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1.
Three-way decomposition is applied for the structural analysis of a complete three-dimensional 15N-NOESY-HSQC of the 128 residues long protein azurin. The procedure presented includes decomposition using the software MUNIN, providing an initial characterization of the complete spectrum by 355 components. This is followed by post-processing yielding a final list of 149 components, 123 of which characterize 1859 NOE peaks from backbone N-H groups. Components from three-way decomposition are defined as direct products of one-dimensional shapes along the three dimensions. Thus, a complete set of distance constraints from this spectrum is obtained by one-dimensional peak picking of the shapes along the NOE dimension. Correctness and completeness of this set of NOEs are tested for all backbone amide groups against both an independent peak picking algorithm and the three-dimensional crystal structure of azurin, and a coincidence of about 95% is observed. Automated `demixing' of components that are `mixed' in a complex manner due to overlap of the HN and/or 15N frequencies is illustrated. 相似文献
2.
Highly resolved multi-dimensional NOE data are essential for rapid and accurate determination of spatial protein structures
such as in structural genomics projects. Four-dimensional spectra contain almost no spectral overlap inherently present in
lower dimensionality spectra and are highly amenable to application of automated routines for spectral resonance location
and assignment. However, a high resolution 4D data set using conventional uniform sampling usually requires unacceptably long
measurement time. Recently we have reported that the use of non-uniform sampling and multi-dimensional decomposition (MDD)
can remedy this problem. Here we validate accuracy and robustness of the method, and demonstrate its usefulness for fully
protonated protein samples. The method was applied to 11 kDa protein PA1123 from structural genomics pipeline. A systematic
evaluation of spectral reconstructions obtained using 15–100% subsets of the complete reference 4D 1H–13C–13C–1H NOESY spectrum has been performed. With the experimental time saving of up to six times, the resolution and the sensitivity
per unit time is shown to be similar to that of the fully recorded spectrum. For the 30% data subset we demonstrate that the
intensities in the reconstructed and reference 4D spectra correspond with a correlation coefficient of 0.997 in the full range
of spectral amplitudes. Intensities of the strong, middle and weak cross-peaks correlate with coefficients 0.9997, 0.9965,
and 0.83. The method does not produce false peaks. 2% of weak peaks lost in the 30% reconstruction is in line with theoretically
expected noise increase for the shorter measurement time. Together with good accuracy in the relative line-widths these translate
to reliable distance constrains derived from sparsely sampled, high resolution 4D NOESY data. 相似文献
3.
Sun ZY Hyberts SG Rovnyak D Park S Stern AS Hoch JC Wagner G 《Journal of biomolecular NMR》2005,32(1):55-60
We describe an efficient NMR triple resonance approach that correlates, at high resolution, protein side-chain and backbone resonances. It relies on the combination of two strategies: joint evolution of aliphatic side-chain proton/carbon coherences using a backbone N–H based HCcoNH reduced dimensionality (RD) experiment and non-uniform sampling (NUS) in two indirect dimensions. A typical data set containing such correlation information can be acquired in 2 days, at very high resolution unfeasible for conventional 4D HCcoNH-TOCSY experiments. The resonances of the aliphatic side-chain protons are unambiguously assigned to their attached carbons through the analysis of the ‘sum’ and ‘difference’ spectra. This approach circumvents the tedious process of manual resonance assignments using HCcH-TOCSY data, while providing additional resolving power of backbone N–H signals. A simple peak-list based algorithm has been implemented in the IBIS software for rapid automated backbone and side-chain assignments. 相似文献
4.
We describe an efficient NMR triple resonance approach for fast assignment of backbone amide resonance peaks in the 15N-HSQC spectrum. The exceptionally high resolutions achieved in the 3D HncocaNH and hNcocaNH experiments together with non-uniform
sampling facilitate error-free sequential connection of backbone amides. Data required for the complete backbone amide assignment
of the 56-residue protein GB1 domain were obtained in 14 h. Data analysis was vastly streamlined using a ‘backbone NH walk’
method to determine sequential connectivities without the need for 13C chemical shifts comparison. Amino acid residues in the sequentially connected NH chains are classified into two groups by
a simple variation of the NMR pulse sequence, and the resulting ‘ZeBra’ stripe patterns are useful for mapping these chains
to the protein sequence. In addition to resolving ambiguous assignments derived from conventional backbone experiments, this
approach can be employed to rapidly assign small proteins or flexible regions in larger proteins, and to transfer assignments
to mutant proteins or proteins in different ligand-binding states. 相似文献
5.
A new strategy is demonstrated that simultaneously enhances sensitivity and resolution in three- or higher-dimensional heteronuclear
multiple quantum NMR experiments. The approach, referred to as mixed-time parallel evolution (MT-PARE), utilizes evolution
of chemical shifts of the spins participating in the multiple quantum coherence in parallel, thereby reducing signal losses
relative to sequential evolution. The signal in a given PARE dimension, t
1, is of a non-decaying constant-time nature for a duration that depends on the length of t
2, and vice versa, prior to the onset of conventional exponential decay. Line shape simulations for the 1H–15N PARE indicate that this strategy significantly enhances both sensitivity and resolution in the indirect 1H dimension, and that the unusual signal decay profile results in acceptable line shapes. Incorporation of the MT-PARE approach
into a 3D HMQC-NOESY experiment for measurement of HN–HN NOEs in KcsA in SDS micelles at 50°C was found to increase the experimental sensitivity by a factor of 1.7±0.3 with a concomitant
resolution increase in the indirectly detected 1H dimension. The method is also demonstrated for a situation in which homonuclear 13C–13C decoupling is required while measuring weak H3′–2′OH NOEs in an RNA oligomer.
Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
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Summary The resolution of spectral frequencies in NMR data obtained from discrete Fourier transformation (DFT) along D constant-time dimensions can be improved significantly through extrapolation of the D-dimensional free induction decay (FID) by multidimensional Bayesian analysis. Starting from Bayesian probability theory for parameter estimation and model detection of one-dimensional time-domain data [Bretthorst, (1990) J. Magn. Reson., 88, 533–551; 552–570; 571–595], a theory for the D-dimensional case has been developed and implemented in an algorithm called BAMBAM (BAyesian Model Building Algorithm in Multidimensions). BAMBAM finds the most probable sinusoidal model to account for the systematic portion of any D-dimensional stationary FID. According to the parameters estimated by the algorithm, the FID is extrapolated in D dimensions prior to apodization and Fourier transformation. Multidimensional Bayesian analysis allows for the detection of signals not resolved by the DFT alone or even by sequential one-dimensional extrapolation from mirror-image linear prediction prior to the DFT. The procedure has been tested with a theoretical two-dimensional dataset and with four-dimensional HN(CO)CAHA (Kay et al. (1992) J. Magn. Reson., 98, 443–450) data from a small protein (8 kDa) where BAMBAM was applied to the 13C and H constant-time dimensions.To whom correspondence should be addressed. 相似文献
8.
NMR spectroscopy is central to atomic resolution studies in biology and chemistry. Key to this approach are multidimensional experiments. Obtaining such experiments with sufficient resolution, however, is a slow process, in part since each time increment in every indirect dimension needs to be recorded twice, in quadrature. We introduce a modified compressed sensing (CS) algorithm enabling reconstruction of data acquired with random acquisition of quadrature components in gradient-selection NMR. We name this approach random quadrature detection (RQD). Gradient-selection experiments are essential to the success of modern NMR and with RQD, a 50 % reduction in the number of data points per indirect dimension is possible, by only acquiring one quadrature component per time point. Using our algorithm (CSRQD), high quality reconstructions are achieved. RQD is modular and combined with non-uniform sampling we show that this provides increased flexibility in designing sampling schedules leading to improved resolution with increasing benefits as dimensionality of experiments increases, with particular advantages for 4- and higher dimensional experiments. 相似文献
9.
MUNIN: Application of three-way decomposition to the analysis of heteronuclear NMR relaxation data**
Dmitry M. Korzhnev Ilghiz V. Ibraghimov Martin Billeter Vladislav Yu. Orekhov 《Journal of biomolecular NMR》2001,21(3):263-268
MUNIN (Multidimensional NMR Spectra Interpretation), a recently introduced approach exploiting the mathematical concept of three-way decomposition, is proposed for separation and quantitative relaxation measurements of strongly overlapped resonances in sets of heteronuclear two-dimensional spectra that result from typical relaxation experiments. The approach is general and may also be applied to sets of two-dimensional spectra with arbitrary modulation along the third dimension (e.g., J-coupling, diffusion). Here, the method is applied for the analysis of 15N rotating frame relaxation data. 相似文献
10.
Peter Schmieder Alan S. Stern Gerhard Wagner Jeffrey C. Hoch 《Journal of biomolecular NMR》1994,4(4):483-490
Summary Nonlinear sampling along the constant-time dimension is applied to the constant-time HNCO spectrum of the dimerization domain of Ga14. Nonlinear sampling was used for the nitrogen dimension, while the carbon and proton dimensions were sampled linearly. A conventional ct-HNCO spectrum is compared with a nonlinearly sampled spectrum, where the gain in experiment time obtained from nonlinear sampling is used to increase the resolution in the carbonyl dimension. Nonlinearly sampled data are processed by maximum entropy reconstruction. It is shown that the nonlinearly sampled spectrum has a higher resolution, although it was recorded in less time. The constant intensity of the signal in the constant-time dimension allows for a variety of sampling schedules. A schedule of randomly distributed sampling points yields the best results. This general method can be used to significantly increase the quality of heteronuclear constant-time spectra. 相似文献
11.
Vladislav Yu. Orekhov Ilghiz V. Ibraghimov Martin Billeter 《Journal of biomolecular NMR》2001,20(1):49-60
A new method, MUNIN (Multi-dimensional NMR spectra interpretation), is introduced for the automated interpretation of three-dimensional NMR spectra. It is based on a mathematical concept referred to as three-way decomposition. An NMR spectrum is decomposed into a sum of components, with each component corresponding to one or a group of peaks. Each component is defined as the direct product of three one-dimensional shapes. A consequence is reduction in dimensionality of the spectral data used in further analysis. The decomposition may be applied to frequency-domain or time-domain data, or to a mixture of these. Features of MUNIN include good resolution in crowded regions and the absence of assumptions about line shapes. Uniform sampling of time-domain data, a prerequisite for discrete Fourier transform, is not required. This opens an avenue for the processing of NMR data that do not follow oscillating behaviour, e.g. from relaxation measurements. The application of MUNIN is illustrated for a 1H-15N-NOESY-HSQC, where each component is defined as the set of all NOE peaks formed by a given amide group. As a result, the extraction of structural information simply consists of one-dimensional peak picking of the shape along the NOE-axis obtained for each amide group. 相似文献
12.
A new isotope-assisted cross-relaxation editing experiment, [1H-13C]DINE-NOESY[1H-15N]HSQC (DINE = Double INEPT Edited), is proposed. It is based on the selectiveinversion of CH/CH3 or CH2 protons in the middle of the mixing time. The experiment sortsout the spin diffusion paths according to the principal mediators, either the CH/CH3 or theCH2 protons. This is useful in the structure refinement process, as it enables proper alignmentof the aliphatic protons in the vicinity of NH protons. 相似文献
13.
Kumaran Baskaran Renate Kirchhöfer Fritz Huber Jochen Trenner Konrad Brunner Wolfram Gronwald Klaus-Peter Neidig Hans Robert Kalbitzer 《Journal of biomolecular NMR》2009,43(4):197-210
A problem often encountered in multidimensional NMR-spectroscopy is that an existing chemical shift list of a protein has
to be used to assign an experimental spectrum but does not fit sufficiently well for a safe assignment. A similar problem
occurs when temperature or pressure series of n-dimensional spectra are to be evaluated automatically. We have developed two different algorithms, AUREMOL-SHIFTOPT1 and
AUREMOL-SHIFTOPT2 that fulfill this task. In the present contribution their performance is analyzed employing a set of simulated
and experimental two-dimensional and three-dimensional spectra obtained from three different proteins. A new z-score based on atom and amino acid specific chemical shift distributions is introduced to weight the chemical shift contributions
in different dimensions properly. 相似文献
14.
The conformation of kappa-carrageenan in solution was studied combining 1H and 13C NMR with molecular mechanics. The experimental conditions were chosen to characterize the disordered conformation of the polymer. Particular attention has been given to explore a wide range of experimental conditions as to the dependence on solvent (water and Me2SO), polymer concentration, temperature, pH, presence of a denaturing agent (guanidinium chloride), and of ions otherwise able to induce conformational order of the carrageenan chains, either in solution (I-) or in the gel state (Rb+). Two-dimensional NOE experiments were analyzed to obtain information on internuclear distances, and molecular mechanics provided the range of energetically accessible conformations. Two inter-residue topological constraints were clearly identified: their combination is rather restricting for the chain and suggests that the disordered conformation of kappa-carrageenan is characterized by an intrinsic stiffness with high values of persistent length and characteristic ratio. They also rule out any postulated interchain hydrogen bonds. In contrast, experiments on the temperature dependence of the chemical shift in Me2SO reveal the existence of two inter-residue intramolecular H-bonds which might contribute positively to the rigidity of the polymer chain. The overall picture emerging from the present results is that of a locally elongated 'loose single helix'. 相似文献
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Reinterpreting maximum entropy in ecology: a null hypothesis constrained by ecological mechanism 下载免费PDF全文
Simplified mechanistic models in ecology have been criticised for the fact that a good fit to data does not imply the mechanism is true: pattern does not equal process. In parallel, the maximum entropy principle (MaxEnt) has been applied in ecology to make predictions constrained by just a handful of state variables, like total abundance or species richness. But an outstanding question remains: what principle tells us which state variables to constrain? Here we attempt to solve both problems simultaneously, by translating a given set of mechanisms into the state variables to be used in MaxEnt, and then using this MaxEnt theory as a null model against which to compare mechanistic predictions. In particular, we identify the sufficient statistics needed to parametrise a given mechanistic model from data and use them as MaxEnt constraints. Our approach isolates exactly what mechanism is telling us over and above the state variables alone. 相似文献
17.
采用多种NMR分析技术,首次对百合甾体皂苷(25R,26R)-26-甲氧基螺甾烷-5-烯-3β-α-L-鼠李糖-(1→2)-[β-D-葡萄糖-(1→6)]-β-D-葡萄糖苷的1H和13C NMR信号进行了全归属,特别是应用选择性的1D TOCSY和1D NOESY核磁共振分析技术,对该化合物1中的氢谱信号严重重叠的糖链进行了详细的分析,提出了一套对甾体皂苷糖链信号进行全归属的核磁共振法.在确认其结构的基础上,建立了核磁共振法(1H NMR)测定该化合物1的纯度,给出了完整的实验条件,线性回归系数为0.9998,重复性实验RSD为0.58%,稳定性实验RSD为0.24%,操作简单、快速准确,且不需要其它对照品,是中药化学对照品纯度研究的一个有益补充. 相似文献
18.
D. B. Amirkulova 《Molecular simulation》2019,45(14-15):1285-1294
ABSTRACTThis review describes recent advances by the authors and others on the topic of incorporating experimental data into molecular simulations through maximum entropy methods. Methods which incorporate experimental data improve accuracy in molecular simulation by minimally modifying the thermodynamic ensemble. This is especially important where force fields are approximate, such as when employing coarse-grain models, or where high accuracy is required, such as when attempting to mimic a multiscale self-assembly process. The authors review here the experiment directed simulation (EDS) and experiment directed metadynamics (EDM) methods that allow matching averages and distributions in simulations, respectively. Important system-specific considerations are discussed such as using enhanced sampling simultaneously, the role of pressure, treating uncertainty, and implementations of these methods. Recent examples of EDS and EDM are reviewed including applications to ab initio molecular dynamics of water, incorporating environmental fluctuations inside of a macromolecular protein complex, improving RNA force fields, and the combination of enhanced sampling with minimal biasing to model peptides 相似文献
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We show that adiabatic fast passage (AFP) pulses are robust refocusing elements of transverse 13C magnetization in multidimensional NMR experiments. A pair of identical AFP pulses can refocus selected parts or a complete 13 C chemical shift range in 13C spectra. In the constant time 13C-1H HSQC, replacement of attenuated rectangular pulses by selective AFP pulses results in a sensitivity enhancement of up to a factor of 1.8. In the 3D CBCA(CO)NH the signal-to-noise ratio is increased by a factor of up to 1.6. 相似文献