A comprehensive analysis of multifield 15N relaxation parameters in proteins: determination of 15N chemical shift anisotropies.

This study deals with the exploitation of the three classical 15N relaxation parameters (the longitudinal relaxation rate, R1, the transverse relaxation rate, R2, and the 1H-15N cross-relaxation rate, sigmaNH) measured at several magnetic fields in uniformly 15N-labeled proteins. Spectral densities involved in R1, R2 and sigmaNH are analyzed according to the functional form A + B/(1 + omega(2) taus(2)), where taus is the correlation time associated with slow motions sensed by the NH vector at the level of the residue to which it belongs. The coefficient B provides a realistic view of the backbone dynamics, whereas A is associated with fast local motions. According to the "model free approach", B can be identified with 2tausS(2) where S is the generalized order parameter. The correlation time taus is determined from the field dependency of the relaxation parameters while A and B are determined through linear equations. This simple data processing is needed for obtaining realistic error bars based on a statistical approach. This proved to be the key point for validating an extended analysis aiming at the determination of nitrogen chemical shift anisotropy. The protein C12A-p8(MTCP1) has been chosen as a model for this study. It will be shown that all data (obtained at five magnetic field strengths corresponding to proton resonance of 400, 500, 600, 700, and 800 MHz) are very consistently fitted provided that a specific effective correlation time associated with slow motions is defined for each residue. This is assessed by small deviations between experimental and recalculated values, which, in all cases, remain within experimental uncertainty. This strategy makes needless elaborate approaches based on the combination of several slow motions or their possible anisotropy. Within the core of the protein taus fluctuates in a relatively narrow range (with a mean value of 6.15 ns and a root-mean-square deviation of 0.36 ns) while it is considerably reduced at the protein extremities (down to approximately 3 ns). To a certain extent, these fluctuations are correlated with the protein structure. A is not obtained with sufficient accuracy to be valuably discussed. Conversely, order parameters derived from B exhibit a significant correlation with the protein structure. Finally, the multi-field analysis of the evolution of longitudinal and transverse relaxation rates has been refined by allowing the 15N chemical shift anisotropy (csa) to vary residue by residue. Within uncertainties (derived here on a statistical basis) an almost constant value is obtained. This strongly indicates an absence of correlation between the experimental value of this parameter obtained for a given residue in the protein, the nature of this residue, and the possible involvement of this residue in a structured area of the protein.     

An 15N NMR spin relaxation dispersion study of the folding of a pair of engineered mutants of apocytochrome b562

15N relaxation dispersion NMR spectroscopy has been used to study exchange dynamics in a pair of mutants of Rd-apocyt b562, a redesigned four-helix-bundle protein. An analysis of the relaxation data over a range of temperatures establishes that exchange in both proteins is best modeled as two-state and that it derives from the folding/unfolding transition. These results are in accord with predictions based on the reaction coordinate for the folding of the protein determined from native-state hydrogen exchange data [Chu, R.; Pei, W.; Takei, J.; Bai, Y. Biochemistry 2002, 41, 7998-8003]. The kinetics and thermodynamics of the folding transition have been characterized in detail. Although only a narrow range of temperatures could be examined, it is clear that the folding rate temperature profile is distinctly non-Arrhenius for both mutants, with the folding barrier for at least one of them entropic.     

Slow dynamics in folded and unfolded states of an SH3 domain.

(15)N relaxation dispersion experiments were applied to the isolated N-terminal SH3 domain of the Drosophila protein drk (drkN SH3) to study microsecond to second time scale exchange processes. The drkN SH3 domain exists in equilibrium between folded (F(exch)) and unfolded (U(exch)) states under nondenaturing conditions in a ratio of 2:1 at 20 degrees C, with an average exchange rate constant, k(ex), of 2.2 s(-1) (slow exchange on the NMR chemical shift time scale). Consequently a discrete set of resonances is observed for each state in NMR spectra. Within the U(exch) ensemble there is a contiguous stretch of residues undergoing conformational exchange on a micros/ms time scale, likely due to local, non-native hydrophobic collapse. For these residues both the F(exch) <--> U(exch) conformational exchange process and the micros/ms exchange event within the U(exch) state contribute to the (15)N line width and can be analyzed using CPMG-based (15)N relaxation dispersion measurements. The contribution of both processes to the apparent relaxation rate can be deconvoluted numerically by combining the experimental (15)N relaxation dispersion data with results from an (15)N longitudinal relaxation experiment that accurately quantifies exchange rates in slow exchanging systems (Farrow, N. A.; Zhang, O.; Forman-Kay, J. D.; Kay, L. E. J. Biomol. NMR 1994, 4, 727-734). A simple, generally applicable analytical expression for the dependence of the effective transverse relaxation rate constant on the pulse spacing in CPMG experiments has been derived for a two-state exchange process in the slow exchange limit, which can be used to fit the experimental data on the global folding/unfolding transition. The results illustrate that relaxation dispersion experiments provide an extremely sensitive tool to probe conformational exchange processes in unfolded states and to obtain information on the free energy landscape of such systems.     

Fast local backbone dynamics of encapsulated ubiquitin

Backbone dynamics of ubiquitin confined within AOT reverse micelles have been evaluated based on analysis of 15N NMR relaxation data. Results indicate that upon encapsulation the protein experiences a slight overall increase in the value of the order parameter, S2, indicating a restriction in the average amplitude of fast local N-H bond vector motion. The largest increases in S2 upon encapsulation were concentrated in the region of beta-sheet 2 and, additionally, at the transitions of secondary structure motifs and loop regions. In addition, statistical analysis of the residue average ratio of the 15N longitudinal and transverse NMR relaxation time constants indicates that chemical exchange contributions to relaxation are consistent with previous aqueous studies. Earlier studies have demonstrated that native protein structure can be maintained in the encapsulated state. These results presented here establish that the dynamical behavior of encapsulated ubiquitin is likewise nativelike and adds important new observations regarding the enhancement of protein stability under confinement.     

Off-resonance R(1rho) NMR studies of exchange dynamics in proteins with low spin-lock fields: an application to a Fyn SH3 domain

An (15)N NMR R(1rho) relaxation experiment is presented for the measurement of millisecond time scale exchange processes in proteins. On- and off-resonance R(1rho) relaxation profiles are recorded one residue at a time using a series of one-dimensional experiments in concert with selective Hartmann-Hahn polarization transfers. The experiment can be performed using low spin-lock field strengths (values as low as 25 Hz have been tested), with excellent alignment of magnetization along the effective field achieved. Additionally, suppression of the effects of cross-correlated relaxation between dipolar and chemical shift anisotropy interactions and (1)H-(15)N scalar coupled evolution is straightforward to implement, independent of the strength of the (15)N spin-locking field. The methodology is applied to study the folding of a G48M mutant of the Fyn SH3 domain that has been characterized previously by CPMG dispersion experiments. It is demonstrated through experiment that off-resonance R(1rho) data measured at a single magnetic field and one or more spin-lock field strengths, with amplitudes on the order of the rate of exchange, allow a complete characterization of a two-site exchange process. This is possible even in the case of slow exchange on the NMR time scale, where complementary approaches involving CPMG-based experiments fail. Advantages of this methodology in relation to other approaches are described.     

Nonnative interactions in the FF domain folding pathway from an atomic resolution structure of a sparsely populated intermediate: an NMR relaxation dispersion study

Several all-helical single-domain proteins have been shown to fold rapidly (microsecond time scale) to a compact intermediate state and subsequently rearrange more slowly to the native conformation. An understanding of this process has been hindered by difficulties in experimental studies of intermediates in cases where they are both low-populated and only transiently formed. One such example is provided by the on-pathway folding intermediate of the small four-helix bundle FF domain from HYPA/FBP11 that is populated at several percent with a millisecond lifetime at room temperature. Here we have studied the L24A mutant that has been shown previously to form nonnative interactions in the folding transition state. A suite of Carr-Purcell-Meiboom-Gill relaxation dispersion NMR experiments have been used to measure backbone chemical shifts and amide bond vector orientations of the invisible folding intermediate that form the input restraints in calculations of atomic resolution models of its structure. Despite the fact that the intermediate structure has many features that are similar to that of the native state, a set of nonnative contacts is observed that is even more extensive than noted previously for the wild-type (WT) folding intermediate. Such nonnative interactions, which must be broken prior to adoption of the native conformation, explain why the transition from the intermediate state to the native conformer (millisecond time scale) is significantly slower than from the unfolded ensemble to the intermediate and why the L24A mutant folds more slowly than the WT.     

Quadrupole central transition 17O NMR spectroscopy of biological macromolecules in aqueous solution

We demonstrate a general nuclear magnetic resonance (NMR) spectroscopic approach in obtaining high-resolution (17)O (spin-5/2) NMR spectra for biological macromolecules in aqueous solution. This approach, termed quadrupole central transition (QCT) NMR, is based on the multiexponential relaxation properties of half-integer quadrupolar nuclei in molecules undergoing slow isotropic tumbling motion. Under such a circumstance, Redfield's relaxation theory predicts that the central transition, m(I) = +1/2 ? -1/2, can exhibit relatively long transverse relaxation time constants, thus giving rise to relatively narrow spectral lines. Using three robust protein-ligand complexes of size ranging from 65 to 240 kDa, we have obtained (17)O QCT NMR spectra with unprecedented resolution, allowing the chemical environment around the targeted oxygen atoms to be directly probed for the first time. The new QCT approach increases the size limit of molecular systems previously attainable by solution (17)O NMR by nearly 3 orders of magnitude (1000-fold). We have also shown that, when both quadrupole and shielding anisotropy interactions are operative, (17)O QCT NMR spectra display an analogous transverse relaxation optimized spectroscopy type behavior in that the condition for optimal resolution depends on the applied magnetic field. We conclude that, with the currently available moderate and ultrahigh magnetic fields (14 T and higher), this (17)O QCT NMR approach is applicable to a wide variety of biological macromolecules. The new (17)O NMR parameters so obtained for biological molecules are complementary to those obtained from (1)H, (13)C, and (15)N NMR studies.     

Hydrogen exchange rates in proteins from water (1)H transverse magnetic relaxation

Access to the fast exchange kinetics of labile protein hydrogens in solution is provided by exchange broadening of the water 1H NMR line. We analyzed the chemical shift modulation contribution of labile hydrogens in bovine pancreatic trypsin inhibitor (BPTI) to the transverse 1H spin relaxation rate, R2, of the bulk solvent. Both the experimental pH dependence and the CPMG dispersion of R2 could be quantitatively accounted for on the basis of known chemical shifts, exchange rates, and ionization constants for BPTI. This analysis provided, for the first time, the hydrogen exchange rate constants for Lys and Arg side chains in a protein and pointed to an internal catalysis of the N-terminal amino protons in BPTI by a salt bridge. The method can be used for mapping the hydrogen exchange rates in protein solutions and biomaterials, which may be important for the control of relaxation-weighted contrast in biological MRI.     

Estimation of protein folding rate from Monte Carlo simulations and entropy capacity

The problem of protein self-organization is one of the most important problems of molecular biology nowadays. Despite the recent success in the understanding of general principles of protein folding, details of this process are yet to be elucidated. Moreover, the prediction of protein folding rates has its own practical value due to the fact that aggregation directly depends on the rate of protein folding. The time of folding has been calculated for 67 proteins with known experimental data at the point of thermodynamic equilibrium between unfolded and native states using a Monte Carlo model where each residue is considered to be either folded as in the native state or completely disordered. The times of folding for 67 proteins which reach the native state within the limit of 10(8) Monte Carlo steps are in a good correlation with the experimentally measured folding rate at the mid-transition point (the correlation coefficient is -0.82). Theoretical consideration of a capillarity model for the process of protein folding demonstrates that the difference in the folding rate for proteins sharing more spherical and less spherical folds is the result of differences in the conformational entropy due to a larger surface of the boundary between folded and unfolded phases in the transition state for proteins with more spherical fold. The capillarity model allows us to predict the folding rate at the same level of correlation as by Monte Carlo simulations. The calculated model entropy capacity (conformational entropy per residue divided by the average contact energy per residue) for 67 proteins correlates by about 78% with the experimentally measured folding rate at the mid-transition point.     

Solution NMR studies of iron(II) spin-crossover complexes

The 1H NMR spectra of a series of mono- and dinuclear pyridine complexes [FeL1(R1/R2)(py)2] and [Fe2L2(R1/R2)(py)4] have been investigated in a mixed toluene-d8/pyridine-d5 solution. The equatorial tetradentade Schiff base like ligands L1(R1/R2) and L2(R1/R2) with a N2O22- coordination sphere for each metal center have been obtained by condensation of a substituted malonodialdehyde (R1/R2 are Me/COOEt, Me/COMe, or OEt/COOEt) with o-phenylenediamine (L1(R1/R2)) or 1,2,4,5-tetraaminobenzene (L2(R1/R2)). The 1H NMR resonances were assigned by comparison of differently substituted complexes in combination with a line-width comparison. The 1H NMR shifts from 188 to 358 K show a strong influence of the spin state of the iron center. The behavior of the pure high-spin iron(II) complexes is close to ideal Curie behavior. Analysis of the resonance shifts of the spin-transition complexes can be used for determining the high-spin mole fraction of the complex in solution at different temperatures. Magnetic susceptibility measurements in solution using the Evans method were made for all six complexes. Significant differences between the spin-transition behavior of the complexes in solution of those in the solid state were found. However, the plots of microeff as a function of temperature obtained using the Evans method and those obtained by interpretation of the NMR shifts were virtually identical. The isotropic shifts of protons in the complexes proved to be suitable tools for following a spin transition in solution. Comparison of the microeff plots of the mono- and dinuclear complexes in solution reveals slight differences between the steepness of the curves that may be attributable to cooperative interactions between the metal centers in the case of the dinuclear complexes.     

Monitoring Backbone Hydrogen‐Bond Formation in β‐Barrel Membrane Protein Folding

β‐barrel membrane proteins are key components of the outer membrane of bacteria, mitochondria and chloroplasts. Their three‐dimensional structure is defined by a network of backbone hydrogen bonds between adjacent β‐strands. Here, we employ hydrogen–deuterium (H/D) exchange in combination with NMR spectroscopy and mass spectrometry to monitor backbone hydrogen bond formation during folding of the outer membrane protein X (OmpX) from E. coli in detergent micelles. Residue‐specific kinetics of interstrand hydrogen‐bond formation were found to be uniform in the entire β‐barrel and synchronized to formation of the tertiary structure. OmpX folding thus propagates via a long‐lived conformational ensemble state in which all backbone amide protons exchange with the solvent and engage in hydrogen bonds only transiently. Stable formation of the entire OmpX hydrogen bond network occurs downhill of the rate‐limiting transition state and thus appears cooperative on the overall folding time scale.     

The protein folding transition-state ensemble from a Gō-like model

Characterizing the structure of transition states (TS) is a first step towards understanding two-state protein folding mechanisms. However, a direct experimental characterization of these states is challenging and indirect information derived from protein engineering methodologies (?-value analysis) is often difficult to interpret. We present here a theoretical study on the nature of the transition state ensemble for three representative proteins covering the major structural classes using a mean-field C(α)-based Gō-model. We identify that transition state ensembles are dominated by local contacts, indicating that most non-local contacts form only upon crossing the macroscopic folding free energy barrier. We demonstrate that the mean ?-value corresponds to the fraction of stabilization energy gained at the barrier-top in two-state-like systems, and that it depends monotonically on the stability conditions. Furthermore, we show that there is a fundamental connection between small destabilization and large ?-values that in turn depends on the location of the mutated residue in the structure. These results that are in agreement with the recent empirical findings highlight the importance of local energetics in determining folding mechanisms.     

Structural characterization of a paramagnetic metal-ion-assembled three-stranded alpha-helical coiled coil

A helical peptide designed to present an all-leucine core upon folding has been shown to exhibit concentration-dependent helicity and to exist as an ill-defined equilibrium population of oligomers. In marked contrast, an identical peptide covalently modified with a 2,2'-bipyridyl group at the N terminus forms a stable three-stranded parallel coiled coil in the presence of transition metal ions. We have employed paramagnetic Ni(2+) and Co(2+) ions to stabilize the trimeric assembly and to exploit their shift and relaxation properties in NMR structural studies. We find that metal-ion binding and helix-bundle folding are tightly coupled. Surprisingly, the three-helix bundle exhibits a dynamic N-terminal region, and a well-structured C-terminal half. The spectra indicate the presence of a dual conformation for the bundle extending from the N terminus to residue 12. The structure of the two isomeric forms has been ascertained from interpretation of NOEs in the Ni(II) complex and (1)H pseudocontact shifts in the Co(II) complex. Two different facial isomers with distinct susceptibility tensors were identified. The bulky leucine side chain at position 3 in the peptide chain appears to play a role in the conformational variation at the N terminus.     

An effective method for the discrimination of motional anisotropy and chemical exchange

Analysis of the ratio of transverse and longitudinal relaxation rates (R2/R1) is an approach commonly used for estimation of overall correlation time and identification of chemical exchange in biological macromolecules. However, this analysis fails to distinguish between chemical exchange and motional anisotropy. We describe a simple method for identifying chemical exchange and motional anisotropy using the product, R1R2. In the slow tumbling regime, the R1R2 product results in a constant value that is independent of overall correlation time and motional anisotropy. This analysis provides a simple method for rapidly estimating and dissociating the effects of motional anisotropy and chemical exchange in NMR heteronuclear spin relaxation data. We demonstrate the utility of the method with 15N relaxation data collected on the proteins E. coli ribonuclease H and the trimeric E. coli membrane associated lipoprotein lpp.     

Multiple-site exchange in proteins studied with a suite of six NMR relaxation dispersion experiments: an application to the folding of a Fyn SH3 domain mutant

The three-site exchange folding reaction of an (15)N-labeled, highly deuterated Gly48Met mutant of the Fyn SH3 domain has been characterized at 25 degrees C using a suite of six CPMG-type relaxation dispersion experiments that measure exchange contributions to backbone (1)H and (15)N transverse relaxation rates in proteins. It is shown that this suite of experiments allows the extraction of all the parameters of this multisite exchange process in a robust manner, including chemical shift differences between exchanging states, from a data set recorded at only a single temperature. The populations of the exchanging folded, intermediate, and unfolded states that are fit are 94, 0.7, and 5%, respectively. Despite the small fraction of the intermediate, structural information is obtained for this state that is consistent with the picture of SH3 domain folding that has emerged from other studies. Taken together, the six dispersion experiments facilitate the complete reconstruction of (1)H-(15)N correlation spectra for the unfolded and intermediate states that are "invisible" in even the most sensitive of NMR experiments.     

Proton magic-angle spinning-NMR investigation of surfactant aqueous suspensions

In this Note we present the advantages of 1H magic-angle spinning nuclear magnetic resonance (MAS-NMR) for the investigation of surfactant suspensions via transverse relaxation rate (R2) measurements. 1H-relaxation rates can be determined by the classical CPMG method from high-resolution spectra obtained either under conditions of liquid-state NMR for monomers and small spherical micelles or by using MAS-NMR for larger aggregates. For a mixture of alkyl dioxyethylene sulfate and alkylbetaine (80:20, w/w), up to a percentage of surfactant in water of 20%, we found that R2 increased, in accordance with an increased micellar size and very likely the formation of an HI phase. However, above 25%, R2 decreased. This result suggests a change from a hexagonal to a lamellar phase that would be difficult to observe by proton NMR without magic-angle spinning because the lines would be very broad, or by light scattering because of sample opacity. This NMR approach seems to have been overlooked by the community of surfactant physical chemists. It can be complementary to other analytical techniques and presents the advantage of not requiring isotopic labeling.     

Role of hydration in the phase transition of polypeptides investigated by NMR and Raman spectroscopy

NMR, Raman spectroscopy and ab initio quantum-chemical calculations have been employed to investigate the role of the hydration water in the inverse temperature transition of elastin-derived biopolymers represented by poly(Gly-Val-Gly-Val-Pro) and poly(Ala-Val-Gly-Val-Pro). Temperature and concentration dependences of the Raman spectra measured for water solutions of polymers and of a low-molecular-weight model have been correlated with the vibrational frequencies calculated at the DFT (B3LYP) and MP2 levels for the peptide segment surrounded by a growing number of water molecules. The results indicate strong hydration before the transition that, in addition to water hydrogen-bonded to amide groups, includes hydrophobic hydration of non-polar groups by a dynamic cluster of several water molecules. According to ¹H longitudinal and transverse relaxation of HOD signals in D₂O solutions, the number of water molecules motionally correlated with the polymer is about 4 per one amino acid residue.     

Mobility of molecules and diagram of the state of a glyceryl monooleate-water system according to NMR data

Transverse relaxation and self-diffusion of molecules in a glyceryl monooleate (monoolein)-D₂O system was studied using pulsed ¹H NMR in a range of water concentrations from 10 to 30 wt % and a range of temperatures from 20 to 90°C. It was noted that self-diffusion is described by one or two self-diffusion coefficients, depending on the temperature and concentration of water, while NMR-relaxation has a complex form. It was determined that with a reduction in the transverse magnetization, a component that has a form similar to Gaussian and relaxation times of 70 to 250 μs is observed at certain temperatures and concentrations of water, confirming the formation of structures in which glyceryl monooleate molecules (GM) are characterized by anisotropic rotational mobility. It was demonstrated that the ranges of the concentrations of water and temperature in which this component is observed correspond to liquid-crystalline phase for lamellar and inverse hexagonal structural organizations of lipids, according to the state diagram obtained by X-ray diffraction. In the state diagram areas corresponding to micellar and cubic structures (characterized by the isotropic rotation of GM molecules in the time scale of NMR), multiexponential decays of magnetization with average relaxation times were noted in the range of 10 to 200 ms. A number of features were discovered with the use of NMR: specimens always contain structures with isotropic rotational mobility in the presence of structures characterized by anisotropic rotational mobility; a change in the fraction of the structures with anisotropic rotational mobility takes place slowly over 5–15 K, not abruptly. Our conclusions regarding the polymorphism of a GM-D₂O system in the presence of anisotropic structures was confirmed by an analysis of the transverse NMR relaxation in an egg phosphatidylcholine-D₂O system, for which the presence of only lamellar liquid-crystalline structure is confirmed by ³¹P NMR.     

Nascent chain dynamics and ribosome interactions within folded ribosome–nascent chain complexes observed by NMR spectroscopy

The folding of many proteins can begin during biosynthesis on the ribosome and can be modulated by the ribosome itself. Such perturbations are generally believed to be mediated through interactions between the nascent chain and the ribosome surface, but despite recent progress in characterising interactions of unfolded states with the ribosome, and their impact on the initiation of co-translational folding, a complete quantitative analysis of interactions across both folded and unfolded states of a nascent chain has yet to be realised. Here we apply solution-state NMR spectroscopy to measure transverse proton relaxation rates for methyl groups in folded ribosome–nascent chain complexes of the FLN5 filamin domain. We observe substantial increases in relaxation rates for the nascent chain relative to the isolated domain, which can be related to changes in effective rotational correlation times using measurements of relaxation and cross-correlated relaxation in the isolated domain. Using this approach, we can identify interactions between the nascent chain and the ribosome surface, driven predominantly by electrostatics, and by measuring the change in these interactions as the subsequent FLN6 domain emerges, we may deduce their impact on the free energy landscapes associated with the co-translational folding process.

NMR measurements of methyl relaxation in translationally-arrested ribosome–nascent chain complexes probe the dynamics of folded nascent polypeptides emerging during biosynthesis and quantify their interaction with the ribosome surface.