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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↗

PubMed2006

Structural features of incremental line-like striations in mandibular condylar cartilage of c-src-deficient mice.

Mandibular condylar cartilage is sensitive to masticatory force, while mice lacking the c-src gene (c-src-deficient mice) have osteopetrosis and tooth eruption failure. The purpose of this study was to investigate the morphology of the mandibular condyle in these mice, which were maintained with a soft-food diet for 240 days after birth. The condylar head in the c-src-deficient mice showed slight deformity in shape before weaning, but showed remarkable undergrowth after weaning. No significant morphological or histological differences were detected between the mandibular condyle in wild-type mice fed soft food and those fed hard food, indicating that osteopetrosis, as well as abnormal masticatory force, influences the morphology of the mouse mandibular condyle, and that malocclusion rather than dietary consistency may have greater influence. After 70 days, incremental line-like striations consisting of cartilaginous and non-cartilaginous layers were detected in the mandibular condyle of the c-src-deficient mice, but not in the tibial growth plate. Immunostaining of aggrecan, collagen types II and X, and osteopontin was detected in the cartilaginous layers, but not in the non-cartilaginous layers showing collagen type I immunostaining. Chondrocyte lacunae were not eroded in the cartilaginous layers, and complete circumferential mineralisation around the lacunae and impaired osteoclast (chondroclast) function can account for this phenomenon. However, repeated cessation of chondrocyte differentiation may be required to completely explain the formation of the striations. These results indicate that the mandibular condyle in the c-src-deficient mice has unique structural features, adding to its deformity.

Aggrecans↗

PubMed2004

Torsadogenic cardiotoxicity of antipsychotic drugs: a structural feature, potentially involved in the interaction with cardiac HERG potassium channels.

Many non-cardiovascular drugs of common clinical use cause, as an unwanted accessory property, the prolongation of the cardiac repolarisation process, due to the block of the HERG (Human Ether-a-go-go Related Gene) potassium channel, responsible for the repolarising I(Kr) current. This delayed cardiac repolarisation process can be often unmasked by a prolongation of the QT interval of the ECG. In these conditions, premature action potentials can generate morphologically anomalous after-polarisations, and trigger a dangerous kind of polymorphic ventricular tachyarrhythmia, known as torsade de pointes, which can evolve in ventricular fibrillation and death. The risk associated with the torsadogenic cardiotoxicity of drugs, which prolong the QT interval has been the topic of documents produced by many health authorities, giving important issues about the preclinical and clinical evaluation of cardiac safety. Besides, public and private research laboratories developed several experimental in vitro or in vivo strategies, aimed to an early recognition of the influence of a drug (or of a drug-candidate) on the HERG channel and/or on the cardiac repolarisation process. Also the identification of a possible pharmacophore model, common in all or at least in numerous torsadogenic drugs, could represent a first step for the development of useful in silico approaches, allowing a preliminary indication about the potential torsadogenic property of a given molecule. In this work, we described the electrophysiological basis of torsade de pointes and listed several pharmacological classes of torsadogenic drugs. Among them, we focused our attention on antipsychotics, with an accurate overview on the experimental and clinical reports about their torsadogenic properties. Moreover, a common structural feature exhibited by these drugs, despite of their remarkable chemical differences, is evidenced by a computational approach and is indicated as a possible "facilitating" requirement for their torsadogenic properties. Together with other remarks, coming from different computational studies, the individuation of a satisfactory "toxicophore" model could be greatly useful, for the theoretical prediction of torsadogenic properties of a given chemical moiety and for the design of new drugs devoid of such an undesired and potentially lethal side-effect.

Animals↗

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↗

PubMed1964

CONCERNING SOME SPECIAL STRUCTURAL FEATURES OF THE COLLAGEN MOLECULE.

A summary of results and ideas concerning special features of the covalent structure of collagen is presented. Our recent data on the nature of aspartyl ester pairs in collagen cross-linking and speculations about how these may function in fiber maturation are discussed. An important new aldehydic component associated with the cross-link sites has been detected and is under investigation. A model of collagen based upon 4 subunits of 25,000 to 30,000 per alpha component has been developed. These subunits appear to be held together in a linear array by three pairs of ester bonds. A more detailed picture of the distribution of "crystalline" and "amorphous" regions along the tropocollagen molecule has been proposed primarily based on the results of analyses of collagen peptide fractions obtained with collagenase. Other topics such as gamma-glutamyl bonds in collagen and results with carbonyl group-detecting reagents which demonstrate the presence of small amounts of alpha-keto acid groups are briefly considered.

Animals↗

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↗

PubMed2006

Search for cyclodextrin-based inhibitors of anthrax toxins: synthesis, structural features, and relative activities.

Recently, using structure-inspired drug design, we demonstrated that aminoalkyl derivatives of beta-cyclodextrin inhibited anthrax lethal toxin action by blocking the transmembrane pore formed by the protective antigen (PA) subunit of the toxin. In the present study, we evaluate a series of new beta-cyclodextrin derivatives with the goal of identifying potent inhibitors of anthrax toxins. Newly synthesized hepta-6-thioaminoalkyl and hepta-6-thioguanidinoalkyl derivatives of beta-cyclodextrin with alkyl spacers of various lengths were tested for the ability to inhibit cytotoxicity of lethal toxin in cells as well as to block ion conductance through PA channels reconstituted in planar bilayer lipid membranes. Most of the tested derivatives were protective against anthrax lethal toxin action at low or submicromolar concentrations. They also blocked ion conductance through PA channels at concentrations as low as 0.1 nM. The activities of the derivatives in both cell protection and channel blocking were found to depend on the length and chemical nature of the substituent groups. One of the compounds was also shown to block the edema toxin activity. It is hoped that these results will help to identify a new class of drugs for anthrax treatment, i.e., drugs that block the pathway for toxin translocation into the cytosol, the PA channel.

Animals↗

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↗