Finite one-dimensional spin systems as models of biopolymers

New models are proposed for describing various properties of biopolymers, especially those of proteins and nucleic acids. Each model is constituted of a set of spins arranged on a chain, and each pair of spins produces an interaction. We examine the transitions of these spin systems between the ground state and the disordered state. It is found that the transitions of the present spin systems demonstrate various properties in response to values of the so-called interaction energy. If we define interaction energy parameters with no so-called frustration, the system exhibits two-state transitions, similar to the folding-unfolding transition of small proteins. The addition of frustrations to the model produces effects similar to those of mutations in proteins. On the other hand, if the interactions between two spins attenuate as a function of their separation along the chain, the transition of the system has characteristics similar to those of nucleic acids. Thus, the present spin systems can offer a unified view of the folding-unfolding transition of biopolymers in terms of differences in the pairwise interactions between spins. Based on our models, we propose a condition for two-state transition behavior for proteins.     

Efficient rotamer elimination applied to protein side-chains and related spin glasses.

Folded proteins and spin glasses share various properties, such as seemingly random interactions between residues (spins), and one might presume that some generic behaviors of spin glasses would also be exhibited in a general way by proteins. But a comparison here shows that the side-chain conformation systems of apo-myoglobin and lysozyme are qualitatively different from specific closely related spin glass systems. This difference is manifest in the number of rotamers that can be identified as definitely not contributing to the global energy minimum. This identification is effected by using a significantly enhanced version of the Dead End Elimination theorem (Desmet, J., M. De Maeyer, B. Hazes, and I. Lasters. 1992. The dead-end elimination theorem and its use in protein side-chain positioning. Nature. 356:539-542), which is much more effective and efficient in eliminating rotamers. In several cases (for proteins, although not for spin glasses) this improved Dead End Elimination theorem succeeded in identifying the absolute global minimum of rotamer conformations, with no statistical uncertainty. The difference between protein and spin glass is due to correlations between the interactions of one residue pair with another pair, and probably will play an important role in the thermodynamic behavior of the protein system.     

Frozen spin targets in ribosomal structure research.

Polarized neutron scattering strongly depends on nuclear spin polarisation, particularly on proton spin polarisation. A single proton in a deuterated environment then is as efficient as 10 electrons in X-ray anomalous diffraction. Neutron scattering from the nuclear spin label is controlled by the polarisation of neutron spins and nuclear spins. Pure deuteron spin labels and proton spin labels are created by NMR saturation. We report on results obtained from the large subunit of E. coli ribosomes which have been obtained at the research reactor of GKSS using the polarized target facility developed by CERN. The nuclear spins were oriented with respect to an external field by dynamic nuclear polarisation. Proton spin polarisations of more than 80% were obtained in ribosomes at temperatures below 0.5 K. At T = 130 mK the relaxation time of the polarized target is one month (frozen spin target). Polarized small-angle neutron scattering of the in situ structure of rRNA and the total ribosomal protein (TP) has been determined from the frozen spin targets of the large ribosomal subunit, which has been deuterated in the TP and rRNA respectively. The results agree with those from neutron scattering in H2O/D2O mixtures obtained at room temperature. This is a necessary prerequisite for the planned determination of the in situ structure of individual ribosomal proteins and especially of that of ribosome bound mRNA and tRNAs.     

Suppression of spin diffusion in selected frequency bands of nuclear Overhauser spectra

Summary A variant of two-dimensional nuclear Overhauser effect spectroscopy (NOESY) is described that yields information about cross-relaxation rates between pairs of spins, while the migration of magnetization through several consecutive steps (spin diffusion via neighboring spins) is largely suppressed. This can be achieved by inserting a doubly-selective inversion pulse in a conventional NOESY sequence.     

Free radical scavenging action of Bio-catalyzer alpha.rho No.11 (Bio-normalyzer) and its by-product.

Bio-catalyzer alpha.rho No.11 (Bio-normalyzer) and its by-product are natural health products made by yeast fermentation of glucose, Carica papaya Linn., Pennisetum pupureum Schum., and Sechium edule Swartz. Their effects on free radicals were examined by electron spin resonance spectrometry using spin trapping agent 5,5-dimethyl-1-pyrroline-1-oxide (DMPO). It was observed that both Bio-catalyzer and its by-product scavenged 95% of DMPO-OH spin adducts (89 x 10(15) spins/ml) generated by FeSO4-H2O2-diethylene triamine pentaacetic acid system at 45.45 mg/ml each. Five percent of DMPO-O2- spin adducts (27 x 10(15) spins/ml) generated by hypoxanthine-xanthine oxidase system and 11% of 1,1-diphenyl-2-picrylhydrazyl radicals (7 x 10(15) spins/ml) were quenched using 25 mg/ml of Bio-catalyzer while 5% of superoxide and nil DPPH radicals were scavenged by its by-product. Vivo tests showed that oral administration of 1-g/kg body weight of Bio-catalyzer significantly inhibited thiobarbituric acid reactive substances formation, which is an index of lipid peroxidation, in the FeCl3-induced epileptic focus of rats. These findings suggest that Bio-catalyzer or its by-product may be useful health foods against neural lipid peroxidation, traumatic epilepsy and aging.     

Detection of conformational changes in Complex III of the respiratory chain by a maleimido spin label

Changes in the conformation of Complex III (CoQH₂-cytochromec reductase) of the mitochondrial respiratory chain were detected upon oxidoreduction using the nitroxide spin label, 3-(maleimidomethyl)-2,2,5,5-tetramethyl-1-pyrrolidinyloxyl. EPR spectra of the spin label show a transition from a greater to a lesser degree of immobilization when the labeled enzyme, reduced either with ascorbate or sodium dithionite, is oxidized with potassium ferricyanide or ferricytochromec. These observations are interpreted to indicate that Complex III is more compact in the reduced state at least in the locality of the spin label. An apparent increase in the concentration of total spins during oxidation of the complex suggests change in the interaction between the spin label and other paramagnetic centers and not an oxidation of spin label, itself, since reduced free spin label could not be reoxidized. Addition of antimycin A had no effect on the EPR spectrum of the spin-labeled enzyme, indicating that this inhibitor does not initiate a conformational change in the region of the spin label. Experiments in which N-ethyl-[2-³H] maleimide was bound to Complex III show that binding occurs primarily to a subunit with a molecular weight of 45,000. Although no qualitative differences were observed, it was found that less radioactivity appears in samples reduced with dithionite than in those reduced with ascorbate. This difference appears to be caused by decomposition products of dithionite.     

Periodicity in the fine structure of histograms during nuclear decay

A theoretical explanation is offered for the appearance of periodicity in the fine structure of histograms describing the processes of nuclear decay. This effect is observed in a sample containing nonpolarized radioactive nuclei, with largely isotropic spin distribution over directions. However, because of fluctuations occurring in any real sample, the number of nuclei having spin directed along some isolated axis would differ somewhat from the number of nuclei with spin directed along another axis. The same is immobile relating to the Earth but rotates in space together with it. At the same time, the nuclear spins, owing to quite weak interaction with the environment, keep their directions in space. Therefore, the spin ensemble rotates both relative to the sample itself and relative to the detector of α-particles directed onto the sample. Since fluctuations in the number of nuclei with spins directed at a certain angle relative to the detector direction affect the fine structure of histograms, the latter proves to depend, among other things, of the rotation of the Earth. Consequently, when the Earth makes a full revolution and the distribution of fluctuations in the number of nuclei with given spin direction returns to the initial one, the shape of the fine structure of histograms will be repeated, and repeated over the same definite time intervals.     

NMR relaxation of protein and water protons in methemoglobin solutions.

Hemoglobin (Hb) proton spins rapidly equilibrate among themselves after an initial excitation, and relax toward thermal equilibrium as a unit. In the diamagnetic form, spin diffusion to nearby methyl relaxation sinks can account for this. For metHb, four strong heme relaxation centers dominate, and spin diffusion must occur over long distances. A sizeable difference in protein T1 is found between H2O and D2O solutions, much more than for diamagnetic Hb, consistent with internal H2O acting as a spin carrier to the heme.     

Quantum magnets with anisotropic infinite range random interactions

Using exact diagonalization techniques, we study the dynamical response of the anisotropic disordered Heisenberg model for systems of S=1/2 spins with infinite range random exchange interactions at temperature T=0. The model can be considered as a generalization, to the quantum case, of the well-known Sherrington-Kirkpatrick classical spin glass model. We also compute and study the behavior of the Edwards Anderson order parameter and energy per spin as the anisotropy evolves from the Ising to the Heisenberg limits.     

Analysis of the Cob(II)alamin-5'-deoxy-3',4'-anhydroadenosyl radical triplet spin system in the active site of diol dehydrase

A triplet spin system (S=1) is detected by low-temperature electron paramagnetic resonance (EPR) spectroscopy in samples of diol dehydrase and the functional adenosylcobalamin (AdoCbl) analogue 5'-deoxy-3',4'-anhydroadenosylcobalamin (anAdoCbl). Different spectra are observed in the presence and absence of the substrate (R,S)-1,2-propanediol. In both cases, the spectra include a prominent half-field transition (DeltaM(S) = 2) that is a hallmark of strongly coupled triplet spin systems. The appearance of 59Co hyperfine splitting in the EPR signals and the positions (g values) of the signals in the spectra show that half of the triplet spin is contributed by the low-spin Co2+ of cob(II)alamin. Line width effects from isotopic labeling (13C and 2H) in the 5'-deoxy-3',4'-anhydroribosyl ring demonstrate that the other half of the spin triplet is from an allylic 5'-deoxy-3',4'-anhydroadenosyl (anhydroadenosyl) radical. The zero-field splitting (ZFS) tensors describing the magnetic dipole-dipole interactions of the component spins of the triplets have rhombic symmetry because of electron spin delocalization within the organic radical component and the proximity of the radical to the low-spin Co2+. The dipole-dipole interaction was modeled as a summation of point-dipole interactions involving the spin-bearing orbitals of the anhydroadenosyl radical and cob(II)alamin. Geometries which are consistent with the ZFS tensors in the presence and absence of the substrate position the 5'-carbon of the anhydroadenosyl radical 3.5 and 4.1 A from Co2+, respectively. Homolytic cleavage of the cobalt-carbon bond of the analogue in the absence of the substrate indicates that, in diol dehydrase, binding of the coenzyme to the protein weakens the bond prior to binding of the substrate.     

Quantum computing with molecular magnets

We discuss the potential of molecular magnets as the building blocks of a quantum computer. The simplification in the control procedure for the quantum gates in many-spin systems coming from the high symmetry is shown to lead to a relatively simple way to address the spin degrees of freedom in molecular magnets. The advantage of an anisotropic effective spin interaction in memory applications is demonstrated on the example of the Grover quantum search algorithm in a generic easy-axis molecular magnet. Electric control of the coupling between the spins is shown to enable two-qubit quantum gates in polyoxometalates.     

电子顺磁共振测量蛋白质分子内选定位点之间距离的方法及应用

蛋白质分子的结构决定了其特性和功能,准确测量蛋白质分子中特殊位点之间的距离对其结构解析至关重要。该文在简要介绍电子顺磁共振(electron paramagnetic resonance,EPR)方法测量蛋白质分子内未偶自旋之间距离基本原理的基础上,重点综述了近年来EPR结合定点自旋标记(site-directed spin label,SDSL)技术在研究蛋白质结构与功能方面的应用情况,归纳了EPR-SDSL方法测量距离的特点和存在问题,并提出了改进用连续波EPR技术测量距离的准确度的思路和实现方法。     

Multiangular method for analysing molecular geometry from nuclear Overhauser effect results

A multiangular method, as an extension of a triangular method, has been developed in order to analyse the local conformation of a molecule in an atomic resolution from nuclear Overhauser effect results. When there is a rigid part in the molecule, and the nuclear Overhauser effect signals are observed between several spins attributed to the rigid part of the molecule and the target spin to be analysed, the geometrical probability density of the target spin can be found by the multiangulation method, using distances between spin pairs. The spin density is illustrated by a set of isograms similar to electron density maps from X-ray crystallographic analyses. The molecular model building is performed based upon the isograms. An application to the conformation analysis of transferred nuclear magnetic resonance results of NAD⁺, which binds to lactose dehydrogenace from Thermus caldophilus GK24, is described.     

Synthesis and properties of chlorophyll-derived nitroxide spin labels

A general synthesis of chlorophyll-derived spin labels is reported. The starting point is chlorophyll a and a long chain spin-labeled alcohol. The four-step synthetic route yields new spin labels in quantities practical for membrane spin-labeling studies. Two examples prepared are 12′-proxyltridecyl pyropheophorbide a and 12′-proxylhexadecyl pyropheophorbide a. The spin labels were purified and characterized by thin-layer chromatography, high-pressure liquid chromatography, mass spectroscopy, nmr and visible spectroscopy, and the number of unpaired spins per molecule. ESR spectral parameters are reported. The chlorophyll-derived spin labels intercalate into fluid phospholipid bilayers and are observed in both the bilayer phase and bound to membrane proteins in chromatophores of the purple photosynthetic bacterium, Rhodopseudomonas sphaeroides.     

Body movements during the off-ice execution of back spins in figure skating

Using an optoelectronic motion capture system, we quantitatively assessed the arrangement of body segments and the displacement of the horizontal projection of the center of mass (CM) in seven skaters performing off-ice back spins on a rotating device (spinner). The position of the CM at the beginning of the spins was not a determining factor, but its rapid stabilization towards the center of the spinner, together with the achievement of a stable arrangement of trunk and limbs, was crucial to get the dynamic equilibrium, necessary for a lasting performance. At full spinning, however, there was an indicative variety of individual body postures. A final deceleration, associable with the loss of body equilibrium, was detected in the last spin of most of skaters.In conclusion, the current investigation demonstrated that the off-ice execution of back spin, a critical movement of ice skating, can be measured in laboratory, thus providing quantitative information to both the skaters and the coaches. The analysis is not invasive, and it may be proposed also for longitudinal evaluations of skating and postural training.     

Partially folded equilibrium intermediate of the villin headpiece HP67 defined by 13C relaxation dispersion

Identification and characterization of ensembles of intermediate states remains an important objective in describing protein folding in atomic detail. The 67-residue villin headpiece, HP67, consists of an N-terminal subdomain (residues 10–42) that transiently unfolds at equilibrium under native-like conditions and a highly stable C-terminal subdomain (residues 43–76). The transition between folded and unfolded states of the N-terminal domain has been characterized previously by ¹⁵N NMR relaxation dispersion measurements (Grey et al. in J Mol Biol 355:1078, 2006). In the present work, ¹³C spin relaxation was used to further characterize backbone and hydrophobic core contributions to the unfolding process. Relaxation of ¹³C^α spins was measured using the Hahn echo technique at five static magnetic fields (11.7, 14.1, 16.4, 18.8, and 21.1 T) and the Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion method at a static magnetic field of 14.1 T. Relaxation of methyl ¹³C spins was measured using CPMG relaxation dispersion experiments at static magnetic fields of 14.1 and 18.8 T. Results for ¹³C and ¹⁵N spins yielded a consistent model in which the partially unfolded intermediate state of the N-terminal subdomain maintains residual structure for residues near the unprotonated His41 imidazole ring and in the interface between the N- and C-terminal subdomains. In addition, a second faster process was detected that appears to represent local dynamics within the folded state of the molecule and is largely confined to the hydrophobic interface between the N- and C-terminal subdomains.     

Ortho-para spin isomers of the protons in the methylene group--possible implications for protein structure

The two hydrogen atoms attached to the carbon in the methylene group are of two different spin configurations, similar to those in the case of water: ortho, where the two proton spins are parallel to each other, and para, where they are antiparallel. The ortho configuration has three degenerate states, while the para configuration is singular, leading to a statistical ratio of these isomers 3:1 ortho/para. Such spin isomers are present in glycine and most chiral amino acids where they may induce broadening of structural zones, a possibility which remains to be assessed. The implications of this neglected possibility could be far-reaching, in particular with respect to protein structure and the origins of biochirality.     

Low T scaling in the binary 2d spin glass

We investigate 2d Ising spin glasses with binary couplings via exact computations of the partition function on lattices with periodic boundary conditions. After introducing the physical issues, we sketch the algorithm to compute the partition function as a polynomial with integer coefficients. This technique is then exploited to obtain the thermodynamic properties of the spin glass. We find an anomalous low temperature scaling of the heat capacity c(v) approximately e(-2beta) and that hyperscaling holds.     

The Mössbauer and magnetic properties of ferritin cores

Background: Mössbauer and magnetization measurements, singly or in combination, extract detailed information on the microscopic or internal magnetism of iron-based materials and their macroscopic or bulk magnetization. The combination of the two techniques affords a powerful investigatory probe into spin relaxation processes of nanosize magnetic systems. The ferritin core constitutes a paradigm of such nano-magnetic system where Mössbauer and magnetization studies have been broadly combined in order to elucidate its composition, the initial steps of iron nucleation and biomineralization, particle growth and core-size distribution. In vivo produced and in vitro reconstituted wild-type and variant ferritins have been extensively studied in order to elucidate structure/function correlations and ferritin’s role in iron overloading or neurodegenerative disorders.Scope of Review: Studies on the initial stages of iron biomineralization, biomimetic synthetic analogues and ferrous ion retention within the ferritin core are presented. The dynamical magnetic properties of ferritin by Mössbauer and magnetization measurements are critically reviewed. The focus is on experiments that reveal the internal magnetic structure of the ferritin core. Novel magnetic measurements on individual ferritin molecules via AFM and nanoSQUID investigations are also mentioned. Major Conclusions: A complex two-phase spin system is revealed due to finite-size effects and non-compensated spins at the surface of the anti-ferromagnetic ferritin core. Below the blocking temperature surface spins participate in relaxation processes much faster than those associated with collective magnetic excitations of interior spins. General Significance: The studies reviewed contribute uniquely to the elucidation of the spin-structure and spin-dynamics of anti-ferromagnetic nanolattices and their possible applications to nano/bio-technology.     

Characterization of molecular mobility in seed tissues: an electron paramagnetic resonance spin probe study.

The relationship between molecular mobility (tauR) of the polar spin probe 3-carboxy-proxyl and water content and temperature was established in pea axes by electron paramagnetic resonance (EPR) and saturation transfer EPR. At room temperature, tauR increased during drying from 10(-11) s at 2.0 g water/g dry weight to 10(-4) s in the dry state. At water contents below 0.07 g water/g dry weight, tauR remained constant upon further drying. At the glass transition temperature, tauR was constant at approximately 10(-4) s for all water contents studied. Above Tg, isomobility lines were found that were approximately parallel to the Tg curve. The temperature dependence of tauR at all water contents studied followed Arrhenius behavior, with a break at Tg. Above Tg the activation energy for rotational motion was approximately 25 kJ/mol compared to 10 kJ/mol below Tg. The temperature dependence of tauR could also be described by the WLF equation, using constants deviating considerably from the universal constants. The temperature effect on tauR above Tg was much smaller in pea axes, as found previously for sugar and polymer glasses. Thus, although glasses are present in seeds, the melting of the glass by raising the temperature will cause only a moderate increase in molecular mobility in the cytoplasm as compared to a huge increase in amorphous sugars.