Program MULDER -- a tool for extracting torsion angles from NMR data

MULDER (Mostly UniversaL Dihedral angle ExtractoR) is a program for extraction of torsion angle information from NMR data. Currently, it can analyze two types of input data: The torsion angle data, where several ³J-coupling constants and/or interatomic distances are combined in order to reduce the torsion angle ambiguity arising from solving the isolated Karplus (or distance) equation, and the sugar pucker data, where the dynamics of five-membered sugar rings is evaluated by postprocessing the results calculated from ³J_(HH) coupling constants by program PSEUROT. Program MULDER can be used either as an alternative to r-MD programs in situations where only specific structural features are studied, or as a preparatory tool in connection with full r-MD structure calculation for extraction of unambiguous torsion angle restraints.     

Heteronuclear coupling constants of hydroxyl protons in a water solution of oligosaccharides: trehalose and sucrose

Relatively few details are known about the conformational preferences of hydroxyl groups in carbohydrates in water solution, though these would be informative about solvation and H-bonding. We show that highly concentrated solutions of sucrose and trehalose exhibit surprisingly well-resolved ¹H NMR spectra in a deuterium oxide–water solvent mixture at subzero temperatures. Measurement conditions are suitable to extract nearly all homonuclear and, for the first time, heteronuclear coupling constants of OH groups of carbohydrates in their natural abundance. For ^2,3J_HO,C coupling constants new, powerful variants of HETLOC and HECADE techniques were applied. The present data do not support the presence of persistent H-bonds in these two cryogenic disaccharides.     

Conformational analysis of methyl 6-O-[(R)- and (S)-1-carboxyethyl]-α-D-galactopyranoside by MM and Langevin dynamics simulations

The conformational space of methyl 6-O-[(R)- and (S)- 1-carboxyethyl]-α-D-galactopyranoside has been investigated. A grid search employing energy minimization at each grid point over the three major degrees of freedom, namely φ, ψ and ω, identified low energy regions. The R-isomer shows five low energy conformers within ca. 1 kcal mol−1 of the global energy minimum. The S-isomer has two conformers within a few tenths of a kcal mol−1 of the global energy minimum. Langevin dynamics simulations have been have been performed at 300 K for 30 ns of each isomer. The φ dihedral angle has as its major conformer (g−1) for the R-isomer whereas it is the (g+) conformer for the S-isomer. For the ψ dihedral angle the (t) conformer has the highest population for both isomers. The dihedral angle ω has the (g+) conformer most highly populated, both for the R- and S-isomer. The above five and two conformational states for the R- and S-isomers, respectively, make up 90% in each case of the populated states during the Langevin dynamics (LD) simulations. Rate constants for the ω dihedral angle have been calculated based on a number correlation function. Three bond homo- and heteronuclear, i.e. proton and carbon-13, coupling constants have been calculated from the dynamics trajectories for comparison to experimental values. The heteronuclear coupling constant H2′,C6 has been measured for the S-isomer and found to be 3.3 Hz. The J value calculated from the LD simulations, namely 2.6 Hz, is in fair agreement with experiment. A comparison to the X-ray structure of the R-isomer shows that the conformation of the crystalline compound occupies the low energy region most highly populated as a single R-conformer (30%) during the LD simulations. This revised version was published online in August 2006 with corrections to the Cover Date.     

B3LYP/6-311++G* * study of structure and spin-spin coupling constant in heparin disaccharide

Structures of heparin disaccharide have been analyzed by DFT using the B3LYP/6-311++G( * *) method. The optimized geometries of two forms of this disaccharide, differing in the conformation ((1)C(4) and (2)S(0)) of the IdoA2S residue, confirmed considerable influences of the sulfate and the carboxylate groups upon the pyranose ring geometries. The computed energies showed that disaccharide having the (1)C(4) form of the IdoA2S residue is more stable than that with the (2)S(0) form. Interatomic distances, bond and torsion angles showed that interconversion of the IdoA2S residue results in geometry changes in the GlcN,6S residue as well. Three-bond proton-proton and proton-carbon spin-spin coupling constants computed for both forms agree with the experimental data and indicate that only two chair forms contribute to the conformational equilibrium in disaccharide. Influences of the charged groups upon the magnitudes of spin-spin coupling constants are also discussed.     

代谢组学：一个迅速发展的新兴学科

对代谢组学的含义,中心任务,研究方法,样品要求,应用及其发展方向进行了简要综述. 系统生物学概念的诞生标志着研究哲学由“还原论”向“整体论”的变化. 系统生物学的中心任务就是要针对生物系统整体 (无论它是生物细胞,多细胞组织,器官还是生物整体),建立定量,普适,整体和可预测 (QUIP) 的认知. 具体而言,系统生物学研究就是要将给定生物系统的基因,转录,蛋白质和代谢水平所发生的事件,相关性及其对所涉及生物过程的意义进行整体性认识. 从而出现了许多的“组”和“组学”的新概念. 但是现已提出的一百多个“组”和“组学”,可以大体归纳为“基因组”/“基因组学”,“转录组”/“转录组学”,“蛋白质组”/“蛋白质组学”和“代谢组”/“代谢组学”四个方面. 显而易见,DNA,mRNA 以及蛋白质的存在为生物过程的发生提供了物质基础 (但这个过程有可能不发生!),而代谢物质所反映的是已经发生了的生物学事件. 因此代谢组学是对一个生物系统进行全面认识的不可缺少的一部分,是全局系统生物学 (global systems biology) 的重要基础,也是系统生物学的一个重要组成部分. 在现有的英文表述中,代谢组学同时存在两个不同的词汇和概念,即metabonomics 和 metabolomics. 尽管前者多用在动物系统而后者多用于植物和微生物系统,但这些概念的本质从他们的定义中能够得到较细致的了解. Metabonomics 的最初定义是就生物系统对生理和病理刺激以及基因改变的代谢应答的定量测定(“the quantitative measurement of the multi-parametric metabolic response of living systems to pathophysiological stimuli or geneticmodifications”). 我们认为这个定义现在可以更广泛地表述为:代谢组学是关于定量描述生物内源性代谢物质的整体及其对内因和外因变化应答规律的科学 (“Metabonomics is the branch of science concerned with the quantitative understandings of themetabolite complement of integrated living systems and its dynamic responses to the changes of both endogenous factors (such asphysiology and development) and exogenous factors (such as environmental factors and xenobiotics).”). 其中心任务包括 (1) 对内源性代谢物质的整体及其动态变化规律进行检测,量化和编录,(2) 确定此变化规律和生物过程的有机联系. Metabolomics 存在多个定义,但其精髓是:对一个生物系统的细胞在给定时间和给定条件下所有小分子代谢物质的定量分析(the quantitativemeasurement of all low molecular weight metabolites in an organism's cells at a specified time under specific environmentalconditions). 因此,metabolomics 可以译作“代谢物组学”. 不难看出,前者是对生物系统进行的整体和动态的认识 (不仅关心代谢物质的整体也关注其动态变化规律),而后者强调分析而且是个静态的认识概念. 因此可以认为,metabolomics 是metabonomics 的一个组成部分 (参看定义). 近年又有人提出了“dynamic metabolomics”的概念,这个概念所表达的含义十分接近“metabonomics”本身的含义. 所以,可以预见,随着这门新兴学科的发展和更深入讨论,这两个概念必将趋向一致. 因此我们建议,在中文表述中将“代谢组学”一词和英文中的 metabonomics 相对应,以避免不必要的混淆和争议. 就细胞系统而言,不仅存在细胞自身的代谢物质组成问题,存在细胞之间代谢物质交换的问题,也存在代谢过程所发生的位点问题. 因此,简单地分析代谢物质的总组成 (即代谢组) 缺乏“整体论”所要求的全面性,其意义有一定局限. 代谢组学属于全局系统生物学 (Global systems biology) 研究方法,便于对复杂体系的整体进行认识. 譬如,一个正常工作的人体包括“人体”本身和与之共同进化而来且共生的消化道微生物群体 (或称菌群),孤立地研究“人体”本身的基因,转录子以及蛋白质当然可以为人们认识人体生物学提供重要信息,但无法提供使人体正常工作不可缺少的菌群的信息. 人体血液和尿液的代谢组却携带着包括菌群在内的每一个细胞的信息,因此代谢组学方法对研究如人体这样复杂的进化杂合体十分有效. 正因如此,代谢组学已经广泛地应用到了包括药物研发,分子生理学,分子病理学,基因功能组学,营养学,环境科学等重要领域. 在代谢组学诞生的过去 6 年里,有关代谢组学的研究论文和专利以指数的形式逐年增长. 可以预见,这门新兴学科将应用到更为广泛的领域.     

Influence of the glycosidic torsion angle on 13C and 15N shifts in guanosine nucleotides: Investigations of G-tetrad models with alternating syn and anti bases

Summary The effect of the glycosidic torsion angle on ¹³C and ¹⁵N shifts of the sugar and base moieties of guanosine nucleotides was investigated by comparing the sites in two model G-tetrad oligodeoxynucleotides that contain guanosine residues alternately with syn and anti bases. The sugar puckering has been shown to be C2-endo for both cases. It was observed that, for the instances with syn bases, the C1 through C4 carbons showed shifts that may be distinguished from those normally found in B-DNA-like structures. C1, C3 and C4 moved to lower field, while C2 moved to higher field. Effects of the change in glycosidic torsion angle were also seen in the shifts of base carbons and nitrogens in the five-membered ring portion of the base. Characterization of the shift variation associated with this conformational change may be useful in developing the use of ¹³C shifts as a tool in conformational analysis of oligonucleotides.Part of the work reported here derives from the Ph.D. Thesis of Karen L. Greene, Emory University, Atlanta, GA, 1991.     

Identification of Lignin and Polysaccharide Modifications in Populus Wood by Chemometric Analysis of 2D NMR Spectra from Dissolved Cell Walls

2D ^13C-^1H HSQC NMR spectroscopy of acetylated cell walls in solution gives a detailed fingerprint that can be used to assess the chemical composition of the complete wall without extensive degradation. We demonstrate how multivariate analysis of such spectra can be used to visualize cell wall changes between sample types as high-resolution 2D NMR loading spectra. Changes in composition and structure for both lignin and polysaccharides can subsequently be interpreted on a molecular level. The multivariate approach alleviates problems associated with peak picking of overlapping peaks, and it allows the deduction of the relative importance of each peak for sample discrimination. As a first proof of concept, we compare Populus tension wood to normal wood. All well established differences in cellulose, hemicellulose, and lignin compositions between these wood types were readily detected, confirming the reliability of the multivariate approach, In a second example, wood from transgenic Populus modified in their degree of pectin methylesterification was compared to that of wild-type trees. We show that differences in both lignin and polysaccharide composition that are difficult to detect with traditional spectral analysis and that could not be a priori predicted were revealed by the multivariate approach. 2D NMR of dissolved cell wall samples combined with multivariate analysis constitutes a novel approach in cell wall analysis and provides a new tool that will benefit cell wall research.     

Integration of spin-state-selective excitation into 2D NMR correlation experiments with heteronuclear ZQ/2Q π rotations for1 JXH

Spin-State-Selective Excitation (S³E), which forexample selectively excites amide proton resonances corresponding toexclusively either the or the spin state of the covalentlybound ¹⁵N atom is employed for E.COSY-type extraction ofheteronuclear J coupling constants. Instead of having one spectrum with twopeaks (corresponding to the or spin state of¹⁵N), S³E generates two spectra, each with onlyone peak for each ¹⁵N nucleus. These two spectra are generatedfrom the same data set, so that there is no reduction in sensitivitycompared to conventional ¹J_NH-resolved methods.Another interesting feature in comparison with conventional methods is that¹J_NH can be suppressed during the evolutionperiod, meaning that no heteronuclear multiplet structure is visible in the₁ frequency dimension. The S³E pulsesequence element is combined with NOESY for measurement of³J_N-H and J_N-Hcoupling constants in either a hetero- or a homonuclear correlated version.Experimental confirmation is obtained using the protein RAP 17-;97(N-terminal domain of ₂-macroglobulin ReceptorAssociated Protein).     

Spin-state-selective coherence transfer via intermediate states of two-spin coherence in IS spin systems: Application to E.COSY-type measurement of J coupling constants

It is demonstrated that a new pulse sequence element, Spin-State-SelectiveCoherence Transfer (S³CT), via an intermediate state ofheteronuclear IS zero- or double-quantum coherence can transfer the twosingle-quantum coherences on one of the spins exclusively to any one of thetwo single-quantum coherences on the other spin. This fact is used for editinginto two subspectra that are most suitable for extraction of homo- orheteronuclear J coupling constants when S³CT is combined withhomonuclear coherence transfer during a mixing period. Experimentalconfirmation is obtained using a ¹⁵N-labeled 58-residue protein,the C-terminal Kunitz domain from human type VI collagen. The J coupling con-stants determined include ³J_HN-H and³J_N-H related to the and¹ angles, respectively.     

Efficient Multiple-Trait Association and Estimation of Genetic Correlation Using the Matrix-Variate Linear Mixed Model

Multiple-trait association mapping, in which multiple traits are used simultaneously in the identification of genetic variants affecting those traits, has recently attracted interest. One class of approaches for this problem builds on classical variance component methodology, utilizing a multitrait version of a linear mixed model. These approaches both increase power and provide insights into the genetic architecture of multiple traits. In particular, it is possible to estimate the genetic correlation, which is a measure of the portion of the total correlation between traits that is due to additive genetic effects. Unfortunately, the practical utility of these methods is limited since they are computationally intractable for large sample sizes. In this article, we introduce a reformulation of the multiple-trait association mapping approach by defining the matrix-variate linear mixed model. Our approach reduces the computational time necessary to perform maximum-likelihood inference in a multiple-trait model by utilizing a data transformation. By utilizing a well-studied human cohort, we show that our approach provides more than a 10-fold speedup, making multiple-trait association feasible in a large population cohort on the genome-wide scale. We take advantage of the efficiency of our approach to analyze gene expression data. By decomposing gene coexpression into a genetic and environmental component, we show that our method provides fundamental insights into the nature of coexpressed genes. An implementation of this method is available at http://genetics.cs.ucla.edu/mvLMM.     

Asymmetric Karplus curves for the protein side-chain <Superscript>3</Superscript><Emphasis Type="Italic">J</Emphasis> couplings

The standard Karplus equation for calculating ³ J coupling constants from any given dihedral angle requires three empirical coefficients be determined that relate to the magnitudes of three modes of the angle dependency of ³ J. Considering cosine modes only (bimodal, unimodal and baseline component), Karplus curves are generally symmetric with respect to the sign of the angle argument. Typically, their primary and secondary maxima differ in amplitude, whereas the two minima are of equal depth. However, chiral molecular topologies, such as those surrounding the main-chain and side-chain torsions in amino-acid residues, preclude, as regards substituent positioning, exact mirror-image conformations from being formed—for any given torsion-angle value. It is therefore unlikely that ³ J couplings assume identical values for the corresponding positive and negative dihedral angles. This suggests that a better empirical fit of the torsion-angle dependency of ³ J could be obtained when removing the constraint of symmetrically identical coupling constants. A sine term added to the Karplus equation allows independent modelling of both curve minima typically located near dihedral-angle values of +90° and −90°. Revisiting an extensive ³ J coupling dataset previously recorded to determine the side-chain torsions χ₁ in the protein flavodoxin, the asymmetric Karplus model accomplishes a more accurate fit to the experimental data. Asymmetries revealed in the angle dependencies exceed the experimental precision in determining ³ J. Accounting for these effects helps improve molecular models. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Conformational preferences in diglycosyl disulfides: NMR and molecular modeling studies

The conformations of several β1→β1′ diglycosyl disulfides were investigated by NMR and computational methods. Experimental data, such as NOEs, proton–proton and proton–carbon-13 coupling constants, measured for solutions in DMSO, are in good agreement with values obtained by MD simulations in explicit DMSO. The disulfide torsion angles (C1–S–S–C1′) preferentially sample values close to either +90° or −90° (+g or −g) and appear as the main metric that determines the conformational behavior of these glycomimetics. There is more conformational freedom around the C1–S and C1′–S′ bonds (Φ and Ω torsions, respectively) and population cluster analysis allowed to identify up to four allowed conformational regions for each of the +g or −g forms. Population analysis of the hydroxylic group rotamers, based on proton–proton and proton–carbon-13 couplings as well as on calculated hydrogen bonding statistics, did not reveal any significant intramolecular hydrogen bonds in DMSO solution.     

Prospects for resonance assignments in multidimensional solid-state NMR spectra of uniformly labeled proteins

Summary The feasibility of assigning the backbone ¹⁵N and ¹³C NMR chemical shifts in multidimensional magic angle spinning NMR spectra of uniformly isotopically labeled proteins and peptides in unoriented solid samples is assessed by means of numerical simulations. The goal of these simulations is to examine how the upper limit on the size of a peptide for which unique assignments can be made depends on the spectral resolution, i.e., the NMR line widths. Sets of simulated three-dimensional chemical shift correlation spectra for artificial peptides of varying length are constructed from published liquid-state NMR chemical shift data for ubiquitin, a well-characterized soluble protein. Resonance assignments consistent with these spectra to within the assumed spectral resolution are found by a numerical search algorithm. The dependence of the number of consistent assignments on the assumed spectral resolution and on the length of the peptide is reported. If only three-dimensional chemical shift correlation data for backbone ¹⁵N and ¹³C nuclei are used, and no residue-specific chemical shift information, information from amino acid side-chain signals, and proton chemical shift information are available, a spectral resolution of 1 ppm or less is generally required for a unique assignment of backbone chemical shifts for a peptide of 30 amino acid residues.     

An evaluation of least-squares fits to COSY spectra as a means of estimating proton—proton coupling constants. I. Simulated test problems

Summary A computational method is described that takes an initial estimate of the chemical shifts, line widths and scalar coupling constants for the protons in a molecule, and refines this estimate so as to improve the least-squares fit between an experimental COSY spectrum and the spectrum simulated from these parameters in the weak-coupling approximation. In order to evaluate the potential of such refinements for estimating these parameters from COSY experiments, the method has been applied to a large number of sample problems which were themselves simulated from standard conformations of the amino acids, along with 25 near-native conformations of the protein bovine pancreatic trypsin inhibitor. The results of this evaluation show that: (i) if the chemical shifts are known to within ca. 0.01 ppm and no noise or artifacts are present in the data, the method is capable of recovering the correct coupling constants, starting from essentially arbitrary values, to within 0.1 Hz in almost all cases. (ii) Although the precision of these estimates of the coupling constants is degraded by the limited resolution, noise and artifacts present in most experimental spectra, the large majority of coupling constants can still be recovered to within 1.0 Hz; the local minimum problem is not made significantly worse by such defects in the data. (iii) The method assigns an effective line width to all the resonances, and in the process can resolve overlapping cross peaks. (iv) The method is not capable of determining the chemical shifts a priori, due to the presence of numerous local minima in the least-squares residual as a function of these parameters.