Determination of Multiple φ-Torsion Angles in Proteins by Selective and Extensive C Labeling and Two-Dimensional Solid-State NMR

We describe an approach to efficiently determine the backbone conformation of solid proteins that utilizes selective and extensive ¹³C labeling in conjunction with two-dimensional magic-angle-spinning NMR. The selective ¹³C labeling approach aims to reduce line broadening and other multispin complications encountered in solid-state NMR of uniformly labeled proteins while still enhancing the sensitivity of NMR spectra. It is achieved by using specifically labeled glucose or glycerol as the sole carbon source in the protein expression medium. For amino acids synthesized in the linear part of the biosynthetic pathways, [1-¹³C]glucose preferentially labels the ends of the side chains, while [2-¹³C]glycerol labels the C^α of these residues. Amino acids produced from the citric-acid cycle are labeled in a more complex manner. Information on the secondary structure of such a labeled protein was obtained by measuring multiple backbone torsion angles φ simultaneously, using an isotropic–anisotropic 2D correlation technique, the HNCH experiment. Initial experiments for resonance assignment of a selectively ¹³C labeled protein were performed using ¹⁵N–¹³C 2D correlation spectroscopy. From the time dependence of the ¹⁵N–¹³C dipolar coherence transfer, both intraresidue and interresidue connectivities can be observed, thus yielding partial sequential assignment. We demonstrate the selective ¹³C labeling and these 2D NMR experiments on a 8.5-kDa model protein, ubiquitin. This isotope-edited NMR approach is expected to facilitate the structure determination of proteins in the solid state.     

13C direct detected COCO-TOCSY: a tool for sequence specific assignment and structure determination in protonless NMR experiments

A novel experiment is proposed to provide inter-residue sequential correlations among carbonyl spins in (13)C detected, protonless NMR experiments. The COCO-TOCSY experiment connects, in proteins, two carbonyls separated from each other by three, four or even five bonds. The quantitative analysis provides structural information on backbone dihedral angles phi as well as on the side chain dihedral angles of Asx and Glx residues. This is the first dihedral angle constraint that can be obtained via a protonless approach. About 75% of backbone carbonyls in Calbindin D(9K), a 75 amino acid dicalcium protein, could be sequentially connected via a COCO-TOCSY spectrum. 49 [Formula: see text] values were measured and related to backbone phi angles. Structural information can be extended to the side chain orientation of aminoacids containing carbonyl groups. Additionally, long range homonuclear coupling constants, (4)J(CC) and (5)J(CC), could be measured. This constitutes an unprecedented case for proteins of medium and small size.     

以液体核磁共振波谱分析与帕金森氏病相关的I93M 突变对人类泛素碳端水解酶结构的影响

人类泛素碳端水解酶（UCH-L1）是涉及帕金森氏病并且在神经元高度表达的蛋白．UCH-L1 的家族性突变与转译后修饰会引起聚集倾向增加与去泛素活性损失,这二者都可能成为致病因素．作者所在实验室之前的研究指出与帕金森氏病相关的突变I93M 显著降低UCH-L1 的折叠稳定性并且加速其构型展开动力学．该研究使用液体核磁共振分析方法,包括侧链甲基化学位移,松弛骨干动力学和残余偶极耦合,以进一步阐明I93M 突变如何影响UCH-L1 的结构和动态．结果显示I93M 显著影响突变位点周围的疏水核心侧链构型．然而,这样的结构扰动并不会影响在纳秒时间尺度的快速骨干动力学．透过残余偶极耦合分析显示UCH-L1 在水溶液中的结构与之前报道的晶体结构有相当显著的偏离,另外I93M 突变也导致超出突变位点的远距离结构扰动．这一系列水溶液结构的分析结果可补充之前已知的晶体学数据,并对UCH-L1 在帕金森氏病相关的基因突变影响并提供详细的见解．     

用核磁共振方法研究金属离子与蛋白质的相互作用

许多蛋白质含有金属离子,金属离子对蛋白质发挥生物学功能起着很大的作用. 金属离子与蛋白质的相互作用以及参与蛋白质功能调节的方式各种各样：有些金属离子高度专一性地与蛋白质紧密结合,对蛋白质发挥生物学功能起着关键性的作用;有些金属离子只是作为蛋白质发挥功能的辅助因子而瞬态地与蛋白质松散结合. 本文简要介绍目前国际上用NMR方法研究抗磁金属离子和顺磁金属离子与蛋白质相互作用的进展,并具体介绍了NMR方法在钙调蛋白、锌指蛋白、朊病毒蛋白等金属离子蛋白研究上的应用.     

Superslow Backbone Protein Dynamics as Studied by 1D Solid-State MAS Exchange NMR Spectroscopy

Superslow backbone dynamics of the protein barstar and the polypeptide polyglycine was studied by means of a solid-state MAS 1D exchange NMR method (time-reverse ODESSA) that can detect reorientation of nuclei carrying anisotropic chemical shift tensors. Experiments were performed on carbonyl 13C in polyglycine (natural abundance) and backbone 15N nuclei in uniformly 15N-enriched barstar within a wide range of temperatures in dry and wet powders for both samples. Two exchange processes were observed in the experiments: molecular reorientation and spin diffusion. Experimental conditions that are necessary to separate these two processes are discussed on a quantitative level. It was revealed that the wet protein undergoes molecular motion in the millisecond range of correlation times, whereas in dry protein and polyglycine molecular reorientations could not be detected. The correlation time of the motion in the wet barstar at room temperature is 50-100 ms; the activation energy is about 80 kJ/mol. Previously, protein motions with such a long correlation time could be observed only by methods detecting chemical exchange in solution (e.g., hydrogen exchange). The application of solid-state MAS exchange spectroscopy provides new opportunities in studying slow biomolecular dynamics that is important for the biological function of proteins.     

Force-extension behavior of folding polymers

The elastic response of flexible polymers made of elements which can be either folded or unfolded, having different lengths in these two states, is discussed. These situations are common for biopolymers as a result of folding interactions intrinsic to the monomers, or as a result of binding of other smaller molecules along the polymer length. Using simple flexible-chain models, we show that even when the energy ε associated with maintaining the folded state is comparable to k _B T, the elastic response of such a chain can mimic usual polymer linear elasticity, but with a force scale enhanced above that expected from the flexibility of the chain backbone. We discuss recent experiments on single-stranded DNA, chromatin fiber and double-stranded DNA with proteins weakly absorbed along its length which show this effect. Effects of polymer semiflexiblity and torsional stiffness relevant to experiments on proteins binding to dsDNA are analyzed. We finally discuss the competition between electrostatic self-repulsion and folding interactions responsible for the complex elastic response of single-stranded DNA. Received 7 August 2002 and Received in final form 7 March 2003 / Published online: 15 April 2003 RID="a" ID="a"e-mail: jmarko@uic.edu     

用异核多维NMR技术研究蛋白质动力学

蛋白质在溶液中的三维空间结构、动力学与蛋白质生物功能的关系是在分子水平上理解生命现象的重要基础. NMR技术在研究蛋白质动力学方面具有独特的优势,所能表征的运动过程相关时间尺度很广. 文章综述了异核多维NMR技术研究蛋白质动力学的实验技术和理论方法,介绍了描述蛋白质动力学的内运动参量的意义和Model-Free 方法,并举例说明¹⁵N弛豫测量实验被用于研究蛋白质及其与配体复合物的动力学.      

蛋白质顺磁标记技术与生物核磁共振中的赝接触位移

未配对电子与蛋白质分子自旋核的作用能提供丰富的长程结构信息,这些顺磁信息通常可用顺磁弛豫增强、赝接触位移和残余偶极耦合描述,其中赝接触位移包含生物大分子内重要的距离和角度信息.稀土离子具有相似的配位化学性质和不同的顺磁物理特性,而大多稀土离子具有磁各向异性,在与大分子作用过程中会产生赝接触位移.由于大多数蛋白质没有顺磁中心,获得这些顺磁信息需要通过定点选择标记蛋白质来实现.该文旨在对近年来蛋白质顺磁标记的方法和进展进行介绍,在顺磁标记基础上阐述赝接触位移在结构生物学中的应用.     

Continuum description of anomalous diffusion on a comb structure

Anomalous diffusion on a comb structure consisting of a one-dimensional backbone and lateral branches (teeth) of random length is considered. A well-defined classification of the trajectories of random walks reduces the original problem to an analysis of classical diffusion on the backbone, where, however, the time of this process is a random quantity. Its distribution is dictated by the properties of the random walks of the diffusing particles on the teeth. The feasibility of applying mean-field theory in such a model is demonstrated, and the equation for the Green’s function with a partial derivative of fractional order is obtained. The characteristic features of the propagation of particles on a comb structure are analyzed. We obtain a model of an effective homogeneous medium in which diffusion is described by an equation with a fractional derivative with respect to time and an initial condition that is an integral of fractional order. Zh. éksp. Teor. Fiz. 114, 1284–1312 (October 1998)     

Experimental Realization of Arbitrary Accuracy Iterative Phase Estimation Algorithms on Ensemble Quantum Computers

We report the first experimental demonstration of a nuclear phase estimation algorithms. Using feedback and iterations, magnetic resonance （NMR） realization of iterative we experimentally obtain the phase with 6 bits of precision on a two-qubit NMR quantum computer. Furthermore, we experimentally demonstrate the effect of gate noise on the iterative phase estimation algorithm. Our experimental results show that errors of measurements of the phase depend strongly on the precision of coupling gates. This experiment can be used as a benchmark for multi-qubit realizations of quantum information processing and precision measurements.     

Estimation of relative order tensors, and reconstruction of vectors in space using unassigned RDC data and its application

Advances in NMR instrumentation and pulse sequence design have resulted in easier acquisition of Residual Dipolar Coupling (RDC) data. However, computational and theoretical analysis of this type of data has continued to challenge the international community of investigators because of their complexity and rich information content. Contemporary use of RDC data has required a-priori assignment, which significantly increases the overall cost of structural analysis. This article introduces a novel algorithm that utilizes unassigned RDC data acquired from multiple alignment media (nD-RDC, n  3) for simultaneous extraction of the relative order tensor matrices and reconstruction of the interacting vectors in space.Estimation of the relative order tensors and reconstruction of the interacting vectors can be invaluable in a number of endeavors. An example application has been presented where the reconstructed vectors have been used to quantify the fitness of a template protein structure to the unknown protein structure. This work has other important direct applications such as verification of the novelty of an unknown protein and validation of the accuracy of an available protein structure model in drug design. More importantly, the presented work has the potential to bridge the gap between experimental and computational methods of structure determination.     

Translocation of knotted proteins through a pore

We report the results of molecular dynamics simulations of translocation of knotted proteins through pores. The protein is pulled into the pore with a constant force, which in many cases leads to the tightening of the knot. Since the radius of tightened knot is larger than that of the pore opening, the tight knot can block the pore thus preventing further translocation of the chain. Analyzing six different proteins, we show that the stuck probability increases with the applied force and that final positions of the tightened knot along the protein backbone are not random but are usually associated with sharp turns in the polypeptide chain. The combined effect of the confining geometry of the pore and the inhomogeneous character of the protein chain leads thus to the appearance of topological traps, which can immobilize the knot and lead to the jamming of the pore.     

Small angle neutron scattering studies on the interaction of cationic surfactants with bovine serum albumin

The structure of the protein-surfactant complex of bovine serum albumin (BSA) and cationic surfactants has been studied by small angle neutron scattering. At low concentrations, the CTAB monomers are observed to bind to the protein leading to an increase in its size. On the other hand at high concentrations, surfactant molecules aggregate along the unfolded polypeptide chain of the protein resulting in the formation of a fractal structure representing a necklace model of micelle-like clusters randomly distributed along the polypeptide chain. The fractal dimension as well as the size and number of micelles attached to the complex have been determined.      

An NMR study of the origin of dioxygen-induced spin-lattice relaxation enhancement and chemical shift perturbation

Due to its depth-dependent solubility, oxygen exerts paramagnetic effects which become progressively greater toward the hydrophobic interior of micelles, and lipid bilayer membranes. This paramagnetic gradient, which is manifested as contact shift perturbations (19F and 13C NMR) and spin-lattice relaxation enhancement (19F and 1H NMR), has been shown to be useful for precisely determining immersion depth, membrane protein secondary structure, and overall topology of membrane proteins. We have investigated the influence of oxygen on 19F and 13C NMR spectra and spin-lattice relaxation rates of a semiperfluorinated detergent, (8,8,8)-trifluoro (3,3,4,4,5,5,6,6,7,7)-difluoro octylmaltoside (TFOM) in a model membrane system, to determine the dominant paramagnetic spin-lattice relaxation and shift-perturbation mechanism. Based on the ratio of paramagnetic spin-lattice relaxation rates of 19F and directly bonded 13C nuclei, we conclude that the dominant relaxation mechanism must be dipolar. Furthermore, the temperature dependence of oxygen-induced chemical shift perturbations in 9F NMR spectra suggests a contact interaction is the dominant shift mechanism. The respective hyperfine coupling constants for 19F and 13C nuclei can then be estimated from the contact shifts <(deltav/v0)19F> and <(deltav/v0)13C>, allowing us to estimate the relative contribution of scalar and dipolar relaxation to 19F and 13C nuclei. We conclude that the contribution to spin-lattice relaxation from the oxygen induced paramagnetic scalar mechanism is negligible.     

Improved Resolution from Double Constant-Time Evolution of 3D and 4D Triple-Resonance Experiments

Triple-resonance NMR experiments are nearly essential for performing backbone assignments of proteins larger than 15 kDa. Our work extends the double constant-time (2CT) evolution scheme to triple-resonance 3D and 4D experiments. The modifications needed to accomplish 2CT evolution in triple resonance experiments are straight forward, are completely general, and consequently, will yield increased resolution for all out-and-back experiments. We expect that the increased resolution of experiments presented here will be useful in the study of larger proteins (>30 kDa) and in the study of highly helical proteins where¹HN,¹⁵N, and¹³C dimensions are poorly dispersed.     

Efficient and accurate estimation of relative order tensors from λ-maps

The rapid increase in the availability of RDC data from multiple alignment media in recent years has necessitated the development of more sophisticated analyses that extract the RDC data’s full information content. This article presents an analysis of the distribution of RDCs from two media (2D-RDC data), using the information obtained from a λ-map. This article also introduces an efficient algorithm, which leverages these findings to extract the order tensors for each alignment medium using unassigned RDC data in the absence of any structural information. The results of applying this 2D-RDC analysis method to synthetic and experimental data are reported in this article. The relative order tensor estimates obtained from the 2D-RDC analysis are compared to order tensors obtained from the program REDCAT after using assignment and structural information. The final comparisons indicate that the relative order tensors estimated from the unassigned 2D-RDC method very closely match the results from methods that require assignment and structural information. The presented method is successful even in cases with small datasets. The results of analyzing experimental RDC data for the protein 1P7E are presented to demonstrate the potential of the presented work in accurately estimating the principal order parameters from RDC data that incompletely sample the RDC space. In addition to the new algorithm, a discussion of the uniqueness of the solutions is presented; no more than two clusters of distinct solutions have been shown to satisfy each λ-map.     

REVIEW: High pressure NMR study of proteins – seeking roots for function,evolution, disease and food applications

NMR experiments at variable pressure reveal a wide range of conformation of a globular protein spanning from within the folded ensemble to the fully unfolded ensemble, herewith collectively called “high-energy conformers”. The observation of “high-energy conformers” in a wide variety of globular proteins has led to the “volume theorem”: the partial molar volume of a protein decreases with the decrease in its conformational order. Since “high-energy conformers” are intrinsically more reactive than the basic folded conformer, they could play decisive roles in all phenomena of proteins, namely function, environmental adaptation and misfolding. Based on the information on high-energy conformers and the rules on their partial volume in its monomeric state and amyloidosis, one may have a general view on what is happening on proteins under pressure. Moreover, one may even choose a high-energy conformer of a protein with pressure as variable for a particular purpose. Bridging “high-energy conformers” to macroscopic pressure effects could be a key to success in pressure application to biology, medicine, food technology and industry in the near future.     

Inozemtsev's hyperbolic spin model and its related spin chain

In this paper we study Inozemtsev's su(m) quantum spin model with hyperbolic interactions and the associated spin chain of Haldane–Shastry type introduced by Frahm and Inozemtsev. We compute the spectrum of Inozemtsev's model, and use this result and the freezing trick to derive a simple analytic expression for the partition function of the Frahm–Inozemtsev chain. We show that the energy levels of the latter chain can be written in terms of the usual motifs for the Haldane–Shastry chain, although with a different dispersion relation. The formula for the partition function is used to analyze the behavior of the level density and the distribution of spacings between consecutive unfolded levels. We discuss the relevance of our results in connection with two well-known conjectures in quantum chaos.     

Fracture of a biopolymer gel as a viscoplastic disentanglement process

We present an extensive experimental study of mode-I, steady, slow crack dynamics in gelatin gels. Taking advantage of the sensitivity of the elastic stiffness to gel composition and history we confirm and extend the model for fracture of physical hydrogels which we proposed in a previous paper (Nature Mater. 5, 552 (2006)), which attributes decohesion to the viscoplastic pull-out of the network-constituting chains. So, we propose that, in contrast with chemically cross-linked ones, reversible gels fracture without chain scission.     

Changes in protein structure and dynamics as a function of hydration from (1)H second moments

We report the proton second moment obtained directly from the Free Induction Decay (FID) of the NMR signal of variously hydrated bovine serum albumin (BSA) and hen egg white lysozyme (HEWL) and from the width of the NMR Z-spectrum of the cross-linked protein gels of different concentrations. The second moment of the proteins decreases in a continuous stepwise way as a function of increasing water content, which suggests that the structural and dynamical changes occur in small incremental steps. Although the second moment is dominated by the short range distances of nearest neighbors, the changes in the second moment show that the protein structure becomes more open with increasing hydration level. A difference between the apparent liquid content of the sample as found from decomposition of the FID and the analytically determined water content demonstrates that water absorbed in the early stages of hydration is motionally immobilized and magnetically indistinguishable from rigid protein protons while at high hydration levels some protein side-chain protons move rapidly contributing to liquid-like component of the NMR signal.