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PubMed2003

A segment alignment approach to protein comparison.

MOTIVATION: Local structure segments (LSSs) are small structural units shared by unrelated proteins. They are extensively used in protein structure comparison, and predicted LSSs (PLSSs) are used very successfully in ab initio folding simulations. However, predicted or real LSSs are rarely exploited by protein sequence comparison programs that are based on position-by-position alignments. RESULTS: We developed a SEgment Alignment algorithm (SEA) to compare proteins described as a collection of predicted local structure segments (PLSSs), which is equivalent to an unweighted graph (network). Any specific structure, real or predicted corresponds to a specific path in this network. SEA then uses a network matching approach to find two most similar paths in networks representing two proteins. SEA explores the uncertainty and diversity of predicted local structure information to search for a globally optimal solution. It simultaneously solves two related problems: the alignment of two proteins and the local structure prediction for each of them. On a benchmark of protein pairs with low sequence similarity, we show that application of the SEA algorithm improves alignment quality as compared to FFAS profile-profile alignment, and in some cases SEA alignments can match the structural alignments, a feat previously impossible for any sequence based alignment methods.

Algorithms↗
PubMed1981

[Structure and localization of sympathetic neurons in the cat spinal cord].

By the method of retrograde axonal transport of horseradish peroxidase (HP) structure and localization of sympathetic neurons sending axons to the cranial cervical ganglion (CCG) have been revealed ipsilaterally in the ventral horns and in 4 nuclei of the spinal cord: nucl ILp, nucl. ILf. nucl. IC, nucl. ICpe. Orientation of the neurons, their number, structure of the nuclei formed by them, degree of the CCG efferentation by the preganglionic fibres, which run from various nuclei, are different. In nucl. ILf two types of neurons have been revealed-triangle and spindle-shaped, they always orienting by their long axis in mediolateral direction. The greatest amount of HP-positive neurons are found in nucl. ILp. They form a well distinquished compact nucleus in the lateral horns. HP-labelled neurons in nucl. ILp are found at the level of segments T1-T8 with their maximal amount at the level of segments T1-T3. HP-positive neurons are detected in nucl. ILf beginning from the segment C8 up to the middle of T4, in nucl. IC-from the segment C8 up to T6, in nucl. ICpe-from the segment C8 up to T5, in the ventral horns-from the segment T1 up to T5. In rostocaudal direction from the segment C8 up to T8 the number of HP-positive neurons is decreasing, but the part of nucl. ILp neurons in the CCG efferentation, comparing to the neurons in other sympathetic structures of the spinal cord, is increasing.

Animals↗
PubMed2005

Structure for localizing electromagnetic waves with a left-handed-medium slab and a conducting plane.

A new structure is proposed for localizing electromagnetic waves and energies with a left-handed-medium (LHM) slab and a perfectly electrically conducting (PEC) plane. When a current source is placed in front of a perfectly matched LHM slab with negative permittivity -epsilon0 and negative permeability -mu0 and a PEC plane is placed at the image point, we show rigorously that all the electromagnetic waves are confined in a region between the source and the PEC plane, and the fields outside the region are completely zero. Such an energy-localization system would be useful in medical treatments that use concentrated optical and microwave energies. However, a perfectly matched LHM is unphysical and does not exist in nature. Hence we further study the loss and retardation effects of LHM on the energy localization. Numerical results are presented for the lossy LHM structure to demonstrate the energy localization.

Journal Article↗
PubMed1999

The human BARX2 gene: genomic structure, chromosomal localization, and single nucleotide polymorphisms.

The BARX genes 1 and 2 are Bar class homeobox genes expressed in craniofacial structures during development. In this report, we present the genomic structure, chromosomal localization, and polymorphic markers in BARX2. The gene has four exons, ranging in size from 85 to 1099 bp. BARX2 is localized on human chromosome 11q25, as determined by radiation hybrid mapping. In the mouse, Barx2 is coexpressed with Pitx2 in several tissues. Based on the coexpression, BARX2 was assumed to be a candidate gene for those cases of Rieger syndrome that cannot be associated with mutations of PITX2. Mutations in PITX2 cause some cases of Rieger syndrome, an autosomal dominant disorder affecting eyes, teeth, and umbilicus. DNA from Rieger patients was subjected to single-strand conformation polymorphism screening of the BARX2 coding region. Three single nucleotide polymorphisms were found in a normal population, although no etiologic mutations were detectable in over 100 cases of Rieger syndrome or in individuals with related ocular disorders.

Alleles↗
PubMed2003

Local layer structures in circular domains of an achiral bent-core mesogen observed by x-ray microbeam diffraction.

The local layer structures have been investigated by x-ray microbeam diffraction in the circular domains of the SmCP phase of a banana-shaped molecule. Originally, the molecules form tilted layers with a certain tilt angle as well as nontilted ones. The application of a low electric field induces a tilted layer with a continuous change of the tilt angle; i.e., the tilted layer gradually changes the tilt angle, finally being upright at the center of circular domains. Upon application of a high electric field, the smectic layer forms a cylindrical-type structure. The layer structure changes from cylindrical to onionlike after turning off the high field.

Journal Article↗
PubMed2003

Local secondary structure content predicts folding rates for simple, two-state proteins.

Many single-domain proteins exhibit two-state folding kinetics, with folding rates that span more than six orders of magnitude. A quantity of much recent interest for such proteins is their contact order, the average separation in sequence between contacting residue pairs. Numerous studies have reached the surprising conclusion that contact order is well-correlated with the logarithm of the folding rate for these small, well-characterized molecules. Here, we investigate the physico-chemical basis for this finding by asking whether contact order is actually a composite number that measures the fraction of local secondary structure in the protein; viz. turns, helices, and hairpins. To pursue this question, we calculated the secondary structure content for 24 two-state proteins and obtained coefficients that predict their folding rates. The predicted rates correlate strongly with experimentally determined rates, comparable to the correlation with contact order. Further, these predicted folding rates are correlated strongly with contact order. Our results suggest that the folding rate of two-state proteins is a function of their local secondary structure content, consistent with the hierarchic model of protein folding. Accordingly, it should be possible to utilize secondary structure prediction methods to predict folding rates from sequence alone.

Kinetics↗
PubMed2004

Complex dynamics of the formation of spatially localized standing structures in the vicinity of saddle-node bifurcations of waves in the reaction-diffusion model of blood clotting.

Local activation in a one-dimensional three-component reaction-diffusion model of blood clotting may lead to a formation of spatially localized standing structures (peaks) via several complex scenarios. In the first scenario, two concentration pulses first propagate from the site of activation, then stop and transform into peaks [Zarnitsina et al., Chaos 11, 57 (2001)]. Here, we examine this scenario, and also describe a different scenario of peak formation. In this scenario, two trigger waves propagate initially in opposite directions away from the site of activation. Then they stop and change direction of propagation toward each other to the activation site, where they interact and form a peak. Both of these scenarios of stable peak formation are observed in the vicinity of saddle-node bifurcation and may be viewed as a memory of the extinct wave modes.

Animals↗
PubMedDate not supplied

The importance of local chemical structure for chemical metabolism by human uridine 5'-diphosphate-glucuronosyltransferase.

The uridine 5'-diphosphate- (UDP-)glucuronosyltransferase (UGT) family of enzymes catalyzes the conjugation of chemicals containing a suitable nucleophilic atom with glucuronic acid. Despite the importance of glucuronidation as an elimination and detoxification mechanism for drugs, environmental chemicals, and endogenous compounds, the structural features of substrates that confer isoform selectivity are poorly understood. The relationship between the local molecular structure of nucleophilic atoms of chemicals and the ability of UGT isoforms to glucuronidate the nucleophilic atoms was investigated here. The proximity of an aromatic ring to the nucleophilic atom was highly associated with a greater likelihood of glucuronidation by most UGT isoforms. Similarly, most UGT isoforms were found to have a statistically significant preference for oxygen over nitrogen as the nucleophilic atom. The converse was established only for UGT1A4. Naïve Bayes models were trained to predict the site of glucuronidation for eight UGT isoforms on the basis of the partial charge and Fukui function of the nucleophilic atom and whether an aromatic ring was attached to the nucleophilic atom. On average, the cross-validated sensitivity and specificity of the models were approximately 75-80%. For all but UGT2B7, the area under the receiver operating characteristics curve of the model was greater than 0.8, indicating strong predictive ability. A chemical diversity analysis of the currently available data indicates bias toward chemicals containing phenolic groups, and it is likely that the availability of chemical data sets with greater diversity will facilitate further insights into the structural features of substrates that confer enzyme selectivity.

Bayes Theorem↗
PubMed2002

The kinetics of cyclization reactions on polyaromatics from first principles.

Ab initio density functional theory calculations are presented on cyclization reactions of polyaromatics involved in coke formation during the thermal cracking of hydrocarbons. During coke formation, cyclization can take place at various sites, differing from each other by the local polyaromatic structure. This local structure also determines the minimum number of carbon atoms that must be added to allow the formation of a new ring. Kinetic parameters are calculated for the various ring-closure reactions by means of transition state theory. The activation energy is largely affected by the local structure of the polycyclic aromatic hydrocarbon, whereas the frequency factor varies significantly in terms of the length of the attached alkyl chain. The calculations, as presented, give a microscopic insight into the mechanisms that contribute to barrier formation and to the value of the frequency factor. The relative importance of cyclization at different sites, under conditions typical for an industrial cracking unit is studied on the basis of the calculated rate constants at various temperatures. The results suggest that the nature of coke formation is autocatalytic: the larger the macroradicals, the faster the subsequent reactions that lead to further growth of the polyaramatic surface. This type of calculation is the first step towards the development of structural relations for the kinetic parameters in terms of the local structure of the coke matrix.

Carbon↗
PubMed1992

FMRFamide-immunoreactive structures in the brain of the brown hagfish, Paramyxine atami: relationship with neuropeptide Y-immunoreactive structures.

Localization of the molluscan cardioexcitatory tetrapeptide FMRFamide (Phe-Met-Arg-Phe-NH2) in the brain and hypophysis of the brown hagfish, Paramyxine atami, was examined by immunohistochemistry specially regarding a possible relationship with neuropeptide Y (NPY). FMRFamide-immunoreactive fibers were demonstrated in many regions of the brain, with the highest density in the diencephalon. However, no immunoreactivity was found in the hypophysis. Labeled cells were chiefly located in the nucleus hypothalamicus of the diencephalon, although a few cells were recognized in the ventrolateral area of the caudal tegmentum. Examination of adjacent sections immunostained alternatively with anti-NPY antiserum and anti-FMRFamide antiserum showed overlapping of the distributional patterns of the immunoreactive structures in the brain. Moreover, the same cells in the nucleus hypothalamicus were immunostained with both antisera. Cross-blocking experiments showed that the FMRF-amide-immunoreactivity is abolished by preabsorption of the antiserum with homologous antigen, but not eliminated completely by pretreatment with appropriate antigens (NPY, avian pancreatic polypeptide and methionine-enkephalin-Arg-Phe). In contrast, the NPY-immunoreactivity was blocked by pretreatment of the antiserum with NPY, pancreatic polypeptide or FMRFamide, although no blocking by enkephalin was observed. Accordingly, the present study shows that, in the brown hagfish, FMRFamide-immunoreactive structures in the brain can be recognized by anti-NPY antiserum.

Amino Acid Sequence↗
PubMed2006

Specific heat functions for the orthorhombic Nd3+ in scheelite type of crystals.

Nd3+ doped scheelite type of crystals have attracted extensive interests because of their applications in solid state lasers, as well as upconversion luminescence and magneto-optical and magnetic properties. Usually, these properties are closely related to the local structures and properties of the Nd3+ impurities in the hosts. Since information about electronic states and local structures of the impurity Nd3+ in the scheelite crystals would be helpful to the understanding of the properties of these materials, theoretical investigations on the specific heat functions and the local structures for these Nd3+ centers are of significance.

Crystallization↗
PubMed2001

Three-dimensional adaptive filtering in magnetic resonance angiography.

In order to enhance 3D image data from magnetic resonance angiography (MRA), a novel method based on the theory of multidimensional adaptive filtering has been developed. The purpose of the technique is to suppress image noise while enhancing important structures. The method is based on local structure estimation using six 3D orientation selective filters, followed by an adaptive filtering step controlled by the local structure information. The complete filtering procedure requires approximately 3 minutes of computational time on a standard workstation for a 256 x 256 x 64 data set. The method has been evaluated using a mathematical vessel model and in vivo MRA data (both phase contrast and time of flight (TOF)). 3D adaptive filtering results in a better delineation of small blood vessels and efficiently reduces the high-frequency noise. Depending on the data acquisition and the original data type, contrast-to-noise ratio (CNR) improvements of up to 179% (8.9 dB) were observed. 3D adaptive filtering may provide an alternative to prolonging the scan time or using contrast agents in MRA when the CNR is low.

Algorithms↗
PubMed2001

EXAFS study of Sb-Te alloy films.

The local structures of three phases; stable compound Sb2Te3, metastable crystalline c-SbTe and amorphous a-SbTe films having the atomic ratio Sb/Te=3: in Sb-Te system have been studied by EXAFS. The c-SbTe has a partly similar local structure to crystalline Sb2Te3. The a-SbTe film has a local structure of NaCl-type, which is topologically analogous to the crystalline form. The amorphous phase has shorter bond distances 2.86A (around Sb-site) and 2.83A (around Te-site) than the corresponding distances 2.89A and 2.87A in the crystalline phase. This unbalanced bond distances between the Sb-site and Te-site implies that site-disordering occurs. Shortening of bond distances in the amorphous phase is due to the relaxation of locally distorted crystalline structure.

Journal Article↗
PubMed2006

Fingerprint recognition by combining global structure and local cues.

As an important feature, orientation field describes the global structure of fingerprints. It provides robust discriminatory information other than traditional widely-used minutiae points. However, there are few works explicitly incorporating this information into fingerprint matching stage, partly due to the difficulty of saving the orientation field in the feature template. In this paper, we propose a novel representation for fingerprints which includes both minutiae and model-based orientation field. Then, fingerprint matching can be done by combining the decisions of the matchers based on the global structure (orientation field) and the local cue (minutiae). We have conducted a set of experiments on large-scale databases and made thorough comparisons with the state-of-the-arts. Extensive experimental results show that combining these local and global discriminative information can largely improve the performance. The proposed system is more robust and accurate than conventional minutiae-based methods, and also better than the previous works which implicitly incorporate the orientation information. In this system, the feature template takes less than 420 bytes, and the feature extraction and matching procedures can be done in about 0.30 s. We also show that the global orientation field is beneficial to the alignment of the fingerprints which are either incomplete or poor-qualitied.

Algorithms↗
PubMed2006

Theoretical investigations of the specific heat functions for the orthorhombic Nd+3 centers in some crystals.

Garnets doped with Nd+3 have attracted extensive interests because of their applications in solid-state lasers, as well as upconversion luminescence and magneto-optical and magnetic properties. Usually, these properties are closely related to the local structures and properties of the Nd+3 impurities in the hosts. Since information about electronic states and local structures of the impurity Nd+3 in the garnets would be helpful to the understanding of the properties of these materials, theoretical investigations on the specific heat functions and the local structures for these Nd+3 centers are of significance.

Crystallography↗
PubMed2005

Local spatial structure and predator-prey dynamics: counterintuitive effects of prey enrichment.

The Lotka-Volterra predator-prey model with prey density dependence shows the final prey density to be independent of its vital rates. This result assumes the community to be well mixed so that encounters between predators and prey occur as a product of the landscape densities, yet empirical evidence suggests that over small spatial scales this may not be the normal pattern. Starting from an individual-based model with neighborhood interactions and movements, a deterministic approximation is derived, and the effect of local spatial structure on equilibrium densities is investigated. Incorporating local movements and local interactions has important consequences for the community dynamics. Now the final prey density is very much dependent on its birth, death, and movement rates and in ways that seem counterintuitive. Increasing prey fecundity or mobility and decreasing the coefficient of competition can all lead to decreases in the final density of prey if the predator is also relatively immobile. However, analysis of the deterministic approximation makes the mechanism for these results clear; each of these changes subtly alters the emergent spatial structure, leading to an increase in the predator-prey spatial covariance at short distances and hence to a higher predation pressure on the prey.

Animal Migration↗
PubMed2004

Structural evidence for guanidine-protein side chain interactions: crystal structure of CutA from Pyrococcus horikoshii in 3 M guanidine hydrochloride.

This study was carried out to investigate the structural perturbation of the protein's local structure by the denaturants under non-denaturing conditions. Crystal structure of CutA from an archaeon Pyrococcus horikosii (PhoCutA), a heavy-metal binding protein, was determined at 1.6-angstroms resolution in the presence of 3 M guanidine HCl (GdnHCl). Native PhoCutA has a large number of short intramolecular hydrogen bonds and salt bridges on the protein surface, of which greater than 90% of hydrogen bonds and all salt bridges were retained in 3 M GdnHCl. Hydrogen bonds that disappeared in the GdnHCl crystal structure were mainly located on the protein surface, especially around the structurally perturbed loop, suggesting interactions between peptide groups and GdnHCl. Only a few GdnH+ ions were observed in the crystal structure, although none at the surface, of the protein. Two GdnH+ ions were observed in the center of the trimeric structure, replacing water molecules, and were hydrogen bonded with Asp84 and Asp86 of each chain. The exterior loop from Tyr39 to Lys44, including Trp40-Trp41, was perturbed structurally. Decreases in temperature factors were observed in beta strand 5 and the N terminus of helix 3. These results suggest the specific bindings of GdnH+ with some acidic residues and the non-specific bindings around Trp residues and peptide groups on the protein surface and that binding of GdnHCl to the native protein is limited, resulting in local structural perturbation.

Archaeal Proteins↗
PubMed1987

Demonstration of the asymmetric effect of CC-1065 on local DNA structure using a site-directed adduct in a 117-base-pair fragment from M13mp1.

Using DNase I and Alu I endonuclease analysis of a site-directed CC-1065-[N3-adenine]DNA adduct in a 117-base-pair fragment from M13mp1 DNA, we have demonstrated that CC-1065 produces an asymmetric effect on DNA conformation that extends more than one helix turn to the 5' side of the covalently modified adenine. CC-1065 is a potent antitumor antibiotic produced by Streptomyces zelensis, which is believed to mediate its cytotoxic effects through covalent binding to DNA. Previous studies have demonstrated that CC-1065 binds covalently to N3 of adenine and lies within the minor groove of DNA spanning a 4-base-pair sequence to the 5' side of the modified adenine. DNase I footprinting of this site-directed CC-1065-DNA adduct on the noncovalently modified strand shows that inhibition of cleavage occurs over a 12-base region, which is bordered on the 3' side by a site of 2-fold enhancement of cleavage. On the covalently modified strand a much less pronounced inhibition/enhancement pattern of cleavage occurs as far as 11 bases to the 5' side of the covalently modified adenine. While Hae III is able to cleave the DNA on both strands on the 3' side of the covalently modified adenine, Alu I is only able to cleave the covalently modified strand on the 5' side of the adduct. By taking into account the recently published structure of DNase I, we are able to interpret these results and develop a model for the effect of CC-1065 on local DNA structure. In this model, we propose selective drug-induced distortion of the covalently modified strand as a consequence of the alkylation of adenine by CC-1065.

Adenine↗