A method for the determination of the three-dimensional structure of fluorescent proteins based on homology modeling and mass spectrometry

In the current work a method for the elucidation of the spatial structure of fluorescent GFP-like proteins is presented. The method is based on combining the results of homology modeling of the overall spatial protein structure and the chromophore structure determined experimentally by mass spectrometry. The approach developed can be used for the determination of the spatial structure of GFP homologues which are difficult to crystallize.     

Identification of RNA-recognizing modules on the surface of ribosomal proteins

Properties of specific interaction between ribosomal proteins and ribosomal RNAs were analyzed and a method for determination of "recognizing modules" on the protein surface was proposed. The method is based on the search of protein atoms making conserved H-bonds with RNA and forming an invariant spatial structure in homologous rRNA-protein complexes and in the isolated protein. A potential of the method is demonstrated on the determination of the recognizing modules on the surfaces of ribosomal proteins S8, S15 and L5.     

Structure elucidation of glycoprotein glycans and of polysaccharides by NMR spectroscopy

The applicability of 1H-NMR spectroscopy for the determination of the primary and tertiary structure of carbohydrate-containing molecules is demonstrated. For classes of known compounds the characterization can be based on chemical shifts observed in 1D NMR spectra with or without the aid of a computer database. For more complex structure determinations 2D NMR techniques are required. Here the application of 2D NMR is demonstrated for the primary structure determination of two bacterial exopolysaccharides, for the spatial structure determination of a disaccharide and a glycoprotein hormone.     

NMR spectroscopy for studying structure and intramolecular dynamics of modified analogs of steroid hormones

Special features of the use of homo- and heteronuclear correlation methods of NMR in one and two dimensions for studying the spatial structure and intramolecular dynamics of modified analogues of steroid hormones (MASH) are considered. The application of these methods to the assignment of resonances in the high-field 1H NMR region and to the determination of the most stereospecifically important parameters, such as the vicinal constants of spin-spin coupling (3JH-H) and nuclear Overhauser effects (NOE), are discussed using the example of NMR studies of some estrogens and androgens at 300 MHz and on the basis of literature data. The most efficient combination of the methods and the necessary modification of each of them may be chosen considering the spectral and relaxation parameters of MASH in liquid medium, including the anisotropy of the overall diffusive motion. The characteristics of MASH are the wide use of correlations through long-range couplings (COSY-45 and DQF-COSY), the application of the 4,5JH-H constants for the determination of spatial structure, and the advantage of heteronuclear HSQC methods with and without 13C decoupling over the corresponding HMQC methods in both resolution and sensitivity. In the conformationally rigid MASH molecules, the anisotropy of the MASH diffusive motion in liquid adversely affects the determination of interproton distances by the calibrating processing method for the NOE difference and NOESY spectra: it results in both overestimated and underestimated distance values depending on the polar angle ratios of the reference and the determined distances. Under certain conditions, conformationally mobile MASH demonstrate the additional contribution of the scalar relaxation mechanism between the indirectly (scalarly) bound protons. This mechanism is responsible for the underestimated values of NOE and the corresponding errors in the distance determination.     

Biomolecular structure prediction at a low resolution using a neural network and the double-iterated kalman filter technique

We report the application of an integrated computational approach for biomolecular structure determination at a low resolution. In particular, a neural network is trained to predict the spatial proximity of C-alpha atoms that are less than a given threshold apart, whereas a Kalman filter algorithm is employed to outline the biomolecular fold, with a constraints set that includes these pairwise atomic distances, and the distances and angles that define the structure as it is known from the protein's sequence. The results for Crambin demonstrate that this integrated approach is useful for molecular structure prediction at a low resolution and may also complement existing experimental distance data for a protein structure determination. © 1996 John Wiley & Sons, Inc.     

Sequential resonance assignments as a basis for determination of spatial protein structures by high resolution proton nuclear magnetic resonance

A general scheme is proposed for the determination of spatial protein structures by proton nuclear magnetic resonance. The scheme relies on experimental observation by two-dimensional nuclear magnetic resonance techniques of complete throughbond and through-space proton-proton connectivity maps. These are used to obtain sequential resonance assignments for the individual residues in the amino acid sequence and to characterize the spatial polypeptide structure by a tight network of semi-quantitative, intramolecular distance constraints.     

Protein structure validation by generalized linear model root-mean-square deviation prediction

Large-scale initiatives for obtaining spatial protein structures by experimental or computational means have accentuated the need for the critical assessment of protein structure determination and prediction methods. These include blind test projects such as the critical assessment of protein structure prediction (CASP) and the critical assessment of protein structure determination by nuclear magnetic resonance (CASD-NMR). An important aim is to establish structure validation criteria that can reliably assess the accuracy of a new protein structure. Various quality measures derived from the coordinates have been proposed. A universal structural quality assessment method should combine multiple individual scores in a meaningful way, which is challenging because of their different measurement units. Here, we present a method based on a generalized linear model (GLM) that combines diverse protein structure quality scores into a single quantity with intuitive meaning, namely the predicted coordinate root-mean-square deviation (RMSD) value between the present structure and the (unavailable) "true" structure (GLM-RMSD). For two sets of structural models from the CASD-NMR and CASP projects, this GLM-RMSD value was compared with the actual accuracy given by the RMSD value to the corresponding, experimentally determined reference structure from the Protein Data Bank (PDB). The correlation coefficients between actual (model vs. reference from PDB) and predicted (model vs. "true") heavy-atom RMSDs were 0.69 and 0.76, for the two datasets from CASD-NMR and CASP, respectively, which is considerably higher than those for the individual scores (-0.24 to 0.68). The GLM-RMSD can thus predict the accuracy of protein structures more reliably than individual coordinate-based quality scores.     

洞庭湖森林生态系统空间结构均质性评价

以东、南、西洞庭湖区域君山岛、龙山、赤山岛龙虎山林场、明朗山、常德林场、和洑林场和桃源县天然次生林为对象,借鉴生态学有关生态系统内部均衡和均质原理,在森林生态系统(斑块)尺度,从空间结构的混交、竞争、空间分布格局3个方面分析提出空间优化的均质性目标、均质性指数及均质性评价方法和评价标准.结果表明:15个洞庭湖湿地调查林分平均均质性评价指数为0.2517.均质性评价的5个等级中处于l级和2级的林分为12个,占80％,处于3级的林分只有3个,仅占20％.说明洞庭湖各林分整体上在空间结构、生长环境和树种优势度等方面不具有明显优势,离理想空间结构差距太大;按照高程不同,洞庭湖湿地从湖沼到丘陵岗地,林分空间结构均质性特征逐渐增强.森林生态系统空间优化均质性目标及均质性指数的提出是森林可持续经营空间途径的拓展,为森林经营的理想空间结构及其表达探索一条新途径.     

空间分布型的形成过程研究

具合影个研究了广义空间分布型和复合空间分布型的形成问题,解释了空间分布型的形成机理,并给出了１１种广义空间分布型和９种复事空间分布型;同时提出了空间分布型的３种判定方法：扩散系数法、空间相关法和参数变动法,它们以可用于区分常见的空间分布型,也可以用于判定分布型的形成过程;为研究空间分布型的形成机理和变化规模提供了有力的手段。以马尾松毛虫的空间分布型的研究结果表明,马尾松毛虫幼虫的空间分布型是复合负     

Spatial Variation in the Bacterial and Denitrifying Bacterial Community in a Biofilter Treating Subsurface Agricultural Drainage

Denitrifying biofilters can remove agricultural nitrates from subsurface drainage, reducing nitrate pollution that contributes to coastal hypoxic zones. The performance and reliability of natural and engineered systems dependent upon microbially mediated processes, such as the denitrifying biofilters, can be affected by the spatial structure of their microbial communities. Furthermore, our understanding of the relationship between microbial community composition and function is influenced by the spatial distribution of samples. In this study we characterized the spatial structure of bacterial communities in a denitrifying biofilter in central Illinois. Bacterial communities were assessed using automated ribosomal intergenic spacer analysis for bacteria and terminal restriction fragment length polymorphism of nosZ for denitrifying bacteria. Non-metric multidimensional scaling and analysis of similarity (ANOSIM) analyses indicated that bacteria showed statistically significant spatial structure by depth and transect, while denitrifying bacteria did not exhibit significant spatial structure. For determination of spatial patterns, we developed a package of automated functions for the R statistical environment that allows directional analysis of microbial community composition data using either ANOSIM or Mantel statistics. Applying this package to the biofilter data, the flow path correlation range for the bacterial community was 6.4 m at the shallower, periodically inundated depth and 10.7 m at the deeper, continually submerged depth. These spatial structures suggest a strong influence of hydrology on the microbial community composition in these denitrifying biofilters. Understanding such spatial structure can also guide optimal sample collection strategies for microbial community analyses.     

Advantages of CCD detectors for de novo three-dimensional structure determination in single-particle electron microscopy

For three-dimensional (3D) structure determination of large macromolecular complexes, single-particle electron cryomicroscopy is considered the method of choice. Within this field, structure determination de novo, as opposed to refinement of known structures, still presents a major challenge, especially for macromolecules without point-group symmetry. This is primarily because of technical issues: one of these is poor image contrast, and another is the often low particle concentration and sample heterogeneity imposed by the practical limits of biochemical purification. In this work, we tested a state-of-the art 4 k x 4 k charge-coupled device (CCD) detector (TVIPS TemCam-F415) to see whether or not it can contribute to improving the image features that are especially important for structure determination de novo. The present study is therefore focused on a comparison of film and CCD detector in the acquisition of images in the low-to-medium ( approximately 10-25 A) resolution range using a 200 kV electron microscope equipped with field emission gun. For comparison, biological specimens and radiation-insensitive carbon layers were imaged under various conditions to test the image phase transmission, spatial signal-to-noise ratio, visual image quality and power-spectral signal decay for the complete image-processing chain. At all settings of the camera, the phase transmission and spectral signal-to-noise ratio were significantly better on CCD than on film in the low-to-medium resolution range. Thus, the number of particle images needed for initial structure determination is reduced and the overall quality of the initial computed 3D models is improved. However, at high resolution, film is still significantly better than the CCD camera: without binning of the CCD camera and at a magnification of 70 kx, film is better beyond 21 A resolution. With 4-fold binning of the CCD camera and at very high magnification (> 300 kx) film is still superior beyond 7 A resolution.     

Mosaic structure of native ant supercolonies

According to the inclusive fitness theory, some degree of positive relatedness is required for the evolution and maintenance of altruism. However, ant colonies are sometimes large interconnected networks of nests, which are genetically homogenous entities, causing a putative problem for the theory. We studied spatial structure and genetic relatedness in two supercolonies of the ant Formica exsecta, using nuclear and mitochondrial markers. We show that there may be multiple pathways to supercolonial social organization leading to different spatial genetic structures. One supercolony formed a genetically homogenous population dominated by a single mtDNA haplotype, as expected if founded by a small number of colonizers, followed by nest propagation by budding and domination of the habitat patch. The other supercolony had several haplotypes, and the spatial genetic structure was a mosaic of nuclear and mitochondrial clusters. Genetic diversity probably originated from long‐range dispersal, and the mosaic population structure is likely a result of stochastic short‐range dispersal of individuals. Such a mosaic spatial structure is apparently discordant with the current knowledge about the integrity of ant colonies. Relatedness was low in both populations when estimated among nestmates, but increased significantly when estimated among individuals sharing the same genetic cluster or haplogroup. The latter association indicates the important historical role of queen dispersal in the determination of the spatial genetic structure.     

The antigen activity and structure of analogues and fragments of angiotensin, which contain enantiomeric forms of amino acids and aza-alpha'-homoamino acids]

The antigen activity of angiotensin, its fragments and analogues, which contain enantiomeric forms of amino acids and aza-alpha'-homoamino acids is studied by cross reactions with specific antibodies, obtained for angiotensin and its central tetrapeptide. It is found that the inclusion of additional NH-group between alpha carbon and carboxyl group of peptide chain, although in few cases radically changes spatial structure of compounds, does not deprivate their antigen activity. The replacement of NH-group to the C-end of the angiotensin molecule by affection the antigen determinant considerably decreases the antigen activity of the analogues. The important role in the determination of the antigen activity play the tyrosine residue and its specific orientation with respect to the antigen molecule. Low molecular weight fragments and analogues of the central part of angiotensin molecule, which have less "rigid" spatial structures, are capable to reorganize their spatial structure during interaction with antibodies.     

桃潜叶蛾在桃园的空间分布型和取样技术研究

应用聚集度指标法、Iwao回归分析和频次比较法．研究了桃树重要害虫桃潜叶蛾成虫的空间分布型。结果表明桃潜叶蛾成虫在桃园呈负二项分布,分析提出了该害虫适宜的调查抽样方法。     

Conformational ensemble of amyloid-forming semenogelin 1 peptide SEM1(68–107) by NMR spectroscopy and MD simulations

SEM1(68–107) is a peptide corresponding to the region of semenogelin 1 protein from 68 to 107 amino acid position. SEM1(68–107) is an abundant component of semen, which participates in HIV infection enhanced by amyloid fibrils forming. To understand the causes influencing amyloid fibril formation, it is necessary to determine the spatial structure of SEM1(68–107). It was shown that the determination of SEM1(68–107) structure is complicated by the non-informative NMR spectra due to the high intramolecular mobility of peptides. The complementary approach based on the geometric restrictions of individual peptide fragments and molecular modeling was used for the determination of the spatial structure of SEM1(68–107). The N- (SEM1(68–85)) and C-terminuses (SEM1(86–107)) of SEM1(68–107) were chosen as two individual peptide fragments. SEM1(68–85) and SEM1(86–107) structures were established with NMR and circular dichroism CD spectroscopies. These regions were used as geometric restraints for the SEM1(68–107) structure modeling. Even though most of the SEM1(68–107) peptide is unstructured, our detailed analysis revealed the following structured elements: N-terminus (70His-84Gln) forms an α-helix, (86Asp-94Thr) and (101Gly-103Ser) regions fold into 3₁₀-helixes. The absence of a SEM1(68–107) rigid conformation leads to instability of these secondary structure regions. The calculated SEM1(68–107) structure is in good agreement with experimental values of hydrodynamic radius and dihedral angles obtained by NMR spectroscopy. This testifies the adequacy of a combined approach based on the use of peptide fragment structures for the molecular modeling formation of full-size peptide spatial structure.     

Automated Protein NMR Structure Determination Using Wavelet De-noised NOESY Spectra

A major time-consuming step of protein NMR structure determination is the generation of reliable NOESY cross peak lists which usually requires a significant amount of manual interaction. Here we present a new algorithm for automated peak picking involving wavelet de-noised NOESY spectra in a process where the identification of peaks is coupled to automated structure determination. The core of this method is the generation of incremental peak lists by applying different wavelet de-noising procedures which yield peak lists of a different noise content. In combination with additional filters which probe the consistency of the peak lists, good convergence of the NOESY-based automated structure determination could be achieved. These algorithms were implemented in the context of the ARIA software for automated NOE assignment and structure determination and were validated for a polysulfide-sulfur transferase protein of known structure. The procedures presented here should be commonly applicable for efficient protein NMR structure determination and automated NMR peak picking. Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.     

A new eigenfunction spatial analysis describing population genetic structure

Several methods of spatial analyses have been proposed to infer the relative importance of evolutionary processes on genetic population structure. Here we show how a new eigenfunction spatial analysis can be used to model spatial patterns in genetic data. Considering a sample of n local populations, the method starts by modeling the response variable (allele frequencies or phenotypic variation) against the eigenvectors sequentially extracted from a geographic distance matrix (n × n). The relationship between the coefficient of determination (R ²) of the models and the cumulative eigenvalues, which we named the spatial signal-representation (SSR) curve, can be more efficient than Moran’s I correlograms in describing different patterns. The SSR curve was also applied to simulated data (under distinct scenarios of population differentiation) and to analyze spatial patterns in alleles from microsatellite data for 25 local populations of Dipteryx alata, a tree species endemic to the Brazilian Cerrado. The SSR curves are consistent with previous phylogeographical patterns of the species, revealing combined effects of isolation-by-distance and range expansion. Our analyses demonstrate that the SSR curve is a useful exploratory tool for describing spatial patterns of genetic variability and for selecting spatial eigenvectors for models aiming to explain spatial responses to environmental variables and landscape features.     

The spatial structure of the axially bound methionine in solution conformations of horse ferrocytochrome c and Pseudomonas aeruginosa ferrocytochrome c 551 by 1H NMR

A generally applicable method for the determination of the spatial structure of the heme iron-bound methionine in c-type ferrocytochromes at atomic resolution is presented. It relies primarily on measurements of nuclear Overhauser effects between the individual hydrogen atoms of the axial methionine, and between individual hydrogens of the methionine and the heme group. Four different methionine conformers, corresponding to the four possible stereospecific assignments for the methionine methylene proton resonances, are generated by a structural interpretation of the nuclear Overhauser effects with the use of an interactive computer graphics technique. A unique structure and unique stereospecific resonance assignments are then obtained by discriminating between these four conformers on the basis of van der Waals' constraints and heme ring current effects on the chemical shifts. The use of the method is illustrated with studies of horse ferrocytochrome c and Pseudomonas aeruginosa ferrocytochrome c 551. Comparison with the crystal structures shows close coincidence between the methionine conformations in solution and in single crystals of these proteins.Abbreviations NMR nuclear magnetic resonance - NOE nuclear Overhauser effect - TOE truncated driven nuclear Overhauser effect