SEARCH · PubMed Health

Results for “structural features”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 865 records · Page 48Linked to original sources

PubMed1994

The maize chromosomal HMGa protein recognizes structural features of DNA and increases DNA flexibility.

The abundant maize high-mobility group protein HMGa belongs to the chromosomal, non-histone proteins and consists of a basic region containing the HMG-box DNA-binding domain and a highly acidic carboxy-terminal tail. The full-length HMGa protein and a truncated version lacking the acidic tail were synthesized in Escherichia coli and tested for their ability to induce DNA-bending in a ligase mediated circularization assay with short DNA fragments. It is shown that the recombinant HMGa protein as well as its truncated form efficiently cause circularization of the tested DNA fragments without an obvious requirement for stable DNA-binding. They bind furthermore preferentially to A/T-rich linear DNA or bent DNA structures such as four-way junctions and DNA minicircles. The DNA-binding properties and the ability to increase DNA flexibility suggest a general role of the HMGa protein in assisting the formation of nucleoprotein complexes, possibly by facilitating interactions of proteins bound to adjacent DNA sites.

Base Sequence↗

PubMed2002

Structural features of glycosyltransferases synthesizing major bilayer and nonbilayer-prone membrane lipids in Acholeplasma laidlawii and Streptococcus pneumoniae.

In membranes of Acholeplasma laidlawii two consecutively acting glucosyltransferases, the (i) alpha-monoglucosyldiacylglycerol (MGlcDAG) synthase (alMGS) (EC ) and the (ii) alpha-diglucosyl-DAG (DGlcDAG) synthase (alDGS) (EC ), are involved in maintaining (i) a certain anionic lipid surface charge density and (ii) constant nonbilayer/bilayer conditions (curvature packing stress), respectively. Cloning of the alDGS gene revealed related uncharacterized sequence analogs especially in several Gram-positive pathogens, thermophiles and archaea, where the encoded enzyme function of a potential Streptococcus pneumoniae DGS gene (cpoA) was verified. A strong stimulation of alDGS by phosphatidylglycerol (PG), cardiolipin, or nonbilayer-prone 1,3-DAG was observed, while only PG stimulated CpoA. Several secondary structure prediction and fold recognition methods were used together with SWISS-MODEL to build three-dimensional model structures for three MGS and two DGS lipid glycosyltransferases. Two Escherichia coli proteins with known structures were identified as the best templates, the membrane surface-associated two-domain glycosyltransferase MurG and the soluble GlcNAc epimerase. Differences in electrostatic surface potential between the different models and their individual domains suggest that electrostatic interactions play a role for the association to membranes. Further support for this was obtained when hybrids of the N- and C-domain, and full size alMGS with green fluorescent protein were localized to different regions of the E. coli inner membrane and cytoplasm in vivo. In conclusion, it is proposed that the varying abilities to bind, and sense lipid charge and curvature stress, are governed by typical differences in charge (pI values), amphiphilicity, and hydrophobicity for the N- and (catalytic) C-domains of these structurally similar membrane-associated enzymes.

Acholeplasma laidlawii↗

PubMed2006

Slicing a protease: structural features of the ATP-dependent Lon proteases gleaned from investigations of isolated domains.

ATP-dependent Lon proteases are multi-domain enzymes found in all living organisms. All Lon proteases contain an ATPase domain belonging to the AAA(+) superfamily of molecular machines and a proteolytic domain with a serine-lysine catalytic dyad. Lon proteases can be divided into two subfamilies, LonA and LonB, exemplified by the Escherichia coli and Archaeoglobus fulgidus paralogs, respectively. The LonA subfamily is defined by the presence of a large N-terminal domain, whereas the LonB subfamily has no such domain, but has a membrane-spanning domain that anchors the protein to the cytoplasmic side of the membrane. The two subfamilies also differ in their consensus sequences. Recent crystal structures for several individual domains and sub-fragments of Lon proteases have begun to illuminate similarities and differences in structure-function relationships between the two subfamilies. Differences in orientation of the active site residues in several isolated Lon protease domains point to possible roles for the AAA(+) domains and/or substrates in positioning the catalytic residues within the active site. Structures of the proteolytic domains have also indicated a possible hexameric arrangement of subunits in the native state of bacterial Lon proteases. The structure of a large segment of the N-terminal domain has revealed a folding motif present in other protein families of unknown function and should lead to new insights regarding ways in which Lon interacts with substrates or other cellular factors. These first glimpses of the structure of Lon are heralding an exciting new era of research on this ancient family of proteases.

Adenosine Triphosphate↗

PubMed1987

Structural features of sulfated glycans from the tunic of Styela plicata (Chordata-Tunicata). A unique occurrence of L-galactose in sulfated polysaccharides.

The sulfated polysaccharides in the tunic of Styela plicata occur as three fractions that differ markedly in molecular mass and chemical composition. The high-molecular-mass fraction has a high galactose content and a strong negative optical rotation while the low-molecular-mass fractions have a higher proportion of amino sugars and glucose. The galactose occurs in these polysaccharides entirely in the L-enantiomeric form. Although L-galactose is a constituent of several polysaccharides, this is the first report of sulfated polysaccharides that contain high amounts of L-galactose, and that lack the D enantiomorph of this sugar. Furthermore, the structure of the high-molecular-mass fraction, which is composed mainly of a core of alpha-L-galactopyranose residues, sulfated at position 3, linked glycosidically though position 1----4, and with non-sulfated L-galactopyranose non-reducing end-units, is unique among other previously described sulfated glycans. These data are of considerable interest as they show an unusual example of possible variants of polyanionic glycans with structure function in living tissues.

Animals↗

PubMed1993

A gene for cytochrome c oxidase subunit II in duck mitochondrial DNA: structural features and sequence evolution.

The gene encoding cytochrome c oxidase subunit II (COXII) was amplified by polymerase chain reaction (PCR) using mitochondrial DNAs (mtDNAs) isolated from two genera of domesticated ducks, Anas platyrhnchos and Cairina muschata, and their intergeneric and intrageneric hybrids as templates. Comparison of the nucleotide sequences from the two different duck lineages shows that they have approximately 91% homology. The nucleotide substitution pattern in the duck COXII gene reveals a high transition/transversion ratio (8.8:1.0) while 93.2% of the nucleotide substitutions are silent. The duck COXII, which uses GUG as the initiation codon, contains 228 amino acid residues. Comparison of the deduced COXII amino acid sequences in duck, chicken, Xenopus laevis, mouse, bovine and human reveals five highly conserved domains. The evolutionary conservation of the primary structure of COXII implies its functional importance.

Amino Acid Sequence↗

PubMed1989

Structural features of T-cell recognition: applications to vaccine design.

T lymphocytes, in contrast to antibodies, appear to recognize primarily a limited number of antigenic sites on any given antigenic protein. We find that a single site can so dominate the T-cell repertoire that the presence or absence of a response to one immunodominant site can make the difference between a high responder and a low responder, even though low responders respond to other sites almost as well as high responders. Besides interaction with major histocompatibility complex (MHC) molecules, the mode by which the antigen is processed into fragments for T-cell recognition also determines which sites are seen. The products of natural processing of the protein appear to be larger than the synthetic peptides and contain structures which hinder binding to certain MHC molecules or to the T-cell receptor. A third factor in immunodominance is the intrinsic structure of the antigenic site. We have shown that amphipathic helices have a higher than random chance of being immunodominant, and have developed a computer program to locate such structures in protein amino acid sequences. We prospectively predicted sites in the malaria circumsporozoite protein and found that the four most widely recognized sites in an endemic area of West Africa were all predicted. Similarly, we identified two helper T-cell sites from the HIV (AIDS virus) envelope, and have now shown that immunization with these elicits enhanced antibody responses to the whole envelope when injected into monkeys. These sites are also recognized by human T cells from volunteers who had been immunized with a recombinant vaccinia virus expressing the HIV envelope. Also, because cytotoxic T lymphocytes (CTLS) may play a critical role in defence against AIDS, we have used a recombinant vaccinia virus and transfectants expressing the HIV envelope gene to induce specific CTLS against the HIV envelope. Using synthetic peptides, we were able to identify the first CTL recognition site in the AIDS virus. These results may contribute to the rational design of vaccines.

Animals↗

PubMed2003

Unique structural features that influence neutrophil emigration into the lung.

Neutrophil emigration in the lung differs substantially from that in systemic vascular beds where extravasation occurs primarily through postcapillary venules. Migration into the alveolus occurs directly from alveolar capillaries and appears to progress through a sequence of steps uniquely influenced by the cellular anatomy and organization of the alveolar wall. The cascade of adhesive and stimulatory events so critical to the extravasation of neutrophils from postcapillary venules in many tissues is not evident in this setting. Compelling evidence exists for unique cascades of biophysical, adhesive, stimulatory, and guidance factors that arrest neutrophils in the alveolar capillary bed and direct their movement through the endothelium, interstitial space, and alveolar epithelium. A prominent path accessible to the neutrophil appears to be determined by the structural interactions of endothelial cells, interstitial fibroblasts, as well as type I and type II alveolar epithelial cells.

Animals↗

PubMed1999

The vsp locus of Mycoplasma bovis: gene organization and structural features.

Major lipoprotein antigens, known as variable membrane surface lipoproteins (Vsps), on the surface of the bovine pathogen Mycoplasma bovis were shown to spontaneously undergo noncoordinate phase variation between ON and OFF expression states. The high rate of Vsp phenotypic switching was also shown to be linked with DNA rearrangements that occur at high frequency in the M. bovis chromosome (I. Lysnyansky, R. Rosengarten, and D. Yogev, J. Bacteriol. 178:5395-5401, 1996). In the present study, 13 single-copy vsp genes organized in a chromosomal cluster were identified and characterized. All vsp genes encode highly conserved N-terminal domains for membrane insertion and lipoprotein processing but divergent mature Vsp proteins. About 80% of each vsp coding region is composed of reiterated coding sequences that create a periodic polypeptide structure. Eighteen distinct repetitive domains of different lengths and amino acid sequences are distributed within the products of the various vsp genes that are subject to size variation due to spontaneous insertions or deletions of these periodic units. Some of these repeats were found to be present in only one Vsp family member, whereas other repeats recurred at variable locations in several Vsps. Each vsp gene is also 5' linked to a highly homologous upstream region composed of two internal cassettes. The findings that rearrangement events are associated with Vsp phenotypic switching and that multiple regions of high sequence similarity are present upstream of the vsp genes and within the vsp coding regions suggest that modulation of the Vsp antigenic repertoire is determined by recombination processes that occur at a high frequency within the vsp locus of M. bovis.

5' Untranslated Regions↗

PubMed1985

The serine proteinase inhibitor from summer squash (Cucurbita pepo): some structural features, stability and proteolytic degradation.

The serine proteinase inhibitor from summer squash seeds (CPTI-II) with Mr of about 3250 contains three disulphide bridges and is unusually resistant to denaturing agents (e.g. 10% trichloroacetic acid at about 100 degrees C), thermolysin and proteinase V8 from Staphylococcus aureus. The inhibitor is digested by pepsin; the digestion of the virgin form proceeds more rapidly than when the peptide bond of the reactive site is broken. The inhibitor is not specifically reduced by sodium borohydride at pH 8.8, and almost full reactivation of the inhibitor reduced by dithiothreitol takes place at pH 8.15 in the presence of EDTA and the reduced + oxidized glutathione system. The inhibitor was crystallized from methanol. CD spectra point to the occurrence of beta-turns in the secondary structure of the inhibitor.

Circular Dichroism↗

PubMed2005

Thermal stability, structural features, and B-to-Z transition in DNA tetraloop hairpins as determined by optical spectroscopy in d(CG)(3)T(4)(CG)(3) and d(CG)(3)A(4)(CG)(3) oligodeoxynucleotides.

NMR and CD data have previously shown the formation of the T(4) tetraloop hairpin in aqueous solutions, as well as the possibility of the B-to-Z transition in its stem in high salt concentration conditions. It has been shown that the stem B-to-Z transition in T(4) hairpins leads to S (south)- to N (north)-type conformational changes in the loop sugars, as well as anti to syn orientations in the loop bases. In this article, we have compared by means of UV absorption, CD, Raman, and Fourier transform infrared (FTIR), the thermodynamic and structural properties of the T(4) and A(4) tetraloop hairpins formed in 5'-d(CGCGCG-TTTT-CGCGCG)-3' and 5'-d(CGCGCG-AAAA-CGCGCG)-3', respectively. In presence of 5M NaClO(4), a complete B-to-Z transition of the stems is first proved by CD spectra. UV melting profiles are consistent with a higher thermal stability of the T(4) hairpin compared to the A(4) hairpin. Order-to-disorder transition of both hairpins has also been analyzed by means of Raman spectra recorded as a function of temperature. A clear Z-to-B transition of the stem has been confirmed in the T(4) hairpin, and not in the A(4) hairpin. With a right-handed stem, Raman and FTIR spectra have confirmed the C2'-endo/anti conformation for all the T(4) loop nucleosides. With a left-handed stem, a part of the T(4) loop sugars adopt a N-type (C3'-endo) conformation, and the C3'-endo/syn conformation seems to be the preferred one for the dA residues involved in the A(4) tetraloop.

Base Pairing↗

PubMed1983

cA lectin gene insertion has the structural features of a transposable element.

The single gene Le1, coding for soybean seed lectin, was compared to le1, a naturally occurring mutant allele containing a 3.4 kb insertion within its coding region. Le1 is devoid of introns and produces a 1.0 kb mRNA. It codes for a signal sequence of 32 amino acids and a mature protein of 253 amino acids. With the exception of six single-base substitutions, the coding and flanking sequences in le1 are identical with those in the uninterrupted gene. The insertion termini are imperfect inverted repeats flanked by a 3 bp duplication of lectin target DNA. Inverted repeats within the lectin gene are located symmetrically with respect to the insertion site and are homologous to a region of the insertion termini. These molecular traits conform with the structural aspects of transposable elements in other organisms and imply some degree of site specificity.

Amino Acids↗

PubMed1996

Structural features of the large subunit rRNA expressed in Plasmodium falciparum sporozoites that distinguish it from the asexually expressed subunit rRNA.

The developmentally regulated transcription of at least two distinct sets of nuclear-encoded ribosomal RNAs is detected in Plasmodium species. The identification of functional differences between the two sets of rRNAs is of interest. To facilitate the search for such differences, we have identified the 5.8S and 28S rRNAs from Plasmodium falciparum that are expressed in the sporozoite stage (S gene) of the parasites' life cycle in the mosquito host and compare them to transcripts expressed in the red blood cells (A gene) of the vertebrate host. This completes the first set of A- and S-type nuclear-encoded rRNA genes for a Plasmodium species. Analysis of the predicted secondary structures of the two units reveals the majority of differences between the A- and S-type genes occur in regions previously known to be variable. However, the predicted secondary structure of both 28S rRNAs indicates 11 positions within conserved areas that are not typical of eucaryotic rRNAs. Although the A-type gene resembles almost all eucaryotes, being atypical in only 4 of the 11 positions, the S gene is variant in 8 of the 11 positions. In three of these positions, the S-type gene resembles the consensus nucleotides for the 23S rRNA from Eubacteria and/or Archaea. A few differences occur in regions associated with ribosome function, in particular the GTPase site where the S-type differs in a base pair and loop from all known sequences. Further, the identification of compensatory changes at conserved points of interactions between the 5.8S-28S rRNAs indicates that transcripts from A- and S-units should not be interchangeable.

Animals↗

PubMed1976

Structural features and protective activity of dexamethasone and pregnenolone-16 alpha-carbonitrile.

Pretreatment with dexamethasone acetate or pregnenolone-16 alpha-carbonitrile markedly diminished the pharmacological effect of zoxazolamine in rats. This prophylactic action was associated with significantly decreased plasma drug levels, which, in turn, were correlated with enhanced hepatic drug biotransformation, induced by the steroids. Dexamethasone proved to be more active than pregnenolone-16 alpha-carbonitrile in this respect. The A-ring conformation as well as the distances of O-3-O-11, O-11-O-17, and the O-3-mean plane C-5-C-17 may be key factors in glucocorticoid activity, and the longer the distances, the greater the potency. These characteristics have no bearing on catatoxic activity for which the 16 alpha-substituent appears to be a structural prerequisite.

Animals↗

PubMedDate not supplied

Characterizing bitterness: identification of key structural features and development of a classification model.

This work describes the first approach in the development of a comprehensive classification method for bitterness of small molecules. The data set comprises 649 bitter and 13 530 randomly selected molecules from the MDL Drug Data Repository (MDDR) which are analyzed by circular fingerprints (MOLPRINT 2D) and information-gain feature selection. The feature selection proposes substructural features which are statistically correlated to bitterness. Classification is performed on the selected features via a naïve Bayes classifier. The substructural features upon which the classification is based are able to discriminate between bitter and random compounds, and thus we propose they are also functionally responsible for causing the bitter taste. Such substructures include various sugar moieties as well as highly branched carbon scaffolds. Cynaropicrine contains a number of the substructural features found to be statistically associated with bitterness and thus was correctly predicted to be bitter by our model. Alternatively, both promethazine and saccharin contain fewer of these substructural features, and thus the bitterness in these compounds was not identified. Two different classes of bitter compounds were identified, namely those which are larger and contain mainly oxygen and carbon and often sugar moieties, and those which are rather smaller and contain additional nitrogen and/or sulfur fragments. The classifier is able to predict 72.1% of the bitter compounds. Feature selection reduces the number of false-positives while also increasing the number of false negatives to 69.5% of bitter compounds correctly predicted. Overall, the method presented here presents both one of the largest databases of bitter compounds presently available as well as a relatively reliable classification method.

Algorithms↗

PubMed1978

Common structural features of different viroids: serial arrangement of double helical sections and internal loops.

The thermodynamic parameters of five different highly purified viroid "species" were determined by applying UV-absorption melting analysis and temperature jump methods. Their thermal denaturation proved to be a highly cooperative process with midpoint-temperatures (Tm) between 48.5 and 51 degrees C in 0.01 M sodium cacodylate, 1 mM EDTA, pH 6.8. The values of the apparent reaction enthalpies of the different viroid species range between 3,140 and 3,770 kJ/mol. Although the cooperativity is as high as found in homogeneous RNA double helices the Tm-value of viroid melting is more than 30 degrees C lower than in the homogeneous RNA. In order to explain this deviation, melting curves were simulated for different models of the secondary structure of viroids using literature values of the thermodynamic parameters of nucleic acids. Our calculations show that the following refinement of our earlier model is in complete accordance with the experimental data: In their native conformation viroids exist as an extended rodlike structure characterized by a series of double helical sections and internal loops. In the different viroid species 250-300 nucleotides out of total 350 nucleotides are needed to interprete the thermodynamic behaviour.

Mathematics↗

PubMed1998

Structural features of the human salivary mucin, MUC7.

Human salivary mucin (MUC7) is characterized by a single polypeptide chain of 357 aa. Detailed analysis of the derived MUC7 peptide sequence reveals five distinct regions or domains: (1) an N-terminal basic, histatin-like domain which has a leucine-zipper segment, (2) a moderately glycosylated domain, (3) six heavily glycosylated tandem repeats each consisting of 23 aa, (4) another heavily glycosylated MUC1- and MUC2-like domain, and (5) a C-terminal leucine-zipper segment. Chemical analysis and semi-empirical prediction algorithms for O-glycosylation suggested that 86/105 (83%) Ser/Thr residues were O-glycosylated with the majority located in the tandem repeats. The high (approximately 25%) proline content of MUC7 including 19 diproline segments suggested the presence of polyproline type structures. CD studies of natural and synthetic diproline-rich peptides and glycopeptides indicated that polyproline type structures do play a significant role in the conformational dynamics of MUC7. In addition, crystal structure analysis of a synthetic diproline segment (Boc-Ala-Pro-OBzl) revealed a polyproline type II extended structure. Collectively, the data indicate that the polyproline type II structure, dispersed throughout the tandem repeats, may impart a stiffening of the backbone and could act in consort with the glycosylated segments to keep MUC7 in a semi-rigid, rod shaped conformation resembling a 'bottle-brush' model.

Amino Acid Sequence↗

PubMed2001

A new class of LINEs (ATLN-L) from Arabidopsis thaliana with extraordinary structural features.

The Arabidopsis thaliana genome has about 250 copies of LINEs (here called ATLNs). Of these, some, called ATLN-Ls, have an extra sequence of about 2 kb in the region downstream of two consecutive open reading frames, orf1 and orf2. Interestingly, the extra sequences in these ATLN-L members have another open reading frame, designated as orf3. Each member is flanked by direct repeats of a target site sequence, showing that ATLN-L members with the three open reading frames have retrotransposed as a unit. The ATLN-L members are also distinct from other ATLN members: orf1 terminates with TAA (or TAG) and is located in the same frame as orf2, and the ATG initiation codon of orf2 is not present in the proximal region. A sequence that may form a pseudoknot structure in ATLN-L mRNA was present in the proximal region of orf2, therefore the TAA (or TAG) termination codon of orf1 is assumed to be suppressed to produce an Orf1-Orf2 transframe protein during the translation of the ATLN-L mRNA. The region between orf2 and orf3 is several hundred bp long, suggesting that orf3 expression is independent of orfl-orf2. The amino acid sequences of the proteins Orf1 and Orf3 are highly homologous in their N-terminal half regions that have a retroviral zinc-finger motif for RNA binding. Orf3, however, has a leucine-zipper motif in addition to the zinc-finger motif. The C-terminal regions of the Orf1 and Orf3 proteins have poor homology, but seem to have nuclear localization signals, suggesting that these proteins are involved in the transfer of ATLN-L mRNA to nuclei. A phylogenetic tree shows that Orf3 proteins form a branch distinct from the branches of the Orf1 proteins encoded by ATLN-L members. This indicates that an ancestor element of ATLN-Ls has incorporated the orf1 frame carried by another ATLN member into its distal region to orf1-orf2 during evolution.

5' Untranslated Regions↗

PubMed1980

Structural features of Bacillus precursor 5S RNA involved in the interaction with RNAase M5.

Mature 5S (m5S) RNA from Bacillus licheniformis specifically and almost completely inhibits in vitro maturation of bacillus precursor 5S (p5S) RNA, showing that the maturation enzyme RNAase M5 can recognize Bacillus m5S RNA. E. coli m5S RNA is a much less efficient inhibitor, whereas S. carlsbergensis 5S RNA inhibits maturation by about 70%. The differences in inhibition can be correlated with the position of the sequence UAGG (residues 101-104 in B. licheniformis m5S RNA) relative to the double-helical region formed by the 5'- and 3'-terminal sequences (molecular stalk) of m5S RNA. Recent experiments by Meyhack and Pace (Biochemistry 17 (1980) 5804-5810) demonstrated this UAGG sequence to be indispensable for processing of p5S RNA. Other elements of secondary and/or tertiary structure are also required, however. The effect of artificially constructed "5S RNA" molecules having defined disturbances in the base-pairing within the molecular stalk on in vitro maturation shows that base-pairing in the immediate neighbourhood of the bonds to be cleaved during maturation is crucial to recognition of p5S RNA by RNAase M5. G.U pairs are tolerated in this region, however, without loss of efficiency in maturation. Base-pairing does not have to extend throughout the complete molecular stalk. The introduction of an A/C combination at the end of the molecular stalk removed from the bonds cleaved by RNAase M5 does not significantly impair the efficiency of maturation.

Bacillus↗