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PubMed1981

Structural features of glutamine substrates for transglutaminases. Specificities of human plasma factor XIIIa and the guinea pig liver enzyme toward synthetic peptides.

Studies on the glutamine substrate specificities of human plasma factor XIIIa and guinea pig liver transglutaminase have been made using variants of the synthetic peptide substrate, Ser-Val-Leu-Ser-Leu-Ser-Gln-Ser-Lys-Val-Leu-Pro-Val-Pro-Glu. The sequence of this effective peptide substrate corresponds to the primary site of factor XIIIa-catalyzed amine incorporation into beta-casein, the most sensitive known macromolecular substrate for this enzyme (Gorman, J.J., and Folk, J.E. (1980) J. Biol. Chem. 255, 419-427). Variations in specificity observed with factor XIIIa for peptides containing single substitutions and multiple substitutions in this sequence are indications that several important determinants for enzyme recognition are contained therein. Among these are several of the hydrophobic amino acid residues and the lysine residue. Less pronounced changes in specificity occur with the liver enzyme and the differences in effects of the various substitutions reveal important differences in specificity requirements of factor XIIIa and the liver enzyme. Comparisons of the activities of the enzymes toward the synthetic peptides to their activities toward macromolecular substrates suggest that higher order macromolecular structural features contribute to specificity.

Amino Acid Sequence↗

PubMed1996

Structural features of thyroid hormone response elements that increase susceptibility to inhibition by an RTH mutant thyroid hormone receptor.

The chicken lysozyme silencer F2 (F2) thyroid hormone response element (TRE) contains an unusual everted palindromic arrangement, has a high affinity for thyroid hormone receptor (TR) homodimers, and is especially sensitive to dominant negative inhibition by, the T3 resistance (RTH) mutant TR beta P453H. We used various TREs and TR mutations to determine the mechanisms for this sensitivity. Changing the F2 orientation from an everted palindrome to a direct repeat with a 4-bp gap (DR+4) (F2-DR) decreased the sensitivity to inhibition at high T3 concentrations, while a loss of this sensitivity occurred with a palindromic arrangement of these same half-sites. F2 contains the dinucleotide TG 5' to each consensus half-site conforming to the optimal TR-binding octamer, YRRGGTCA. A T to A change in position 1 of both F2 half-sites markedly reduced T3-induction, yet only slightly reduced TR homodimer or TR-retinoid X receptor (RXR) heterodimer binding. The TR beta ninth heptad mutation, L428R, prevents TR heterodimerization with RXR and eliminates the inhibitory effect of the P453H mutant TR on the F2-DR, but not the F2 element. Structural features of a TRE that favor strong TR binding of both TR homodimers and TR-RXR heterodimers containing the mutant TR, such as the everted palindromic conformation or the optimal TR-binding consensus octamer, enhance the sensitivity of a TRE to inhibition by the mutant TR. Thus, both half-site orientation and sequence contribute to the sensitivity of a given TRE to dominant negative inhibition by a mutant TR.

Amino Acid Sequence↗

PubMedDate not supplied

Structural features of cultured epithelial cells from the adult rat epididymis.

Epithelial cells isolated from the caput epididymidis of adult rats were placed in primary culture and examined daily for ten days for changes in external anatomy, reorganization of cytoskeletal components, maintenance of characteristic cytoplasmic features, and response to media formulated to minimize nonepithelial cell proliferation. Significant cell attachment to the substrate began after the first 24 hours of culture. After attachment, the cells underwent a progressive flattening and became closely applied to the substrate. This was accompanied by a redistribution of microvilli on the cell surface and a reorganization of cytoskeletal elements within the cell. After flattening, the cultured cells displayed an extensive array of 10-nm filaments which were associated with the desmosomes attaching adjacent cells. Immunofluorescence studies demonstrated that these were keratin-containing intermediate filaments and 2-D gel electrophoresis of intact cells and cell cytoskeletons revealed that a family of "keratin-like" polypeptides were major components of the cells. Epithelial cell attachment, morphology, and maintenance in the primary culture were unaffected by D-valine, cytosine arabinoside, or both; however, these agents, either individually or in combination, reduced significantly the number of cells incorporating 3H-thymidine. These data show that isolated epithelial cells retain some differentiated structural features that characterize the intact cell and that enriched cultures of epithelial cells can be maintained under conditions where fibroblast proliferation is inhibited.

Animals↗

PubMed2000

DNA breakage detection-FISH (DBD-FISH) in human spermatozoa: technical variants evidence different structural features.

Non-irradiated and X-irradiated (80 Gy) human spermatozoa were processed for in situ DNA breakage detection-FISH (DBD-FISH) of the whole genome, following two alternative variations of the basic technique. In the first, cells were initially incubated in the alkaline unwinding solution for transformation of DNA breaks into single-stranded DNA (ssDNA) to be hybridized, followed by the lysing solutions for protein removal. In the second, incubation in the lysing solutions was carried out before the denaturation step. The first approach yielded two subpopulations. While most sperm nuclei were faintly labeled and had chromocenters, a small subpopulation was strongly and homogeneously labeled, due to extensive DNA breakage. X-ray exposure increased the surface and mean fluorescence intensity. Otherwise, when the denaturation step was performed after protein extraction, all sperm nuclei yielded strong and dispersed FISH signals. Protein removal allows access of the unwinding solution to the DNA, which has abundant alkali-labile sites, and thus gives rise to large areas of ssDNA that are labeled by FISH. X-ray exposure increased the dispersion of FISH signals but decreased their mean fluorescence intensity. A linear dose-response was generated using the second experimental variant, being 30 Gy the lowest dose for detecting induction of damage by X-rays in mature sperm chromatin. These results indicate that DBD-FISH is not only useful for in situ detection of DNA breakage but also for revealing structural features of chromatin.

DNA↗

PubMed2003

Evolutionary history, structural features and biochemical diversity of the NlpC/P60 superfamily of enzymes.

BACKGROUND: Peptidoglycan is hydrolyzed by a diverse set of enzymes during bacterial growth, development and cell division. The N1pC/P60 proteins define a family of cell-wall peptidases that are widely represented in various bacterial lineages. Currently characterized members are known to hydrolyze D-gamma-glutamyl-meso-diaminopimelate or N-acetylmuramate-L-alanine linkages. RESULTS: Detailed analysis of the N1pC/P60 peptidases showed that these proteins define a large superfamily encompassing several diverse groups of proteins. In addition to the well characterized P60-like proteins, this superfamily includes the AcmB/LytN and YaeF/YiiX families of bacterial proteins, the amidase domain of bacterial and kinetoplastid glutathionylspermidine synthases (GSPSs), and several proteins from eukaryotes, phages, poxviruses, positive-strand RNA viruses, and certain archaea. The eukaryotic members include lecithin retinol acyltransferase (LRAT), nematode developmental regulator Egl-26, and candidate tumor suppressor H-rev107. These eukaryotic proteins, along with the bacterial YaeF/poxviral G6R family, show a circular permutation of the catalytic domain. We identified three conserved residues, namely a cysteine, a histidine and a polar residue, that are involved in the catalytic activities of this superfamily. Evolutionary analysis of this superfamily shows that it comprises four major families, with diverse domain architectures in each of them. CONCLUSIONS: Several related, but distinct, catalytic activities, such as murein degradation, acyl transfer and amide hydrolysis, have emerged in the N1pC/P60 superfamily. The three conserved catalytic residues of this superfamily are shown to be equivalent to the catalytic triad of the papain-like thiol peptidases. The predicted structural features indicate that the N1pC/P60 enzymes contain a fold similar to the papain-like peptidases, transglutaminases and arylamine acetyltransferases.

Amino Acid Sequence↗

PubMed1999

Structural features contributing to complex formation between glycogen phosphorylase and phosphorylase kinase.

A polyclonal antibody was generated against a peptide corresponding to a region opposite the regulatory face of glycogen phosphorylase b (P-b), providing a probe for detecting and quantifying P-b when it is bound to its activating kinase, phosphorylase kinase (PhK). Using both direct and competition enzyme-linked immunosorbent assays (ELISAs), we have measured the extent of direct binding to PhK of various forms of phosphorylase, including different conformers induced by allosteric effectors as well as forms differing at the N-terminal site phosphorylated by PhK. Strong interactions with PhK were observed for both P-b', a truncated form lacking the site for phosphorylation, and P-a, the phosphorylated form of P-b. Further, the binding of P-b, P-b', and P-a was stimulated a similar amount by Mg(2+), or by Ca(2+) (both being activators of PhK). Our results suggest that the presence and conformation of P-b's N-terminal phosphorylation site do not fully account for the protein's affinity for PhK and that regions distinct from that site may also interact with PhK. Direct ELISAs detected the binding of P-b by a truncated form of the catalytic gamma subunit of PhK, consistent with the necessary interaction of PhK's catalytic subunit with its substrate P-b. In contrast, P-b' bound very poorly to the truncated gamma subunit, suggesting that the N-terminal phosphorylatable region of P-b may be critical in directing P-b to PhK's catalytic subunit and that the binding of P-b' by the PhK holoenzyme may involve more than just its catalytic core. The sum of our results suggests that structural features outside the catalytic domain of PhK and outside the phosphorylatable region of P-b may both be necessary for the maximal interaction of these two proteins.

Adenosine Monophosphate↗

PubMed1998

Reconstitution of core light-harvesting complexes of photosynthetic bacteria using chemically synthesized polypeptides. 2. Determination of structural features that stabilize complex formation and their implications for the structure of the subunit complex.

Chemically synthesized polypeptides have been utilized with a reconstitution assay to determine the role of specific amino acid side chains in stabilizing the core light-harvesting complex (LH1) of photosynthetic bacteria and its subunit complex. In the preceding paper [Meadows, K. A., Parkes-Loach, P. S., Kehoe, J. W., and Loach, P. A. (1998) Biochemistry 37, 3411-3417], it was demonstrated that 31-residue polypeptides (compared to 48 and 54 amino acids in the native polypeptides) having the same sequence as the core region of the beta-polypeptide of Rhodobacter sphaeroides (sph beta 31) or Rhodospirillum rubrum (rr beta 31) could form subunit-type complexes. However, neither polypeptide interacted with the native alpha-polypeptides to form a native LH1 complex. In this paper, it is demonstrated that larger segments of the native Rb. sphaeroides beta-polypeptide possess native behavior in LH1 formation. Polypeptides were synthesized that were six (sph beta 37) and ten amino acids (sph beta 41) longer than sph beta 31. Although sph beta 37 exhibited behavior nearly identical to that of sph beta 31, sph beta 41 behaved more like the native polypeptide. In the case of rr beta 31, a polypeptide with four additional amino acids toward the C terminus was synthesized (rr beta 35). Because LH1-forming behavior was not recovered with this longer polypeptide, one or more of the three remaining amino acids at the C-terminal end of the native beta-polypeptide seem to play an important role in LH1 stabilization in Rs. rubrum. Three analogues of the core region of the Rb. sphaeroides beta-polypeptide were synthesized, in each of which one highly conserved amino acid was changed. Evidence was obtained that the penultimate amino acid, a Trp residue, is especially important for subunit formation. When it was changed to Phe, the lambda Max of the subunit shifted from 823 to 811 nm and the association constant decreased about 500-fold. Changing each of two other amino acids had smaller effects on subunit formation. Changing Trp to Phe at the location six amino acid residues toward the C terminus from the His coordinated to Bchl resulted in an approximately 10-fold decrease in the association constant for subunit formation but did not affect the formation of a LH1-type complex compared to sph beta 31. Finally, changing Arg to Leu at the location seven amino acid residues toward the C terminus from the His coordinated to Bchl decreased the association constant for subunit formation by about 30-fold. In this case, no LH1-type complex could be formed. On the basis of these results, in comparison with the crystal structure of the LH2 beta-polypeptide of Rhodospirillum molischianum, two possible structures for the subunit complex are suggested.

Amino Acid Sequence↗

PubMed1993

Structural features and properties of an extraordinarily stable hairpin-turn structure of d(GCGAAGC).

The extraordinarily stable hairpin-like structure formed by a short DNA fragment, d(GCGAAGC), has been studied by NMR spectroscopy and UV melting behaviour. The fragment is folded back between A4 and A5, and forms two terminal G-C base pairs and a non-Watson-Crick G-A base pair. All the nucleotides adopt C2'-endo sugar puckers. Both G1C2G3A4 and A5G6C7 moieties have characteristics of B-form geometry and within each moiety all the bases are involved in extensive base-base interactions. Distortion from B-form occurs in only the three torsion angles between A4 and A5 residues, which causes a sharp turn in the structure. There is no clear distinction between a stem and a loop region, as observed in usual hairpin structures, so that we classify it as a turn (hairpin-turn) structure. In addition to the thermal stability, this fragment is more stable towards the attack of some nucleases than other single-stranded as well as usual hairpin DNA fragments.

Hot Temperature↗

PubMed2001

Crystal structure of a mutant hERalpha ligand-binding domain reveals key structural features for the mechanism of partial agonism.

The crystal structure of a triple cysteine to serine mutant ERalpha ligand-binding domain (LBD), complexed with estradiol, shows that despite the presence of a tightly bound agonist ligand, the protein exhibits an antagonist-like conformation, similar to that observed in raloxifen and 4-hydroxytamoxifen-bound structures. This mutated receptor binds estradiol with wild type affinity and displays transcriptional activity upon estradiol stimulation, but with limited potency (about 50%). This partial activity is efficiently repressed in antagonist competition assays. The comparison with available LBD structures reveals key features governing the positioning of helix H12 and highlights the importance of cysteine residues in promoting an active conformation. Furthermore the present study reveals a hydrogen bond network connecting ligand binding to protein trans conformation. These observations support a dynamic view of H12 positioning, where the control of the equilibrium between two stable locations determines the partial agonist character of a given ligand.

Cloning, Molecular↗

PubMed2003

The structure and thermal motion of the B800-850 LH2 complex from Rps.acidophila at 2.0A resolution and 100K: new structural features and functionally relevant motions.

The structure at 100K of integral membrane light-harvesting complex II (LH2) from Rhodopseudomonas acidophila strain 10050 has been refined to 2.0A resolution. The electron density has been significantly improved, compared to the 2.5A resolution map, by high resolution data, cryo-cooling and translation, libration, screw (TLS) refinement. The electron density reveals a second carotenoid molecule, the last five C-terminal residues of the alpha-chain and a carboxy modified alpha-Met1 which forms the ligand of the B800 bacteriochlorophyll. TLS refinement has enabled the characterisation of displacements between molecules in the complex. B850 bacteriochlorophyll molecules are arranged in a ring of 18 pigments composed of nine approximate dimers. These pigments are strongly coupled and at their equilibrium positions the excited state dipole interaction energies, within and between dimers, are approximately 370cm(-1) and 280cm(-1), respectively. This difference in coupling energy is similar in magnitude to changes in interaction energies arising from the pigment displacements described by TLS tensors. The displacements appear to be non-random in nature and appear to be designed to optimise the modulation of pigment energy interactions. This is the first time that LH2 pigment displacements have been quantified experimentally. The calculated energy changes indicate that there may be significant contributions to inter-pigment energy interactions from molecular displacements and these may be of importance to photosynthetic energy transfer.

Bacterial Proteins↗

PubMed2000

Common structural features in gramicidin and other ion channels.

This review compares and contrasts the structures of several different types of ion channels with known three-dimensional structures, including gramicidin and the family of peptaibol channels, as well as the Streptomyces lividans potassium channel, to reveal common features in their structures that relate to their functional roles in ion binding and transport across membranes. Specifically, the locations of aromatic amino acids, the dimensions of the molecules, the multimeric nature of the channels and the roles of hydrogen bonds in stabilising such structures, the means by which the channels open and close, and the chemical nature of the groups which make up the channel lumen are discussed. The emphasis is on the commonality of features found in model channels, which may ultimately be found in other biological channel structures.

Amino Acid Sequence↗

PubMed1992

Structural features of the pore formed by Staphylococcus aureus alpha-toxin inferred from chemical modification and primary structure analysis.

Staphylococcus aureus alpha-toxin makes cells and model membranes permeable to ions and uncharged molecules by opening oligomeric pores of uniform size. Its primary sequence reveals peculiar features which give some hints on the structure of the pore. A flexible region separating the toxin into two halves, several amphiphilic beta-strands and two amphiphilic alpha-helices long enough to span the hydrophobic core of the lipid bilayer are predicted. In analogy to bacterial porins, we propose that the inner walls of the pore are, at least in part, built by an amphiphilic beta-barrel. The model is consistent with circular dichroism data and with the electrophysiological properties of the pore. Functional information on this toxin were obtained by chemical modification of its four histidine residues. Specific carbethoxylation suggested they have different roles: one is required for specific receptor binding, one for oligomerisation and two for unspecific lipid binding. A tentative assignment of each histidine to its specific role is done on the basis of the structural predictions. A functionally related hemolysin, Aeromonas hydrophyla aerolysin, reveals remarkably similar features including the presence and location of histidines involved in receptor binding and oligomerisation.

Bacterial Toxins↗

PubMedDate not supplied

[Functional changes and structural features of the testis in patients after acute parotid orchitis].

Structural changes and functional features of the testes were studied in 20 patients who had had parotid orchitis (PO) 6 months to 1.5 years before the study. The examination including ultrasonography of the testes, investigation of ejaculate, radioimmunoassay for serum testosterone, FSH, LH brought out a significant reduction of the mean volume and echogenicity of the affected testicles by 44.7 and 50%, respectively, in 15 patients; a 58.2% decrease in the number of spermatozoa in ml; a 71.2% rise in FSH level in 6 patients. Morphometry of biopsy specimen of the testicles on the affected side has shown that mean sectional area of the tubules has diminished by 40%, the spermatogenesis index--by 77.1% while the volume of the intertubular connective tissue increased by 47.7%. Thus, after acute PO, the patients develop atrophic changes in the testes and a decline in spermatogenic function up to secretory infertility.

Acute Disease↗

PubMed1977

[Structural features of the brain stem reticular formation, hippocampus and limbic region of the cortex].

The paper compares the structural reorganization of reticular formation of the brain stem with the cortical structures of the limbic system--hippocamp and limbic cortex in the mammalian comparative order (a hedgehog, a rabbit, a cat, a dog, a dolphin, a monkey, a man). In all the studied links of the limbico-reticular system the author revealed general regularity: the main trend of a structural development is expressed in the intensification of their structural heterogeneity: nuclei are divided in subnuclei, areas in subareas, layers in sublayers. In all structures these features are expressed more vividly in their phylogenetic new parts. Besides, changes of the brain caudal sections--reticular formation are relatively less expressed than the rostral sections, i.e. hippocamp and limbic cortex.

Animals↗

PubMed2002

Structural features of arabinoxylans from bajra (pearl millet).

Structures of arabinoxylans (AX) from bajra, from a variety known to have characteristic quality in the making of roti, an unleavened flat bread, were elucidated by a combination of methylation analysis, (13)C NMR, FT-IR, etc. Arabinoxylans isolated from barium hydroxide-extracted polysaccharides and hemicellulose B had a backbone of xylose residues with beta-(1,4) linkages and were branched mainly through alpha-(1,3) linkages by arabinofuranosyl residues. Completely branched xylose residues were also present. The AX from bajra characteristically had large numbers of branches, and this may be one of the reasons for the crispiness of the rotis.

Gas Chromatography-Mass Spectrometry↗

PubMed2000

Predicting protein function from structure: unique structural features of proteases.

We have noted consistent structural similarities among unrelated proteases. In comparison with other proteins of similar size, proteases have smaller than average surface areas, smaller radii of gyration, and higher C(alpha) densities. These findings imply that proteases are, as a group, more tightly packed than other proteins. There are also notable differences in secondary structure content between these two groups of proteins: proteases have fewer helices and more loops. We speculate that both high packing density and low alpha-helical content coevolved in proteases to avoid autolysis. By using the structural parameters that seem to show some separation between proteases and nonproteases, a neural network has been trained to predict protease function with over 86% accuracy. Moreover, it is possible to identify proteases whose folds were not represented during training. Similar structural analyses may be useful for identifying other classes of proteins and may be of great utility for categorizing the flood of structures soon to flow from structural genomics initiatives.

Endopeptidases↗

PubMedDate not supplied

[Structural features of immunoglobulin G from leukemic cattle].

Structural peculiarities of immunoglobulin G (IgG) in cattle with leukemia were studied using the method of dansyl-finger prints and proteolytic fragmentation with pepsin. It is stated that the protein from the blood of leukemic animals differs from the similar IgG subfraction of healthy animals in the amount of peptides: their number is 39 in sick animals, 41--in healthy ones. The studied protein is splitted into three fragments under the effect of pepsin. The molecular mass of F(ab1)2- and Fc1-fragments isolated from the hydrolyzate is 94 and 51 kDa, respectively. Fab-, Fc- and F(ab')2-, Fc'-fragments manifest a complete antigenic identity. The antibody activity is inherent only in the F(ab')2-fragment; it reacts positively in the precipitation test together with monospecific antiserum against IgG, typical of the malignant growth. This confirms a supposition that structural peculiarities of the protein typical of the malignant growth and isolated from the blood of cattle with leukemia depend on changes in the protein Fab-fragment.

Animals↗

PubMed1995

Ciliate telomerase RNA structural features.

Telomerase RNA is an integral part of telomerase, the ribonucleoprotein enzyme that catalyzes the synthesis of telomeric DNA. The RNA moiety contains a templating domain that directs the synthesis of a species-specific telomeric repeat and may also be important for enzyme structure and/or catalysis. Phylogenetic comparisons of telomerase RNA sequences from various Tetrahymena spp. and hypotrich ciliates have revealed two conserved secondary structure models that share many features. We have cloned and sequenced the telomerase RNA genes from an additional six Tetrahymena spp. (T. vorax, T. borealis, T. australis, T. silvana, T. capricornis and T. paravorax). Inclusion of these sequences, most notably that from T. paravorax, in a phylogenetic comparative analysis allowed us to more narrowly define structural elements that may be necessary for a minimal telomerase RNA. A primary sequence element, positioned 5' of the template and conserved between all previously known ciliate telomerase RNAs, has been reduced from 5'-(C)UGUCA-3' to the 4 nt sequence 5'-GUCA-3'. Conserved secondary structural features and the impact they have on the general organization of ciliate telomerase RNAs is discussed.

Animals↗