A critical evaluation of models for complex molecular dynamics: application of NMR studies of double- and single-stranded DNA

The nature of internal and overall motions in native (double-stranded) and denatured (single-stranded) DNA fragments 120–160 base pairs (bp) long is examined by molecular-dynamics modeling using ¹³C-nmr spin-relaxation data obtained over the frequency range of 37–125 MHz. The broad range of ¹³C frequencies is required to differentiate among various models. Relatively narrow linewidths, large nuclear Overhauser enhancements (NOEs), and short T₁ values all vary significantly with frequency and indicate the presence of rapid, restricted internal motions on the nanosecond time scale. For double-stranded DNA monomer fragments (147 bp, 24 Å diam at 32°C), the overall motion is that of an axially symmetric cylinder (τ_x = ～10^?6 s;τ_Z = ～1.8 × 10^?8s), which is in good agreement with values calculated from hydrodynamic theory (τ_x = ～1.8 × 10^?6 s; τ_Z = ～2.7 × 10^?8 s). The DNA internal motion can be modeled as restricted amplitude internal diffusion of individual C? H vectors of deoxyribose methine carbons C1′, C3′, and C4′, either with conic boundary conditions (τ_w = ～4 × 10^?9 s, θ_cone = ～21°) or as a bistable jump (τ_A = τ_B = ～2 × 10^?9 s, θ = ～15°). We discuss the critical role in molecular-dynamics modeling played by the angle (β) that individual C? H vectors make with the long axis of the DNA helix. Heat denaturation brings about increases in both the rate and amplitude of the internal motion (described by the wobble model with τ_W = ～0.2 × 10^?9 s, θ_cone = ～50°), and overall motion is affected by becoming essentially isotropic (τ_x = τ_Z = ～5 × 10^?8 s) for the single-stranded molecules. Since ¹³C-nmr data obtained at various DNA concentrations for C2′ of the deoxyribose ring is not described well by the above models, a new model incorporating an additional internal motion is proposed to take into account the rapid, extensive, and weakly coupled motion of C2′.     

Molecular mobility of polypeptides containing proline as determined by 13C magnetic resonance

The molecular conformations and dynamics of poly(L -prolyl), poly(hydroxyl-L -prolyl), poly(L -prolyl-glycyl), poly(hydroxyl-L -prolyl), and poly(glycyl-glycyl-L -prolyl-glycyl), in aqueous solution, have been studied using ¹³C pulse Fourier transform nmr spectroscopy. From a measurement of the intensities of major and minor resonances in the spectra of the copolypeptides, it was determined that 15–20% of the glycyl-prolyl and glycyl-hydroxyprolyl peptide bonds are cis. Effective rotational correlation times (τ_eff), obtained from measurements of spin-lattice relaxation times (T₁) of individual backbone and side-chain carbons, demonstrated that backbone reorientation is approximately isotropic for the five polypeptides and is characterized by correlation times of ca. 0.3–0.6 nanoseconds as a result of rapid segmental motion. In a given polypeptide glycyl and pyrrolidine residues were found to have the same backbone correlation times, but backbone carbon τ_eff values did decrease as the glycyl content of the peptides increased. A semi-quantitative analysis of C^β, C^γ, and C^δ correlation times suggests that rapid ring motion in both prolyl and hydroxyprolyl involves primarily C^γ and C^β, with the prolyl ring being more mobile than the hydroxyprolyl ring.     

The conformation of oxytocin in dimethylsulfoxide as revealed by carbon-13 spin-lattice relaxation times

Information was obtained on rates of overall molecular reorientation and segmental motion of amino acid sidechains of oxytocin in dimethylsulfoxide by determination of spin-lattice relaxation times (T₁) at 25 MHz for carbon-13 in natural abundance in the hormone. The T₁ values of the α-carbons of amino acid residues located in the 20-membered ring of oxytocin are all about 50 msec. The overall correlation time for the hormone backbone was estimated to be 8.8 × 10^?10 sec. The sidechains of Tyr, Ile and Gln undergo segmental motion with respect to the backbone of the ring. The T₁ value of the α-carbon of the Leu residue is greater than for any α-carbon in the ring, indicating an increased mobility of the backbone of the C-terminal acyclic peptide as compared to the ring. The β- and γ-carbons of the Pro residue undergo an exo-endo interconversion with regard to the plane formed by α-carbon, δ-carbon and N atom of the Pro pyrollidine ring. These data are discussed in light of results from other experimental and theoretical studies, including carbon-13 spin-lattice relaxation times for oxytocin in aqueous solution.     

13C-NMR off-resonance rotating frame spin-lattice relaxation studies of bovine lens γ-crystallin self association: effect of ‘macromolecular crowding’

The NMR technique of ¹³C off-resonance rotating frame spin-lattice relaxation, which provides an accurate assessment of the effective rotational correlation time (τ_0,eff) for macromolecular rotational diffusion, was applied to the study of γ-crystallin association as a function of protein concentration and temperature. Values of the effective rotational correlation time for γ-crystallin rotational diffusion were obtained at moderate to high protein concentrations (80–350 mg/ml) and at temperatures above, and below, the cold cataract phase transition temperature. With increasing concentration γ-crystallin was observed to increasingly associate as reflected by larger values of τ_0,eff Decreasing temperature in the range of 35 to 22°C was found to result in no change in the temperature corrected value of τ_0,eff at a γ-crystallin concentration of 80 mg/ml, whereas at temperatures of 18°C or below, this parameter was approx. twofold larger, suggesting the occurrence of a well defined phase transition, which correlated well with the cold cataract phase transition temperature. At higher protein concentrations, by contrast, τ_0,eff (temperature corrected) was found to increase by approx. 1.6- to 2-times in the temperature interval 35°C to 22°C, a result consistent with the dependence of the cold cataract phase transition temperature on γ-crystallin concentration. Analysis of intensity ratio dispersion curves, using an assumed model of isodesmic association, permitted the estimation of the association constant characterizing the aggregation under particular conditions of concentration and temperature. The significant increase in the value of the association constant with moderate increases in protein concentration was rationalized by invoking the effect of ‘macromolecular crowding’. The results obtained in this study suggest that in the intact lens, where high protein concentrations prevail, γ-crystallin is unlikely to be found in the monomeric state, but more likely, as a significantly aggregated species, representing a broad molecular weight distribution.     

Temperature and field dependent 1H-NMR relaxation data as probes of prostaglandin motional parameters in aqueous media

Proton resonance correlation times (τ_eff) for PGF₂α and a more rigid analog have been derived from the field-strength dependence of spinlattice relaxation times (T_1D) using 200 and 500 MHz observation. Those hydrogens showing τ_eff less than the value calculated for whole molecule tumbling (which applies for H-5 → H-15) also show a significantly greater temperature dependence for T_1D at 500 MHz. Minor wagging may occur at the C-7 and C-10 methylenes, and gradually increasing segmental motion is observed toward both side chain termini. A current model for the aqueous geometry of PGF₂α is developed from this data and studies of relaxation rate changes upon specific deuteration.     

A 13C spin-lattice relaxation study of dipeptides containing glycine and proline: mobility of the cyclic proline side chain.

Molecular dynamics of the cyclic dipeptides cyclo(Gly-L -Pro), cyclo-(L-Pro-L -Pro), and cyclo(L-Pro-D-Pro) and the linear dipeptides L-Pro-Gly and cis and trans Gly-L -Pro were studied in neutral aqueous solution by ¹³C nuclear magnetic resonance. Spinlattice relaxation times (T₁) were determined for each individual carbon atom. The correlation times, τ, were derived from a semiquantitative analysis of the T₁ data. The correlation times of the proline ring carbons, β, γ, and δ suggest that the cyclic dipeptides have more restriction of conformational freedom in the proline ring than the linear dipeptides. This effect is most pronounced on the γ carbon.     

Cyclic peptides. XVIII. 13C spin-lattice relaxation times of (X-pro-Y)2 cyclic hexapeptides

¹³C spin-lattice relaxation times (T₁'s) of four cyclic hexapeptides of sequence, (X-L -Pro-Y)₂, are reported. The T₁'s of the protonated carbons, which undergo dipolar relaxation, are interpreted qualitatively in terms of the overall tumbling motion of the molecule and in terms of internal motion. It is found that three of the cyclic hexapeptides, those which adopt all-trans β-conformers, tumble isotropically and appear to lack internal motion in the peptide backbone. The method of Torchia and Lyerla was applied to these compounds in order to compare the mobility of the proline rings. The results show that the sequence and particular type of β-turn present affect the internal motion of the Pro ring. Data on a fourth cyclic hexapeptide, which occurs in a conformation with two-cis X-Pro bonds, suggests that internal motion of the backbone contributes an additional frequency component to the motion of the Y residue α-carbons. A consideration of the mobility of the proline rings in the conformer with two-cis peptide bonds revealed that they are significantly more rigid in the two-cis structure than in the all-trans.     

Histone-induced conformational changes in DNA as probed by quasi-elastic light scattering.

Quasi-elastic light scattering as measured by intensity fluctuation (self-beat) spectroscopy in the time domain can be profitably used to follow both the translational diffusion D and the dominant internal flexing mode τ_int of DNA and its complexes with various histones in aqueous salt solutions. Without histones, DNA is found to have D = 1.6 × 10^?8 cm²/sec and τ_int ? 5 × 10^?4 sec in 0.8 M NaCl, 2 M urea at 20°C. Total histone as well as fraction F2A induce supercoiling (D = 2.6 × 10^?8 cm²/sec, τ_int ? 2.8 × 10^?4 sec) whereas fraction F1 induces uncoiling (D = 1.0 × 10^?8 cm²/sec, τ_int ? 9.4 × 10^?4 sec). Upon increasing the salt concentration to 1.5 M the DNA–histone complex dissociates (D = 1.8 × 10^?8 cm²/sec). Upon decreasing the salt concentration to far below 0.8 M, the DNA–histone complex eventually precipitates as a chromatin gel.     

Dielectric studies on water in solutions of purified lecithin vesicles

The complex permittivity of sonicated aqueous solutions of purified dimyristoylphosphatidylcholine has been measured as a function of frequency between 3 kHz and 40 GHz. The dielectric spectrum of the samples shows two dispersion/absorption regions, one centered at about 80 MHz the other at about 20.GHz (30°C). Otherwise than in previous studies no additional dispersion/absorption process has been found at frequencies below 10 MHz.The complex dielectric spectrum of the samples is discussed with respect to the dynamical state of solvent water in solutions of single-bilayer vesicles. The main relaxation time of the solvent water, τ₁ ((2πτ₁)^?1 ≈ 20 GHz), is smaller than that of pure water, τ_W, at the same temperature. This effect results from the action of internal depolarizing fields which obviously overcompensate and enhancement of τ₁ due to specific solute/solvent interactions (hydration) as had been previously found with micellar solutions of lysolecithins.It cannot be excluded, that some solvent water shows unusual dynamical behaviour. If there exists a substantial amount of such motionally perturbed water, however, it must be characterized by a relaxation time close to that of the phosphorylcholine zwitterions, τ₂ ((2πτ₂)^?1 ≈ 80 MHz).     

A comparison of 15N NMR relaxation measurements with a molecular dynamics simulation: Backbone dynamics of the glucocorticoid receptor DNA-binding domain

The rapid motions of the backbone of the DNA-binding domain of the glucocorticoid receptor (GR DBD) have been investigated using proton-detected heteronuclear NMR experiments on ¹⁵N-labeled protein at pH 6.0 and with a 200 psec molecular dynamics simulation of hydrated GR DBD. The experimental data were interpreted in terms of a generalized order parameter (S²) and an effective correlation time (τ_e) for the internal motion of each amide bond. A back calculation, using the same model, yielded the {¹H}-¹⁵N nuclear Overhauser effects (NOEs) and the ¹⁵N spin-lattice relaxation times (T₁) from the simulated data. The rapid motions of the backbone turned out to be rather limited and uniform throughout the protein, with a somewhat reduced mobility in the two major α-helical regions and a slightly enhanced flexibility for some residues in the first zinc coordinating region. The agreement between the experimental and simulated S²-values was as good as quantitative for most of the residues, except for some residues that were subject to a more large-scale, and in the simulation thus poorly sampled, motion. Examples of such motions that were found in the simulation include jumps of the amide bond of Ile-487 between the charged oxygens of the side chain of Asp-485 and less distinct large scale motions for some of the residues in the extended regions, that were shown to give rise to noisy and/or fast decaying internal reorientational correlation functions. For these residues large differences in the simulated and experimental τ_e-values were found, indicating that motions on different time scales were dominating in the experimental and simulated values. The lower (<0.7) experimental NOEs for these residues could not be reproduced in the simulation and were shown to be a consequence of the lower τ_e-values estimated in the simulation. By combining information from the simulation and the experiment a more complete picture of the motions for these residues can be obtained as is illustrated with an estimation of the jump angle and jump frequency for the amide bond of Ile-487. © 1993 Wiley-Liss, Inc.     

Molecular states in single-stranded adenylate chains by relaxation analysis

The single-strand helix-coil transition in various oligo- and polyadenylates is characterized by means of an improved cable temperature-jump technique. In all the polymers studied {poly(rA), poly(dA), poly[A(m^2′)] and poly[A(e^2′)]} helix-coil relaxation is observed in the time range from 30 to 1000 nsec. Relaxation-time constants observed at wavelengths λ<280 nm (τ_α) are different from those found at λ >280 nm (τβ), indicating the presence of more than two conformational states. The time constants τ_α increase in the series poly(dA), poly[A(m^2′)], constants τ_β/τ_α is approximately 2.5, except in poly(dA) where τ_β/τ_α ≈ 9. Relaxation measurements with r(A)_n- oligomers show a decrease in conformational mobility with increasing chain length. The relaxation curves also demonstrate that “internal” residues have lower reaction rates than residues at the ends of the oligomer chain. Measurement in D₂O reveal a solvent isotope effect for τ_α of +87% for poly(rA), and of +53% for poly(dA), whereas no isotope effect is found in τ_β. The absence of “slow” relaxation processes in the model compound 9,9′ -trimethylenebisadenine shows that the relatively low rate of the single-strand helix-coil transitions is due to the coupling of base stacking with the folding of the sugar–phosphate chain. The absence of a seprate relaxation process (corresponding to τ_β) in 9,9′-trimethylenebisadenine, as well as in the dinucleotides ApC and CpA, suggests that this relaxation process is dependent upon the presence of both the sugar–phosphate chain and of adjacent adenine bases. The experimental data provide evidence that there is more than one ordered conformation in various single-stranded oligo- and polyadenylates and that the transition between these conformations is influenced by the sugar conformation.     

An empirical relationship between rotational correlation time and solvent accessible surface area

Structure–dynamics interrelationships are important in understanding protein function. We have explored the empirical relationship between rotational correlation times (τ_c and the solvent accessible surface areas (SASA) of 75 proteins with known structures. The theoretical correlation between SASA and τ_c through the equation SASA = K_rτ_c ^(2/3) is also considered. SASA was determined from the structure, τ_c ^calc was determined from diffusion tensor calculations, and τ_c ^expt was determined from NMR backbone¹³ C or ¹⁵N relaxation rate measurements. The theoretical and experimental values of τ_c correlate with SASA with regression analyses values of K_r as 1696 and 1896 m²s^-(2/3), respectively, and with corresponding correlation coefficients of 0.92 and 0.70.     

Sensitivity and the available free space per molecule in the unit cell

Invoking the known link between impact sensitivity and compressibility, we have expanded upon an earlier preliminary study of the significance of the available free space per molecule in the unit cell, ΔV. We express ΔV as V_eff – V_int, where V_eff corresponds to zero free space, V_eff = molecular mass/density. V_int is the intrinsic gas phase molecular volume. We demonstrate that V_int can be appropriately defined as the volume enclosed by the 0.003 au contour of the molecule’s electronic density; this produces packing coefficients that have the range and average value found crystallographically. Measured impact sensitivities show an overall tendency to increase as ΔV becomes larger. For nitramines, the dependence upon ΔV is rather weak; we interpret this as indicating that a single overriding factor dominates their initiation mechanism, e.g., N-NO₂ rupture. (An analogous situation appears to hold for many organic azides.) In addition to the conceptual significance of identifying ΔV as a factor in impact sensitivity, the present results allow rough estimates of relative sensitivities that are not known.     

Dynamic studies of the unwinding of a DNA-like strand

Following Simon and Zimm's recent work, both molecular dynamic and Monte Carlo methods are used to simulate on a computer the unwinding of a DNA-like (N + 1)-unit helical strand. The strand unwinding is assumed to obey (N + 1)-coupled Langevin equations of motion (N = 10–50). The present computer “experiment” was done to elaborate dependence of unwinding behavior of the helix upon (i) configurations of its complementary strand [represented here by a square cylinder (Simon-Zimm model), a circular cylinder, and a fixed helix (double-helical model)]; (ii) interstrand potentials (a hard-cylinder potential, an inverse twelfth-power soft repulsion with or without an inverse third-power attractive tail); (iii) amplitudes of the Brownian motions, and (iv) the molecular weights of the unwinding strand. We found that (i) the Brownian motions strongly couple with the interstrand potentials to produce a shorter “unwinding time” (τ₀) (which characterizes an expotential decay of the unwinding) for a longer renged repulsive potential (without the Brownian motions, no such effect was present); (ii) addition of an attractive tail to the repulsive potentials further reinforces the unwinding, thereby giving a reduced value of τ₀; (iii) τ₀ can be expressed as a product of two factors–unwinding time for a one-dimensional spring-bead model, which mostly accounts for the N ²-dependence in τ₀, and a factor which depends on the Brownian motions and the interstrand potentials; (iv) among the three models described above, under similar situations, the three-dimensional double-helical model has the smallest τ₀; and (v) unless the maximum Brownian displacement exceeds a certain value, the unwinding around a square cylinder takes place in a (unrealistic) stair-step manner whose τ₀ decreases with increase in the Brownian displacements. The N ²-dependence of τ₀ agrees with the Simon and Zimm's machine results as well as Crother's experimental data on T2 DNA; however, it contradicts experimental data of Massie and Zimm, and others. Further possible improvements in connection with the computer simulation are suggested.     

Characterization of the dynamic behavior of r(ACC) and r(AAC) with NMR relaxation data and both metropolis monte carlo and molecular dynamics simulations

The solution-state behavior of two triribonucleotides, adenylyl(3′-5′) adenylyl (3′-5′) cytidine [r(AAC)] and adenylyl (3′-5′) cytidylyl (3′-5′) cytidine [r(ACC)], was studied with spectroscopic and molecular modeling methods. Melting temperatures of 299 and 294 K for r(AAC) and r(ACC), respectively, were obtained from ultraviolet absorption (UV) and circular dichroism (CD) temperature profiles of the order-disorder transition. The behavior of the Raman marker modes is consistent with greater stability of r(AAC) compared to that of r(ACC). Nuclear magnetic resonance (nmr) relaxation data (homonuclear cross-relaxation rates, proton selective and nonselective longitudinal relaxation times, and carbon longitudinal relaxation times) were measured at 283, 296, and 318 K for both trimers. In parallel, the major types of conformations were explored with Metropolis Monte Carlo (MMC) and molecular dynamics (MD) simulations to obtain representations of both slow and fast events. Fitting of experimental data showed that although the MMC conformations do not represent an exhaustive list of conformers in solution, the canonical helical form (A-RNA type) should coexist at low temperature with significant populations of other less classical conformers such as half-stacked (HS), bulged (BU), and reverse-stacked (RS). Fitting of the experimental relaxation data ensemble at 283 K led to very different representations for the two trimers. r(AAC) was shown to have a fairly compact, rigid structure (angular order parameter, S²_ang ∼ 0.9, correlation time for internal motion, τ_e ∼ 0.1 ns), which undergoes fairly rapid overall tumbling characterized by the correlation time τ_c ∼ 0.6 ns, whereas r(ACC) exhibits much more flexibility (S²_ang ∼ 0.7, τ_e ∼ 0.1 ns) and slower molecular reorientation (τ_c ∼ 1.0 ns). The values of S²_ang tended to confirm that large amplitude fluctuations did not occur on the relaxation timescale (ns). In the course of this paper, a widely accepted concept was shown to be questionable. As regards the nmr relaxation data, simulations show that for fairly small nucleic acids (τ_c < 2.0 ns) the second term of the model-free spectral densities is not negligible for representative motional models (S²_ang values < 0.9 and τ_e values in the 0.05–0.2 ns range). The difference in the dynamic behavior of r(AAC) and r(ACC) can be explained by the greater propensity of the A-A sequence to stack as compared to that of A-C. © 1996 John Wiley & Sons, Inc.     

Heating of tissues by microwaves: A model analysis

We consider the thermal response times for heating of tissue subject to nonionizing (microwave or infrared) radiation. The analysis is based on a dimensionless form of the bioheat equation. The thermal response is governed by two time constants: one(τ₁) pertains to heat convection by blood flow, and is of the order of 20–30 min for physiologically normal perfusion rates; the second (τ₂) characterizes heat conduction and varies as the square of a distance that characterizes the spatial extent of the heating. Two idealized cases are examined. The first is a tissue block with an insulated surface, subject to irradiation with an exponentially decreasing specific absorption rate, which models a large surface area of tissue exposed to microwaves. The second is a hemispherical region of tissue exposed at a spatially uniform specific absorption rate, which models localized exposure. In both cases, the steady-state temperature increase can be written as the product of the incident power density and an effective time constant τ_eff, which is defined for each geometry as an appropriate function of τ₁ and τ₂. In appropriate limits of the ratio of these time constants, the local temperature rise is dominated by conductive or convective heat transport. Predictions of the block model agree well with recent data for the thresholds for perception of warmth or pain from exposure to microwave energy. Using these concepts, we developed a thermal averaging time that might be used in standards for human exposure to microwave radiation, to limit the temperature rise in tissue from radiation by pulsed sources. We compare the ANSI exposure standards for microwaves and infrared laser radiation with respect to the maximal increase in tissue temperature that would be allowed at the maximal permissible exposures. A historical appendix presents the origin of the 6-min averaging time used in the microwave standard. Bioelectromagnetics 19:420–428, 1998. © 1998 Wiley-Liss, Inc.     

Molecular mobilities of soluble components in the aqueous phase of chromaffin granules

NMR relaxation times have been used to characterize molecular motion and intermolecular complexes in the aqueous phase of bovine chromaffin granules. Partially relaxed ¹³C and proton spectra have been obtained at 3 and 25°C. T₁ measurements of five protonated carbons on epinephrine (C₂, C₅, C₆ CHOH and NCH₃) give a correlation time of 0.15 (10^?9) s at 25°C for the catechol ring and methine carbon, while the effective correlation time for the NCH₃ group is somewhat shorter due to its internal degree of rotational freedom. Resonances of protonated carbons on the soluble protein chromogranin give very similar corerlation times: 0.20 (10^?9) s for the peptide α-carbon and 0.2 (10^?9) s for the methylene sidechain carbons of glutamic acid. The correlation time (τ_R) of ATP was not measured direrctly using ¹³C T₁ data due to the weakness of its spectrum, but its reorinetation appears to be substantially slower than that of epinephrine or chromogranin. This conclusion is based on three observations: (1) the qualitative temperature dependence of T₁ for H₂ and H₈ on the adenine ring places τ_R for ATP to the right of the T₁ minimum, or τ_R ? 1.0 (10^?9) s; (2) ¹³C resonances of ATP have anomalously low amplitudes compared with epinphrine resonances, a fact that is readily explained only if ATP undergoes substantially slower reorientation; and (3) a comparision of the T₁ data on H₈ on chromaffin granules and in a dilute aqueous solution, where ρ_R for ATP cam be measured directly, indicates that τ_R ～ 1.0 (10^?9 s at 25°C in the granules. The relaxation data are consistent with the concept of a storage complex based on electrostatic interaction between a polyion (chromogranin) and its counterious (ATP and epinephrine), in which ATP cross-links cationic sidechains of the protein.     

Traceable components of terrestrial carbon storage capacity in biogeochemical models

Biogeochemical models have been developed to account for more and more processes, making their complex structures difficult to be understood and evaluated. Here, we introduce a framework to decompose a complex land model into traceable components based on mutually independent properties of modeled biogeochemical processes. The framework traces modeled ecosystem carbon storage capacity (X_ss) to (i) a product of net primary productivity (NPP) and ecosystem residence time (τ_E). The latter τ_E can be further traced to (ii) baseline carbon residence times (τ′_E), which are usually preset in a model according to vegetation characteristics and soil types, (iii) environmental scalars (ξ), including temperature and water scalars, and (iv) environmental forcings. We applied the framework to the Australian Community Atmosphere Biosphere Land Exchange (CABLE) model to help understand differences in modeled carbon processes among biomes and as influenced by nitrogen processes. With the climate forcings of 1990, modeled evergreen broadleaf forest had the highest NPP among the nine biomes and moderate residence times, leading to a relatively high carbon storage capacity (31.5 kg cm^?2). Deciduous needle leaf forest had the longest residence time (163.3 years) and low NPP, leading to moderate carbon storage (18.3 kg cm^?2). The longest τ_E in deciduous needle leaf forest was ascribed to its longest τ′_E (43.6 years) and small ξ (0.14 on litter/soil carbon decay rates). Incorporation of nitrogen processes into the CABLE model decreased X_ss in all biomes via reduced NPP (e.g., ?12.1% in shrub land) or decreased τ_E or both. The decreases in τ_E resulted from nitrogen‐induced changes in τ′_E (e.g., ?26.7% in C₃ grassland) through carbon allocation among plant pools and transfers from plant to litter and soil pools. Our framework can be used to facilitate data model comparisons and model intercomparisons via tracking a few traceable components for all terrestrial carbon cycle models. Nevertheless, more research is needed to develop tools to decompose NPP and transient dynamics of the modeled carbon cycle into traceable components for structural analysis of land models.     

Desulfovibrio gigas ferredoxin II: redox structural modulation of the [3Fe–4S] cluster

Desulfovibrio gigas ferredoxin II (DgFdII) is a small protein with a polypeptide chain composed of 58 amino acids, containing one Fe₃S₄ cluster per monomer. Upon studying the redox cycle of this protein, we detected a stable intermediate (FdII_int) with four ¹H resonances at 24.1, 20.5, 20.8 and 13.7 ppm. The differences between FdII_ox and FdII_int were attributed to conformational changes resulting from the breaking/formation of an internal disulfide bridge. The same ¹H NMR methodology used to fully assign the three cysteinyl ligands of the [3Fe–4S] core in the oxidized state (DgFdII_ox) was used here for the assignment of the same three ligands in the intermediate state (DgFdII_int). The spin-coupling model used for the oxidized form of DgFdII where magnetic exchange coupling constants of around 300 cm⁻¹ and hyperfine coupling constants equal to 1 MHz for all the three iron centres were found, does not explain the isotropic shift temperature dependence for the three cysteinyl cluster ligands in DgFdII_int. This study, together with the spin delocalization mechanism proposed here for DgFdII_int, allows the detection of structural modifications at the [3Fe-4S] cluster in DgFdII_ox and DgFdII_int.