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PubMed2002

Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory.

A theory of elastic normal modes is described for the exploration of global distortions of biological structures and their assemblies based upon low-resolution image data. Structural information at low resolution, e.g. from density maps measured by cryogenic electron microscopy (cryo-EM), is used to construct discrete multi-resolution models for the electron density using the techniques of vector quantization. The elastic normal modes computed based on these discretized low-resolution models are found to compare well with the normal modes obtained at atomic resolution. The quality of the normal modes describing global displacements of the molecular system is found to depend on the resolution of the synthetic EM data and the extent of reductionism in the discretized representation. However, models that reproduce the functional rearrangements of our test set of molecules are achieved for realistic values of experimental resolution. Thus large conformational changes as occur during the functioning of biological macromolecules and assemblies can be elucidated directly from low-resolution structural data through the application of elastic normal mode theory and vector quantization.

Adenylate Kinase↗
PubMed1976

Subunit symmetry of tetrameric phosphorylase a.

Native crystallographic data of tetrameric phosphorylase a crystals, space group P21, have been collected photographically to 3 A resolution. These data have been used in Patterson search methods in reciprocal and real space. The tetramers were found to exhibit molecular 222 symmetry. The cross vector between the centres of the two symmetry related tetramers in the unit cell was determined by two different translation function methods. On the basis of these rotation and translation function results a model for the arrangement of monomers within the tetramer and of tetramers in the unit cell is proposed; The 222 symmetry of the tetrameric molecule is found only when high resolution diffraction data are included (i.e. higher than 6 A). At lower resolution other symmetries dominate. Calculations with the proposed model have shown that these spurious symmetries result from the nonspecific overlap of protein-protein and solvent-solvent cross vectors. These results emphasize the importance of high resolution data when noncrystallographic symmetry of globular proteins is studied.

Chemical Phenomena↗
PubMed2025

A hierarchical, count-based model highlights challenges in scATAC-seq data analysis and points to opportunities to extract finer-resolution information.

BACKGROUND: Data from Single-cell Assay for Transposase Accessible Chromatin with Sequencing (scATAC-seq) is highly sparse. While current computational methods feature a range of transformation procedures to extract meaningful information, major challenges remain. RESULTS: Here, we discuss the major scATAC-seq data analysis challenges such as sequencing depth normalization and region-specific biases. We present a hierarchical count model that is motivated by the data generating process of scATAC-seq data. Our simulations show that current scATAC-seq data, while clearly containing physical single-cell resolution, are too sparse to infer true informational-level single-cell, single-region of chromatin accessibility states. CONCLUSIONS: While the broad utility of scATAC-seq at a cell type level is undeniable, describing it as fully resolving chromatin accessibility at single-cell resolution, particularly at individual locus level, may overstate the level of detail currently achievable. We conclude that chromatin accessibility profiling at true single-cell, single-region resolution is challenging with current data sensitivity, but that it may be achieved with promising developments in optimizing the efficiency of scATAC-seq assays.

Single-Cell Analysis↗
PubMed1992

Combining experimental information from crystal and solution studies: joint X-ray and NMR refinement.

Joint refinement of macromolecules against crystallographic and nuclear magnetic resonance (NMR) observations is presented as a way of combining experimental information from the two methods. The model of interleukin-1 beta derived by the joint x-ray and NMR refinement is shown to be consistent with the experimental observations of both methods and to have crystallographic R value and geometrical parameters that are of the same quality as or better than those of models obtained by conventional crystallographic studies. The few NMR observations that are violated by the model serve as an indicator for genuine differences between the crystal and solution structures. The joint x-ray-NMR refinement can resolve structural ambiguities encountered in studies of multidomain proteins, in which low- to medium-resolution diffraction data can be complemented by higher resolution NMR data obtained for the individual domains.

Amino Acid Sequence↗
PubMed2007

High-resolution fMRI investigation of the medial temporal lobe.

The medial temporal lobe (MTL) is critical for declarative memory formation. Several theories of MTL function propose functional distinctions between the different structures of the MTL, namely the hippocampus and the surrounding cortical areas. Furthermore, computational models and electrophysiological studies in animals suggest distinctions between the subregions of the hippocampus itself. Standard fMRI resolution is not sufficiently fine to resolve activity on the scale of hippocampal subregions. Several approaches to scanning the MTL at high resolutions have been made, however there are limitations to these approaches, namely difficulty in conducting group-level analyses. We demonstrate here techniques for scanning the MTL at high resolution and analyzing the high-resolution fMRI data at the group level. To address the issue of cross-participant alignment, we employ the ROI-LDDMM alignment technique, which is demonstrated to result in smaller alignment errors when compared with several other common normalization techniques. Finally, we demonstrate that the pattern of activation obtained in the high-resolution functional data is similar to that obtained at lower resolution, although the spatial extent is smaller and the percent signal change is greater. This difference in the pattern of activation may be due to less partial volume sampling in the high-resolution data, resulting in more accentuated regions of activation.

Adult↗
PubMed1985

Structure of alpha-chymotrypsin refined at 1.68 A resolution.

Diffraction data for alpha-chymotrypsin crystals at -10 degrees C were measured at 1.68 A resolution and refined by restrained structure-factor least-squares refinement. The two independent chymotrypsin molecules in the crystallographic asymmetric unit were refined independently. The overall structure of alpha-chymotrypsin is little changed from published co-ordinates. The root-mean-square shift of C alpha co-ordinates is 0.42 A, co-ordinates for the two molecules showing a root-mean-square difference of 0.19 A. Certain regions with high disorder (residues 9 to 14, 73 to 79) remain difficult to interpret and several side-chains are disordered. Some water molecule positions have been changed. The absence of the tosyl group has made a significant difference to the refined structure at the active site. This now agrees closely with other enzymes of the trypsin family that have been refined at high resolution. There is a strong hydrogen bond between N epsilon 2 (His57) and O gamma (Ser195) in the free enzyme, in line with the published description of the charge relay system.

Amino Acid Sequence↗
PubMed1994

On the application of direct methods to oligonucleotide crystallography.

The direct methods program SAYTAN was applied to simulated data at various resolutions from three oligonucleotides. Success in solving the structures was found to depend more upon the resolution of the data than upon errors in the data or the complexity of the structure. Collecting the data at a reduced temperature has little effect, unless it alters the mosaicity of the crystal or changes the resolution of the data. The presence of a heavy atom dramatically improved the phase refinement, particularly at low resolution.

Journal Article↗
PubMed1984

Analysis of emission tomographic scan data: limitations imposed by resolution and background.

The proper analysis of positron emission tomographic scan data requires a careful knowledge of the limitations of the tomographic system used so that scan data can be collected and sampled in a manner consistent with those limitations. The present investigation was undertaken to clarify some of the limitations imposed by resolution. The usual imaging situation, e.g., 218FDG , C15O2, or 15O2 , involves imaging structures of limited size in all three dimensions which may appear either warm or cool in relation to some background level of activity. In emission tomography the importance of adequate data sampling within a given plane has been frequently emphasized. Little attention, however, has been given to proper z axis sampling for clinical scanning. The actual selection of regions of interest from scans can have a significant impact on the subsequent statistical analysis. Previous work on this subject has experimentally examined the relationship of object size to quantitative estimation in the hot spot-cold background situation for the one- and two-dimensional cases. Approximate three-dimensional recovery coefficients for the hot spot-cold background situation have been calculated. An examination of the factors discussed above, three-dimensional objects with varying contrast, z axis sampling, and selection of regions of interest, has not yet been addressed in the literature. The purpose of the present investigation is to examine these factors.

Background Radiation↗
PubMedDate not supplied

Intensity-modulated parametric mapping for simultaneous display of rapid dynamic and high-spatial-resolution breast MR imaging data.

Contrast material-enhanced magnetic resonance (MR) imaging of the breast has variable specificity for differentiation of breast cancer from other enhancing conditions. Two principal strategies to improve its specificity are rapid dynamic MR imaging and high-spatial-resolution MR imaging. A method was developed of combining contemporaneously acquired dynamic and high-spatial-resolution MR imaging data into a single integrated display. Whole-breast rapid dynamic data were condensed into a color map by using pharmacokinetic analysis. The pharmacokinetic results were combined with the high-spatial-resolution images with a new technique that preserves underlying morphologic details. This new method was evaluated by five radiologists for eight breast lesions, and the results were compared with those of the standard method of overlaying parametric map data. The radiologists' ratings showed a statistically significant preference for the intensity-modulated parametric map display method over the overlaid parametric display method for 10 of the 12 evaluation criteria. The new method enabled simultaneous visualization of pharmacokinetic and morphologic information, facilitated assessment of lesion extent, and improved the suppression of noise in the pharmacokinetic data. The ability to simultaneously assess both dynamic and high-spatial-resolution features may ultimately improve the specificity of breast MR imaging.

Breast Neoplasms↗
PubMed2006

Multivariate curve resolution of time course microarray data.

BACKGROUND: Modeling of gene expression data from time course experiments often involves the use of linear models such as those obtained from principal component analysis (PCA), independent component analysis (ICA), or other methods. Such methods do not generally yield factors with a clear biological interpretation. Moreover, implicit assumptions about the measurement errors often limit the application of these methods to log-transformed data, destroying linear structure in the untransformed expression data. RESULTS: In this work, a method for the linear decomposition of gene expression data by multivariate curve resolution (MCR) is introduced. The MCR method is based on an alternating least-squares (ALS) algorithm implemented with a weighted least squares approach. The new method, MCR-WALS, extracts a small number of basis functions from untransformed microarray data using only non-negativity constraints. Measurement error information can be incorporated into the modeling process and missing data can be imputed. The utility of the method is demonstrated through its application to yeast cell cycle data. CONCLUSION: Profiles extracted by MCR-WALS exhibit a strong correlation with cell cycle-associated genes, but also suggest new insights into the regulation of those genes. The unique features of the MCR-WALS algorithm are its freedom from assumptions about the underlying linear model other than the non-negativity of gene expression, its ability to analyze non-log-transformed data, and its use of measurement error information to obtain a weighted model and accommodate missing measurements.

Algorithms↗
PubMed1996

Peptide aldehyde complexes with wheat serine carboxypeptidase II: implications for the catalytic mechanism and substrate specificity.

The structures of two ternary complexes of wheat serine carboxypeptidase II (CPD-WII), with a tetrapeptide aldehyde and a reaction product arginine, have been determined by X-ray crystallography at room temperature and -170 degrees. The peptide aldehydes, antipain and chymostatin, form covalent adducts with the active-site serine 146. The CPD-WII antipain arginine model has a standard crystallographic R-factor of 0.162, with good geometry at 2.5 A resolution for data collected at room temperature. The -170 degrees C model of the chymostatin arginine complex has an R-factor of 0.174, with good geometry using data to 2.1 A resolution. The structures suggest binding subsites N-terminal to the scissile bond. All four residues of chymostatin are well-localized in the putative S1 through S4 sites, while density is apparent only in S1 and S2 for antipain. In the S1 site, Val340 and 341, Phe215 and Leu216 form a hydrophobic binding surface, not a pocket, for the P1 phenylalanyl side-chain of chymostatin. The P1 arginyl of antipain also binds at this site, but the positive charge appears to be stabilized by additional solvent molecules. Thus, the hybrid nature of the S1 site accounts for the ability of CPD-WII to accept both hydrophobic and basic residues at P1. Hydrogen bonds to the peptide substrate backbone are few and are made primarily with side-chains on the enzyme. Thus, substrate recognition by CPD-WII appears to have nothing in common with that of the other families of serine proteinases. The hemiacetal linkages to the essential Ser146 are of a single stereoisomer with tetrahedral geometry, with an oxygen atom occupying the "oxyanion hole" region of the enzyme. This atom accepts three hydrogen bonds, two from the polypeptide backbone and one from the positively-charged amino group of bound arginine, and must be negatively charged. Thus, the combination of ligands forms an excellent approximation to the oxyanion intermediate formed during peptide hydrolysis. Surprisingly, the (R) stereochemistry at the hemiacetal linkage is opposite to that expected by comparison to previously determined structures of peptide aldehydes complexed with Streptomyces griseus proteinase A. This is shown to be a consequence of the approximate mirror symmetry of the arrangement of catalytic groups in the two families of serine proteases and suggests that the stereochemical course of the two enzymatic reactions differ in handedness.

Aldehydes↗
PubMed1987

Ultrasonic studies of proton-transfer reactions at the catalytic site of alpha-chymotrypsin.

Ultrasonic relaxation measurements for alpha-chymotrypsin in phosphate, sulfite and arsenate buffers exhibit a high peak of absorption at neutral pH. The analysis is based on: comparison of the relaxation measurements for the enzyme and for the zymogen and inhibited enzyme; X-ray and neutron diffraction data, and high-resolution NMR data. The ultrasonic relaxation is shown to result mainly from a proton-transfer reaction that involves the histidine at the catalytic site (His-57). The question is raised of whether the enhanced ultrasonic effect observed in the enzyme is indicative of a property that plays a part in the catalytic activity.

Binding Sites↗
PubMed1983

Structure of oxidized poplar plastocyanin at 1.6 A resolution.

The structure of poplar plastocyanin in the oxidized (CuII) state at pH 6.0 has been refined, using 1.6 A resolution counter data. The starting co-ordinates were obtained from the 2.7 A electron density map computed with phases derived by the multiple isomorphous replacement method. The model was refined successively by constrained real space, unrestrained reciprocal space, and restrained reciprocal space least-squares methods. The final residual R value is 0.17 for 8285 reflections (I greater than 2 sigma (I)). It is estimated that the root-mean-square standard deviation of the atomic positions is 0.1 A when averaged over all atoms, and 0.05 A for the Cu ligand atoms alone. The refined structure retains all the essential features of the 2.7 A model. The co-ordination geometry of the copper atom is confirmed as being distorted tetrahedral. The two Cu-N(His) bonds, 2.10 and 2.04 A, are within the range normally found in low molecular weight CuII complexes with Cu-N(imidazole) bonds. The Cu-S(Cys) bond, 2.13 A, is also normal, but the Cu-S(Met) bond, 2.90 A, is sufficiently long to raise important questions about its significance. The hydrogen-bonding and secondary structure can now be assigned confidently. Forty-four water molecules are included in the final model. Repetition of the refinement, using new data to 1.9 A resolution recorded from crystals at pH 4.2, has led to a residual R value of 0.16 for 6060 reflections (I greater than sigma (I)). There are few significant changes in the structure of poplar CuII-plastocyanin between pH 6.0 and pH 4.2. In particular, the geometry of the copper site is not affected. The observed changes in redox behaviour of plastocyanin at low pH are therefore unlikely to be connected with structural changes in the oxidized form of the protein. A number of features of the molecular structure appear to be directly related to the function of plastocyanin as an electron carrier in photosynthesis. Comparison between the known amino acid sequences of 67 plant plastocyanins reveals 52 conserved and 11 conservatively substituted residues in a total of 99. If three algal plastocyanin sequences are included in the comparison, there are still 26 conserved and 12 conservatively substituted residues. In many cases, the importance of these residues in determining the tertiary structure can be rationalized.

Amino Acid Sequence↗
PubMed2002

Multi-detector row and volume-rendered CT of the normal and accessory flow pathways of the thoracic systemic and pulmonary veins.

Multi-detector row computed tomography (CT) and volume rendering can be used as an interpretive aid to present the systemic and pulmonary venous anatomy of the thorax. Both of these venous systems are routinely imaged in clinical practice and are important in interpretation of diagnostic images in health and disease. Multi-detector row CT and three-dimensional volume rendering provide high-quality near-isotropic data (ie, the longitudinal resolution approximates the in-plane resolution). The data sets allow tailored postprocessing to produce images optimized for these vessels, which are often not fully appreciated at planar axial imaging alone. Venous structures of the thorax that can be demonstrated with multi-detector row CT and volume rendering include the jugular veins; the subclavian and brachiocephalic veins; the internal and lateral thoracic veins; the superior and inferior venae cavae; the coronary sinus, the cardiac and pericardiophrenic veins, and vein grafts; the azygos, hemiazygos, and accessory hemiazygos veins; the intercostal veins; the pulmonary veins; and other thoracic veins.

Azygos Vein↗
PubMed2003

Single-pollen analysis by laser-induced breakdown spectroscopy and Raman microscopy.

The application of laser-induced breakdown spectroscopy to the analysis of single biological microparticles (bioaerosols) is described, exemplified here for a range of pollens. Spectra were recorded by exposure of the pollen to a single laser pulse from a Nd:YAG laser (lambda = 1064 nm, Ep approximately 30 mJ). The intensities of the single-pulse laser-induced breakdown spectra fluctuated dramatically, but an internal signal calibration procedure was applied that referenced elemental line intensities to the carbon matrix of the sample (represented by molecular bands of CN and C2). This procedure allowed us to determine relative element concentration distributions for the different types of pollen. These pollens exhibited some distinct concentration variations, for both major and minor (trace) elements in the biomatrix, through which ultimately individual pollens might be identified and classified. The same pollen samples were also analyzed by Raman microscopy, which provided molecular compositional data (even with spatial resolution). These data allowed us to distinguish between biological and nonbiological specimens and to obtain additional classification information for the various pollen families, complementing the laser-induced breakdown spectroscopy measurement data.

Aerosols↗
PubMed2004

Phylogenetic relationships of Iberian Aphodiini (Coleoptera: Scarabaeidae) based on morphological and molecular data.

A phylogeny of Iberian Aphodiini dung beetles was reconstructed based on morphological and molecular data. The data set included a total of 84 variable characters from wing venation, mouthparts, genitalia, and external morphology, as well as mitochondrial partial cytochrome c oxidase I (COI), complete tRNA-Leu (UUR), and partial cytochrome c oxidase II (COII) gene nucleotide sequences (1210 positions). Phylogenetic trees based on molecular data were relatively more resolved than those based on morphological characters. The Bayesian analysis of combined molecular and morphological data provided resolution not achieved by each data set separately. Ammoecius and Aphodius are the first lineages that branch off from the tree, followed by Acrossus, Nimbus, and Heptaulacus. The remaining studied taxa are recovered in a more derived clade that lacks internal resolution. Reconstructed trees based on molecular data showed relatively short internal nodes that were weakly supported. Such pattern may reflect a rapid radiation at the origin of the tribe Aphodiini, but also saturation of mutational changes. Several tests were conducted to discern between both competing hypotheses, as well as to assess the effect of incomplete taxon sampling.

Animals↗
PubMed2002

The structures of Micrococcus lysodeikticus catalase, its ferryl intermediate (compound II) and NADPH complex.

The crystal structure of the bacterial catalase from Micrococcus lysodeikticus has been refined using the gene-derived sequence both at 0.88 A resolution using data recorded at 110 K and at 1.5 A resolution with room-temperature data. The atomic resolution structure has been refined with individual anisotropic atomic thermal parameters. This has revealed the geometry of the haem and surrounding protein, including many of the H atoms, with unprecedented accuracy and has characterized functionally important hydrogen-bond interactions in the active site. The positions of the H atoms are consistent with the enzymatic mechanism previously suggested for beef liver catalase. The structure reveals that a 25 A long channel leading to the haem is filled by partially occupied water molecules, suggesting an inherent facile access to the active site. In addition, the structures of the ferryl intermediate of the catalase, the so-called compound II, at 1.96 A resolution and the catalase complex with NADPH at 1.83 A resolution have been determined. Comparison of compound II and the resting state of the enzyme shows that the binding of the O atom to the iron (bond length 1.87 A) is associated with increased haem bending and is accompanied by a distal movement of the iron and the side chain of the proximal tyrosine. Finally, the structure of the NADPH complex shows that the cofactor is bound to the molecule in an equivalent position to that found in beef liver catalase, but that only the adenine part of NADPH is visible in the present structure.

Amino Acid Sequence↗
PubMed2000

[Analysis of multi-wavelength overlapping chromatographic data by orthogonal projection resolution].

Orthogonal projection resolution(OPR) has been proved to be a high performance chromatographic data processing technique. In this paper, it is applied to the resolution of multi-wavelength chromatographic overlapping peaks. When the highest number of degree of overlapping in chromatogram is less than or equal to the number of wavelengths used, a real resolved chromatogram can be completely obtained from multi-wavelength chromatographic overlapping peaks by this method. When based on dual wavelength chromatographic data analysis, a new method, namely dual wavelength characteristic information analysis (DWCI), used for the base line correction, determination of number of components and region of pure components signal. Analysis of overlapping cases of every components in the overlapping chromatogram is also proposed. DWCI has been successfully used for the analysis of overlapping chromatogram with dual peaks of three components and with single peak of two components. But based on single wavelength chromatographic data, the analysis of these overlapping peaks is a very difficult and complicated problem.

English Abstract↗