Structural alignment
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This paper presents the utilization of progressive alignment principle for positional adjustment of a set of genomic signals with different lengths. The new method of multiple alignment of signals based on dynamic time warping is tested for the purpose of evaluating the similarity of different length genes in phylogenetic studies. Two sets of phylogenetic markers were used to demonstrate the effectiveness of the evaluation of intraspecies and interspecies genetic variability. The part of the proposed method is modification of pairwise alignment of two signals by dynamic time warping with using correlation in a sliding window. The correlation based dynamic time warping allows more accurate alignment dependent on local homologies in sequences without the need of scoring matrix or evolutionary models, because mutual similarities of residues are included in the numerical code of signals.
- MeSH
- algoritmy MeSH
- bakteriální RNA genetika MeSH
- druhová specificita MeSH
- fylogeneze MeSH
- genom bakteriální * MeSH
- genomika metody MeSH
- počítačové zpracování signálu MeSH
- RNA ribozomální 18S genetika MeSH
- sekvenční seřazení metody MeSH
- výpočetní biologie metody MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
In this paper, we present a novel algorithm for measuring protein similarity based on their 3-D structure (protein tertiary structure). The algorithm used a suffix tree for discovering common parts of main chains of all proteins appearing in the current research collaboratory for structural bioinformatics protein data bank (PDB). By identifying these common parts, we build a vector model and use some classical information retrieval (IR) algorithms based on the vector model to measure the similarity between proteins--all to all protein similarity. For the calculation of protein similarity, we use term frequency × inverse document frequency ( tf × idf ) term weighing schema and cosine similarity measure. The goal of this paper is to introduce new protein similarity metric based on suffix trees and IR methods. Whole current PDB database was used to demonstrate very good time complexity of the algorithm as well as high precision. We have chosen the structural classification of proteins (SCOP) database for verification of the precision of our algorithm because it is maintained primarily by humans. The next success of this paper would be the ability to determine SCOP categories of proteins not included in the latest version of the SCOP database (v. 1.75) with nearly 100% precision.
- MeSH
- algoritmy MeSH
- data mining metody MeSH
- databáze proteinů MeSH
- lidé MeSH
- proteiny chemie MeSH
- reprodukovatelnost výsledků MeSH
- strukturní homologie proteinů MeSH
- terciární struktura proteinů MeSH
- umělá inteligence MeSH
- výpočetní biologie metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- MeSH
- acetabulum chirurgie patofyziologie MeSH
- chirurgie s pomocí počítače metody přístrojové vybavení trendy MeSH
- lidé MeSH
- miniinvazivní chirurgické výkony metody statistika a číselné údaje MeSH
- náhrada kyčelního kloubu metody statistika a číselné údaje MeSH
- výsledky a postupy - zhodnocení (zdravotní péče) metody statistika a číselné údaje MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- srovnávací studie MeSH
A wealth of evidence provides support for magnetic alignment (MA) behavior in a variety of disparate species within the animal kingdom, in which an animal, or a group of animals, show a tendency to align the body axis in a consistent orientation relative to the geomagnetic field lines. Interestingly, among vertebrates, MA typically coincides with the north-south magnetic axis, however, the mean directional preferences of an individual or group of organisms is often rotated clockwise from the north-south axis. We hypothesize that this shift is not a coincidence, and future studies of this subtle, yet consistent phenomenon may help to reveal some properties of the underlying sensory or processing mechanisms, that, to date, are not well understood. Furthermore, characterizing the fine structure exhibited in MA behaviors may provide key insights to the biophysical substrates mediating magnetoreception in vertebrates. Therefore, in order to determine if a consistent shift is exhibited in taxonomically diverse vertebrates, we performed a meta-analysis on published MA datasets from 23 vertebrate species that exhibited an axial north-south preference. This analysis revealed a significant clockwise shift from the north-south magnetic axis. We summarize and discuss possible competing hypotheses regarding the proximate mechanisms underlying the clockwise shifted MA and conclude that the most likely cause of such a shift would be a lateralization in central processing of magnetic information.
- MeSH
- druhová specificita MeSH
- funkční lateralita fyziologie MeSH
- magnetické jevy * MeSH
- obratlovci fyziologie MeSH
- orientace * MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
Tuberculosis, the second leading infectious disease killer after HIV, remains a top public health priority. The causative agent of tuberculosis, Mycobacterium tuberculosis (Mtb), which can cause both acute and clinically latent infections, reprograms metabolism in response to the host niche. Phosphoenolpyruvate carboxykinase (Pck) is the enzyme at the center of the phosphoenolpyruvate-pyruvate-oxaloacetate node, which is involved in regulating the carbon flow distribution to catabolism, anabolism, or respiration in different states of Mtb infection. Under standard growth conditions, Mtb Pck is associated with gluconeogenesis and catalyzes the metal-dependent formation of phosphoenolpyruvate. In non-replicating Mtb, Pck can catalyze anaplerotic biosynthesis of oxaloacetate. Here, we present insights into the regulation of Mtb Pck activity by divalent cations. Through analysis of the X-ray structure of Pck-GDP and Pck-GDP-Mn2+ complexes, mutational analysis of the GDP binding site, and quantum mechanical (QM)-based analysis, we explored the structural determinants of efficient Mtb Pck catalysis. We demonstrate that Mtb Pck requires presence of Mn2+ and Mg2+ cations for efficient catalysis of gluconeogenic and anaplerotic reactions. The anaplerotic reaction, which preferably functions in reducing conditions that are characteristic for slowed or stopped Mtb replication, is also effectively activated by Fe2+ in the presence of Mn2+ or Mg2+ cations. In contrast, simultaneous presence of Fe2+ and Mn2+ or Mg2+ inhibits the gluconeogenic reaction. These results suggest that inorganic ions can contribute to regulation of central carbon metabolism by influencing the activity of Pck. Furthermore, the X-ray structure determination, biochemical characterization, and QM analysis of Pck mutants confirmed the important role of the Phe triad for proper binding of the GDP-Mn2+ complex in the nucleotide binding site and efficient catalysis of the anaplerotic reaction.
- MeSH
- aktivace enzymů MeSH
- fosfoenolpyruvátkarboxykinasa (závislá na ATP) chemie genetika metabolismus MeSH
- glukoneogeneze MeSH
- katalýza MeSH
- kationty dvojmocné MeSH
- kineze MeSH
- konformace proteinů MeSH
- lidé MeSH
- molekulární modely MeSH
- molekulární sekvence - údaje MeSH
- multimerizace proteinu MeSH
- mutace MeSH
- Mycobacterium tuberculosis enzymologie genetika MeSH
- nukleotidy metabolismus MeSH
- sekvence aminokyselin MeSH
- sekvenční seřazení MeSH
- vazebná místa MeSH
- vodíková vazba MeSH
- vztahy mezi strukturou a aktivitou MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
BACKGROUND: Pelvic floor muscles have potential to influence relative pelvic alignment. Side asymmetry in pelvic floor muscle tension is claimed to induce pelvic malalignment. However, its nature and amplitude are not clear. There is a need for non-invasive and reliable assessment method. An intervention experiment of unilateral pelvic floor muscle activation on healthy females was performed using image data for intra-subject comparison of normal and altered configuration of bony pelvis. METHODS: Sequent magnetic resonance imaging of 14 females in supine position was performed with 1.5 T static body coil in coronal orientation. The intervention, surface functional electrostimulation, was applied to activate pelvic floor muscles on the right side. Spatial coordinates of 23 pelvic landmarks were localized in each subject and registered by specially designed magnetic resonance image data processing tool (MPT2006), where individual error calculation; data registration, analysis and 3D visualization were interfaced. FINDINGS: The effect of intervention was large (Cohen's d=1.34). We found significant differences in quantity (P<0.01) and quality (P=0.02) of normal and induced pelvic displacements. After pelvic floor muscle activation on the right side, pelvic structures shifted most frequently to the right side in ventro-caudal direction. The right femoral head, the right innominate and the coccyx showed the largest displacements. INTERPRETATION: The consequences arising from the capacity of pelvic floor muscles to displace pelvic bony structures are important to consider not only in management of malalignment syndrome but also in treatment of incontinence. The study has demonstrated benefits associated with processing of magnetic resonance image data within pelvic region with high localization and registration reliability.
- MeSH
- dospělí MeSH
- interpretace obrazu počítačem metody MeSH
- kosterní svaly anatomie a histologie MeSH
- lidé MeSH
- magnetická rezonanční tomografie metody MeSH
- pánev anatomie a histologie MeSH
- pánevní dno anatomie a histologie MeSH
- subtrakční technika MeSH
- vylepšení obrazu metody MeSH
- Check Tag
- dospělí MeSH
- lidé MeSH
- ženské pohlaví MeSH
Receptor proteins at the cell surface regulate the ability of natural killer cells to recognize and kill a variety of aberrant target cells. The structural features determining the function of natural killer receptor proteins 1 (NKR-P1s) are largely unknown. In the present work, refined homology models are generated for the C-type lectin-like extracellular domains of rat NKR-P1A and NKR-P1B, mouse NKR-P1A, NKR-P1C, NKR-P1F, and NKR-P1G, and human NKR-P1 receptors. Experimental data on secondary structure, tertiary interactions, and thermal transitions are acquired for four of the proteins using Raman and infrared spectroscopy. The experimental and modeling results are in agreement with respect to the overall structures of the NKR-P1 receptor domains, while suggesting functionally significant local differences among species and isoforms. Two sequence regions that are conserved in all analyzed NKR-P1 receptors do not correspond to conserved structural elements as might be expected, but are represented by loop regions, one of which is arranged differently in the constructed models. This region displays high flexibility but is anchored by conserved sequences, suggesting that its position relative to the rest of the domain might be variable. This loop may contribute to ligand-binding specificity via a coupled conformational transition.
- MeSH
- aminokyselinové motivy MeSH
- fylogeneze MeSH
- konzervovaná sekvence MeSH
- krysa rodu rattus MeSH
- lektinové receptory NK-buněk - podrodina B chemie klasifikace MeSH
- lidé MeSH
- molekulární sekvence - údaje MeSH
- myši inbrední C57BL MeSH
- myši MeSH
- Ramanova spektroskopie MeSH
- sekvence aminokyselin MeSH
- sekvenční seřazení MeSH
- simulace molekulární dynamiky MeSH
- spektroskopie infračervená s Fourierovou transformací MeSH
- strukturní homologie proteinů MeSH
- terciární struktura proteinů MeSH
- termodynamika MeSH
- vazebná místa MeSH
- zvířata MeSH
- Check Tag
- krysa rodu rattus MeSH
- lidé MeSH
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Pepsin-family aspartic peptidases are biosynthesized as inactive zymogens in which the propeptide blocks the active site until its proteolytic removal upon enzyme activation. Here, we describe a novel dual regulatory function for the propeptide using a set of crystal structures of the parasite cathepsin D IrCD1. In the IrCD1 zymogen, intramolecular autoinhibition by the intact propeptide is mediated by an evolutionarily conserved exosite on the enzyme core. After activation, the mature enzyme employs the same exosite to rebind a small fragment derived from the cleaved propeptide. This fragment functions as an effective natural inhibitor of mature IrCD1 that operates in a pH-dependent manner through a unique allosteric inhibition mechanism. The study uncovers the propeptide-binding exosite as a target for the regulation of pepsin-family aspartic peptidases and defines the structural requirements for exosite inhibition.
- MeSH
- aktivace enzymů MeSH
- alosterická regulace MeSH
- katalytická doména MeSH
- kathepsin D chemie metabolismus MeSH
- kinetika MeSH
- klíšťata enzymologie MeSH
- koncentrace vodíkových iontů MeSH
- krystalografie rentgenová MeSH
- ligandy MeSH
- peptidy chemie metabolismus MeSH
- prekurzory enzymů chemie metabolismus MeSH
- sekvence aminokyselin MeSH
- sekvenční seřazení MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
Heteronuclear and homonuclear direct (D) and indirect (J) spin-spin interactions are important sources of structural information about nucleic acids (NAs). The Hamiltonians for the D and J interactions have the same functional form; thus, the experimentally measured apparent spin-spin coupling constant corresponds to a sum of J and D. In biomolecular NMR studies, it is commonly presumed that the dipolar contributions to Js are effectively canceled due to random molecular tumbling. However, in strong magnetic fields, such as those employed for NMR analysis, the tumbling of NA fragments is anisotropic because the inherent magnetic susceptibility of NAs causes an interaction with the external magnetic field. This motional anisotropy is responsible for non-zero D contributions to Js. Here, we calculated the field-induced D contributions to 33 structurally relevant scalar coupling constants as a function of magnetic field strength, temperature and NA fragment size. We identified two classes of Js, namely (1)JCH and (3)JHH couplings, whose quantitative interpretation is notably biased by NA motional anisotropy. For these couplings, the magnetic field-induced dipolar contributions were found to exceed the typical experimental error in J-coupling determinations by a factor of two or more and to produce considerable over- or under-estimations of the J coupling-related torsion angles, especially at magnetic field strengths >12 T and for NA fragments longer than 12 bp. We show that if the non-zero D contributions to J are not properly accounted for, they might cause structural artifacts/bias in NA studies that use solution NMR spectroscopy.
