Geometry dependent two-dimensional heteronuclear multiplet effects in paramagnetic proteins

We report experimental observation and numerical simulation of a two-dimensional multiplet effect in the heteronuclear correlation spectrum of a paramagnetic protein that depends on molecular geometry. This effect arises as a consequence of cross-correlated relaxation involving the Curie spin relaxation and internuclear dipolar relaxation mechanisms. It also manifests itself in resolution and sensitivity improvement in transverse relaxation optimised spectroscopy (TROSY) kind of experiments. Characteristic multiplet patterns in heteronuclear coupled two-dimensional NMR spectra encode directional information for the heteronuclear bond with respect to the paramagnetic center. These patterns, which are simulated here using Redfield's relaxation theory, can be used to obtain a new type of geometry restriction for structure determination and refinement of paramagnetic macromolecular systems.     

顺磁物质对土壤低场核磁共振信号特征及含水量测定的影响

核磁共振(NMR)技术由于具有高效快速、不破坏土壤结构且对人体无害等优点,逐渐被应用到土壤学相关领域研究中。然而,土壤中顺磁物质的存在对核磁共振信号特征的影响仍不明确。本研究旨在揭示顺磁物质对不同类型土壤低场核磁共振(LF-NMR)信号特征和土壤含水量测定的影响。结果表明:土壤水的LF-NMR信号量最高可达150左右,土壤矿物、有机质和微生物等固相物质的LF-NMR信号量基本不超过0.3,相对可以忽略。质地和顺磁物质对土壤水的LF-NMR信号量测量有更大影响。LF-NMR仪器存在弛豫时间监测盲区,信号量损失主要是由于顺磁物质加速了水中氢质子的弛豫过程,导致小孔隙中水分反馈的极快的LF-NMR信号不能被监测设备捕获。对于顺磁物质含量较少的壤性潮土(1.2%)和黏壤性黑土(1.3%),LF-NMR信号量损失不大,其与土壤含水量呈线性关系;但对于黏粒含量(45.3%)和顺磁物质含量(4.0%)较高的黏性红壤,测定中会损失一部分LF-NMR信号量,监测到的LF-NMR信号量与土壤含水量不再呈线性关系。此外,外源添加顺磁物质(3.0 g·L^-1的MnCl₂溶液)也会降低黑土和红壤中可被监测的LF-NMR信号量,黑土和红壤的信号量最大损失率分别为41.0%和46.7%,极大地改变其与土壤含水量之间的定量关系。因此,在利用LF-NMR测量富含顺磁物质(>1.3%)或有外源顺磁物质进入的黏性土壤的含水量时,应先通过校正降低顺磁物质等对LF-NMR信号量的影响。研究结果对利用低场核磁共振技术准确分析土壤水分分布及土壤孔隙结构具有重要意义。     

Cross correlation rates between Curie spin and dipole-dipole relaxation in paramagnetic proteins: the case of cerium substituted calbindin D9k

Cross correlation rates between Curie spin relaxation and H-N dipole-dipole coupling (^CS,DD _HM,HN) have been determined for a calcium binding protein, Calbindin D_9k, in which one of the two calcium ions is substituted with cerium(III). ^CS,DD _HM,HNvalues depend on both the metal-to-proton distances and the M-H-N angles and can be used as an additional constraint in order to refine the solution structure of paramagnetic metalloproteins. For this purpose, we have implemented a new module (CCR-DYANA) in a version of the program DYANA (PARAMAGNETIC-DYANA), which can be used together with other paramagnetism-based constraints such as pseudocontact shifts, residual dipolar couplings and hyperfine based Karplus relationships. This integrated structure calculation protocol has the advantage that different paramagnetic-based constraints are treated by the same algorithm in a way that the efficiency of each class of constraints can be analyzed and compared.     

Measurement of 15N relaxation in the detergent-solubilized tetrameric KcsA potassium channel

A set of TROSY-HNCO (tHNCO)-based 3D experiments is presented for measuring ¹⁵N relaxation parameters in large, membrane-associated proteins, characterized by slow tumbling times and significant spectral overlap. Measurement of backbone ¹⁵N R ₁, R _1ρ, ¹⁵N–{¹H} NOE, and ¹⁵N CSA/dipolar cross correlation is demonstrated and applied to study the dynamic behavior of the homotetrameric KcsA potassium channel in SDS micelles under conditions where this channel is in the closed state. The micelle-encapsulated transmembrane domain, KcsA^TM, exhibits a high degree of order, tumbling as an oblate ellipsoid with a global rotational correlation time, τ_c = 38 ± 2.5 ns, at 50 °C and a diffusion anisotropy, , corresponding to an aspect ratio a/b ≥ 1.4. The N- and C-terminal intracellular segments of KcsA exhibit considerable internal dynamics (S ² values in the 0.2–0.45 range), but are distinctly more ordered than what has been observed for unstructured random coils. Relaxation behavior in these domains confirms the position of the C-terminal helix, and indicates that in SDS micelles, this amphiphilic helix does not associate into a stable homotetrameric helical bundle. The relaxation data indicate the absence of elevated backbone dynamics on the ps–ns time scale for the 5-residue selectivity filter, which selects K⁺ ions to enter the channel. Electronic Supplementary Material Supplementary material is available to authorised users in the online version of this article at . An erratum to this article can be found at     

Electron paramagnetic resonance spectroscopy as a probe of coordination structure in green heme systems: iron chlorins and iron formylporphyrins reconstituted into myoglobin

A series of ferric low-spin derivatives of myoglobin containing its natural prosthetic group, iron protoporphyrin IX, and reconstituted with iron heme s (a formyl-substituted porphyrin) and iron methylchlorin have been examined using low-temperature electron paramagnetic resonance (EPR) spectroscopy. Good agreement is observed between the EPR properties of parallel derivatives of natural myoglobin and heme s-myoglobin. Likewise, the EPR properties of parallel adducts of three types of iron chlorins, methylchlorin-myoglobin, sulfyomyoglobin (a myoglobin derivative known to contain a chlorin macrocycle) and synthetic chlorin models are similar to each other. The ferric chlorin systems are shown to exhibit increased tetragonality and decreased rhombicity values relative to protoporphyrin/formylporphyrin systems. Thus, EPR spectroscopy is a very useful technique with which to probe the coordination structure of naturally occurring iron chlorin proteins and the method can be used to distinguish between proteins containing iron formylporphyrins and iron chlorin prosthetic groups.     

Determination of dihedral Psi angles in large proteins by combining NH(N)/C(alpha)H(alpha) dipole/dipole cross-correlation and chemical shifts

We propose a strategy based on the combination of experimental NH(N)/C(alpha)H(alpha) dipole/dipole cross-correlated relaxation rates and chemical shift analysis for the determination of Psi torsion angles in proteins. The method allows the determination of a dihedral angle that is not easily accessible by nuclear magnetic resonance (NMR). The measurement of dihedral angle restraints can be used for structure calculation, which is known to improve the quality of NMR structures. The method is of particular interest in the case of large proteins, for which spectral assignment of the nuclear Overhauser effect spectra, and therefore straightforward structural determination, is out of reach. One advantage of the method is that it is reasonably simple to implement, and could be used in association with other methods aiming at obtaining structural information on complex systems, such as residual dipolar coupling measurements. An illustrative example is analyzed in the case of the 30-kDa protein 6-phosphogluconolactonase.     

Electron paramagnetic resonance study of structural changes in the O photointermediate of bacteriorhodopsin

The structural changes of bacteriorhodopsin during its photochemical cycle, as revealed by crystal structures of trapped intermediates, have provided insights to the proton translocation mechanism. Because accumulation of the last photointermediate, O, appears to be hindered by lattice forces in the crystals, the only information about the structure of this state is from suggested analogies with the determined structures of the non-illuminated D85S mutant and wild-type bacteriorhodopsin at low pH. We used electron paramagnetic resonance spectroscopy of site-directed spin labels at the extracellular protein surface in membranes to test these models. Spin-spin dipolar interactions in the authentic O state compared to the non-illuminated state revealed that the distance between helices C and F increases by ca 4 Angstroms, there is no distance change between helices D and F, and the distance between helix D and helix B of the adjacent monomer increases. Further, the mobility changes of single labels indicate that helices E and F move outward from the proton channel at the center of the protein, and helix D tilts inward. The overall pattern of movements suggests that the model at acid pH is a better representation of the O state than D85S. However, the mobility analysis of spin-labels on the B-C interhelical loop indicates that the antiparallel beta-sheet maintains its ordered secondary structure in O, instead of the predicted disorder in the two structural models. During decay of the O state, the last step of the photocycle, a proton is transferred from Asp85 to proton release complex in the extracellular proton channel. The structural changes in O suggest the need of large conformational changes to drive the Arg82 side-chain back to its initial orientation towards Asp85, and to rearrange the numerous water molecules in this region in order to conduct the proton away from Asp85.     

Dielectric behavior of water in biological solutions: studies on myoglobin, human low-density lipoprotein, and polyvinylpyrrolidone

The dielectric behavior of the aqueous solutions of three widely differing macromolecules has been investigated: myoglobin, polyvinylpyrrolidone (PVP), and human serum low-density lipoprotein (LDL). It was not possible to interpret unambiguously the dielectric properties of the PVP solution in terms of water structure. The best interpretation of the dielectric data on the myoglobin and LDL solutions was that, in both cases, the macromolecule attracts a layer of water of hydration one or two water molecules in width. For LDL, this corresponds to a hydration factor of only 0.05 g/g, whereas for myoglobin the figure is nearer 0.6 g/g. With myoglobin, part of the water of hydration exhibits its dispersion at frequencies of a few GHz, and the rest disperses at lower frequencies, perhaps as low as 10-12 MHz. The approximate constancy of the width of the hydration shell for two molecules as dissimilar in size as LDL and myoglobin confirms that the proportion of water existing as water of hydration in a biological solution depends critically on the size of the macromolecules as well as on their concentration.     

Lipid chain-length dependence for incorporation of alamethicin in membranes: electron paramagnetic resonance studies on TOAC-spin labeled analogs

Alamethicin is a 19-residue hydrophobic peptide, which is extended by a C-terminal phenylalaninol but lacks residues that might anchor the ends of the peptide at the lipid-water interface. Voltage-dependent ion channels formed by alamethicin depend strongly in their characteristics on chain length of the host lipid membranes. EPR spectroscopy is used to investigate the dependence on lipid chain length of the incorporation of spin-labeled alamethicin in phosphatidylcholine bilayer membranes. The spin-label amino acid TOAC is substituted at residue positions n = 1, 8, or 16 in the sequence of alamethicin F50/5 [TOAC(n), Glu(OMe)(7,18,19)]. Polarity-dependent isotropic hyperfine couplings of the three TOAC derivatives indicate that alamethicin assumes approximately the same location, relative to the membrane midplane, in fluid diC(N)PtdCho bilayers with chain lengths ranging from N = 10-18. Residue TOAC(8) is situated closest to the bilayer midplane, whereas TOAC(16) is located farther from the midplane in the hydrophobic core of the opposing lipid leaflet, and TOAC(1) remains in the lipid polar headgroup region. Orientational order parameters indicate that the tilt of alamethicin relative to the membrane normal is relatively small, even at high temperatures in the fluid phase, and increases rather slowly with decreasing chain length (from 13 degrees to 23 degrees for N = 18 and 10, respectively, at 75 degrees C). This is insufficient for alamethicin to achieve hydrophobic matching. Alamethicin differs in its mode of incorporation from other helical peptides for which transmembrane orientation has been determined as a function of lipid chain length.     

Similarities between intra- and intermolecular hydrogen bonds in RNA kissing complexes found by means of cross-correlated relaxation

The bond lengths and dynamics of intra- and intermolecular hydrogen bonds in an RNA kissing complex have been characterized by determining the NMR relaxation rates of various double- and triple-quantum coherences that involve an imino proton and two neighboring nitrogen-15 nuclei belonging to opposite bases. New experiments allow one to determine the chemical shift anisotropy of the imino protons. The bond lengths derived from dipolar relaxation and the lack of modulations of the nitrogen chemical shifts indicate that the intermolecular hydrogen bonds which hold the kissing complex together are very similar to the intramolecular hydrogen bonds in the double-stranded stem of the RNA.     

Light-dependent and -independent behavioral effects of extremely low frequency magnetic fields in a land snail are consistent with a parametric resonance mechanism

Exposure to extremely low frequency (ELF) magnetic fields has been shown to attenuate endogenous opioid peptide mediated antinociception or “analgaesia” in the terrestrial pulmonate snail, Cepaea nemoralis. Here we examine the roles of light in determining this effect and address the mechanisms associated with mediating the effects of the ELF magnetic fields in both the presence and absence of light. Specifically, we consider whether the magnetic field effects involve an indirect induced electric current mechanism or a direct effect such as a parametric resonance mechanism (PRM). We exposed snails in both the presence and absence of light at three different frequencies (30, 60, and 120 Hz) with static field values (B_DC) and ELF magnetic field amplitude (peak) and direction (B_AC) set according to the predictions of the PRM for Ca²⁺. Analgaesia was induced in snails by injecting them with an enkephalinase inhibitor, which augments endogenous opioid (enkephalin) activity. We found that the magnetic field exposure reduced this opioid-induced analgaesia significantly more if the exposure occurred in the presence rather than the absence of light. However, the percentage reduction in analgaesia in both the presence and absence of light was not dependent on the ELF frequency. This finding suggests that in both the presence and the absence of light the effect of the ELF magnetic field was mediated by a direct magnetic field detection mechanism such as the PRM rather than an induced current mechanism. Bioelectromagnetics 18:284–291, 1997. © 1997 Wiley-Liss, Inc.     

Cell volume dependence of 1H spin-echo NMR signals in human erythrocyte suspensions: The influence of in situ field gradients

The ¹H spin-echo NMR signal amplitudes and intensities of low molecular weight solutes in the cytoplasm and extracellular fluid of suspensions of human erythrocytes were shown to depend on the osmotic pressure of the media. At low osmotic pressure (220 mosM/kg) freeze-thaw lysis of the cells resulted in signal enhancement which was greatest for extracellular molecules, but both intra- and extracellular species were almost equally enhanced at 580 mosM/kg. This effect is due to field gradients formed at cell boundaries as a result of differences in magnetic susceptibility between the medium and the cytoplasm. T₂ values measured using the Carr-Purcell-Meiboom-Gill pulse sequence, with τ = 0.0003 s, depended little on cell volume and absolute changes in volume magnetic susceptibility were also small. The mean field gradients, calculated from data obtained on cell suspensions at different osmotic pressures, were in the range 0.25–1.98 G/cm and 0.89–2.09 G/cm for intra- and extracellular compartments, respectively. The maintenance of isotonicity of the extracellular fluid during metabolic studies of cell suspensions is important in order to avoid artefacts in the determination of metabolite concentrations when using the spin-echo technique. Conversely it may be possible to perform transport measurements using spin-echo NMR to monitor the cell volume changes which occur during the transmembrane migration of molecules.     

Spatial distribution of cytoplasmic domains of the Mg-transporter MgtE,in a solution lacking Mg,revealed by paramagnetic relaxation enhancement

MgtE is a prokaryotic Mg²⁺ transporter that controls cellular Mg²⁺ concentrations. We previously reported crystal structures of the cytoplasmic region of MgtE, consisting of 2 domains, that is, N and CBS, in the Mg²⁺-free and Mg²⁺-bound forms. The Mg²⁺-binding sites lay at the interface of the 2 domains, making the Mg²⁺-bound form compact and globular. In the Mg²⁺-free structure, however, the domains are far apart, and the Mg²⁺-binding sites are destroyed. Therefore, it is unclear how Mg²⁺-free MgtE changes its conformation to accommodate Mg²⁺ ions. Here, we used paramagnetic relaxation enhancement (PRE) to characterize the relative orientation of the N and CBS domains in the absence of Mg²⁺ in solution. When the residues on the surface of the CBS domain were labeled with nitroxide tags, significant PRE effects were observed for the residues in the N domain. No single structure satisfied the PRE profiles, suggesting that the N and CBS domains are not fixed in a particular orientation in solution. We then conducted ensemble simulated annealing calculations in order to obtain the atomic probability density and visualize the spatial distribution of the N domain in solution. The results indicate that the N domain tends to occupy the space near its position in the Mg²⁺-bound crystal structure, facilitating efficient capture of Mg²⁺ with increased intracellular Mg²⁺ concentration, which is necessary to close the gate.     

Structure and dynamics of the force-generating domain of myosin probed by multifrequency electron paramagnetic resonance

Spin-labeling and multifrequency EPR spectroscopy were used to probe the dynamic local structure of skeletal myosin in the region of force generation. Subfragment 1 (S1) of rabbit skeletal myosin was labeled with an iodoacetamide spin label at C707 (SH1). X-and W-band EPR spectra were recorded for the apo state and in the presence of ADP and nucleotide analogs. EPR spectra were analyzed in terms of spin-label rotational motion within myosin by fitting them with simulated spectra. Two models were considered: rapid-limit oscillation (spectrum-dependent on the orientational distribution only) and slow restricted motion (spectrum-dependent on the rotational correlation time and the orientational distribution). The global analysis of spectra obtained at two microwave frequencies (9.4 GHz and 94 GHz) produced clear support for the second model and enabled detailed determination of rates and amplitudes of rotational motion and resolution of multiple conformational states. The apo biochemical state is well-described by a single structural state of myosin (M) with very restricted slow motion of the spin label. The ADP-bound biochemical state of myosin also reveals a single structural state (M*, shown previously to be the same as the post-powerstroke ATP-bound state), with less restricted slow motion of the spin label. In contrast, the extra resolution available at 94 GHz reveals that the EPR spectrum of the S1.ADP.V_i-bound biochemical state of myosin, which presumably mimics the S1.ADP.P_i state, is resolved clearly into three spectral components (structural states). One state is indistinguishable from that of the ADP-bound state (M*) and is characterized by moderate restriction and slow motion, with a mole fraction of 16%. The remaining 84% (M**) contains two additional components and is characterized by fast rotation about the x axis of the spin label. After analyzing EPR spectra, myosin ATPase activity, and available structural information for myosin II, we conclude that post-powerstroke and pre-powerstroke structural states (M* and M**) coexist in the S1.ADP.V_i biochemical state. We propose that the pre-powerstroke state M** is characterized by two structural states that could reflect flexibility between the converter and N-terminal domains of myosin.     

Hatching fraction and timing of resting stage production in seasonal environments: effects of density dependence and uncertain season length

Many organisms survive unfavourable seasons as resting stages, some of which hatch each favourable season. Hatching fraction and timing of resting stage production are important life history variables. We model life cycles of freshwater invertebrates in temporary pools, with various combinations of uncertain season length and density‐dependent fecundity. In deterministic density‐independent conditions, resting stage production begins suddenly. With uncertain season length and density independence, resting stage production begins earlier and gradually. A high energetic cost of resting stages favours later resting stage production and a lower hatching fraction. Deterministic environments with density dependence allow sets of coexisting strategies, dominated by pairs, each switching suddenly to resting stage production on a different date, usually earlier than without density dependence. Uncertain season length and density dependence allow a single evolutionarily stable strategy, around which we observe many mixed strategies with negatively associated yield (resting stages per initial active stage) and optimal hatching fraction.     

Physiological and psychological effects of walking on young males in urban parks in winter

Background

Interaction with nature has a relaxing effect on humans. Increasing attention has been focused on the therapeutic effects of urban green space; however, there is a lack of evidence-based field research. This study provided scientific evidence supporting the physiological and psychological effects of walking on young males in urban parks in winter.

Findings

Subjects (13 males aged 22.5 ± 3.1 years) were instructed to walk predetermined 15-minute courses in an urban park (test) and in the city area (control). Heart rate and heart rate variability (HRV) were measured to assess physiological responses. The semantic differential (SD) method, Profile of Mood States (POMS), and State-Trait Anxiety Inventory (STAI) were used to determine psychological responses.Heart rate was significantly lower and the natural logarithm of the high frequency component of HRV was significantly higher when walking through the urban park than through the city area. The results of three questionnaires indicated that walking in the urban park improved mood and decreased negative feelings and anxiety.

Conclusions

Physiological and psychological data from this field experiment provide important scientific evidence regarding the health benefits of walking in an urban park. The results support the premise that walking in an urban park has relaxing effects even in winter.     

Dynamical characterization of residual and non-native structures in a partially folded protein by (15)N NMR relaxation using a model based on a distribution of correlation times

A spectral density model based on a truncated lorentzian distribution of correlation times is used to analyze the nanosecond time-scale dynamics of the partially unfolded domain 2 of annexin I from its (15)N NMR relaxation parameters measured at three magnetic field strengths. The use of a distribution of correlation times enables the characterization of the dynamical features of the NH bonds of the protein in terms of heterogeneity of dynamical states in the nanosecond range. The variation along the sequence of the two dynamical parameters introduced, namely the center and the width of the distribution, points out the different types of residual secondary structures present in the D2 domain. Moreover, it allows a physically sensible interpretation of the dynamical behavior of the different residual helices and of the non-native structures. Also, a striking correspondence is found between the parameters obtained using an extended Lipari and Szabo model and the parameters obtained using the distribution of correlation times. This result led us to propose a specific interpretation of the model-free order parameter for internal motions in the nanosecond range in the case of unfolded states.     

The effects of a weak permanent magnetic field on the lipid composition and content in the onion leaves of various ages

We have studied the effects of a weak permanent magnetic field (PMF) with strength of 403 A/m on the composition and content of polar and neutral lipids and the composition of their fatty acids (FAs). The lipids were isolated from the third, fourth, and fifth leaves of onion (Allium cepa L., cv. Arzamasskii) plants, and their composition was determined using TLC and GLC techniques. Plants growth under the conditions of a natural geomagnetic field served as a control. Most intense changes in the lipid content induced by PMF were observed in the fourth onion leaf. The content of total lipids and that of polar lipids (glyco-and phospholipids) changed, whereas the content of neutral lipids either decreased or remained unchanged. The phospholipid/sterol ratio increased, causing an increase in the fluidity of the membrane lipid bilayer. PMF induced an increase in the concentration of linolenic acid and the relative content of total unsaturated FAs. The effects of PMF on the content and composition of lipids in the third and fifth onion leaves were less pronounced, demonstrating differences between the leaves of various ages in their sensitivity to the effects of magnetic field. It is concluded that changes in the weak PMF within the limits of changes in the strength of geomagnetic field in the course of evolution can affect biochemical and physiological processes of plants.     

Mutual information analysis of mutation,nonlinearity, and triple interactions in proteins

Mutations are the cause of several diseases as well as the underlying force of evolution. A thorough understanding of their biophysical consequences is essential. We present a computational framework for evaluating different levels of mutual information (MI) and its dependence on mutation. We used molecular dynamics trajectories of the third PDZ domain and its different mutations. Nonlinear MI between all residue pairs are calculated by tensor Hermite polynomials up to the fifth order and compared with results from multivariate Gaussian distribution of joint probabilities. We show that MI is written as the sum of a Gaussian and a nonlinear component. Results for the PDZ domain show that the Gaussian term gives a sufficiently accurate representation of MI when compared with nonlinear terms up to the fifth order. Changes in MI between residue pairs show the characteristic patterns resulting from specific mutations. Emergence of new peaks in the MI versus residue index plots of mutated PDZ shows how mutation may change allosteric pathways. Triple correlations are characterized by evaluating MI between triplets of residues. We observed that certain triplets are strongly affected by mutation. Susceptibility of residues to perturbation is obtained by MI and discussed in terms of linear response theory.