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At least 631 records · Page 35Linked to original sources
PubMed1997

Patterns, structures, and amino acid frequencies in structural building blocks, a protein secondary structure classification scheme.

To study local structures in proteins, we previously developed an autoassociative artificial neural network (autoANN) and clustering tool to discover intrinsic features of macromolecular structures. The hidden unit activations computed by the trained autoANN are a convenient low-dimensional encoding of the local protein backbone structure. Clustering these activation vectors results in a unique classification of protein local structural features called Structural Building Blocks (SBBs). Here we describe application of this method to a larger database of proteins, verification of the applicability of this method to structure classification, and subsequent analysis of amino acid frequencies and several commonly occurring patterns of SBBs. The SBB classification method has several interesting properties: 1) it identifies the regular secondary structures, alpha helix and beta strand; 2) it consistently identifies other local structure features (e.g., helix caps and strand caps); 3) strong amino acid preferences are revealed at some positions in some SBBs; and 4) distinct patterns of SBBs occur in the "random coil" regions of proteins. Analysis of these patterns identifies interesting structural motifs in the protein backbone structure, indicating that SBBs can be used as "building blocks" in the analysis of protein structure. This type of pattern analysis should increase our understanding of the relationship between protein sequence and local structure, especially in the prediction of protein structures.

Amino Acid Sequence↗
PubMed2002

Interaction between transient change in local muscle structure and segmented leg motor responses.

We investigated the interaction between transient change in the local structure of gastrocnemius muscle fibers and the segmented leg motor responses elicited by toes-up rotation of the support surface. The gastrocnemius muscle in healthy young subjects underwent a sustained 2-min, isometric stretch (Prestretch group), followed immediately by the rotations. Analysis showed that the prestretch affected the amplitude of the monosynaptic but not the automatic components of the medial gastrocnemius muscle responses (monosynaptic response: 93 +/- 20% of the mean of the last three rotations in the Prestretch group compared to 174 +/- 42% in the Control group; automatic response: 128 +/- 18% in the Prestretch group versus 123 +/- 31% in the Control group). The shortened tibialis anterior muscle response and the onset latencies of responses were not affected by prestretching the gastrocnemius muscle. The prestretch effect on the amplitude of the monosynaptic (mediated by group Ia afferents) but not the automatic gastrocnemius muscle response (mediated by group II afferents) suggests that the automatic component of the muscle response to platform rotations has a stronger supraspinal influence than the monosynaptic response and is thus less affected by local events such as prolonged stretching.

Adult↗
PubMed1986

Localization of structural proteins in African swine fever virus particles by immunoelectron microscopy.

Seven African swine fever virus structural proteins were localized in the virion by immunoelectron microscopy. African swine fever virus-infected cells were incubated, before or after embedding and thin sectioning, with monoclonal antibodies specific for different structural proteins, and after labeling with protein A-gold complexes, the samples were examined in the electron microscope. Proteins p14 and p24 were found in the external region of the virion, proteins p12, p72, p17, and p37 were found in the intermediate layers, and protein p150 was found in the nucleoid and in one vertex. A monoclonal antibody that recognized protein p150 as well as p220, a virus-induced, nonstructural protein, could also bind to a component present in the nucleus of both uninfected and virus-infected cells.

African Swine Fever Virus↗
PubMed1997

Chromosome localization and structure of the murine cyclin G1 gene promoter sequence.

Cyclins play an essential role in the control of the cell cycle. In this study the murine cyclin G1 gene expression, structure, and chromosomal localization were examined. Genes with high homology to murine cyclin G1 were detected in various mammals, including human, monkey, rat, dog, cow, and rabbit, but not in yeast or chicken. Cyclin G1 gene was expressed in all murine tissues examined, with the highest levels in cardiac and skeletal muscle. A 10,366-bp genomic DNA fragment encompassing the promoter region and the 5'-flanking region of the gene was cloned and sequenced. Three putative binding sites for the myocyte enhancer factor-2 family of transcription factors were revealed. Furthermore, an upstream p53-binding site was localized to nucleotides -252 to -233 and a new putative p53-binding site was identified in the first intronic region at nucleotides 275 to 294. By fluorescence in situ hybridization, the cyclin G1 gene was mapped to mouse chromosome 11B1.1. This region is homologous with human chromosome 5q31-q32, consistent with the recent mapping of the human cyclin G1 gene to chromosome 5q32-q34. Localization of murine cyclin G1 will facilitate determination of gene linkage and the identification of synteny groups in mammals and of DNA elements in or near this gene that mediate its tissue expression or development-specific pattern of expression.

Amino Acid Sequence↗
PubMed2003

Native structural propensity in cellular retinoic acid-binding protein I 64-88: the role of locally encoded structure in the folding of a beta-barrel protein.

A central question in protein folding is the relative importance of locally encoded structure and cooperative interactions among residues distant in sequence. We have been exploring this question in a predominantly beta-sheet protein, since beta-structure formation clearly relies on both local and global sequence information. We present evidence that a 24-residue peptide corresponding to two linked hairpins of cellular retinoic acid-binding protein I (CRABP I) adopts significant native structure in aqueous solution. Prior work from our laboratory showed that the two turns contained in this fragment (turns III and IV) had the highest tendency of any of the eight turns in this anti-parallel beta-barrel to fold into native turns. In addition, the primary sequence of these two turns is well conserved throughout the structural family to which CRABP I belongs, and residues in the turns and their associated hairpins participate in a network of conserved long-range interactions. We propose that the strong local-sequence biases within the chain segment comprising turns III and IV favor longer-range interactions that are crucial to the folding and native-state stability of CRABP I, and may play a similar role in related intracellular lipid-binding proteins (iLBPs).

Amino Acid Sequence↗
PubMed2003

Recurring features of local tertiary structural elements in RNA molecules exemplified by hepatitis D virus RNA.

Elements of local tertiary structure in RNA molecules are important in understanding structure-function relationships. The loop E motif, first identified in several eukaryotic RNAs at functional sites which share an exceptional propensity for UV crosslinking between specific bases, was subsequently shown to have a characteristic tertiary structure. Common sequences and secondary structures have allowed other examples of the E-loop motif to be recognized in a number of RNAs at sites of protein binding or other biological function. We would like to know if more elements of local tertiary structure, in addition to the E-loop, can be identified by such common features. The highly structured circular RNA genome of the hepatitis D virus (HDV) provides an ideal test molecule because it has extensive internal structure, a UV-crosslinkable tertiary element, and specific sites for functional interactions with proteins including host PKR. We have now found a UV-crosslinkable element of local tertiary structure in antigenomic HDV RNA which, although differing from the E-loop, has a very similar pattern of sequence and secondary structure to the UV-crosslinkable element found in the genomic strand. Despite the fact that the two structures map close to one another, the sequences comprising them are not the templates for each other. Instead, the template regions for each element are additional sites for potential higher order structure on their respective complementary strands. This wealth of recurring sequences interspersed with base-paired stems provides a context to examine other RNA species for such features and their correlations with biological function.

Binding Sites↗
PubMed2006

Local electronic structure around a single Kondo impurity.

The local electronic structure due to the adsorption of Co on Cu111 is studied using an embedded cluster model, in which the crystal background is taken into account via an effective density functional theory (DFT)-based potential. This approach goes beyond the usual single-impurity Anderson model, where the ground state consists of a singly occupied impurity whose moment is compensated by the background conduction electrons. Ab initio correlated wave function calculations for the embedded cluster provide an alternative picture for this ground state and indicate that the quenching of the Co magnetic moment is due to the formation of metal-metal bonds with the Cu substrate. Low-lying excitations are also studied within the embedding model, and our results are discussed in the context of scanning tunneling microscopy experiments (Manoharan, H. C.; Lutz, C. P.; Eigler, D. M. Nature 2000, 403, 512), which find a sharp tunneling resonance localized in the vicinity of the Co adatom.

Adsorption↗
PubMed1995

Localized solution structure refinement of an F45W variant of ubiquitin using stochastic boundary molecular dynamics and NMR distance restraints.

The local structure within an 8-A radius around residue 45 of a recombinant F45W variant of human ubiquitin has been determined using 67 interproton distance restraints measured by two-dimensional proton NMR. Proton chemical shift evidence indicates that structural perturbations due to the F45W mutation are minimal and limited to the immediate vicinity of the site of mutation. Simulated annealing implemented with stochastic boundary molecular dynamics was applied to refine the structure of Trp 45 and 10 neighboring residues. The stochastic boundary method allowed the entire protein to be reassembled from the refined coordinates and the outlying unrefined coordinates with little distortion at the boundary. Refinement began with four low-energy indole ring orientations of F45W-substituted wild-type (WT) ubiquitin crystal coordinates. Distance restraints were derived from mostly long-range NOE cross peaks with 51 restraints involving the Trp 45 indole ring. Tandem refinements of 64 structures were done using either (1) upper and lower bounds derived from qualitative inspection of NOE crosspeak intensities or (2) quantitative analysis of cross-peak heights using the program MARDIGRAS. Though similar to those based on qualitative restraint, structures obtained using quantitative NOE analysis were superior in terms of precision and accuracy as measured by back-calculated sixth-root R factors. The six-membered portion of the indole ring is nearly coincident with the phenyl ring of the WT and the indole NH is exposed to solvent. Accommodation of the larger ring is accompanied by small perturbations in the backbone and a 120 degrees rotation of the chi 2 dihedral angle of Leu 50.

Computer Graphics↗
PubMed1996

Fourier transform infrared spectroscopy and site-directed isotope labeling as a probe of local secondary structure in the transmembrane domain of phospholamban.

Phospholamban is a 52-amino acid residue membrane protein that regulates Ca(2+)-ATPase activity in the sarcoplasmic reticulum of cardiac muscle cells. The hydrophobic C-terminal 28 amino acid fragment of phospholamban (hPLB) anchors the protein in the membrane and may form part of a Ca(2+)-selective ion channel. We have used polarized attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy along with site-directed isotope labeling to probe the local structure of hPLB. The frequency and dichroism of the amide I and II bands appearing at 1658 cm-1 and 1544 cm-1, respectively, show that dehydrated and hydrated hPLB reconstituted into dimyristoylphosphatidycholine bilayer membranes is predominantly alpha-helical and has a net transmembrane orientation. Specific local secondary structure of hPLB was probed by incorporating 13C at two positions in the protein backbone. A small band seen near 1614 cm-1 is assigned to the amide I mode of the 13C-labeled amide carbonyl group(s). The frequency and dichroism of this band indicate that residues 39 and 46 are alpha-helical, with an axial orientation that is approximately 30 degrees relative to the membrane normal. Upon exposure to 2H2O (D2O), 30% of the peptide amide groups in hPLB undergo a slow deuterium/hydrogen exchange. The remainder of the protein, including the peptide groups of Leu-39 and Leu-42, appear inaccessible to exchange, indicating that most of the hPLB fragment is embedded in the lipid bilayer. By extending spectroscopic characterization of PLB to include hydrated, deuterated as well as site-directed isotope-labeled hPLB films, our results strongly support models of PLB that predict the existence of an alpha-helical hydrophobic region spanning the membrane domain.

Amino Acid Sequence↗
PubMed1995

Disulfide mutants of barnase. II: Changes in structure and local stability identified by hydrogen exchange.

The hydrogen exchange behaviour of two stabilised disulfide mutants of barnase has been examined using NMR H/2H exchange measurements. The choice of experimental conditions is crucial in experiments to study the effects of mutations on local and global stability and dynamic behaviour of proteins. If exchange conditions allow both local and global unfolding events to be examined, then a comparison of three proteins (two mutants and wild-type) allows the effect of a mutation on the folded state to be ascribed to specific increases or decreases in local stability. This method was used to examine the effect of an introduced crosslink on the folded state of two different disulfide mutants of barnase, and the results are related to structural studies. It is found that disulfide bonds can stabilise or destabilise local structures as well as having an effect upon global stability. The effects of the mutations on exchange rate constants of protons are compared with the effects on the structure upon the introduction of the disulfide bonds. In the protein with a disulfide bond between residues 43 and 80, some local exchange rate constants are higher, reflecting local destabilisation at the site of the disulfide bond, associated with small structural rearrangements. In the protein with a disulfide bond between residues 85 and 102, amide protons of the adjacent loop are protected to a considerable extent. This is not associated with a structural rearrangement yet indicates that this disulfide bond has an effect on the stability of this loop.

Bacillus↗
PubMed2006

Structural diversity of protein segments follows a power-law distribution.

The local structures of protein segments were classified and their distribution was analyzed to explore the structural diversity of proteins. Representative proteins were divided into short segments using a sliding L-residue window. Each set of local structures consisting of consecutive 1-31 amino acids was classified using a single-pass clustering method. The results demonstrate that the local structures of proteins are very unevenly distributed in the protein universe. The distribution of local structures of relatively long segments shows a power-law behavior that is formulated well by Zipf's law, implying that a protein structure possesses recursive and fractal characteristics. The degree of effective conformational freedom per residue as well as the structure entropy per residue decreases gradually with an increasing value of L and then converges to constant values. This suggests that the number of protein conformations resides within the range between 1.2L and 1.5L and that 10- to 20-residue segments are already proteinlike in terms of their structural diversity.

Amino Acid Motifs↗
PubMed2003

Local genetic structure in a white-bearded manakin population.

Local genetic structure was studied in lekking white-bearded manakins in a study area on northern Trinidad, West Indies. The study population consisted of nine leks, at which a total of 238 birds were caught. By genotyping the individuals at eight polymorphic microsatellite loci we inferred some males on leks to be related (r = 0.25) as we found an average number of 14.8 half-sib relationships and two full-sib relationships per lek. We found that the sampled birds belonged to one genetic population that was slightly inbred (FIS and FIT = 0.02). Kinship coefficients decreased with increasing geographical distance, indicating that related birds displayed at the same or nearby leks. However, leks did not consist of only one family group because the average genetic distance (aij) between males within leks was higher than when comparing males on leks within close proximity. These patterns suggest limited male dispersal, that some type of kin recognition process between individuals may exist in this species and that males on leks may be more likely to establish themselves as territory-holding birds if a relative is already present.

Alleles↗
PubMed1981

Immunoglobulins of colostrum. V. Localization of structural differences between serum and colostral ovine and bovine IgG1 and IgG2 immunoglobulins.

Studies on localization of structural differences between ovine and bovine serum and colostral IgG immunoglobulins are described. Comparison of heterogeneity, susceptibility to proteolytic enzymes, peptide maps, amino acid compositions, and antigenic properties of immunoglobulins and their Fab and Fc fragments and H and L chains showed that structural differences are localized in the Fc region. The strongest differences were found in case of IgG2. It was also shown that no Fc fragments could be obtained from bovine serm IgG2 and ovine serum and colostral IgG2 due to their susceptibility to papain and trypsin. The results obtained confirmed our suggestion that colostral IgG2 are locally synthesized in mammary glands, whereas colostral IgG1 might be a mixed population of molecules locally synthesized and transferred from the serum.

Amino Acids↗
PubMed2003

Improving appearance model matching using local image structure.

We show how non-linear representations of local image structure can be used to improve the performance of model matching algorithms in medical image analysis tasks. Rather than represent the image structure using intensity values or gradients, we use measures that indicate the reliability of a set of local image feature detector outputs. These features are image edges, corners, and gradients. Feature detector outputs in flat, noisy regions tend to be ignored whereas those near strong structure are favoured. We demonstrate that combinations of these features give more accurate and reliable matching between models and new images than modelling image intensity alone. We also show that the approach is robust to non-linear changes in contrast, such as those found in multi-modal imaging.

Algorithms↗
PubMed1990

Relations between protein sequence and structure and their significance.

The relation between amino acid sequence and local structure in proteins is investigated. The local structures considered are either the four classes of secondary structure (H, E, T and C) or four classes of local conformations defined using measures of conformational similarity based on distances between C alpha atoms. The classes are obtained by applying an automatic clustering procedure to short polypeptide fragments of uniform length from a database of 75 known protein structures. The thrust of our investigation consists of systematically searching the database for simple amino acid patterns of the type Gly-X-Ala-X-X-Val, where X denotes an arbitrary residue. Patterns that are nearly always associated with the same structure are retained. Finding many such associations, we then evaluate by a statistical approach how many among them are non-random and compare the results for different definitions of local structure. A similar comparison is made for the predictive value of retained associations, which is assessed using an internal test based on dividing the database into "learning" and "test" subsets. While we find that local structures defined by conformational similarity are not superior to secondary structure for prediction purposes, they help us gain insight into the factors that influence the predictive value of derived associations. A major conclusion is that the number of retained associations is in large excess over the number expected from a random correlation between sequence and structure, irrespective of how local conformation is defined. However, only a very small number of these associations can be earmarked as reliable using statistical criteria, due to the limited size of the database. We find, for instance, that the pattern Ala-Ala-X-X-Lys reliably characterizes helix, and the pattern Val-X-Val-X-X-X-Ala reliably characterizes extended structure and beta-strand. The possibility is discussed that these and other reliable associations correspond to regions of the polypeptide chain whose conformations are locally determined and that these regions may play a role in folding.

Amino Acid Sequence↗
PubMed1986

Base sequence, local helix structure, and macroscopic curvature of A-DNA and B-DNA.

Given a specified DNA sequence and starting with an idealized conformation for the double helix (A-DNA or B-DNA), the dependence of conformational energy on variations in the local geometry of the double helix can be examined by computer modeling. By averaging over all thermally accessible states, it is possible to determine 1) how the optimum local structure differs from the initial idealized conformation and 2) the energetic costs of small structural deformations. This paper describes such a study. Tables are presented for the prediction of helix twist angles and base pair roll angles for both A-DNA and B-DNA when the sequence has been specified. Local deviations of helix parameters from their average values can accumulate to produce a net curvature of the molecule, a curvature that can be sharp enough to be experimentally detectable. As an independent check on the method, the calculations provide predictions for the longitudinal compressibility (Young's modulus) and the average torsional stiffness, both of which are in good agreement with experimental values. In examining the role of sequence-dependent variations in helix structure for the recognition of specific sequences by proteins, we have calculated the energy needed to deform the self-complementary hexanucleotide d(CAATTG) to match the local geometry of d(GAATTC), which is the sequence recognized by the EcoRI restriction endonuclease. That energy would be sufficient to reduce the binding of the incorrect sequence to the protein by over 2 orders of magnitude relative to the correct sequence.

Base Composition↗
PubMed1999

Using information theory to discover side chain rotamer classes: analysis of the effects of local backbone structure.

An understanding of the regularities in the side chain conformations of proteins and how these are related to local backbone structures is important for protein modeling and design. Previous work using regular secondary structures and regular divisions of the backbone dihedral angle data has shown that these rotamers are sensitive to the protein's local backbone conformation. In this preliminary study, we demonstrate a method for combining a more general backbone structure model with an objective clustering algorithm to investigate the effects of backbone structures on side chain rotamer classes and distributions. For the local structure classification, we use the Structural Building Blocks (SBB) categories, which represent all types of secondary structure, including regular structures, capping structures, and loops. For classification of side chain data, we use Minimum Message Length (MML) clustering from information theory. We show an example of how MML clustering on data classified by backbone SBBs can reveal different distributions of rotamer classes among the SBBs. Using these preliminary results, some of the characteristics of a rotamer library created using MML clustering on SBB dependent rotamer data are demonstrated.

Computational Biology↗
PubMed2001

EELFS study of the cementite local atomic structure.

The changes in the nearest - neighbour surroundings of carbon atoms in the cementite Fe3C lattice due to the heat treatment are analysed by the Extended Energy Loss Fine Structure (EELFS) method. To study the local atomic structure of the carbon steel U15 after different heat treatment regimes the electron energy loss spectra above the C K edge and Fe L2,3 edge were measured. The measured experimental EELFS spectra were treated by the standard for the Extended X - ray Absorption Fine Structure method procedure using Fourier transformation to obtain the parameters of the nearest - neighbour atomic surroundings. Qualitatively the assumption was made that the number of the iron atoms in the carbon atom nearest - neighbour surroundings changes due to the heat treatment, the evidence of which was the change in the ratio of the first two feature intensities of the atomic radial distribution function. This assumption is consistent well with the previous Mössbauer data.

Journal Article↗