured compared to models with classical magneto-dipolar radiation losses. Assuming that the initial magnetic field is given by a lognormal distribution, our optimal model has mean strength 〈log B0[G]〉 ≈ 13.0–13.2 with width σ(log B0) = 0.6–0.7. However, there are strong correlations between parameters. This degeneracy in the parameter space can be broken by an independent estimate of the pulsar birth rate or by future studies correlating this information with the population in other observational bands (X-rays and γ-rays).

Population synthesis of isolated neutron stars with magneto-rotational evolution – II. From radio-pulsars to magnetars

Population synthesis studies constitute a powerful method to reconstruct the birth distribution of periods and magnetic fields of the pulsar population. When this method is applied to populations in different wavelengths, it can break the degeneracy in the inferred properties of initial distributions that arises from single-band studies. In this context, we extend previous works to include X-ray thermal emitting pulsars within the same evolutionary model as radio-pulsars. We find that the cumulative distribution of the number of X-ray pulsars can be well reproduced by several models that, simultaneously, reproduce the characteristics of the radio-pulsar distribution. However, even considering the most favourable magneto-thermal evolution models with fast field decay, lognormal distributions of the initial magnetic field overpredict the number of visible sources with periods longer than 12 s. We then show that the problem can be solved with different distributions of magnetic field, such as a truncated lognormal distribution, or a binormal distribution with two distinct populations. We use the observational lack of isolated neutron stars (NSs) with spin periods P > 12 s to establish an upper limit to the fraction of magnetars born with B > 1015 G (less than 1 per cent). As future detections keep increasing the magnetar and high-B pulsar statistics, our approach can be used to establish a severe constraint on the maximum magnetic field at birth of NSs.

Derivation of the spin Hamiltonians for Fe in MgO

A method to calculate the effective spin Hamiltonian for a transition metal impurity in a non-magnetic insulating host is presented and applied to the paradigmatic case of Fe in MgO. In the first step we calculate the electronic structure employing standard density functional theory (DFT), based on generalized gradient approximation (GGA), using plane waves as a basis set. The corresponding basis of atomic-like maximally localized Wannier functions is derived and used to represent the DFT Hamiltonian, resulting in a tight-binding model for the atomic orbitals of the magnetic impurity. The third step is to solve, by exact numerical diagonalization, the N electron problem in the open shell of the magnetic atom, including both effects of spin–orbit and Coulomb repulsion. Finally, the low energy sector of this multi-electron Hamiltonian is mapped into effective spin models that, in addition to the spin matrices S, can also include the orbital angular momentum L when appropriate. We successfully apply the method to Fe in MgO, considering both the undistorted and Jahn–Teller (JT) distorted cases. Implications for the influence of Fe impurities on the performance of magnetic tunnel junctions based on MgO are discussed.

Applications of spin resonance techniques to the study of radiation effects,

Includes bibliography.

Enhanced spin injection efficiency in ferromagnet/semiconductor tunnel junctions

Within the ballistic transport picture, we have investigated the spin-polarized transport properties of a ferromagnetic metal/two-dimensional semiconductor (FM/SM) hybrid junction and an FM/FM/SM structure using quantum tunnelling theory. Our calculations indicate explicitly that the low spin injection efficiency (SIE) from an FM into an SM, compared with a ferromagnet/normal metal junction, originates from the mismatch of electron densities in the FM and SM. To enhance the SIE from an FM into an SM, we introduce another FM film between them to form FM/FM/SM double tunnel junctions, in which the quantum interference effect will lead to the current polarization exhibiting periodically oscillating behaviour, with a variation according to the thickness of the middle FM film and/or its exchange energy strength. Our results show that, for some suitable values of these parameters, the SIE can reach a very high level, which can also be affected by the electron density in the SM electrode.

Microcin J25 has a threaded sidechain-to-backbone ring structure and not a head-to-tail cyclized backbone

Microcin J25 is a 21 amino acid bacterial peptide that has potent antibacterial activity against Gram-negative bacteria, resulting from its interaction with RNA polymerase. The peptide was previously proposed to have a head-to-tail cyclized peptide backbone and a tight globular structure (Blond, A., Peduzzi, J., Goulard, C., Chiuchiolo, M. J., Barthelemy, M., Prigent, Y., Salomon, R. A., Farias, R. N., Moreno, F. & Rebuffat, S. Eur. J. Biochem. 1999, 259, 747-755). It exhibits remarkable thermal stability for a peptide of its size lacking disulfide bonds and in part this was previously proposed to derive from its macrocyclic structure. We show here that in fact the peptide does not have a head-to-tail cyclic structure but rather a side chain to backbone cyclization between Glu8 and the N-terminus. This creates an embedded ring that is threaded by the C-terminal tail of the molecule, forming a noose-like feature. The three-dimensional structure deduced from NMR data suggests that slippage of the noose is prevented by two aromatic residues flanking the embedded ring. Unthreading does not occur even when the molecule is enzymatically digested with thermolysin. The new structural interpretation fully accounts for previously reported NMR and biophysical data and is consistent with the remarkable stability of this potent antimicrobial peptide.

Solution structure of the cyclotide palicourein: Implications for the development of a pharmaceutical framework

The cyclotides are a family of disulfide-rich proteins from plants. They have the characteristic structural features of a circular protein backbone and a knotted arrangement of disulfide bonds. Structural and biochemical studies of the cyclotides suggest that their unique physiological stability can be loaned to bioactive peptide fragments for pharmaceutical and agricultural development. In particular, the cyclotides incorporate a number of solvent-exposed loops that are potentially suitable for epitope grafting applications. Here, we determine the structure of the largest known cyclotide, palicourein, which has an atypical size and composition within one of the surface-exposed loops. The structural data show that an increase in size of a palicourein loop does not perturb the core fold, to which the thermodynamic and chemical stability has been attributed. The cyclotide core fold, thus, can in principle be used as a framework for the development of useful pharmaceutical and agricultural bioactivities.