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PubMed1997

Structural features of the kringle domain determine the intracellular degradation of under-gamma-carboxylated prothrombin: studies of chimeric rat/human prothrombin.

Vitamin K antagonists such as warfarin inhibit the vitamin K-dependent gamma-glutamyl carboxylation during protein processing and block the secretion of under-gamma-carboxylated prothrombin (FII) in the rat but not in the human or bovine. Under-gamma-carboxylated prothrombin is also secreted from warfarin-treated human (HepG2) cell cultures but is degraded in the endoplasmic reticulum in warfarin-treated rat (H-35) cell cultures. This differential response to warfarin has been shown to be determined by the structural difference in the proteins rather than by the origin of the cell line. When recombinant rat prothrombin (rFII) and human prothrombin (hFII) were expressed in a transformed human kidney cell line (HEK293), secretion of rFII but not hFII was drastically decreased in response to warfarin. To determine the structural signal required for this differential response, chimeric cDNAs with the propeptide/Gla domains, kringle domain, and serine protease domain exchanged between rFII and hFII were generated (FIIRHH and FIIHRR, FIIRRH and FIIHHR, FIIRHR and FIIHRH) and expressed in both warfarin-treated HEK293 cells and HepG2 cells. The presence of the hFII kringle domain changed the stability of rFII to that of hFII, and the rFII kringle domain changed the stability of hFII to that of rFII. The kringle domain therefore is critical in determining the metabolic fate of under-gamma-carboxylated prothrombin precursors during processing. Prothrombin contains two kringle structures, and expression of additional rFII/hFII chimeras (FIIHrhH and FIIHhrH, FIIRrhR, and FIIRhrR) was used to determine that the first of the two kringles plays a more important role in the recognition process.

Animals↗

PubMed2005

Probing the pH-dependent structural features of alpha-KTx12.1, a potassium channel blocker from the scorpion Tityus serrulatus.

Potassium channels are widespread in living cells and are involved in many diseases. The scorpion toxin alpha-KTx(12.1) interacts with various K(+) channels, suggesting its capacity to match diverse channel pores. It is recognized that tissue injuries may affect the pH at toxins site of action, thereby modulating both protein conformation and activity. To better understand its molecular mechanism of action, we studied alpha-KTx(12.1) using pH as a tool to explore its plasticity and NMR in combination with MD calculations to detect it. The toxin solution structure consists of an alpha-helix and a triple-stranded beta-sheet stabilized by four disulfide bridges. The NMR results show, in addition, that His28 possesses an unusually low pK(a) of 5.2. The best set of protein conformers is obtained at pH 4.5, while at pH 7.0, the reduced number of NOEs resulting from a faster hydrogen exchange does not allow to reach a good structural convergence. Nonetheless, MD calculations show that the toxin structure does not vary significantly in that pH range, while conformational changes and modifications of the surface charge distribution occur when His28 is fully protonated. Moreover, essential dynamics analysis reveals variations in the toxin's coherent motions. In conclusion, His28, with its low pK(a) value, provides alpha-KTx(12.1) with the ability to preserve its active conformation over a wide pH interval, thus expanding the range of cellular conditions where the toxin can fully exhibit its activity. Overall, the results further underline the role of histidine as a natural controller of proteins' functionality.

Amino Acid Sequence↗

PubMed2004

Structural features of Escherichia coli heat-stable enterotoxin that activates membrane-associated guanylyl cyclase.

Heat-stable enterotoxin (ST), a small peptide of 18 or 19 amino acid residues produced by enterotoxigenic Escherichia coli, is the cause of acute diarrhea in infants and travelers in developing countries. ST triggers a biological response by binding to a membrane-associated guanylyl cyclase C (GC-C) which is located on intestinal epithelial cell membranes. This binding causes an increase in the concentration of cGMP as a second messenger in cells and activates protein kinase A and cystic fibrosis transmembrane conductance regulator. Here we describe the crystal structure of an ST at 0.89 A resolution. The molecule has a ring-shaped molecular architecture consisting of six peptide molecules with external and internal diameters of approximately 35 and 7 A, respectively and a thickness of approximately 11 A. The conserved residues at the central portion of ST are distributed on the outer surface of the ring-shaped peptide hexamer, suggesting that the hexamer may be implicated in the association with GC-C through these invariant residues.

Amino Acid Sequence↗

PubMed1995

Two hnRNP-associated proteins share common structural features with the adenoviral 72-kDa protein.

Using our anti-hnRNP monoclonal antibody library Y. Lutz, M. Jacob, and J.-P. Fuchs (1988) Exp. Cell Res., 175, 108-124; P. Mähl, Y. Lutz, E. Puvion, and J.-P. Fuchs, (1989) J. Cell Biol. 109, 1921-1935, we investigated by immunocytofluorescence the fate of a series of speckled-distributed nuclear antigens, after HeLa cells were infected with adenovirus type 2. Although the speckled pattern, which corresponds to the nucleoplasmic fibrillogranular network, including the interchromatin-granule clusters, was still observed during most of the infectious cycle, several antibodies also revealed additional, increasingly fluorescent virus-induced structures. In noninfected cells, two of these antibodies, termed 3F2 and 2A5, recognize two antigens of 33 and 31 kDa, respectively. Western blot analysis showed that this increasing amount of fluorescence observed in infected cells did not reflect an accumulation of the 33- and 31-kDa antigens, but is actually due to the fact that both antibodies also recognize the multifunctional adenovirus 72-kDa single-stranded DNA-binding protein (DBP). Immunoelectron microscopy analyses, including sequential double-labeling, indeed showed that this additional signal precisely colocalizes with the viral 72-kDa DBP, which essentially accumulates over the entire surface of the virus-induced single-stranded DNA accumulation sites. Taken together, our data show that two host-specific hnRNP-associated antigens share common epitopes with the viral 72-kDa DBP.

Adenoviruses, Human↗

PubMed2006

Magnesium-cationic dummy atom molecules enhance representation of DNA polymerase beta in molecular dynamics simulations: improved accuracy in studies of structural features and mutational effects.

Human DNA polymerase beta (pol beta) fills gaps in DNA as part of base excision DNA repair. Due to its small size it is a convenient model enzyme for other DNA polymerases. Its active site contains two Mg(2+) ions, of which one binds an incoming dNTP and one catalyzes its condensation with the DNA primer strand. Simulating such binuclear metalloenzymes accurately but computationally efficiently is a challenging task. Here, we present a magnesium-cationic dummy atom approach that can easily be implemented in molecular mechanical force fields such as the ENZYMIX or the AMBER force fields. All properties investigated here, namely, structure and energetics of both Michaelis complexes and transition state (TS) complexes were represented more accurately using the magnesium-cationic dummy atom model than using the traditional one-atom representation for Mg(2+) ions. The improved agreement between calculated free energies of binding of TS models to different pol beta variants and the experimentally determined activation free energies indicates that this model will be useful in studying mutational effects on catalytic efficiency and fidelity of DNA polymerases. The model should also have broad applicability to the modeling of other magnesium-containing proteins.

Binding Sites↗

PubMed1993

Structural features of lipoarabinomannan from Mycobacterium bovis BCG. Determination of molecular mass by laser desorption mass spectrometry.

It was recently shown that mycobacterial lipoarabinomannan (LAM) can be classified into two types (Chatterjee, D., Lowell, K., Rivoire B., McNeil M. R., and Brennan, P. J. (1992) J. Biol. Chem. 267, 6234-6239) according to the presence or absence of mannosyl residues (Manp) located at the nonreducing end of the oligoarabinosyl side chains. These two types of LAM were found in a pathogenic Mycobacterium tuberculosis strain and in an avirulent M. tuberculosis strain, respectively, suggesting that LAM with Manp characterizes virulent and "disease-inducing strains." We now report the structure of the LAM from Mycobacterium bovis Bacille Calmette-Guérin (BCG) strain Pasteur, largely used throughout the world as vaccine against tuberculosis. Using an up-to-date analytical approach, we found that the LAM of M. bovis BCG belongs to the class of LAMs capped with Manp. By means of two-dimensional homonuclear and heteronuclear scalar coupling NMR analysis and methylation data, the sugar spin system assignments were partially established, revealing that the LAM contained two types of terminal Manp and 2-O-linked Manp. From the following four-step process: (i) partial hydrolysis of deacylated LAM (dLAM), (ii) oligosaccharide derivatization with aminobenzoic ethyl ester, (iii) HPLC purification, (iv) FAB/MS-MS analysis; it was shown that the dimannosyl unit alpha-D-Manp-(1-->2)-alpha-D-Manp is the major residue capping the termini of the arabinan of the LAM. In this report, LAM molecular mass determination was established using matrix-assisted UV-laser desorption/ionization mass spectrometry which reveals that the LAM molecular mass is around 17.4 kDa. The similarity of the LAM structures between M. bovis BCG and M. tuberculosis H37Rv is discussed in regard to their function in the immunopathology of mycobacterial infection.

Antigens, Bacterial↗

PubMed2000

Structural features of Ag[AuF4] and Ag[AuF6] and the stuctural relationship of Ag[AgF4]2 and Au[AuF4]2 to Ag[AuF4]2.

Synchrotron radiation X-ray powder diffraction data (SPDD) have been obtained for Ag[AgF4]2, Au[AuF4]2, Ag[AuF4], and Ag[AuF6]. Ag[AgF4]2 and Au[AuF4]2 are isostructural with Ag[AuF4]2, space group (SG) P2(1)/n, Z = 2, with the following: for Ag[AgF4]2 a = 5.04664(8), b = 11.0542(2), c = 5.44914(9) A, beta = 97.170(2) degrees; for Au[AuF4]2 a = 5.203(2), b = 11.186(3), c = 5.531(2) A, beta = 90.55(2) degrees. The structure of Ag[AgF4]2 was refined successfully (SPDD) applying the Rietveld method, yielding the following interatomic distances (A): AgII-F = 2.056(12), 2.200(13), 2.558(13); AgIII-F = two at 1.846(12), others = 1.887(12), 1.909(13), 2.786-(12), 2.796(12), 2.855(12). AgAuF4, like other AA'F4 salts (A = Na-Rb; A' = Ag, Au), crystallizes in the KBrF4 structure type, SG I4/mcm (140), Z = 4 with a = 5.79109(6), c = 10.81676(7) A. SPDD gave (in A) four AuIII-F = 1.89(1) and eight AgI-F = 2.577(7). SPDD for AgAuF6 confirmed that it has the LiSbF6 structure, SG R3, Z = 3, with a = 5.2840(2), c = 15.0451(6) A.

Journal Article↗

PubMed1976

Origin, concentration and structural features of human mammary gland cells cultured from breast secretions.

This study traced the origin of cells observed in human breast secretion samples obtained during lactation and describes the appearance of these cells following prolonged maintenance in vitro. Human milk contains a large number of single vacuolated foam celsl and a small proportion of non-vacuolated epithelial cells in clusters. Foam cells are identified by their large size, the polarity of their cytoplasmic organelles, the variation in number and size of lipid vacuoles and the condensed chromatin of their eccentrically located nucleus. Both cell types originate by exfoliation from the mammary gland. This was established by comparing the structural characteristics of cells isolated from milk with those of the cuboidal cell linings of ducts and alveoli in lactating mammary tissue. Relatively pure populations of foam cells could be established from early lactation samples (3-7 days post/partum) while non-vacuolated epithelial cell clusters were more frequently cultured from late lactation specimens (1-10 days postweaning). Foam cells did not divide and lost cytoplasmic organization during prolonged culture. In contrast, non-vacuolated epithelium in clusters proliferated to form colonies of polygonal cells. These results, which imply that foam cells are an active form of the non-vacuolated mammary cells in clusters, call attention to one system for the study of the complex hormonal interactions necessary to induce and maintain lactation.

Animals↗

PubMed2005

Structural features and nucleotide-binding capability of the C subunit are integral to the regulation of the eukaryotic V1Vo ATPases.

V-ATPases (vacuolar ATPases) are responsible for acidification of intracellular compartments and, in certain cases, proton transport across the plasma membrane of eukaryotic cells. They are composed of a catalytic V1 sector, in which ATP hydrolysis takes place, and the Vo sector, which functions in proton conduction. The best established mechanism for regulating the V-ATPase activity in vivo involves reversible dissociation of the V1 and Vo domains, in which subunit C is intimately involved. In the last year, impressive progress has been made in elucidating the structure of the C subunit and its arrangement inside the V-ATPase. Nucleotide occupancy by subunit C, followed by conformational changes of this subunit has shed light on the mechanism of V-ATPase regulation.

Adenosine Triphosphate↗

PubMed1985

Structural features of the hisT operon of Escherichia coli K-12.

The DNA sequence of a 2,3-kilobase segment of the E. coli hisT operon was determined. Analysis of the sequence indicated that the upstream gene in the operon encodes a 36,364-dalton polypeptide, which runs aberrantly on SDS-polyacrylamide gels. The distal hisT gene encodes the tRNA modification enzyme, pseudouridine synthase I, which was shown to have a polypeptide molecular mass of 30,399 daltons. The DNA sequence was consistent with the phenotypes and hisT expression of mutant operons. Analysis of the sequence and genetic complementation experiments demonstrated that the upstream and hisT genes are evolutionarily, structurally, and functionally unrelated; however, translation signals for the two genes overlap, which is consistent with genetic evidence suggesting translational coupling. Codon usage in the upstream gene is radically different from the hisT gene and may underlie the differential expression observed from the operon. Gene-inactivation experiments and S1-mapping of in vivo transcripts indicated that the operon contains an additional upstream gene. S1-mapping experiments also confirmed the presence of an internal promoter, which might be stringently controlled. Taken together, these results show that the structure of the hisT operon is complex and suggest that the operon might be regulated at several levels.

Amino Acid Sequence↗

PubMed1997

Conservation of structural features reveals the existence of a large family of inhibitory cell surface receptors and noninhibitory/activatory counterparts.

Immunoreceptor tyrosine-based inhibition motifs (ITIMs) consist of a 6-amino acid stretch (ILV)xYxx(LV). ITIMs are expressed in the intracytoplasmic domain of transmembrane receptors, which extinguish cell activation induced by receptors bearing immunoreceptor tyrosine-based activation motifs. The recent identification of new members of the ITIM-bearing receptor family (such as the signal-regulatory proteins) extends the ITIM concept to the negative regulation of growth factor- and oncogene-induced activation in nonhemopoietic cells. In addition, it appears that a feature of the family of ITIM-bearing receptors is the existence of noninhibitory/activatory counterparts devoid of intracytoplasmic ITIMs and characterized by the presence of a charged amino acid residue in their transmembrane domain.

Animals↗

PubMed2001

In vitro bioactivity and structural features of mildly heat-treated sol-gel-derived silica fibers.

The ability of sol-gel-derived silica fibers heat treated at a low temperature to induce formation of bone-like calcium phosphate (HCA) on their surfaces provides alternatives for the design of novel biomaterials, for example as implants used in tissue guiding or bone repairs. In this study, dry spinning was used to prepare the sol-gel fibers, which were heat-treated at 175 degrees and 250 degrees C. In addition, the differences in the surface topography (in a nanometer scale) of different fibers with respect to their in vitro bioactivity were studied. The structure of the fibers was varied using three different factors: (1) spinnable sols having varying structures and sizes of silica polymers to establish varying viscosity levels; (2) aging of green-state fibers; and (3) heat treatment of fibers. The in vitro bioactivity and solubility tests were done in simulated body fluid (SBF). To monitor surface topography and roughness of the heat-treated silica fibers, a scanning probe microscopy (SPM) with tapping mode AFM was used. Different fibers obtained clearly different properties. The fibers spun at about eta > 3.0 Pas had the best properties with respect to bioactivity, especially when they were heat-treated at 175 degrees C. It was found that surface structure in a nanometer scale was the most important factor controlling the in vitro bioactivity of heat-treated silica fibers. The correct proportions between the peaks and peak distances at the surfaces are suggested to be important with respect to in vitro bioactivity. The results indicate that peak distance distribution between 5-50 nm, especially between 5-20 nm, together with a peak height > or = 1 nm is most favorable for calcium phosphate formation.

Absorbable Implants↗

PubMed1975

Structural features of double-stranded polyribonucleotides required for immunological specificity and interferon induction.

Purified antibody to poly(adenylic acid)-poly(uridylic acid) was used in quantitative microcomplement fixation assays to detect conformational variations among several double-helical polyribonucleotide analogs of poly(adenylic acid)-poly(uridylic acid) or poly(inosinic acid)-poly(cytidylic acid) that had been previously evaluated for their ability to induce interferon. Modification at the furanose 2'-position of one or both strands resulted in a dramatic decrease in serological reactivity. Most modifications of the bases caused smaller serological changes, and no base modification caused complete loss of reactivity. The reaction patterns support the conclusion that the structure of the furanose and the overall conformation of the helix are critical in the formation of antigenic determinants. The backbones of both strands appear to be involved in forming a single antigenic site, and base modifications may alter the steric relationship between the backbones. In addition, the same structural changes that substantially alter recognition by antibody also lead to large changes in the interferon-inducing ability of the nucleic acid.

Antigen-Antibody Reactions↗

PubMed2006

Aurelin, a novel antimicrobial peptide from jellyfish Aurelia aurita with structural features of defensins and channel-blocking toxins.

A novel 40-residue antimicrobial peptide, aurelin, exhibiting activity against Gram-positive and Gram-negative bacteria, was purified from the mesoglea of a scyphoid jellyfish Aurelia aurita by preparative gel electrophoresis and RP-HPLC. Molecular mass (4296.95 Da) and complete amino acid sequence of aurelin (AACSDRAHGHICESFKSFCKDSGRNGVKLRANCKKTCGLC) were determined. Aurelin has six cysteines forming three disulfide bonds. The total RNA was isolated from the jellyfish mesoglea, RT-PCR and cloning were performed, and cDNA was sequenced. A 84-residue preproaurelin contains a putative signal peptide (22 amino acids) and a propiece of the same size (22 amino acids). Aurelin has no structural homology with any previously identified antimicrobial peptides but reveals partial similarity both with defensins and K+ channel-blocking toxins of sea anemones and belongs to ShKT domain family.

Amino Acid Sequence↗

PubMed1996

How structural features influence the biomembrane permeability of peptides.

Successful drug development requires not only optimization of specific and potent pharmacological activity at the target site, but also efficient delivery to that site. Many promising new peptides with novel therapeutic potential for the treatment of AIDS, cardiovascular diseases, and CNS disorders have been identified, yet their clinical utility has been limited by delivery problems. Along with metabolism, a major factor contributing to the poor bioavailability of peptides is thought to be inefficient transport across cell membranes. At the present time, the reasons for this poor transport are poorly understood. To explore this problem, we have designed experiments focused on determining the relationship between peptide structure and peptide transport across various biological membranes both in vitro and in vivo. Briefly, peptides that varied systematically in chain length, lipophilicity, and amide bond number were prepared. Permeability results with these solutes support a model in which the principal determinant of peptide transport is the energy required to desolvate the polar amides in the peptide for the peptide to enter and diffuse across the cell membrane. Further impacting on peptide permeability is the presence of active, secretory transport systems present in the apical membrane of intestinal epithelial and brain endothelial cells. In Caco-2 cell monolayers, a model of the human intestinal mucosa, this pathway displayed substrate specificity, saturation, and inhibition. Similar results have been shown in vivo in both rat intestinal and blood-brain barrier absorption models. The presence of such systems serves as an additional transport barrier by returning a fraction of absorbed peptide back to the lumen.

Animals↗

PubMed1984

The immune response to Epstein-Barr nuclear antigen: conformational and structural features of antibody binding to synthetic peptides.

Naturally developing human antibodies to the Epstein-Barr nuclear antigen recognize synthetic peptides containing sequences from the unusual glycine-alanine region of this protein. We tested antibody binding to a series of peptides of from five to 20 amino acids in length. Peptides as small as seven amino acids could bind but optimal results required chain lengths of 15. Binding was extremely sensitive to small changes in the length and sequence of the peptide, and also to the temp of the reaction. The changes can be ascribed to two factors: (1) deletion of the site of antigen binding and (2) loss of peptide secondary structure.

Amino Acid Sequence↗

PubMedDate not supplied

Structural features and regulatory properties of the brain glutamate decarboxylases.

It is widely recognized that the two major forms of GAD present in adult vertebrate brains are each composed of two major sequence domains that differ in size and degree of similarity. The amino-terminal domain is smaller and shows little sequence identity between the two forms. This domain is thought to mediate the subcellular targeting of the two GADs. Substantial parts of the amino-terminal domain appear to be exposed and flexible, as shown by proteolysis experiments and the locations of posttranslational modifications. The carboxyl-terminal sequence domain contains the catalytic site and shows substantial sequence similarity between the forms. The interaction of GAD with its cofactor, pyridoxal-5' phosphate (pyridoxal-P), plays a key role in the regulation of GAD activity. Although GAD(65) and GAD(67) interact differently with pyridoxal-P, their cofactor-binding sites contain the same set of nine putative cofactor-binding residues and have the same basic structural fold. Thus the cofactor-binding differences cannot be attributed to fundamental structural differences between the GADs but must result from subtle modifications of the basic cofactor-binding fold. The presence of another conserved motif suggests that the carboxyl-terminal domain is composed of two functional domains: the cofactor-binding domain and a small domain that closes when the substrate binds. Finally, GAD is a dimeric enzyme and conserved features of GADs superfamily of pyridoxal-P proteins indicate the dimer-forming interactions are mediated mainly by the carboxyl-terminal domain.

Animals↗

PubMed1995

Structural features of isolated M2 helices of nicotinic receptors. Simulated annealing via molecular dynamics studies.

The nicotinic acetylcholine receptor is an integral membrane protein and a ligand-gated cation channel. It has stoichiometry alpha 2 beta gamma delta, the subunits arranged symmetrically around an approximate five-fold axis. Five M2 helices, one from each subunit, form a parallel helix bundle surrounding a central pore. Simulated annealing via restrained molecular dynamics (SA/MD) has been employed to generate ensembles of isolated M2 transmembrane helices. Four ensembles of two different M2 helix sequences, M2 delta and M2 gamma, have been generated by SA/MD. The ensembles differed in their treatment of electrostatic interactions. Analysis of the simulated structures showed that intra-helical H-bonds were more strongly conserved in the C-terminal (and more hydrophobic) segment of M2 helices. Conformations of polar sidechains have been analyzed, placing particular emphasis on EK (and QK) pairs at the N-termini of M2 delta (and M2 gamma) helices. Conformations of EK sidechain pairs were obtained for the high resolution structures in the protein database in order to guide our analysis of simulated structures. Serine and threonine sidechain conformations in the M2 models also have been determined. Implications of studies of isolated M2 helices for models of the intact pore region of the nicotinic receptor are discussed.

Amino Acid Sequence↗