Structure determination in "shiftless" solid state NMR of oriented protein samples

An efficient formalism for calculating protein structures from oriented-sample NMR data in the torsion-angle space is presented. Angular anisotropies of the NMR observables are treated by utilizing an irreducible spherical basis of rotations. An intermediate rotational transformation is introduced that greatly speeds up structural fitting by rendering the dependence on the torsion angles Φ and Ψ in a purely diagonal form. Back-calculation of the simulated solid-state NMR spectra of protein G involving 15N chemical shift anisotropy (CSA), and 1H-15N and 1Hα-13Cα dipolar couplings was performed by taking into account non-planarity of the peptide linkages and experimental uncertainty. Even a relatively small (to within 1 ppm) random variation in the CSA values arising from uncertainties in the tensor parameters yields the RMSD's of the back-calculated structures of more than 10 ?. Therefore, the 15N CSA has been substituted with heteronuclear dipolar couplings which are derived from the highly conserved bond lengths and bond angles associated with the amino-acid covalent geometry. Using the additional 13Cα-15N and 13C'-15N dipolar couplings makes it possible to calculate protein structures entirely from "shiftless" solid-state NMR data. With the simulated "experimental" uncertainty of 15 Hz for protein G and 120 Hz for a helical hairpin derived from bacteriorhodopsin, back-calculation of the synthetic dipolar NMR spectra yielded a converged set of solutions. The use of distance restraints dramatically improves structural convergence even if larger experimental uncertainties are assumed.     

15N chemical shift anisotropy in protein structure refinement and comparison with NH residual dipolar couplings

Recent methods of aligning proteins which were developed in order to measure residual dipolar couplings (RDCs) in solution can also be used for additional applications such as measuring the 15N CSA in the form of chemical shift differences, Deltadelta. A new XPLOR-NIH module has been developed and implemented for NMR structure refinement using the 15N Deltadelta data as restraints. The results of this refinement are shown using the protein Bax. This method should be amenable to any protein which can be studied by NMR. An analysis comparing the structural information provided by NH RDCs and the 15N Deltadelta is included.     

Atomic refinement using orientational restraints from solid-state NMR

We describe a procedure for using orientational restraints from solid-state NMR in the atomic refinement of molecular structures. Minimization of an energy function can be performed through either (or both) least-squares minimization or molecular dynamics employing simulated annealing. The energy, or penalty, function consists of terms penalizing deviation from "ideal" parameters such as covalent bond lengths and terms penalizing deviation from orientational data. Thus, the refinement strives to produce a good fit to orientational data while maintaining good stereochemistry. The software is in the form of a module for the popular refinement package CNS and is several orders of magnitude faster than previous software for refinement with orientational data. The short computer time required for refinement removes one of the difficulties in protein structure determination with solid-state NMR.     

Atomic refinement with correlated solid-state NMR restraints

The orientation data provided by solid-state NMR can provide a great deal of structural information about membrane proteins. The quality of the information provided is, however, somewhat degraded by sign degeneracies in measurements of the dipolar coupling tensor. This is reflected in the dipolar coupling penalty function used in atomic refinement, which is less capable of properly restraining atoms when dipolar sign degeneracies are present. In this report we generate simulated solid-state NMR data using a variety of procedures, including back-calculation from crystal structures of alpha-helical and beta-sheet membrane proteins. We demonstrate that a large fraction of the dipolar sign degeneracies are resolved if anisotropic dipolar coupling measurements are correlated with anisotropic chemical shift measurements, and that all sign degeneracies can be resolved if three data types are correlated. The advantages of correlating data are demonstrated with atomic refinement of two test membrane proteins. When refinement is performed using correlated dipolar couplings and chemical shifts, perturbed structures converge to conformations with a larger fraction of correct dipolar signs than when data are uncorrelated. In addition, the final structures are closer to the original unperturbed structures when correlated data are used in the refinement. Thus, refinement with correlated data leads to improved atomic structures. The software used to correlate dipolar coupling and chemical shift data and to set up energy functions and their derivatives for refinement, CNS-SS02, is available at our web site.     

Structural fitting of PISEMA spectra of aligned proteins

An algorithm for fitting protein structures to PISEMA spectra is described, and its application to helical proteins in aligned samples is demonstrated using both simulated and experimental results. The formulation of the algorithm in terms of rotation operators yields compact recursion relations that provide a fast and effective way of obtaining peptide plane orientations from chemical and torsion angle constraints. The algorithm in combination with experimental solid-state NMR data results in a method for determining the backbone structures of proteins, since it yields the orientation of a helix as a whole, including its tilt and twist angles, and describes kinks and curves with atomic resolution. Although the algorithm can be applied in an "assignment-free" manner to spectra of uniformly labeled proteins, the precision of the structural fitting is improved by the addition of assignment information, for example the identification of resonances by residue type from spectra of selectively labeled proteins.     

水化磷脂层中蛋白质和多肽的高分辨固体核磁共振波谱学

有序样品的固体核磁共振(NMR)已快速发展成测定蛋白质和多肽在“仿真”水化磷脂层中高分辨结构的重要谱学方法. 由于与膜相连的蛋白质和多肽的结构、动力学和功能往往都和其周边自然环境密切相关,因此人们把蛋白质和多肽有序排列于水化磷脂层中进行固体NMR测量, 从而获得与取向相关的各向异性自旋相互作用. 这些取向约束可作为结构参数重构蛋白质在水化磷脂层中的高分辨三维结构. 近十年来在样品制备,NMR探头和实验方法方面的显著发展,极大地促进了有序样品的固体NMR的发展,并使之成为测定与膜相连的蛋白质和多肽结构的有效方法. 该综述介绍有序样品的固体NMR谱学方法,并总结此领域里的最新研究进展.     

Separation of 47Ti and 49Ti solid-state NMR lineshapes by static QCPMG experiments at multiple fields

Experimental procedures are proposed and demonstrated that separate the spectroscopic contribution from both (47)Ti and (49)Ti in solid-state nuclear magnetic resonance spectra. These take advantage of the different nuclear spin quantum numbers of these isotopes that lead to different "effective" radiofrequency fields for the central transition nutation frequencies when these nuclei occur in sites with a significant electric field gradient. Numerical simulations and solid-state NMR experiments were performed on the TiO(2) polymorphs anatase and rutile. For anatase, the separation of the two isotopes at high field (21.1T) facilitated accurate determination of the electric field gradient (EFG) and chemical shift anisotropy (CSA) tensors. This was accomplished by taking advantage of the quadrupolar interaction between the EFG at the titanium site and the different magnitudes of the nuclear quadrupole moments (Q) of the two isotopes. Rutile, having a larger quadrupolar coupling constant (C(Q)), was examined by (49)Ti-selective experiments at different magnetic fields to obtain spectra with different scalings of the two anisotropic tensors. A small chemical shielding anisotropy (CSA) of -30 ppm was determined.     

First principles NMR calculations of phenylphosphinic acid C6H5HPO(OH): assignments, orientation of tensors by local field experiments and effect of molecular motion

The complete set of NMR parameters for (17)O enriched phenylphosphinic acid C(6)H(5)HP( *)O(*OH) is calculated from first principles by using the Gauge Including Projected Augmented Wave (GIPAW) approach [C.J. Pickard, F. Mauri, All-electron magnetic response with pseudopotentials: NMR chemical shifts, Phys. Rev. B 63 (2001) 245101/1-245101/13]. The analysis goes beyond the successful assignment of the spectra for all nuclei ((1)H, (13)C, (17)O, (31)P), as: (i) the (1)H CSA (chemical shift anisotropy) tensors (magnitude and orientation) have been interpreted in terms of H bonding and internuclear distances. (ii) CSA/dipolar local field correlation experiments have allowed the orientation of the direct P-H bond direction in the (31)P CSA tensor to be determined. Experimental and calculated data were compared. (iii) The overestimation of the calculated (31)P CSA has been explained by local molecular reorientation and confirmed by low temperature static (1)H-->(31)P CP experiments.     

Optimal control based NCO and NCA experiments for spectral assignment in biological solid-state NMR spectroscopy

We present novel pulse sequences for magic-angle-spinning solid-state NMR structural studies of (13)C,(15)N-isotope labeled proteins. The pulse sequences have been designed numerically using optimal control procedures and demonstrate superior performance relative to previous methods with respect to sensitivity, robustness to instrumental errors, and band-selective excitation profiles for typical biological solid-state NMR applications. Our study addresses specifically (15)N to (13)C coherence transfers being important elements in spectral assignment protocols for solid-state NMR structural characterization of uniformly (13)C,(15)N-labeled proteins. The pulse sequences are analyzed in detail and their robustness towards spin system and external experimental parameters are illustrated numerically for typical (15)N-(13)C spin systems under high-field solid-state NMR conditions. Experimentally the methods are demonstrated by 1D (15)N-->(13)C coherence transfer experiments, as well as 2D and 3D (15)N,(13)C and (15)N,(13)C,(13)C chemical shift correlation experiments on uniformly (13)C,(15)N-labeled ubiquitin.     

Solid-state 31P CP/MAS and static 65Cu NMR characterization of polycrystalline copper(I) dialkyldithiophosphate clusters

Polycrystalline tetra-nuclear Cu4[S2P(O-i-C3H7)2]4, hexa-nuclear Cu6[S2P(OC2H5)2]6, and octa-nuclear Cu8[S2P(O-i-C4H9)2]6(S) complexes were synthesized and analyzed by means of solid-state 31P CP/MAS and 65Cu static NMR spectroscopy. The symmetries of the electronic environments around each P-site were estimated from the 31P chemical shift anisotropy (CSA) parameters, Deltaaniso and eta. The 65Cu chemical shift and quadrupolar splitting parameters obtained from the experimental 65Cu NMR spectra of the polycrystalline Cu(I)-complexes are presented. A solid-state NMR approach for the elucidation of the stereochemistry of poly-nuclear Cu(I) dithiophosphate complexes, when the structural analysis of the systems by single-crystal X-ray diffraction is not readily available, is proposed.     

Sample optimization and identification of signal patterns of amino acid side chains in 2D RFDR spectra of the alpha-spectrin SH3 domain

Future structural investigations of proteins by solid-state CPMAS NMR will rely on uniformly labeled protein samples showing spectra with an excellent resolution. NMR samples of the solid alpha-spectrin SH3 domain were generated in four different ways, and their (13)C CPMAS spectra were compared. The spectrum of a [u-(13)C, (15)N]-labeled sample generated by precipitation shows very narrow (13)C signals and resolved scalar carbon-carbon couplings. Linewidths of 16-19 Hz were found for the three alanine C(beta )signals of a selectively labeled [70% 3-(13)C]alanine-enriched SH3 sample. The signal pattern of the isoleucine, of all prolines, valines, alanines, and serines, and of three of the four threonines were identified in 2D (13)C-(13)C RFDR spectra of the [u-(13)C, (15)N]-labeled SH3 sample. A comparison of the (13)C chemical shifts of the found signal patterns with the (13)C assignment obtained in solution shows an intriguing match.     

Assigning solid-state NMR spectra of aligned proteins using isotropic chemical shifts

A method for assigning solid-state NMR spectra of membrane proteins aligned in phospholipid bicelles that makes use of isotropic chemical shift frequencies and assignments is demonstrated. The resonance assignments are based on comparisons of 15N chemical shift differences in spectra obtained from samples with their bilayer normals aligned perpendicular and parallel to the direction of the applied magnetic field.     

SOLUTION STRUCTURE DETERMINATION OF PROTEINS BY SOLUTION NMR:Application to a Envelope Protein, LAP2

Recent advances in multidimensional NMR to obtain resonance assignments, interproton distance and torsion angle restraints, and restraints that characterize long range order, coupled with new methods of structure refinement, have permitted solution structures of proteins to be rapidly and quickly determined.     

'q-Titration' of long-chain and short-chain lipids differentiates between structured and mobile residues of membrane proteins studied in bicelles by solution NMR spectroscopy

'q-Titration' refers to the systematic comparison of signal intensities in solution NMR spectra of uniformly (15)N labeled membrane proteins solubilized in micelles and isotropic bicelles as a function of the molar ratios (q) of the long-chain lipids (typically DMPC) to short-chain lipids (typically DHPC). In general, as q increases, the protein resonances broaden and correspondingly have reduced intensities due to the overall slowing of protein reorientation. Since the protein backbone signals do not broaden uniformly, the differences in line widths (and intensities) enable the narrower (more intense) signals associated with mobile residues to be differentiated from the broader (less intense) signals associated with "structured" residues. For membrane proteins with between one and seven trans-membrane helices in isotropic bicelles, we have been able to find a value of q between 0.1 and 1.0 where only signals from mobile residues are observed in the spectra. The signals from the structured residues are broadened so much that they cannot be observed under standard solution NMR conditions. This q value corresponds to the ratio of DMPC:DHPC where the signals from the structured residues are "titrated out" of the spectrum. This q value is unique for each protein. In magnetically aligned bilayers (q>2.5) no signals are observed in solution NMR spectra of membrane proteins because the polypeptides are "immobilized" by their interactions with the phospholipid bilayers on the relevant NMR timescale (～10(5)Hz). No signals are observed from proteins in liposomes (only long-chain lipids) either. We show that it is feasible to obtain complementary solution NMR and solid-state NMR spectra of the same membrane protein, where signals from the mobile residues are present in the solution NMR spectra, and signals from the structured residues are present in the solid-state NMR spectra. With assigned backbone amide resonances, these data are sufficient to describe major features of the secondary structure and basic topology of the protein. Even in the absence of assignments, this information can be used to help establish optimal experimental conditions.     

Automatic assignment of NOESY cross peaks and determination of the protein structure of a new world scorpion neurotoxin using NOAH/DIAMOD

The 3D NMR structures of the scorpion neurotoxin, CsE-v5, were determined from the same NOESY spectra with NOAH/DIAMOD, an automated assignment and 3D structure calculation software package, and with a conventional manual assignment combined with a distance geometry/simulated annealing (X-PLOR) refinement method. The NOESY assignments and the 3D structures obtained from the two independent methods were compared in detail. The NOAH/DIAMOD program suite uses feedback filtering and self-correcting distance geometry methods to automatically assign NOESY spectra and to calculate the 3D structure of a protein. NOESY cross peaks were automatically picked using a standard software package and combined with 74 manually assigned NOESY peaks to start the NOAH/DIAMOD calculations. After 63 NOAH/DIAMOD cycles, using REDAC procedures in the last 8 cycles, and final FANTOM constrained energy minimization, a bundle of 20 structures with the smallest target functions has a RMSD of 0.81 A for backbone atoms and 1.11 A for all heavy atoms to the mean structure. Despite some missing chemical shifts of side chain protons, 776 (including 74 manually assigned) of 1130 NOE peaks were unambiguously assigned, 150 peaks have more than one possible assignment compatible with the bundle structures, and only 30 peaks could not be assigned within the given chemical shift tolerance ranges in either the D1 or the D2 dimension. The remaining 174, mainly weak NOE peaks were not compatible with the final 20 best bundle structures at the last NOAH/DIAMOD cycle. The automatically determined structures agree well with the structures determined independently using the conventional method and the same NMR spectra, with the mean RMSD in well-defined regions of 0.84 A for bb and 1.48 A for all heavy atoms from residues 2-5, 18-26, 32-36, and 39-45. This study demonstrates the potential of the NOAH/DIAMOD program suite to automatically assign NMR data for proteins and determine their structure.     

13C CP MAS NMR and GIAO-CHF calculations of coumarins

13C cross-polarization magic-angle spinning NMR spectra were recorded for a series of solid coumarins. Ab initio calculations of shielding constants were performed with the use of GIAO-CHF method. The combined CPMAS NMR and theoretical approach was successful in characterizing solid-state conformations of coumarins; a relationship sigma (ppm) = -1.032 xdelta + 205.28 (R(2) = 0.9845) can be used to obtain structural information for coumarins, for which solid-state NMR or crystal structure data are not available.     

Chemical shift anisotropy selective inversion

Magic angle spinning (MAS) is used in solid-state NMR to remove the broadening effects of the chemical shift anisotropy (CSA). In this work we investigate a technique that can reintroduce the CSA in order to selectively invert transverse magnetization. The technique involves an amplitude sweep of the radio frequency field through a multiple of the spinning frequency. The selectivity of this inversion mechanism is determined by the size of the CSA. We develop a theoretical framework to describe this process and demonstrate the CSA selective inversion with numerical simulations and experimental data. We combine this approach with cross-polarization (CP) for potential applications in multi-dimensional MAS NMR.     

High-resolution local field spectroscopy with internuclear correlations

Establishing correlations among distant (>3 Å) spins remains an outstanding problem for both spectral assignment and elucidation of interhelical contacts in solid-state NMR of oriented membrane proteins. Here we present a pulse sequence which incorporates the previously established mismatched Hartmann–Hahn mixing of dilute spins via the proton bath together with high-resolution local field spectroscopy. In addition to providing structural information, the use of dipolar couplings in the indirect dimension helps eliminate the spectral crowdedness compared to the standard homonuclear correlation techniques. The proposed pulse sequence may find its use in assigning protein spectra in uniaxially oriented membrane environments.     

Quantitative study of the effects of chemical shift tolerances and rates of SA cooling on structure calculation from automatically assigned NOE data

The calculation of protein structures from nuclear magnetic resonance (NMR) data has been greatly facilitated by improvements in software for the automatic assignment of NOESY spectra. Nevertheless, for larger proteins, resonance overlap may lead to an overwhelming number of assignment options per peak. Although most software for automatic NOESY assignment can deal with a certain level of assignment ambiguity, structure calculations fail when this becomes too high. Reducing the number of assignment options per peak by reducing the chemical shift tolerances can lead to correct assignments being excluded, and thus also to incorrect structures. We have investigated, systematically, for three proteins of different size, the influence of the chemical shift tolerance limits (Delta) and of the number of simulated annealing (SA) cooling steps on the performance of the software ARIA. Large tolerance windows, and the correspondingly high levels of ambiguity, did not cause problems when appropriately slower cooling was used in our SA protocol. In cases where a high percentage of well-converged structures was not achieved, we demonstrate that it is more productive to calculate fewer structures whilst applying slow cooling, than to calculate many structures with fast cooling. In this way, high-quality structures were obtained even for proteins whose NMR spectra showed great degeneracy, and where there was much inconsistency in peak alignment between different samples. The method described herein opens the way to the automated structure determination of larger proteins from NMR data.     

高分子化学位移的量化计算与固体NMR实验研究

该文以2种不同立构聚丙烯（iPP和sPP）为讨论对象,首先研究了量化计算方法在预测高分子¹³C 各向同性和各向异性化学位移（CSA）中的应用,然后讨论了近年来发展的测定¹³C CSA粉末线形的2种重要固体NMR实验技术（SUPER和RAI）的特点和实验优化问题. 最后,利用可获得接近无扭曲线形的SUPER技术测定了等规立构聚丙烯样品的¹³C CSA粉末线形,并与量化计算理论结果比较. 结果表明：¹³C 各向同性化学位移及CSA粉末线形的理论计算结果均与固体NMR实验结果有很好的符合,预示通过¹³C CSA量化计算结合固体NMR实验是阐明高分子微观结构的有力工具.