Measurement of relaxation rates of N(H) and H(alpha) backbone protons in proteins with tailored initial conditions.

Several methods are presented for the selective determination of spin-lattice and spin-spin relaxation rates of backbone protons in labeled proteins. The relaxation rates of amide protons in (15)N labeled proteins can be measured by using two-way selective cross-polarization (SCP). The measurement of H(alpha) relaxation rates can be achieved by combining this method with homonuclear Hartmann-Hahn transfer using doubly selective irradiation. Various schemes for selective or nonselective inversion of the longitudinal proton magnetization lead to different initial recovery rates. The methods have been applied to lysine K6 in (15)N-labeled human ubiquitin and to leucine L5 in (15)N- and (13)C-labeled octapeptide YG*G*F*LRRI (GFL) in which the marked residues are (15)N- and (13)C-labeled.     

The role of (15)N CSA and CSA/dipole cross-correlation in (15)N relaxation in solid proteins

The influence of the (15)N CSA on (15)N longitudinal relaxation is investigated for an amide group in solid proteins in powder form under MAS. This contribution is determined to be typically 20-33% of the overall longitudinal relaxation rate, at 11.74 and 16.45 T, respectively. The improved treatment is used to analyze the internal dynamics in the protein Crh, in the frame of a motional model of diffusion in a cone, using the explicit average sum approach. Significant variations with respect to the determined dynamics parameters are observed when properly accounting for the contribution of (15)N CSA fluctuations. In general, the fit of experimental data including CSA led to the determination of diffusion times (tau(w)) which are longer than when considering only an (15)N-(1)H dipolar relaxation mechanism. CSA-Dipole cross-correlation is shown to play little or no role in protonated solids, in direct contrast to the liquid state case.     

Temperature dependence of protein backbone motion from carbonyl 13C and amide 15N NMR relaxation

The NMR spin-lattice relaxation rate (R1) and the rotating-frame spin-lattice relaxation rate (R1rho) of amide 15N and carbonyl 13C (13C') of the uniformly 13C- and 15N-labeled ubiquitin were measured at different temperatures and field strengths to investigate the temperature dependence of overall rotational diffusion and local backbone motion. Correlation between the order parameter of the N-H vector, SNH2, and that of the carbonyl carbon, S2C', was investigated. The effective S2C' was estimated from the direct fit of the experimental relaxation rates and from the slope of 2R2-R1 vs. B2 using Lipari-Szabo formalism. The average SNH2 decreased by 5.9%, while the average S2C' decreased by 4.6% from 15 to 47 degrees C. At the extreme low and high temperatures the difference in the temperature dependence of the order parameters vanishes. At the intermediate temperatures they do not change by the same amount but they follow the same trend. On the same peptide plane along the protein sequence, S2C' and SNH2 are highly correlated. The results suggest that fast local motion experienced at the site of the N-H vector and carbonyl nucleus is more complicated than previously thought and it cannot be easily described by one single type of motion in a broad range of temperature.     

Separation of anisotropy and exchange broadening using (15)N CSA-(15)N-(1)H dipole-dipole relaxation cross-correlation experiments

Based on the measurement of cross-correlation rates between (15)N CSA and (15)N-(1)H dipole-dipole relaxation we propose a procedure for separating exchange contributions to transverse relaxation rates (R(2) = 1/T(2)) from effects caused by anisotropic rotational diffusion of the protein molecule. This approach determines the influence of anisotropy and chemical exchange processes independently and therefore circumvents difficulties associated with the currently standard use of T(1)/T(2) ratios to determine the rotational diffusion tensor. We find from computer simulations that, in the presence of even small amounts of internal flexibility, fitting T(1)/T(2) ratios tends to underestimate the anisotropy of overall tumbling. An additional problem exists when the N-H bond vector directions are not distributed homogeneously over the surface of a unit sphere, such as in helix bundles or beta-sheets. Such a case was found in segment 4 of the gelation factor (ABP 120), an F-actin cross-linking protein, in which the diffusion tensor cannot be calculated from T(1)/T(2) ratios. The (15)N CSA tensor of the residues for this beta-sheet protein was found to vary even within secondary structure elements. The use of a common value for the whole protein molecule therefore might be an oversimplification. Using our approach it is immediately apparent that no exchange broadening exists for segment 4 although strongly reduced T(2) relaxation times for several residues could be mistaken as indications for exchange processes.     

REDCRAFT: a tool for simultaneous characterization of protein backbone structure and motion from RDC data

REDCRAFT, a new open source software tool that accommodates the analysis of RDC data for simultaneous structure and dynamics characterization of proteins is presented in this article. Simultaneous consideration of structure and motion is believed to be necessary for accurate representation of the solution-state of a protein. REDCRAFT is designed to primarily utilize RDC data from multiple alignment media in two stages. During Stage-I, a list of possible torsion angles joining any two neighboring peptide planes is ranked based on their fitness to experimental constraints; in Stage-II, a dipeptide fragment is extended by addition of one peptide plane at a time. The algorithm adopted by REDCRAFT is very efficient and can produce a structure for an 80 residue protein within two hours on a typical desktop computer. REDCRAFT exhibits robustness with respect to noise and missing data. REDCRAFT describes the overall alignment of the molecule in the form of an order tensor matrix and is capable of identifying peptide fragments with internal dynamics. Identification of the location of internal motion will permit a more accurate structural representation. Experimental data from two proteins as well as simulated data are presented to illustrate the capabilities of REDCRAFT in both structure determination and identification of the dynamical regions.     

Simple and accurate determination of global tau(R) in proteins using (13)C or (15)N relaxation data

In the study of protein dynamics by (13)C or (15)N relaxation measurements different models from the Lipari-Szabo formalism are used in order to determine the motion parameters. The global rotational correlation time tau(R) of the molecule must be estimated prior to the analysis. In this Communication, the authors propose a new approach in determining an accurate value for tau(R) in order to realize the best fit of R(2) for the whole sequence of the protein, regardless of the different type of motions atoms may experience. The method first determines the highly structured regions of the sequence. For each corresponding site, the Lipari-Szabo parameters are calculated for R(1) and NOE, using an arbitrary value for tau(R). The chi(2) for R(2), summed over the selected sites, shows a clear minimum, as a function of tau(R). This minimum is used to better estimate a proper value for tau(R).     

Pulse sequences for measurement of one-bond (15)N-(1)H coupling constants in the protein backbone.

A set of three improved two-dimensional (2D) NMR methods for measuring one-bond (15)N-(1)H coupling constants in the protein backbone is presented. They are tailored to suit the size of the TROSY effect, i.e., the degree of interference between dipolar and chemical shift anisotropy relaxation mechanisms. The methods edit 2D spectra into two separate subspectra corresponding to the two possible spin states of the coupling partner. Cross talk between the two subspectra is a second order effect in the difference between the actual coupling constants and the one used in setting the pertinent delays of the pulse sequences. This relatively high degree of editing accuracy makes the methods useful for applications to molecules subjected to weak alignment where the one-bond coupling constants are linear combinations of a scalar J and a residual dipolar contribution containing important structural information. A demonstration of the new methods is shown for the (15)N-labeled protein chymotrypsin inhibitor 2 in a lipid bicelle mixture.     

Generalization of the N(p)N(n)N(p)N(n) scheme and the structure of the valence space

The N(p)N(n) scheme, which has been extensively applied to even-even nuclei, is found to be a very good benchmark for odd-even, even-odd, and doubly-odd nuclei as well. There are no apparent shifts in the correlations for these four classes of nuclei. The compact correlations highlight the deviant behavior of the Z = 78 nuclei and are used to deduce effective valence proton numbers near Z = 64 as well as to study the evolution of the Z = 64 subshell gap.     

Efficient and accurate determination of the overall rotational diffusion tensor of a molecule from (15)N relaxation data using computer program ROTDIF

We present a computer program ROTDIF for efficient determination of a complete rotational diffusion tensor of a molecule from NMR relaxation data. The derivation of the rotational diffusion tensor in the case of a fully anisotropic model is based on a six-dimensional search, which could be very time consuming, particularly if a grid search in the Euler angle space is involved. Here, we use an efficient Levenberg-Marquardt algorithm combined with Monte Carlo generation of initial guesses. The result is a dramatic, up to 50-fold improvement in the computational efficiency over the previous approaches. This method is demonstrated on a computer-generated and real protein systems. We also address the issue of sensitivity of the diffusion tensor determination from (15)N relaxation measurements to experimental errors in the relaxation rates and discuss possible artifacts from applying higher-symmetry tensor model and how to recognize them.     

Transverse NMR relaxation as a probe of mesoscopic structure

Transverse NMR relaxation in a macroscopic sample is shown to be extremely sensitive to the structure of mesoscopic magnetic susceptibility variations. Such a sensitivity is proposed as a novel kind of contrast in the NMR measurements. For suspensions of arbitrary-shaped paramagnetic objects, the transverse relaxation is found in the case of a small dephasing effect of an individual object. Strong relaxation rate dependence on the objects' shape agrees with experiments on whole blood. Demonstrated structure sensitivity is a generic effect that arises in NMR relaxation in porous media, biological systems, as well as in kinetics of diffusion limited reactions.     

Nuclear orientation as a tool for studying the structure of very unstable nuclei

With the availability of modern isotope separator on-line systems it has become possible to make broad and systematic studies of low-energy low-spin nuclear structure. A vital ingredient in such a program is unique spin-parity assignments to all low-lying levels. A most desirable complement to spin-parity information is detailed spectroscopic information. Obtaining such information far from stability is difficult because of low activity production. Nuclear orientation provides a means for obtaining spin assignments usingsingles measurements. This is less demanding on source intensities than - angular correlation coincidence measurements. Further, nuclear orientation can provide information on magnetic moments and on multipole mixing ratios. A number of structural problems are discussed: the need for unique spin assignments in systematics schemes; the need to distinguish between E2+E0 and M1 transitions; the importance of measuring E2-M1 mixing ratios; and the value of magnetic moment information. Particular emphasis is placed on the desirability of obtaining such information in the neutron-deficient Pt, Au, Hg, Tl, Pb and Bi isotopes, based upon the experimental program at the UNISOR facility.Work supported in part by U.S.Dept. of Energy, Contract No. DE-AS05-80ER10599.     

New (15)N NMR exchange experiments for the unambiguous assignment of (1)H(N)/(15)N resonances of proteins in complexes in slow chemical exchange with free form

The potentialities of a 2D proton-detected heteronuclear exchange experiment to assign the nitrogen and amide proton resonances in a uniformly (15)N-enriched macromolecule involved in a complex, starting from the free form assignments, are demonstrated on a protein-DNA complex. This 2D experiment is further extended to a 3D experiment in the case of severe superpositions.     

15N(p,po)15N and the levels of 16O for Ex = 14.8–18.6 MeV

Angular distributions of cross section and analyzing power for elastic scattering of protons from ¹⁵N have been measured for E_p = 2.7–7.0 MeV. A phase-shift analysis of the data yields spin-parity assignments and level parameters for seventeen states of ¹⁶O in the excitation energy region 14.8–18.6MeV. Three of the resonances have not previously been identified, among them being a broad J^π = 2^? level at E_p = 6.1 MeV which is almost certainly the analog of the 2^? 1p1h state with configuration ($\text{d}{}_{\mathrm{<mtext>3</mtext><mtext>2</mtext>}}\text{,}\text{p}{}_{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}{}^{\mathrm{?1}}$) at E_x ∽ 5.0 MeV in ¹⁶N. The broad level previously reported near E_p = 5.0 MeV has been observed and its parameters determined. A resonance analysis of the phase shifts yielded values of E_r, Γ and Γ_p for all of the levels. The J^π assignments are in agreement with previously reported values. For resonances having J = l, the data can usually be fit with a resonant phase shift corresponding to either J = l + 1 or J = l ? 1, in addition to the phase shift for J = l. Which of the two spurious-J solutions occurs seems to depend on whether the partial wave through which the resonant state is formed is $\text{J = l +}\text{1}\text{2}\text{or}\text{J = l ?}\text{1}\text{2}$.     

Test for the shell-model-Weinberg treatment of the reaction15N(n,n′)15N* with a separable interaction

A modification of Weinberg's method in connection with the Born approximation was first employed by Ebenhöhet al. to describe the reaction¹⁵N(n, n′)¹⁵N^* using a delta-force as residual interaction. This method is now applied to the same reaction but using a surface-delta-interaction. For this separable interaction also the exact solution of the problem is presented. We were not interested in adjusting any parameters to obtain optimal agreement with experiment. Only the results of these two approaches are compared. The good agreement may give confidence in the application of the modified Weinberg method in connection with non-separable interactions.     

Reactions p(d, p)d and p(d, p)pn as a tool for studying the short-range internal structure of the deuteron

In recent years, the deuteron structure at short distances has often been treated from the point of view of nonnucleonic degrees of freedom. In this study, measurements of T-odd polarization observables by using a tensorially polarized deuteron beam and a polarized proton target or a proton polarimeter are proposed as a means for seeking quark configurations inside the deuteron.     

13C solid state NMR investigation of structural relaxation of the polymer backbone in poly (ethylmethacrylate)

Geometry and time scale of structural relaxation of poly(n-alkylmethacrylates) above the glass transition is studied by temperature dependent one- and two-dimensional 13C-NMR spectroscopy. The geometry of the isotropization of the polymer backbone as deduced from detailed analysis of spectral line shapes is identified as random angular jumps. Analysis of echo decays confirms that at a given temperature this isotropization can adequately be described with a single correlation time. The results are discussed in terms of conformational memory and local structure recently identified in these polymeric glasses.     

Uptake of [(15)N] Ammonium and [(15)N]Nitrate in a 140-Year-Old Spruce Stand (Picea abies) in the Fichtelgebirge (NE Bavaria)

Abstract In April 1994 a (15)N tracer pulse study was started in a 140-year-old spruce stand (Picea abies [L.] Karst.) located at the Fichtelgebirge (NE Bavaria). Highly enriched (98%) [(15)N]ammonium and [(15)N]nitrate were applied simulating wet deposition. For two growing seasons the pathways and dynamics of the tracer were followed in all compartments of spruce (needles and twigs of all age classes, stem wood and bark, roots) and understorey vegetation and in soils of the organic (L/Of and Oh) and mineral horizons (A(0-5) and A(5-10)). By variations of the application time on different plots within the growing season (spring, summer and autumn) a seasonal effect of labelling on uptake and distribution patterns was tested. First results of this tracer study indicate that young and old spruce stands do not differ basically in pattern of uptake and distribution of mineral nitrogen. There are indications that spruce uses preferentially ammonium versus nitrate and that the ratio of ammonium/nitrate which is being consumed depends on the ammonium/nitrate ratio in the soil solution. The uptake rates decrease within the growing season.     

Protein Backbone N Relaxation Rates as a Tool for the Diagnosis of Structure Quality

In the work reported herein we define a structure validation factor that depends on protein backbone ¹⁵N relaxation rates. This is an alternative method to the previously defined quality factors derived from anisotropic chemical shifts or residual dipolar couplings. We have used the structure dependence of ¹⁵N relaxation rates of anisotropically tumbling proteins to calculate this structure diagnosis factor and have used it to demonstrate the improvement of protein structures refined with residual dipolar couplings.     

Isolation of NO(3)(-)-N as 1-phenylazo-2-naphthol (Sudan-1) for measurement of delta(15)N

The conversion of nitrate (NO(3)(-)) to 1-phenylazo-2-naphthol (Sudan-1) has been examined as a method for natural abundance measurement of delta(15)N of NO(3)(-). The reaction results in dilution of NO(3)(-)-N with only one reagent-derived N and the product is readily concentrated from dilute samples by reverse phase chromatography. There is systematic isotopic fractionation during the reaction, but this can be allowed for by analysing known NO(3)(-) standards along with each sample set. Sudan-1 prepared from surface water samples containing approximately 50 &mgr;g NO(3)(-)-N can be analysed by automated continuous flow isotope ratio mass spectrometry with a precision of 0.2 per thousand (one standard deviation) and the accuracy is not affected by interference from other nitrogenous species in the sample or reagents. Copyright 1999 John Wiley & Sons, Ltd.