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PubMed2002

An efficient branch-and-bound algorithm for the assignment of protein backbone NMR peaks.

NMR resonance assignment is one of the key steps in solving an NMR protein structure. The assignment process links resonance peaks to individual residues of the target protein sequence, providing the prerequisite for establishing intra- and inter-residue spatial relationships between atoms. The assignment process is tedious and time-consuming, which could take many weeks. Though there exist a number of computer programs to assist the assignment process, many NMR labs are still doing the assignments manually to ensure quality. This paper presents a new computational method based on our recent work towards automating the assignment process, particularly the process of backbone resonance peak assignment. We formulate the assignment problem as a constrained weighted bipartite matching problem. While the problem, in the most general situation, is NP-hard, we present an efficient solution based on a branch-and-bound algorithm with effective bounding techniques and a greedy filtering algorithm for reducing the search space. Our experimental results on 70 instances of (pseudo) real NMR data derived from 14 proteins demonstrate that the new solution runs much faster than a recently introduced (exhaustive) two-layer algorithm and recovers more correct peak assignments than the two-layer algorithm.

Algorithms↗

PubMed2005

Isolation of a cotton reversibly glycosylated polypeptide (GhRGP1) promoter and its expression activity in transgenic tobacco.

Reversibly glycosylated polypeptides (RGPs) are thought to be involved in polysaccharide metabolism. A cDNA of the cotton (Gossypium hirsutum) RGP gene, designated GhRGP1, has previously been characterized, and is preferentially expressed in fiber cells. In order to investigate its temporal and spatial control, we isolated a 624bp fragment upstream of the GhRGP1 coding sequence using a polymerase chain reaction (PCR)-based genomic walking method, transcriptionally fused the 624bp promoter sequence to the beta-glucuronidase (GUS) gene, and analyzed the stable gene expression in tobacco (Nicotiana tabacum). In 4-week-old transgenic tobacco plants, the highest expression level was observed in roots, and the GUS activity was 1.13- and 6.65-fold higher than that in stems and leaves, respectively. In the reproductive growth stage, the GUS expression level was highest in the pistils and the GUS activity in the stigmas and styles were 17.6-fold higher than that in the ovaries. High GUS activity was also detected in the anthers. In addition, histochemical staining for GUS activity on transgenic tobacco plants further indicated a higher expression in the trichomes, seeds and vascular tissues of stems. Abiotic stress treatments on transgenic tobacco plants showed that wounding and dehydration induced GUS expression. These results demonstrated the spatial and temporal regulation of a cotton RGP promoter in a model plant, and provided an important insight into the factors that control the fiber development and stress responses of the gene.

Base Sequence↗

PubMed2003

Virtual 3D IVUS vessel model for intravascular brachytherapy planning. I. 3D segmentation, reconstruction, and visualization of coronary artery architecture and orientation.

Intravascular brachytherapy (IVB) can significantly reduce the risk of restenosis after interventional treatment of stenotic arteries, if planned and applied correctly. To facilitate computer-based IVB planning, a three-dimensional vessel model has been derived from information on coronary artery segments acquired by intravascular ultrasound (IVUS) and biplane angiography. Part I describes the approach of model construction and presents possibilities of visualization. The vessel model is represented by a voxel volume. Polygonal information about the vessel wall structure is derived by segmentation from a sequence of IVUS images automatically acquired ECG gated during pull back of the IVUS transducer. To detect horizontal, vertical, and radial contours, modified Canny-Edge and Shen-Castan filters are applied on Cartesian and polar coordinate representations of the IVUS tomograms as edge detectors. The spatial course of the vessel wall layers is traced in reconstructed longitudinal IVUS scans. By resampling the sequence of IVUS frames the voxel volume is obtained. For this purpose the frames are properly located in space and augmented with additional intermediate frames generated by interpolation. Their spatial location and orientation is derived from biplane X-ray angiography which is performed simultaneously. For resampling, two approaches are proposed: insertion of the vertices of the rectangular goal grid into the cells of a deformed hexahedral mesh derived from the IVUS sequence, and insertion of the vertices of the hexahedral mesh into the cells of the rectangular grid. Finally, the vessel model is visualized by methods of combined volume and polygon rendering. The segmentation process is verified as being in good agreement with results obtained by manual contour tracing with a commercial system. Our approach of construction of the vessel model has been implemented into an interactive software system, 3D IVUS-View, serving as the basis of a future system for intracoronary brachytherapy treatment planning being currently under development (Part II).

Algorithms↗

PubMedDate not supplied

[Model of the spatial structure of peptide T].

The spatial structure model of peptide T (AIDS reproduction inhibitor, the amino acid sequence of which corresponds to the fragment into the binding site of the virus protein gp120 with T4 receptor) is proposed. Peptide structure modelling has been carried out by the previously developed method based on joint usage of the molecular mechanics algorithms and NMR spectroscopy data. To build the model, two-dimensional nuclear Overhauser effect spectroscopy data for RNase A homologous fragment 22-26 were taken from the literature. The result of the presented work was a set consisting of six types of low-energy structures with different spatial packing of the peptide main chain. All structural types have been shown to be characterized by the lack of strict determination of the side chain conformations of the amino acid residues that can be realized in a few states providing approximately equal (within the given type) stabilization of one main chain form. At the same time, despite the definite differences, all of the selected structures were characterized by the presence of two consecutive reverse polypeptide chain turns at the C-terminal pentapeptide fragment. This site is supposed to be responsible for the peptide binding with T4 receptor and the antiviral effect.

Algorithms↗

PubMed2004

Microbial communities and their interactions in biofilm systems: an overview.

Several important advances have been made in the study of biofilm microbial populations relating to their spatial structure (or architecture), their community structure, and their dependence on physicochemical parameters. With the knowledge that hydrodynamic forces influence biofilm architecture came the realization that metabolic processes may be enhanced if certain spatial structures can be forced. An example is the extent of plasmid-mediated horizontal gene transfer in biofilms. Recent in situ work in defined model systems has shown that the biofilm architecture plays a role for genetic transfer by bacterial conjugation in determining how far the donor cells can penetrate the biofilm. Open channels and pores allow for more efficient donor transport and hence more frequent cell collisions leading to rapid spread of the genes by horizontal gene transfer. Such insight into the physical environment of biofilms can be utilized for bioenhancement of catabolic processes by introduction of mobile genetic elements into an existing microbial community. If the donor organisms themselves persist, bioaugmentation can lead to successful establishment of newly introduced species and may be a more successful strategy than biostimulation (the addition of nutrients or specific carbon sources to stimulate the authochthonous population) as shown for an enrichment culture of nitrifying bacteria added to rotating disk biofilm reactors using fluorescent in situ hybridization (FISH) and microelectrode measurements of NH4+, NO2-, NO3-, and O2. However, few studies have been carried out on full-scale systems. Bioaugmentation and bioenhancement are most successful if a constant selective pressure can be maintained favoring the promulgation of the added enrichment culture. Overall, knowledge gain about microbial community interactions in biofilms continues to be driven by the availability of methods for the rapid analysis of microbial communities and their activities. Molecular tools can be grouped into those suitable for ex situ and in situ community analysis. Non-spatial community analysis, in the sense of assessing changes in microbial populations as a function of time or environmental conditions, relies on general fingerprinting methods, like DGGE and T-RFLP, performed on nucleic acids extracted from biofilm. These approaches have been most useful when combined with gene amplification, cloning and sequencing to assemble a phylogenetic inventory of microbial species. It is expected that the use of oligonucleotide microarrays will greatly facilitate the analysis of microbial communities and their activities in biofilms. Structure-activity relationships can be explored using incorporation of 13C-labeled substrates into microbial DNA and RNA to identify metabolically active community members. Finally, based on the DNA sequences in a biofilm, FISH probes can be designed to verify the abundance and spatial location of microbial community members. This in turn allows for in situ structure/function analysis when FISH is combined with microsensors, microautoradiography, and confocal laser scanning microscopy with advanced image analysis.

Bacteria↗

PubMed1993

[MRI techniques applied to the diagnosis of hepatic tumors].

We know that the contrast of MR images can be better than that of CT scans. In the spin echo mode, sequences with long TR and long TE provide great contrast, while, conversely, sequences with short TR and TE produce images with a greater anatomical fidelity. This dual performance, a notion that had never been expressed as explicitly in imaging, has led to distinguishing between the roles of MRI for detection and tissue characterization (diagnosis and nature). While the choice of an appropriate sequence for characterization has apparently been made immediately with a modulation of T2 weighting, the selection of a detection sequence is less easy. The number of parameters involved (signal-to-noise and contrast-to-noise ratios, spatial resolution, artifacts, imaging time) and the compromise arrangements needed to take them into account explain the lack of consensus as to the optimal sequence for detection. Instead of becoming simpler with time, the issue is increasingly complex, as now fast imaging has been developed in addition to conventional spin echo imaging, and may even supersede it.

Humans↗

PubMed2003

Automated protein NMR resonance assignments.

NMR resonance peak assignment is one of the key steps in solving an NMR protein structure. The assignment process links resonance peaks to individual residues of the target protein sequence, providing the prerequisite for establishing intra- and inter-residue spatial relationships between atoms. The assignment process is tedious and time-consuming, which could take many weeks. Though there exist a number of computer programs to assist the assignment process, many NMR labs are still doing the assignments manually to ensure quality. This paper presents (1) a new scoring system for mapping spin systems to residues, (2) an automated adjacency information extraction procedure from NMR spectra, and (3) a very fast assignment algorithm based on our previous proposed greedy filtering method and a maximum matching algorithm to automate the assignment process. The computational tests on 70 instances of (pseudo) experimental NMR data of 14 proteins demonstrate that the new score scheme has much better discerning power with the aid of adjacency information between spin systems simulated across various NMR spectra. Typically, with automated extraction of adjacency information, our method achieves nearly complete assignments for most of the proteins. The experiment shows very promising perspective that the fast automated assignment algorithm together with the new score scheme and automated adjacency extraction may be ready for practical use.

Algorithms↗

PubMed1973

Three-dimensional structure of the Fab' fragment of a human immunoglobulin at 2,8-A resolution.

The structure of the Fab' fragment of a human myeloma immunoglobulin was determined by x-ray crystallographic analysis at 2.8-A resolution. The Fourier map of the electron density was correlated with the aminoacid sequence to obtain a three-dimensional model. Four globular subunits, which correspond to the homology regions of the light and heavy chains, are arranged in a tetrahedral configuration. These subunits closely resemble each other, sharing a basic pattern of polypeptide chain folding. In each subunit, long sequences of tightly packed, hydrogen bonded polypeptide chain run parallel to the major axis of the subunit. No helical conformation can be seen. Different patterns of interchain disulfide linkage and unusual intrachain disulfide bonds that have been observed in other immunoglobulins can be explained with this model. The regions of hypervariable sequences in the light and heavy chains occur at one end of the molecule, in close spatial proximity.

Amino Acid Sequence↗

PubMed2004

Photochemical ligation of DNA conjugates through anthracene cyclodimer formation and its fidelity to the template sequences.

Anthracene readily forms photoadducts, anthracene dimers, and this photodimerization reaction has been well characterized. In general, however, the reaction requires close proximity and certain spatial alignment of both reaction partners. DNA could provide an ideal scaffold for accelerating the photocyclic addition. We synthesized a number of anthracene-DNA conjugates. The sequences of the conjugates, 5'AntODNn and 3'AntODNn (the length of methylene linkers: n = 3 or 6), were designed to bind adjacent sequences of the template with the anthracene units directed such that they stacked with each other. The conjugates were only dimerized in the presence of the template by light irradiation. The efficiency was affected by one-base displacement in the template sequence.

Anthracenes↗

PubMed2001

A predictive model for regulatory sequences directing liver-specific transcription.

The identification and interpretation of the regulatory signals within the human genome remain among the greatest goals and most difficult challenges in genome analysis. The ability to predict the temporal and spatial control of transcription is likely to require a combination of methods to address the contribution of sequence-specific signals, protein-protein interactions and chromatin structure. We present here a new procedure to identify clusters of transcription factor binding sites characteristic of sequence modules experimentally verified to direct transcription selectively to liver cells. This algorithm is sufficiently specific to identify known regulatory sequences in genes selectively expressed in liver, promising acceleration of experimental promoter analysis. In combination with phylogenetic footprinting, this improvement in the specificity of predictions is sufficient to motivate a scan of the human genome. Potential regulatory modules were identified in orthologous human and rodent genomic sequences containing both known and uncharacterized genes.

Animals↗

PubMed2001

The sheep genome contributes to localization of control elements in a human gene with complex regulatory mechanisms.

Genes that show complex tissue-specific and temporal control by regulatory elements located outside their promoters present a considerable challenge to identify the sequences involved. The rapid accumulation of genomic sequence information for a number of species has enabled a comparative phylogenetic approach to find important regulatory elements. For some genes, which show a similar pattern of expression in humans and rodents, genomic sequence information for these two species may be sufficient. Others, such as the cystic fibrosis transmembrane conductance regulator (CFTR) gene, show significant divergence in expression patterns between mouse and human, necessitating phylogenetic approaches involving additional species. The ovine CFTR gene has a temporal and spatial expression pattern that is very similar to that of human CFTR. Comparative genomic sequence analysis of ovine and human CFTR identified high levels of homology between the core elements in several potential regulatory elements defined as DNase I hypersensitive sites in human CFTR. These data provide a case for the power of an artiodactyl genome to contribute to the understanding of human genetic disease.

Animals↗

PubMed1992

Classification of pathologies by reduced sequential potential maps.

Body surface potential mapping (BSPM) is an electrocardiographic measuring technique which produces the data as a series of three-dimensional maps. These maps are assumed to contain information which may help classify subjects for diagnostic purposes more effectively than standard ECGs. As quantitative classification of the complete sequences of maps is complex and cumbersome, the present study uses extracted features which characterise the data. The features, which have been presented and evaluated in a recent work, have been extracted after the maps were processed by a compression technique which conserved the spatial details of the maps. The compression by two-level thresholding converted the sequences of maps into sequences of annuli, from which the following features were extracted: time indices, velocity vector magnitude, loci in three-dimensional space of the centres of mass and cross-correlation coefficients between successive annuli in the sequence. Here, three different classification methods are applied to these features: statistical methods, the Fisher linear discriminant method and visual inspection. BSPMs from 54 subjects are used: 25 normal, 11 WPW syndrome and 18 CAD cases. It is found that by applying a decision role which comprises all features, the procedure offers a completely accurate classification of the subjects to their groups. The three-dimensional centre of mass is found to be the single best classifier; successfully categorising 20/25 of the normals 17/18 of the CAD patients and 11/11 of the WPW patients.

Action Potentials↗

PubMed1996

[How good is spatial orientation with rigid endoscopic optics? Study of micromanipulation in the nasal cavity].

Rigid endoscopes are used as an alternative to the operating microscope for visual control during paranasal sinus surgery. Since the view through the endoscope is monocular, perception of depth (stereopsis) through the operating microscope must be expected to be superior due to the binocular view afforded. To investigate whether monocular visualization through an endoscope is a disadvantage in paranasal sinus surgery, we compared stereoacuity in a model of the nasal cavity, using a head lamp, an operating microscope and a 0 degree Hopkin's endoscope. Twenty volunteers had to touch defined points in a spatial model of the nasal cavity. Under binocular vision with a head lamp, performance was significantly better than with the microscope or the endoscope. Manipulations were performed with the same speed under microscopic and endoscopic control, although under microscopic guidance more faults in point sequence were made than with the endoscope. Various monocular phenomena seem to allow sufficient spatial orientation through the endoscope, so that monocular visualization does not appear to be a disadvantage for quick and safe manipulations during functional endoscopic sinus surgery.

Depth Perception↗

PubMed2002

Point of attachment and sequence of immobilized peptide-acridine conjugates control affinity for nucleic acids.

Screening of combinatorial libraries by spatial arraying strategies requires library members to be solid-phase immobilized. However, for nucleic acid ligands that bind via intercalation, immobilization may inhibit binding if the tethering functionality is present at the edge of the heterocyle that approaches the duplex during the binding reaction. We report here a method for immobilizing peptide-acridine conjugates (PACs) via either their C- or their N-terminus, corresponding to functionalization at either the 4- or the 9-position of acridine, respectively, and for assaying the nucleic acid binding properties of the resulting resins. We find that both the amino acid sequence of the PAC as well as its point of attachment to the solid support are important in determining affinity for duplex nucleic acids. These results have implications for the design of future on-bead and microarray-based selections and in understanding the nucleic acid binding of functionalized intercalators.

Amino Acids↗

PubMed2003

Computational assignment of protein backbone NMR peaks by efficient bounding and filtering.

NMR resonance assignment is one of the key steps in solving an NMR protein structure. The assignment process links resonance peaks to individual residues of the target protein sequence, providing the prerequisite for establishing intra- and inter-residue spatial relationships between atoms. The assignment process is tedious and time-consuming, which could take many weeks. Though there exist a number of computer programs to assist the assignment process, many NMR labs are still doing the assignments manually to ensure quality. This paper presents a new computational method based on the combination of a suite of algorithms for automating the assignment process, particularly the process of backbone resonance peak assignment. We formulate the assignment problem as a constrained weighted bipartite matching problem. While the problem, in the most general situation, is NP-hard, we present an efficient solution based on a branch-and-bound algorithm with effective bounding techniques using two recently introduced approximation algorithms. We also devise a greedy filtering algorithm for reducing the search space. Our experimental results on 70 instances of (pseudo) real NMR data derived from 14 proteins demonstrate that the new solution runs much faster than a recently introduced (exhaustive) two-layer algorithm and recovers more correct peak assignments than the two-layer algorithm. Our result demonstrates that integrating different algorithms can achieve a good tradeoff between backbone assignment accuracy and computation time.

Algorithms↗

PubMed2006

Analysis of posttranslational modifications of proteins by tandem mass spectrometry.

Protein activity and turnover is tightly and dynamically regulated in living cells. Whereas the three-dimensional protein structure is predominantly determined by the amino acid sequence, posttranslational modification (PTM) of proteins modulates their molecular function and the spatial-temporal distribution in cells and tissues. Most PTMs can be detected by protein and peptide analysis by mass spectrometry (MS), either as a mass increment or a mass deficit relative to the nascent unmodified protein. Tandem mass spectrometry (MS/MS) provides a series of analytical features that are highly useful for the characterization of modified proteins via amino acid sequencing and specific detection of posttranslationally modified amino acid residues. Large-scale, quantitative analysis of proteins by MS/MS is beginning to reveal novel patterns and functions of PTMs in cellular signaling networks and biomolecular structures.

Mass Spectrometry↗

PubMedDate not supplied

[Evolutionary conservatism of the molecular structure of gamma-crystallins of vertebrates].

Homology of 18 amino acid sequences of lens gamma-crystallins of several vertebrates: frog, mouse, rat, calf and human being--has been considered. Pair sequence homology varies in the range from 57 to 100%, the mean value is equal to 74%. The spatial structures have been determined only for two calf gamma-crystallins. The protein molecule consists of four-fold repeated "motifs" (patterns) which are joint in two domains. After comparison of 18 gamma-crystallin sequences it was found that "motifs" domains and whole protein molecules have about 10, 30 and 58% conservative residues, respectively, that seem to be related to the evolution of these structural units. Structure analysis shows that almost all the conservative residues have an important structural meaning and play a basic role in the domain and molecular structure organization. This result allows us to make a conclusion about the homology of spatial structures of all considered gamma-crystallins of vertebrates.

Amino Acid Sequence↗

PubMed1990

Rokitansky sequence in association with the facio-auriculo-vertebral sequence: part of a mesodermal malformation spectrum?

We report on a 4-year-old first-born monozygotic twin girl with a hypoplastic left face, mandible and zygoma, left microtia without an external auditory canal, a U-shaped cleft palate, right ectopic-fused kidneys, a blindly ending vaginal pouch, and absent uterus. We review 3 other cases with the manifestations of the Rokitansky and the facio-auriculo-vertebral sequence. The anomalies in these disorders can be thought of as deriving from an early defect or disruption in fetal mesoderm or its progenitor tissue at the time of primitive streak formation. They are frequently associated with other mesodermally derived defects or sequences and may together represent an extended polytopic field defect. While such speculation on how these spatially separated anomalies develop is probably simplistic, the concept of a mesodermal "malformation" spectrum is helpful in reminding the clinician to look for other mesodermal defects when one mesodermally derived defect or sequence is detected.

Abnormalities, Multiple↗