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PubMed2005

First QSAR report on FSH receptor antagonistic activity: quantitative investigations on physico-chemical and structural features among 6-amino-4-phenyltetrahydroquinoline derivatives.

A quantitative attempt has been made to correlate the structure-activity relationship (SAR) among the recently reported 6-amino-4-phenyltetrahydroquinoline derivatives as antagonists for the Gs-protein-coupled human follicle-stimulating hormone (FSH) receptor. The compounds used for the present study have been reported to show high antagonistic efficacy in vitro using a CHO-hFSHR(luc) assay. Our QSAR investigations revealed a hydrophobic type of interactions between these ligands and the FSH receptor, hence confirming the presence of a lipophilic pocket on the active site of the target structure. The positive coefficient of ClogP variable in our derived QSAR model suggests that more hydrophobic ligands are crucial for their FSH receptor antagonistic efficacy. In exploring the structural requirements among these congeners, we found an amide linkage as conducive to their FSH receptor antagonistic activity. Also, an unsubstituted 4-phenyl ring of the tetrahydroquinoline scaffold is favorable for their FSH receptor antagonistic activity. The results discussed herein could be useful in understanding the nature of interactions of these newly identified ligands as FSH receptor antagonists and in designing more potent ligands based on this novel 6-amino-4-phenyltetrahydroquinoline scaffold.

Models, Chemical↗

PubMed2005

Classification of spider neurotoxins using structural motifs by primary structure features. Single residue distribution analysis and pattern analysis techniques.

In recent years the data on the novel structures of spider toxins have been greatly increasing. The sequence data should be classified. We introduced two primary structure analysis techniques-single residue distribution analysis (SRDA) and pattern analysis for classifying spider polypeptide toxins with molecular weight less than 10kDa. For multiple sequence alignment, we also introduced three novel sequence representation formats named as a simple record, motif record and a pattern record, which can be useful for large-scale analysis of structures. About 300 sequences of spider toxins were analyzed and nine primary structure motifs were identified. New classification of spider toxins was proposed on the basis of previously described principal structural motif (PSM) and extra structural motif (ESM) [Kozlov, S.A., Malyavka, A.A., McCutchen, B., Lu, A., Schepers, E., Herrmann, R., Grishin, E.V., 2005. A novel strategy for the identification of toxin-like structures in spider venom. Proteins 59 (1), 131-140]. Five main structural classes were revealed, and for putative ion channel inhibitors from the most numerous classes 1, 2, and 3, five-digital personal ID numbers were introduced. A reference table with simple, motif and pattern representation sequence formats was created for all analyzed structures.

Amino Acid Motifs↗

PubMed1985

Evidence of random structural features in the heparin polymer.

The first use of computer-simulation studies to examine heparin's structure has been reported. The product distributions obtained when porcine mucosal heparins were depolymerized with heparinase have been compared to computer-simulated distributions. The modeled distribution was relatively unaffected by the polydispersity and molecular weight of heparin. However, the percent of heparinase-cleavable glycosidic linkages and their distribution throughout the polymer resulted in a marked change in the simulated product distribution. The similarity between experimentally observed and computer-simulated product distributions is consistent with the random distribution of heparinase-cleavable sites in porcine mucosal heparin. Finally, a random distribution of N-acetyl residues with respect to heparinase-cleavable sites was experimentally observed.

Animals↗

PubMed1994

Goldfish tyrosinase related protein I (TRP-1): deduced amino acid sequence from cDNA and comments on structural features.

Previous workers have shown that mammals have tyrosinase and tyrosinase related proteins (TRPs) that share common structural domains, all of which are not present in microbial tyrosinases. We report here the deduced amino acid sequence of a TRP from fish that is highly homologous to mammalian TRP-1. Examination of the structures of these vertebrate tyrosinases and TRPs shows that, aside from the conserved cysteine-rich and histidine-rich domains previously noted, there are a large number of conserved prolines and glycines, leading to an abundance of turns and few conserved helical regions. These tyrosinases and TRP-1s also have in their cytosolic tails a consensus sequence that is not present in any other protein. It is proposed that this sequence may participate in directing these proteins to the melanosomes.

Amino Acid Sequence↗

PubMed1984

A family of small nucleoplasmic RNAs with common structural features.

The four small nucleoplasmic RNAs designated as U1, U2, U4 and U5 RNA have a common structural domain or domain A. It is characterized by the presence of consensus sequence Pu-A-(U)5-G-Pup in a free single-stranded region and of the sequence Py-N-Py-Gp in the top loop of a hairpin located at the 3' end of the free region. Domain A is likely to be involved in a function common to the four small RNAs. Other domains possibly involved in the specific function of U1 and U5 RNAs are also presented. Several molecular forms of a same U RNA may be found in a same cellular type. These variant U RNAs are particularly numerous for U5 RNA. The possible origin of such new molecular forms is discussed in relation to multigene families for U RNAs. U1, U2, U4 and U5 RNAs are capped (with trimethylguanosine) and the consensus sequence for their 6 first nucleotides is A-(Py)5p. Thus, their 5' end resembles that of premessenger RNA, also capped (with monomethylguanosine) and bearing A-(Py)5p. Both classes of RNA are synthesized by RNA polymerase B, but the presence of a "TATA box" upstream of the capsite has not yet been demonstrated for U RNA genes. U1, U2, U4 and U5 RNAs bear a sequence C-Py-Pu at their 3' end or very close to it. This trinucleotide might be part of a site of post-transcriptional cleavage of U RNA precursors.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed1991

Structural features of neurons in whole grafts of the rat inferior colliculus.

The inferior colliculus (IC) is a midbrain structure that receives ascending auditory input from brainstem nuclei via the lateral lemniscus, sends efferent fibers to the medial geniculate body of thalamus and receives descending projections from auditory cortex. In the rat, the IC consists of dorsal and external cortices surrounding the central nucleus of IC (CNIC) which is populated by discoid and stellate neurons; the CNIC has a laminar appearance arising from organization of lemniscal fibers and processes of discoid cells. The IC of adult rats was chosen for implantation of whole grafts of E16-17 caudal tectum into unilateral lesion sites. Dendritic and somal architecture of graft neurons was examined 1 to 4.5 months following implantation using rapid Golgi, HRP and Nissl methods. The CNIC of rat is dominated by principal neurons with relatively flattened dendritic fields. In grafts of caudal tectum the most common neuron class observed possesses flattened dendritic arbors which often parallel one another. These neurons also resemble CNIC neurons of host tissue adjacent to the graft border. Spine formations appear on both proximal and distal dendrites of this neural type in both normal and implanted tissues. In addition, comparable somal features of graft neurons include ovoid or fusiform shapes with regular nuclear membranes as found in the normal colliculus. In Golgi stained material fewer stellate class neurons appear as in the normal CNIC, although stellate cell classes are more abundant in the pericentral areas of normal tissue. Both neuron populations are retrogradely labelled in graft and normal IC after HRP injection into the medial geniculate body. These features suggest that the graft core typically consists of prototypic CNIC cells. Other features of neuron and glial cell density vary in graft material which also shows a complex network of vasculature. These results demonstrate that whole grafts of caudal tectum placed into the inferior colliculus can form organized neural architecture similar to the normal CNIC. The somal, dendritic and spine features of these neurons form a potential substrate for connectional and functional properties which establish this preparation as suitable for further investigation as a model for development and recovery of function in the central auditory system.

Animals↗

PubMed1996

The adenylosuccinate synthetase from the hyperthermophilic archaeon Pyrococcus species displays unusual structural features.

The first example of a hyperthermophilic adenylosuccinate synthetase is reported, which is an enzyme that must maintain its folded structure at temperatures as high as 102 degrees C. The amino acid sequence of this key enzyme has been determined after cloning and sequencing the purA-like gene from the archaeal Pyrococcus sp. strain ST700. The corresponding protein displays two unexpected features: (1) it is 21% shorter than the homologous mesophilic enzymes and this shortening corresponds to the loss of two alpha-helices and three beta-strands present in the Escherichia coli enzyme; (2) surprisingly, the archaeal adenylosuccinate synthetase has a significant number of substitutions in residues that are conserved in all other homologous enzymes from bacteria to man. In E. coli, the conserved residues have been described as essential for catalytic activity and/or for maintaining the folded structure of the homodimer. Despite these drastic differences, the purA-like archaeal gene seems to be normally expressed and its product functions in vivo in bacteria, since it complemented an E. coli purA auxotroph. The archaeal adenylosuccinate synthetase appears to be a good example of a bona fide orthologous protein. Reconstruction of phylogenetic trees showed that the archaeal gene is equally distantly related to both eukaryotes and bacteria, independently of the numerous substitutions observed at critical positions.

Adenylosuccinate Synthase↗

PubMed2007

The first pure LambdaHT rotamer of a complex with a cis-[metal(nucleotide)2] unit: a cis-[Pt(amine)2(nucleotide)2] LambdaHT rotamer with unique molecular structural features.

cis-[PtA2(nucleotide)2] complexes (A2 stands for two amines or a diamine) have been extensively investigated as model compounds for key cisplatin-DNA adducts. All cis-[metal(nucleotide/nucleoside)2] complexes with guanine and related purines characterized in the solid state thus far have the DeltaHT conformation (head-to-tail orientation of the two bases and right-handed chirality). In sharp contrast, the LambdaHT conformation (left-handed chirality) dominates in acidic and neutral aqueous solutions of cis-[PtA2(5'-GMP)2] complexes. Molecular models and solution experiments indicate that the LambdaHT conformer is stabilized by 5'-phosphate/N1H hydrogen-bond interactions between cis nucleotides with the normal anti conformation. However, this evidence, while compelling, is indirect. At last, conditions have been defined to allow crystallization of this elusive conformer. The structure obtained reveals three unique features not present in all other cis-[PtA2(nucleotide)2] solid-state structures: a LambdaHT conformation, very strong hydrogen-bond interactions between the phosphate and N1H of cis nucleotides, and a very small dihedral angle between the planes of the two guanines lying nearly perpendicular to the coordination plane. These new results indicate that, because there are no local base-base repulsions precluding the LambdaHT conformer, global forces rather than local interactions account for the predominance of the DeltaHT conformer over the LambdaHT conformer in the solid state and in both inter- and intrastrand HT crosslinks of oligonucleotides and DNA.

Cisplatin↗

PubMed1993

Starch- and glycogen-debranching and branching enzymes: prediction of structural features of the catalytic (beta/alpha)8-barrel domain and evolutionary relationship to other amylolytic enzymes.

Sequence alignment and structure prediction are used to locate catalytic alpha-amylase-type (beta/alpha)8-barrel domains and the positions of their beta-strands and alpha-helices in isoamylase, pullulanase, neopullulanase, alpha-amylase-pullulanase, dextran glucosidase, branching enzyme, and glycogen branching enzymes--all enzymes involved in hydrolysis or synthesis of alpha-1,6-glucosidic linkages in starch and related polysaccharides. This has allowed identification of the transferase active site of the glycogen debranching enzyme and the locations of beta-->alpha loops making up the active sites of all enzymes studied. Activity and specificity of the enzymes are discussed in terms of conserved amino acid residues and loop variations. An evolutionary distance tree of 47 amylolytic and related enzymes is built on 37 residues representing the four best conserved beta-strands of the barrel. It exhibits clusters of enzymes close in specificity, with the branching and glycogen debranching enzymes being the most distantly related.

Amino Acid Sequence↗

PubMed1999

Structural features of protein-nucleic acid recognition sites.

We analyzed the atomic models of 75 X-ray structures of protein-nucleic acid complexes with the aim of uncovering common properties. The interface area measured the extent of contact between the protein and nucleic acid. It was found to vary between 1120 and 5800 A2. Despite this wide variation, the interfaces in complexes of transcription factors with double-stranded DNA could be broken up into recognition modules where 12 +/- 3 nucleotides on the DNA side contact 24 +/- 6 amino acids on the protein side, with interface areas in the range 1600 +/- 400 A2. For enzymes acting on DNA, the recognition module is on average 600 A2 larger, due to the requirement of making an active site. As judged by its chemical and amino acid composition, the average protein surface in contact with the DNA is more polar than the solvent accessible surface or the typical protein-protein interface. The protein side is rich in positively charged groups from lysine and arginine side chains; on the DNA side the negative charges from phosphate groups dominate. Hydrogen bonding patterns were also analyzed, and we found one intermolecular hydrogen bond per 125 A2 of interface area in high-resolution structures. An equivalent number of polar interactions involved water molecules, which are generally abundant at protein-DNA interfaces. Calculations of Voronoi atomic volumes, performed in the presence and absence of water molecules, showed that protein atoms buried at the interface with DNA are on average as closely packed as in the protein interior. Water molecules contribute to the close packing, thereby mediating shape complementarity. Finally, conformational changes accompanying association were analyzed in 24 of the complexes for which the structure of the free protein was also available. On the DNA side the extent of deformation showed some correlation with the size of the interface area. On the protein side the type and size of the structural changes spanned a wide spectrum. Disorder-to-order transitions, domain movements, quaternary and tertiary changes were observed, and the largest changes occurred in complexes with large interfaces.

Amino Acids↗

PubMed1997

Structural features of membrane fusion between influenza virus and liposome as revealed by quick-freezing electron microscopy.

The structure of membrane fusion intermediates between the A/PR/8(H1N1) strain of influenza virus and a liposome composed of egg phosphatidylcholine, cholesterol, and glycophorin was studied using quick-freezing electron microscopy. Fusion by viral hemagglutinin protein was induced at pH 5.0 and 23 degrees C. After a 19-s incubation under these conditions, small protrusions with a diameter of 10-20 nm were found on the fractured convex faces of the liposomal membranes, and small pits complementary to the protrusions were found on the concave faces. The protrusions and pits corresponded to fractured parts of outward bendings of the lipid bilayer or "microprotrusions of the lipid bilayer." At the loci of the protrusions and pits, liposomal membranes had local contacts with viral membranes. In many cases both the protrusions and the pits were aligned in regular polygonal arrangements, which were thought to reflect the array of hemagglutinin spikes on the viral surface. These structures were induced only when the medium was acidic with the virus present. Based on these observations, it was concluded that the microprotrusions of the lipid bilayer are induced by hemagglutinin protein. Furthermore, morphological evidence for the formation of the "initial fusion pore" at the microprotrusion was obtained. The protrusion on the convex face sometimes had a tiny hole with a diameter of <4 nm in the center. The pits transformed into narrow membrane connections <10 nm in width, bridging viruses and liposomes. The structures of the fusion pore and fusion neck with larger sizes were also observed, indicating growth of the protrusions and pits to distinct fusion sites. We propose that the microprotrusion of the lipid bilayer is a fusion intermediate induced by hemagglutinin protein, and suggest that the extraordinarily high curvature of this membrane structure is a clue to the onset of fusion. The possible architecture of the fusion intermediate is discussed with regard to the localization of intramembrane particles at the microprotrusion.

Acids↗

PubMed1999

Structural features and bleeding activity of commercial low molecular weight heparins: neutralization by ATP and protamine.

Differences in the structure of three low molecular weight heparins (LMWHs) have been observed by applying physico-chemical methods as well as enzymatic degradation with bacterial heparinase and heparitinase II. The production of enoxaparin maintains the internal structure of the parent heparin with the exception of the unsaturated nonreducing end. In contrast, the production of dalteparin and nadroparin removes part of their nonsulfated uronic acid residues and, unlike enoxaparin and unfractionated heparin (UFH), these LMWHs also contain regions that remain resistant to the action of heparitinase II. Enoxaparin has a lower molecular weight distribution than dalteparin and nadroparin and is composed of at least four discrete molecular weight populations. A rat-tail model demonstrated that LMWHs applied topically or injected intravenously had a lower bleeding potency when compared with UFH treatment. The bleeding potencies of the different LMWHs were similar. Furthermore, adenosine triphosphate (ATP) completely neutralized bleeding caused by LMWHs and UFH in the animal model when applied topically and significantly reduced bleeding in heparinized surgical patients undergoing cardiopulmonary bypass surgery.

Adenosine Triphosphate↗

PubMed1990

Structural features of the amplified N-myc oncogene detected by micrococcal nuclease digestion of neuroblastoma cell nuclei.

The structure of chromatin containing amplified N-myc in neuroblastoma and retinoblastoma cells was investigated using micrococcal nuclease digestion of isolated nuclei. The size distribution of DNA fragments containing N-myc, produced by micrococcal nuclease digestion of nuclei, was determined and compared to that of DNA containing the structural gene for dihydrofolate reductase. A perturbation of the native structure of chromatin containing N-myc was evident from the association of N-myc with more extensively digested DNA when compared with chromatin containing dihydrofolate reductase.

Cell Nucleus↗

PubMed1976

Lipophosphonoglycan of the plasma membrane of A canthamoeba castellanii. Inositol and phytosphingosine content and general structural features.

Lipophosphonoglycan, a major component of the plasma membrane of Acanthamoeba castellanii, has now been shown to contain 8% inositol and 13% C25- and C24-phytosphingosines in addition to the previously identified content of neutral sugars (26%), amino sugars (3%), aminophosphonates (10%), acidhydrolyzable phosphate (3%), and long chain fatty acids (14%). The fatty acids and phytosphingosines are in ceramide groups. Lipophosphonoglycan can be separated by dodecyl sulfate-polyacrylamide electrophoresis into two major components that are similar in composition except for different oligosaccharide groups. A tentative structural model incorporating these features is proposed in which each of the two components of lipophosphonoglycan is conceived as an oligomeric inositol-containing glycosphingolipid.

Amoeba↗

PubMed1992

Phylogeny of the p68c-ets-1 amino-terminal transactivating domain reveals some highly conserved structural features.

The chicken c-ets-1 locus gives rise to two distinct transcription factors differing only in their structurally and functionally unrelated N-termini. One of these transcription factors, p54c-ets-1, contains a specific, short (27 amino acids), hydrophilic N-terminus encoded by a single exon, I54, that is widely conserved among vertebrates. The other one, p68c-ets-1, the cellular counterpart of the viral ets oncogene product, differs in the replacement of the I54 by two exons, termed alpha and beta, encoding a larger (71 amino acids), hydrophobic N-terminus which, in contrast to I54, exhibits properties of a transactivating domain. To date the alpha and beta exons have only been found in chicken. Here, we demonstrate the existence of the alpha and beta exons in other avian species (quail and duck) and the existence of the alpha exon in reptiles (turtle). However, none of them could be detected in mammals. Our results strongly suggest that, in contrast to the phylogenetically well-conserved I54 exon, the alpha exon is restricted to reptilian species (birds and 'true' reptiles), whereas the beta exon is detectable so far only in birds. Comparison of their amino acid sequences reveals that the alpha exon and to a much greater extent the beta exon have diverged faster than the I54 exon. In addition, we show that the N- and C-terminal thirds of the alpha exon and the highly hydrophobic nature of the alpha beta-encoded sequence are heavily conserved features and thus likely to be required for function as a transactivating domain in p68c-ets-1 and possibly in the viral P135gag-myb-ets transforming protein.

Amino Acid Sequence↗

PubMed2005

The prokaryotic enzyme DsbB may share key structural features with eukaryotic disulfide bond forming oxidoreductases.

Three different classes of thiol-oxidoreductases that facilitate the formation of protein disulfide bonds have been identified. They are the Ero1 and SOX/ALR family members in eukaryotic cells, and the DsbB family members in prokaryotic cells. These enzymes transfer oxidizing potential to the proteins PDI or DsbA, which are responsible for directly introducing disulfide bonds into substrate proteins during oxidative protein folding in eukaryotes and prokaryotes, respectively. A comparison of the recent X-ray crystal structure of Ero1 with the previously solved structure of the SOX/ALR family member Erv2 reveals that, despite a lack of primary sequence homology between Ero1 and Erv2, the core catalytic domains of these two proteins share a remarkable structural similarity. Our search of the DsbB protein sequence for features found in the Ero1 and Erv2 structures leads us to propose that, in a fascinating example of structural convergence, the catalytic core of this integral membrane protein may resemble the soluble catalytic domain of Ero1 and Erv2. Our analysis of DsbB also identified two new groups of DsbB proteins that, based on sequence homology, may also possess a catalytic core similar in structure to the catalytic domains of Ero1 and Erv2.

Bacterial Proteins↗

PubMed2000

Conserved structural features in class I major fimbrial subunits (Pilin) in gram-negative bacteria. Molecular basis of classification in seven subfamilies and identification of intrasubfamily sequence signature motifs which might Be implicated in quaternary structure.

Type 1 and P-pili are prototype members of Class I fimbriae produced by Gram-negative bacteria. Despite common structural characteristics, the low level of amino acid sequence conservation among the Class I major fimbrial subunits (pilins) indicates considerable evolutionary distance between members of this superfamily. We highlight here structural relatedness between Class I pilins from their two-dimensional sequence analysis using hydrophobic cluster analysis (HCA) and secondary structure predictions (PHD program). We present evidence that all members of the Class I pilin family have clear structural relatedness and suggest that classification based on phylogenetic analysis of Class I pilins into seven subfamilies correlates with differences in structural properties of the amino acid sequences. Using a sensitive alignment process (HCA), we identified 29 residues in topohydrophobic positions which probably play a prominent role in folding. The most striking aspects that distinguish the different pilin subfamilies are (i) large variation in the length of the loops connecting the structurally conserved regions and (ii) intrasubfamily sequence signature motifs located on regions predicted to be in the beta-conformation. We suggest that these "intrasubfamily sequence signature motifs" are part of interactive surfaces which participate in subunit-subunit interactions. These motifs prove highly useful in characterizing and classifying new Class I fimbriae that have not yet been described and whose sequence diverges appreciably from those of characterized groups. (After the submission of our manuscript, the experimental structure of Class I pilus subunits was published. In light of these actual pilin structures, a comparison has been made between the predicted results and the crystal structure in the Note Added in Proof.)

Amino Acid Motifs↗

PubMed1989

Hydroxyl radical footprints reveal novel structural features around the NF I binding site in adenovirus DNA.

We have identified a number of as yet unknown structural abnormalities of the NF I-DNA binding site within the inverted terminal repetition of adenovirus DNA by probing it with a hydroxyl radical footprinting technique. NF I binding alters the accessibility of the deoxyribose moieties to hydroxyl radicals both at the 3' and at the 5' side of the recognition sequence 5'-TGG(N)6GCCAA-3'. A smooth bend at the 5' side of the binding sequence is already present in naked linear DNA and it is further enhanced by protein binding. This could be demonstrated not only by hydroxyl radical footprinting but also by studying the temperature dependent mobility during gel electrophoresis of DNA fragments carrying the NF I binding site at circularly permutated positions. We propose that the bent conformation at this site is responsible for facilitating protein/DNA interactions.

Adenoviruses, Human↗