AssignFit: a program for simultaneous assignment and structure refinement from solid-state NMR spectra

AssignFit is a computer program developed within the XPLOR-NIH package for the assignment of dipolar coupling (DC) and chemical shift anisotropy (CSA) restraints derived from the solid-state NMR spectra of protein samples with uniaxial order. The method is based on minimizing the difference between experimentally observed solid-state NMR spectra and the frequencies back calculated from a structural model. Starting with a structural model and a set of DC and CSA restraints grouped only by amino acid type, as would be obtained by selective isotopic labeling, AssignFit generates all of the possible assignment permutations and calculates the corresponding atomic coordinates oriented in the alignment frame, together with the associated set of NMR frequencies, which are then compared with the experimental data for best fit. Incorporation of AssignFit in a simulated annealing refinement cycle provides an approach for simultaneous assignment and structure refinement (SASR) of proteins from solid-state NMR orientation restraints. The methods are demonstrated with data from two integral membrane proteins, one α-helical and one β-barrel, embedded in phospholipid bilayer membranes.     

Application of solid-state NMR restraint potentials in membrane protein modeling

We have developed a set of orientational restraint potentials for solid-state NMR observables including (15)N chemical shift and (15)N-(1)H dipolar coupling. Torsion angle molecular dynamics simulations with available experimental (15)N chemical shift and (15)N-(1)H dipolar coupling as target values have been performed to determine orientational information of four membrane proteins and to model the structures of some of these systems in oligomer states. The results suggest that incorporation of the orientational restraint potentials into molecular dynamics provides an efficient means to the determination of structures that optimally satisfy the experimental observables without an extensive geometrical search.     

先进固体NMR技术研究高分子结构与动力学

随着固体NMR理论和谱仪硬件技术的不断发展,近年来固体NMR技术在高分子多尺度结构与动力学研究领域中正发挥着越来越重要的作用. 多脉冲及高速魔角旋转（MAS）等质子高分辨技术的发展使得高灵敏度的¹H谱可有效地用于高分子化学结构与链间相互作用的检测;基于化学键（J-耦合）相关和通过空间（偶极耦合）相互作用的各种二维异核相关谱NMR新技术,使得复杂高分子的链结构得以严格解析. 基于MAS下同核和异核偶极-偶极相互作用、化学位移各向异性等各向异性相互作用重聚的系列新技术,使得研究者可在采用高分辨¹H或¹³C 检测信号的同时检测准静态下的各向异性相互作用,进而获得与之密切相关的结构和动力学信息. 通过质子偶极滤波技术可有效检测多相聚合物中的界面相与相区尺寸、高分子共混物中的相容性等问题. 在动力学的研究中,通过质子间自旋扩散的有效压制技术和化学位移各向异性的重聚,目前已经可以有效地获取链段上单个化学键的快速局域运动以及链段的超慢分子运动. 上述丰富的多尺度NMR技术可以使研究者在不同空间和时间尺度上对高分子聚合物的微观结构、相分离和动力学行为等进行详细的研究,进而阐明高分子微观结构与宏观性能的关联. 该文以固体NMR中最主要的2类核（¹H和¹³C）的检测技术为主线,简单介绍近年来固体NMR领域的一些最新研究进展及其在高分子结构和动力学研究中的应用.     

Experimental aspects of multidimensional solid-state NMR correlation spectroscopy.

The experimental parameters critical for the implementation of multidimensional solid-state NMR experiments that incorporate heteronuclear spin exchange at the magic angle are discussed. This family of experiments is exemplified by the three-dimensional experiment that correlates the (1)H chemical shift, (1)H-(15)N dipolar coupling, and (15)N chemical shift frequencies. The broadening effects of the homonuclear (1)H-(1)H dipolar couplings are suppressed using flip-flop (phase- and frequency-switched) Lee-Goldburg irradiations in both the (1)H chemical shift and the (1)H-(15)N dipolar coupling dimensions. The experiments are illustrated using the (1)H and (15)N chemical shift and dipolar couplings in a single crystal of (15)N-acetylleucine.     

The roles of homonuclear line narrowing and the1H amide chemical shift tensor in structure determination of proteins by solid-state NMR spectroscopy

The seminal contributions of Ulrich Haeberlen to homonuclear line narrowing and the determination of¹H chemical shift tensors are crucial for protein structure determination by solid-state nuclear magnetic resonance spectroscopy. The¹H chemical shift is particularly important in spectra obtained on oriented samples of membrane proteins as a mechanism for providing dispersion among resonances that are not resolved with the¹H-¹⁵N dipolar coupling and¹⁵N chemical shift frequencies. This is demonstrated with three-dimensional experiments on uniformly¹⁵N-labeled samples of Magainin antibiotic peptide and the protein Vpu from HIV-1 in oriented lipid bilayers. These experiments enable resonances in two-dimensional¹H-¹⁵N dipolar coupling/¹⁵N chemical shift planes separated by¹H chemical shift frequencies to be resolved and analyzed. These three-dimensional spectra are compared to one-dimensional spectra of full-length Vpu, the cytoplasmic domain of Vpu, and Magainin, as well as to two-dimensional spectra of fd coat protein and Colicin El polypeptide. The¹H amide chemical shift tensor provides valuable structural information, and this is demonstrated with its contributions to orientational restrictions to one of the in-plane helical residues of Magainin.     

Direct refinement against proton-proton dipolar couplings in NMR structure determination of macromolecules

The computational tools necessary for making use of (1)H-(1)H dipolar couplings in macromolecular structure refinement are presented. Potentials are described for direct refinement against (1)H-(1)H dipolar couplings of known sign as well as of unknown sign. In addition, a multiple potential is developed for prochiral protons whose stereospecific assignments are unknown. The utility of direct (1)H-(1)H dipolar coupling refinement is illustrated using the small protein ubiquitin. It is shown that direct (1)H-(1)H dipolar coupling refinement leads to improvements in the precision, accuracy, and quality of the resulting structures.     

A 2D MAS solid-state NMR method to recover the amplified heteronuclear dipolar and chemical shift anisotropic interactions

A two-dimensional solid-state NMR method for the measurement of chemical shift anisotropy tensors of X nuclei (15N or 13C) from multiple sites of a polypeptide powder sample is presented. This method employs rotor-synchronized pi pulses to amplify the magnitude of the inhomogeneous X-CSA and 1H-X dipolar coupling interactions. A combination of on-resonance and magic angle rf irradiation of protons is used to vary the ratio of the magnitudes of the 1H-X dipolar and X-CSA interactions which are recovered under MAS, in addition to suppressing the 1H-1H dipolar interactions. The increased number of spinning sidebands in the recovered anisotropic interactions is useful to determine the CSA tensors accurately. The performance of this method is examined for powder samples of N-acetyl-(15)N-L-valine (NAV), N-acetyl-15N-L-valyl-15N-L-leucine (NAVL), and alpha-13C-L-leucine. The sources of experimental errors in the measurement of CSA tensors and the application of the pulse sequences under high-field fast MAS operations are discussed.     

Measurement of Cross Correlation between Dipolar Coupling and Chemical Shift Anisotropy in the Spin Relaxation ofC,N-Labeled Proteins

We present a simple method for extracting interference effects between chemical shift anisotropy (CSA) and dipolar coupling from spin relaxation measurements in macromolecules, and we apply this method to extracting cross-correlation rates involving interference of amide¹⁵N CSA and¹⁵N–¹H dipolar coupling and interference of carbonyl¹³C′ CSA and¹⁵N–¹³C′ dipolar coupling, in a small protein. A theoretical basis for the interpretation of these rates is presented. While it proves difficult to quantitatively separate the structural and dynamic contributions to these cross-correlation rates in the presence of anisotropic overall tumbling and a nonaxially symmetric chemical shift tensor, some useful qualitative correlations of data with protein structure can be seen when simplifying assumptions are made.     

Separating structure and dynamics in CSA/DD cross-correlated relaxation: a case study on trehalose and ubiquitin

We present two new sensitivity enhanced gradient NMR experiments for measuring interference effects between chemical shift anisotropy (CSA) and dipolar coupling interactions in a scalar coupled two-spin system in both the laboratory and rotating frames. We apply these methods for quantitative measurement of longitudinal and transverse cross-correlation rates involving interference of (13)C CSA and (13)C-(1)H dipolar coupling in a disaccharide, alpha,alpha-D-trehalose, at natural abundance of (13)C as well as interference of amide (15)N CSA and (15)N-(1)H dipolar coupling in uniformly (15)N-labeled ubiquitin. We demonstrate that the standard heteronuclear T(1), T(2), and steady-state NOE autocorrelation experiments augmented by cross-correlation measurements provide sufficient experimental data to quantitatively separate the structural and dynamic contributions to these relaxation rates when the simplifying assumptions of isotropic overall tumbling and an axially symmetric chemical shift tensor are valid.     

Recoupled polarization transfer heteronuclear 1H-13C multiple-quantum correlation in solids under ultra-fast MAS.

A new approach for high-resolution solid-state heteronuclear multiple-quantum MAS NMR spectroscopy of dipolar-coupled spin-12 nuclei is introduced. The method is a heteronuclear chemical shift correlation technique of abundant spins, like 1H with rare spins, like 13C in natural abundance. High resolution is provided by ultra-fast MAS and high magnetic fields, high sensitivity being ensured by a direct polarization transfer from the abundant protons to 13C. In a rotor-synchronized variant, the method can be used to probe heteronuclear through-space proximities, while the heteronuclear dipolar coupling constant can quantitatively be determined by measuring multiple-quantum spinning-sideband patterns. By means of recoupling, even weak heteronuclear dipolar interactions are accessible. The capabilities of the technique are demonstrated by measurements on crystalline L-tyrosine hydrochloride salt.     

质子化学位移各向异性的测量

测量质子化学位移各向异性（CSA）有助于表征分子结构与其动力学,但由于¹H-¹H同核偶极耦合相互作用很强及质子各向异性化学位移较小,测量质子化学位移各向异性仍具有巨大挑战,特别是对含有多种质子的生物大分子,如蛋白质.本文简要综述了测量质子化学位移各向异性的方法,包括同核去耦慢速魔角旋转方法、超快魔角旋转方法、对称重耦（RN_n^v）方法、xCSA方法以及量子化学计算方法.我们重点介绍了在高速魔角旋转条件下蛋白质氨基质子化学位移各向异性的测量及它们与氢键长度、蛋白质二级结构之间的关系.     

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.     

Determination of NMR interaction parameters from double rotation NMR

It is shown that the anisotropic NMR parameters for half-integer quadrupolar nuclei can be determined using double rotation (DOR) NMR at a single magnetic field with comparable accuracy to multi-field static and MAS experiments. The (17)O nuclei in isotopically enriched l-alanine and OPPh(3) are used as illustrations. The anisotropic NMR parameters are obtained from spectral simulation of the DOR spinning sideband intensities using a computer program written with the GAMMA spin-simulation libraries. Contributions due to the quadrupolar interaction, chemical shift anisotropy, dipolar coupling and J coupling are included in the simulations. In l-alanine the oxygen chemical shift span is 455 +/- 20 ppm and 350 +/- 20 ppm for the O1 and O2 sites, respectively, and the Euler angles are determined to an accuracy of +/- 5-10 degrees . For cases where effects due to heteronuclear J and dipolar coupling are observed, it is possible to determine the angle between the internuclear vector and the principal axis of the electric field gradient (EFG). Thus, the orientation of the major components of both the EFG and chemical shift tensors (i.e., V(33) and delta(33)) in the molecular frame may be obtained from the relative intensity of the split DOR peaks. For OPPh(3) the principal axis of the (17)O EFG is found to be close to the O-P bond, and the (17)O-(31)P one-bond J coupling ((1)J(OP)=161 +/- 2 Hz) is determined to a much higher accuracy than previously.     

Quadrupole effects of spin-3/2 nuclei on the solid-state magic-angle spinning nuclear magnetic resonance spectra of spin-1/2 nuclei Deviations from first-order theory and implications concerning the sign of the indirect coupling constant

The effect of the interaction between spin-3/2 and spin-1/2 nuclei on solid-state magic-angle spinning nuclear magnetic resonance (MAS NMR) spectra of the latter is studied in cases where deviations from first-order theory are expected. A comparison is made between the exact and first-order perturbation approaches. Both dipolar and indirect (iso- and anisotropic) coupling interactions are considered. Implications regarding ¹³C,^35,37Cl, ³¹P,^63,65Cu and ¹¹⁹Sn,^35,37Cl cases are discussed. It is shown that in the latter two cases the sign of the indirect coupling constant J can be derived.     

Accurate measurement of H(N)-H(alpha) residual dipolar couplings in proteins.

A method for accurately measuring H(N)-H(alpha) residual dipolar couplings is described. Using this technique, both the sign and magnitude of the coupling can be determined easily. Residual dipolar coupling between H(N)(i)-H(alpha)(i) and H(N)(i)-H(alpha)(i-1) were measured for the FK506 binding protein complexed to FK506. The experimental values were in excellent agreement with predictions based on an X-ray crystal structure of the protein/ligand complex, suggesting that these residual dipolar couplings will provide accurate structural constraints for the refinement of protein structures determined by NMR.     

Triple resonance experiments for aligned sample solid-state NMR of (13)C and (15)N labeled proteins

Initial steps in the development of a suite of triple-resonance (1)H/(13)C/(15)N solid-state NMR experiments applicable to aligned samples of (13)C and (15)N labeled proteins are described. The experiments take advantage of the opportunities for (13)C detection without the need for homonuclear (13)C/(13)C decoupling presented by samples with two different patterns of isotopic labeling. In one type of sample, the proteins are approximately 20% randomly labeled with (13)C in all backbone and side chain carbon sites and approximately 100% uniformly (15)N labeled in all nitrogen sites; in the second type of sample, the peptides and proteins are (13)C labeled at only the alpha-carbon and (15)N labeled at the amide nitrogen of a few residues. The requirement for homonuclear (13)C/(13)C decoupling while detecting (13)C signals is avoided in the first case because of the low probability of any two (13)C nuclei being bonded to each other; in the second case, the labeled (13)C(alpha) sites are separated by at least three bonds in the polypeptide chain. The experiments enable the measurement of the (13)C chemical shift and (1)H-(13)C and (15)N-(13)C heteronuclear dipolar coupling frequencies associated with the (13)C(alpha) and (13)C' backbone sites, which provide orientation constraints complementary to those derived from the (15)N labeled amide backbone sites. (13)C/(13)C spin-exchange experiments identify proximate carbon sites. The ability to measure (13)C-(15)N dipolar coupling frequencies and correlate (13)C and (15)N resonances provides a mechanism for making backbone resonance assignments. Three-dimensional combinations of these experiments ensure that the resolution, assignment, and measurement of orientationally dependent frequencies can be extended to larger proteins. Moreover, measurements of the (13)C chemical shift and (1)H-(13)C heteronuclear dipolar coupling frequencies for nearly all side chain sites enable the complete three-dimensional structures of proteins to be determined with this approach.     

Solid-state NMR spectroscopy of a membrane protein in biphenyl phospholipid bicelles with the bilayer normal parallel to the magnetic field

Bicelles composed of the long-chain biphenyl phospholipid TBBPC (1-tetradecanoyl-2-(4-(4-biphenyl)butanoyl)-sn-glycero-3-PC) and the short-chain phospholipid DHPC align with their bilayer normals parallel to the direction of the magnetic field. In contrast, in typical bicelles the long-chain phospholipid is DMPC or DPPC, and the bilayers align with their normals perpendicular to the field. Samples of the membrane-bound form of the major coat protein of Pf1 bacteriophage in TBBPC bicelles are stable for several months, align magnetically over a wide range of temperatures, and yield well-resolved solid-state NMR spectra similar to those obtained from samples aligned mechanically on glass plates or in DMPC bicelle samples "flipped" with lanthanide ions so that their bilayer normals are parallel to the field. The order parameter of the TBBPC bicelle sample decreases from approximately 0.9 to 0.8 upon increasing the temperature from 20 degrees C to 60 degrees C. Since the frequency spans of the chemical shift and dipolar coupling interactions are twice as large as those obtained from proteins in DMPC bicelles without lanthanide ions, TBBPC bicelles provide an opportunity for structural studies with higher spectral resolution of the metal-binding membrane proteins without the risk of chemical or spectroscopic interference from the added lanthanide ions. In addition, the large temperature range of these samples is advantageous for the studies of membrane proteins that are unstable at elevated temperatures and for experiments requiring measurements as a function of temperature.     

Distance measurements in spin-1/2 systems by 13C and 31P solid-state NMR in dense dipolar networks

In this article solid-state NMR methods for the determination of internuclear dipole-dipole couplings between homonuclear spin-1/2 nuclei are presented. They are suitable for relatively dense dipolar networks which are still dominated by 2-spin interactions. C-/R-symmetry theory is applied to create a double-quantum average Hamiltonian using phase-modulated radio-frequency irradiation and magic-angle sample-rotation. Symmetry derived pulse sequences with improved compensation against chemical shift anisotropies were found assuming a small isotropic chemical shift difference and using numerical calculations of the spin dynamics. Moreover it is shown that a constant time procedure can be used to acquire reliable double-quantum build-up curves even in systems in which damping obscures oscillations in their symmetric build-up curve. This technique is demonstrated on four crystalline model compounds with 31P and 13C spin systems typical for inorganic and biological applications. Comparison to crystal structure data indicates that the distances derived this way from 31P and 13C double-quantum NMR carry only small systematic errors caused for example by anisotropic J-coupling, dipolar contributions from adjacent spins and relaxation.     

Direct Refinement against Proton–Proton Dipolar Couplings in NMR Structure Determination of Macromolecules

The computational tools necessary for making use of ¹H–¹H dipolar couplings in macromolecular structure refinement are presented. Potentials are described for direct refinement against ¹H–¹H dipolar couplings of known sign as well as of unknown sign. In addition, a multiple potential is developed for prochiral protons whose stereospecific assignments are unknown. The utility of direct ¹H–¹H dipolar coupling refinement is illustrated using the small protein ubiquitin. It is shown that direct ¹H–¹H dipolar coupling refinement leads to improvements in the precision, accuracy, and quality of the resulting structures.     

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.