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D A Parry

Publications and source records attributed to D A Parry.

At least 19 recordsLinked to original sources
PubMed1992

Molecular structure of the human desmoplakin I and II amino terminus.

Desmoplakins (DPs) I and II are closely related proteins found in the innermost region of the desmosomal plaque, which serves as a cell surface attachment site for cytoplasmic intermediate filaments. Overlapping cDNA clones comprising 9.2 kilobases of DP-I, predicted to encode a full-length 310-kDa polypeptide (2677 amino acid residues), have now been identified. Here we report the predicted protein sequence and structural analysis of the N terminus of DP, extending our previous study of the rod and carboxyl domains. The N terminus contains groups of heptad repeats that are predicted to form at least two major alpha-helical-rich bundles. Unlike the rod and carboxyl domains, the N terminus did not display a periodic distribution of charged residues. Northern blot mapping and genomic sequence analysis were also undertaken to examine the organization of the DP mRNAs. A 1-kilobase intron was located at the 3' boundary of a DP-I-specific region; however, instead of an intron at the 5' junction, a possible splice donor site was observed within a potential coding sequence, suggesting alternative RNA splicing from an internal donor site.

Amino Acid Sequence↗
PubMed1992

Intermediate filament structure.

In the past year, several new developments concerning the structure of intermediate filament proteins and their assembly into intact intermediate filaments have been made: the coiled-coil structure of a rod domain has been elucidated; the basis of the chain interaction and its role in intermediate filament assembly has been specified; the organization of nearest-neighbour molecules in keratin intermediate filaments has been determined; and the glycine loop structures of the terminal domains of epidermal keratin chains have been defined. In addition, mutations in intermediate filament chains that promote pathology have been reported for the first time.

Animals↗
PubMed1992

Analysis of the three-alpha-helix motif in the spectrin superfamily of proteins.

Members of the spectrin superfamily of proteins contain different numbers of homologous repeats arranged in tandem. Each of these consists of a three-alpha-helix motif, comprising two similarly and one oppositely directed alpha-helical segment joined by nonhelical linkers of characteristic length. The right-handed alpha-helices each display a heptad repeat in their amino acid sequences indicative of left-handed coiled-coil-like packing. We have calculated the potential number of inter-helix ionic interactions that specify the spatial arrangement of the helices in the motif in terms of both the handedness of helix connectivity (left or right) and the relative axial stagger between the three alpha-helices. All of the models examined were constrained to have optimal coiled-coil packing. For alpha-spectrin and alpha-actinin the results provide strong support for a left-handed connectivity of the three helices and axial repeat lengths of 5.05 and 6.24 nm, respectively. Furthermore, the axial staggers between homologous segments in the preferred models are identical. The insights provided into the topography of this widespread tertiary fold may prove of value to those concerned with the problem of de novo protein design.

Actinin↗
PubMed1992

Comparative structural analysis of desmoplakin, bullous pemphigoid antigen and plectin: members of a new gene family involved in organization of intermediate filaments.

Desmoplakins (DP) and bullous pemphigoid antigen (BPA) are major plaque components of the desmosome and hemidesmosome, respectively. These cell adhesion structures are both associated intimately with the intermediate filament (IF) network. Structural analyses of DP and BPA sequences have indicated that these molecules are likely to form extended dumbbell-shaped dimers with a central rod and globular end domains. Recent sequence data have indicated that the N-terminal domains of both DP and BPA (like their C-terminal domains) are highly related: the former contain regions of heptad repeats that are predicted to form several alpha-helical bundles. Comparisons of DP and BPA protein sequences with that of plectin (PL), a 466 kDa IF-associated protein, have also revealed large scale homology. Identities between their N-terminal domains are: DP:BPA = 35%, DP:PL = 32%, BPA:PL = 40%, suggesting that BPA is more closely related to PL than DP in this region. In the C-terminal domains, which contain a 38-residue repeating motif, however, DP and PL are closer relatives (identities: DP:BPA = 38%, BPA:PL = 40%, DP:PL = 49%). The central domains of all three proteins have extensive heptad repeat substructure, express the same periodic distribution of charged residues, and are predicted to form two-stranded alpha-helical coiled-coil ropes. These observations suggest that DP, BPA and PL belong to a new gene family encoding proteins involved in IF organization.

Amino Acid Sequence↗
PubMed1992

Control of collagen fibril diameters in tissues.

It is proposed that radial growth of collagen fibrils, which takes place in all connective tissues to varying extents, according to the tensile stresses exerted on them, proceeds mainly by aggregation of protofibrils (approximately 10 nm) and existing fibrils. In young tissues, fibrils are prevented from making frequent intimate contacts which would lead to aggregation by abundant interfibrillar proteoglycan, that keeps the fibrils apart. Collagen fibrils are probably unable to fuse except when the molecules within them are packed in the same sense, i.e. fusing fibrils are parallel. The roughly equal numbers of parallel and antiparallel fibrils seen in several tissues must limit radial fibril growth in older tissues, where proteoglycan is usually less abundant. Possible origins of the balance of fibril polarities, which must be conserved after fibril nucleation on cell or non-cell templates, are analysed. The two controlling factors, ambient proteoglycan and fibril polarity, working against the tendency of fibrils to fuse, account for many features of the observed distributions of collagen fibril diameters in diverse tissues and at different ages.

Collagen↗
PubMed1992

Structure of desmoplakin and its association with intermediate filaments.

Desmoplakins (DPs) I and II are two major related proteins located in the desmosomal plaque where they have been proposed to play a role in attaching intermediate filaments (IF) to the inner cell surface. The predicted amino acid sequence of DP was obtained by analysis of overlapping cDNA clones. Computer-aided analysis suggests that DPI will form a dumbbell-shaped homodimer, with a central alpha-helical coiled coil rod domain of 132 nm and two globular end domains. The DPII molecule is missing 599 residues from the central domain, resulting in a rod about one third the length of DPI. The carboxyl terminus comprises three subdomains each containing almost 5 repeats of a 38 residue repeating motif with a periodicity in acidic and basic residues similar to that found in the rod domain of IF proteins. This suggests a possible mechanism by which these proteins might interact. The amino terminus contains groups of heptad repeats that are predicted to form at least two major alpha-helical rich bundles. A series of c-myc-tagged mammalian expression vectors encoding specific predicted domains of DPI were transiently expressed in COS-7 cells. Light and electron microscopical observations revealed that DP polypeptides including the 90 kDa carboxyl terminal globular domain of DPI specifically colocalized with and ultimately resulted in the complete disruption of keratin and vimentin IF. This effect was specific for the carboxyl terminus, as the expression of the 95 kDa rod domain of DPI did not visibly alter IF networks.(ABSTRACT TRUNCATED AT 250 WORDS)

Cell Adhesion Molecules↗
PubMed1991

Comparison of molecularly cloned bullous pemphigoid antigen to desmoplakin I confirms that they define a new family of cell adhesion junction plaque proteins.

Bullous pemphigoid is a subepidermal blistering disease in which patients have autoantibodies against the plaque of the hemidesmosome. Starting with a previously isolated 2-kilobase (kb) cDNA for bullous pemphigoid antigen (BPA), we used primer extension of keratinocyte mRNA to isolate overlapping cDNAs with a combined open reading frame of 6.3 kb, encoding most (243 kDa) of the BPA, but lacking the far amino terminus. Analysis of this amino acid sequence revealed a carboxyl-terminal domain containing two regions of 174 and 176 residues with high sequence identity. Most of the amino-terminal two-thirds of BPA is predicted to be in an alpha-helical conformation in which two chains would aggregate into a coiled-coil rod structure. BPA and desmoplakin I, a desmosome plaque protein, show remarkable sequence and structural homology. In its carboxyl-terminal domain, desmoplakin I also has 176 residue repeats with 40% sequence identity to those in BPA. The repeats in both molecules have a regular linear distribution of acidic and basic residues with a period of 9.5, the same as that found in the 1B segment of keratin filaments, suggesting a means of ionic interaction between keratin and these plaque proteins. Also, desmoplakin I, like BPA, is predicted to have a rod domain, which in both proteins has similar regular charge periodicities, suggesting a means of ionic self-aggregation. These findings extend those of Green et al. (Green, K. J., Parry, D. A. D., Steinert, P. S., Virata, L. A., Wagner, R. M., Angst, B. D., and Nilles, L. A. (1990) J. Biol. Chem. 265, 2603-2612) which show that BPA and desmoplakin I represent the first members of a new family of adhesion junction plaque proteins.

Amino Acid Sequence↗
PubMed1991

Three-stranded alpha-fibrous proteins: the heptad repeat and its implications for structure.

Amino acid sequence data have been collected for the coiled-coil rod domains of three-stranded alpha-fibrous proteins--fibrinogen, laminin, tenascin, macrophage scavenger receptor protein and the leg fibre protein from bacteriophage. Such domains are characterized by a heptad substructure in which apolar residues occur alternately three and four residues apart. The distribution of residues in each position of the heptad has been analysed, and the results compared with those obtained for the two-stranded alpha-fibrous proteins, which include the intermediate filament and myosin families. Distinctions can be drawn between the sequences in two- and three-stranded coiled-coil structures and these provide criteria that will prove useful in predicting secondary and tertiary structure purely from sequence data.

Amino Acid Sequence↗
PubMed1991

Structural analysis and expression of human desmoglein: a cadherin-like component of the desmosome.

Desmosomes are adhesive cell junctions found in great abundance in tissues that experience mechanical stress. The transmembrane desmosomal glycoproteins have been proposed to play a role in cell adhesion; desmoglein I (DGI) is a major member of this class of desmosomal molecules. However, evidence supporting a role for DGI in cell adhesion or in the plaque is lacking. In order to begin to understand DGI function we have identified human cDNA clones encoding the entire mature polypeptide of 1000 amino acids. Our data suggest that like the bovine DGI molecule human DGI is highly related to the calcium-dependent class of cell adhesion molecules known as cadherins. Four related extracellular domains located in the amino-terminal domain of the molecule contain putative calcium binding sites originally identified in the cadherins. The highest degree of similarity between human N-cadherin and human DGI, and likewise between bovine DGI and human DGI, is greatest in the most amino-terminal extracellular domain. This suggests a conserved functional role for the extracellular domains, perhaps in calcium-mediated cell adhesion. The cytoplasmic portion of the molecule contains a cadherin-like region and, like bovine DGI, a carboxy-terminal tail that is not present in the cadherins, comprising three additional domains. One of these contains a novel repeating motif of 29 +/- 1 residues, first identified in bovine DGI. Each of the highly homologous repeating units is likely to consist of two beta-strands and two turns with special characteristics. Five amino acids that are identical in bovine and human DGI lie in the second of the two predicted beta-strands, and intriguingly contain putative target sites for protein kinase C. On the basis of structural analysis, a model predicting the disposition of human DGI domains in the desmosome is proposed. Northern analysis suggests that unlike bovine epidermis, which expresses a single mRNA of reported size approximately 7.6 kb, human foreskin and cultured keratinocytes display a complex pattern with bands of approximately 7.2, 4.0 and 3.0 kb. Each of these cross-hybridizing mRNAs is coordinately expressed in normal human keratinocytes in response to long-term culture and increased calcium.

Amino Acid Sequence↗
PubMed1990

Structure of the human desmoplakins. Implications for function in the desmosomal plaque.

Desmoplakins (DPs) I and II are two major related proteins located in the innermost portion of the desmosomal plaque where it is thought they may play a role in attaching intermediate filaments (IF) to the cell surface. We have isolated and sequenced human cDNA clones encoding two major DP domains and a portion of a third. These clones can be divided into two classes that we believe to represent DPI and DPII cDNAs; our evidence suggests that the DPII message is derived at least in part from the processing of a larger transcript encoded by a single gene. Computer-aided analysis of the DPI-predicted amino acid sequence indicates that the central domain, which contains the heptad repeat characteristic of many alpha-fibrous proteins, will participate in the formation of a coiled coil dimer approximately 130 nm in length. The periodicity of acidic and basic residues in the rod suggests that DPI will aggregate with itself or similar molecules into higher order filamentous structures. The carboxyl terminus contains three regions with significant homology, each of which comprises almost five repeats of a 38-residue motif. It is likely that these regions each fold into a compact globular conformation stabilized by intrachain ionic interactions. Comparison of the predicted amino acid sequence of a cDNA encoding a portion of the 230-kDa bullous pemphigoid antigen (Stanley, J. R., Tanaka, T., Mueller, S., Klaus-Kovtun, V., and Roop, D. (1988) J. Clin. Invest. 82, 1864-1870) with DP revealed the presence of a 38-residue repeat with striking similarity to that of the DPs. Significantly, the periodicity in acidic and basic residues of these domains is the same as that found in the 1B rod domain of IF proteins. This suggests the possibility that the DPs might interact with IF via their common periodicity of charged residues.

Amino Acid Sequence↗
PubMed1990

Structural features in the heptad substructure and longer range repeats of two-stranded alpha-fibrous proteins.

Considerable sequence data have been collected from the intermediate filament proteins and other alpha-fibrous proteins including myosin, tropomyosin, paramyosin, desmoplakin and M-protein. The data show that there is a clear preference for some amino acids to occur in specific positions within the heptad substructure that characterizes the sequences which form the coiled-coil rod domain in this class of proteins. The results also indicate that although there are major similarities between the various proteins there are also key differences. In all cases, however, significant regularities in the linear disposition of the acidic and the basic residues in the coiled-coil segments can be related to modes of chain and molecular aggregation. In particular a clear trend has been observed which relates the mode of molecular aggregation to the number of interchain ionic interactions per heptad pair.

Amino Acids↗
PubMed1989

Characterization of a cDNA clone encoding human filaggrin and localization of the gene to chromosome region 1q21.

Filaggrins are an important class of intermediate filament-associated proteins that interact with keratin intermediate filaments of terminally differentiating mammalian epidermis. They show wide species variations and their aberrant expression has been implicated in a number of keratinizing disorders. We have isolated a cDNA clone encoding human filaggrin and used this to demonstrate that the human gene encodes a polyprotein precursor containing numerous tandem filaggrin repeats. This structure is similar to that of mouse; however, the human filaggrin repeat is much longer (972 base pairs; 324 amino acids) and shows little sequence homology to the mouse protein. Also, data presented here reveal that the human filaggrin repeats show considerable sequence variations; such polymorphism is not found in the mouse. Furthermore, chromosomal mapping data revealed that the human gene is located at 1q21, indicating that the polymorphism is confined to a single locus. By peptide mapping, we define a short linker sequence within the human filaggrin repeat that is excised by proteolysis to yield functional molecules. Finally, we show by in situ hybridization that human filaggrin precursor gene expression is tightly regulated at the transcriptional level in terminally differentiating epidermis and that this represents a useful system in which to study intermediate filament-intermediate filament-associated protein interactions as well as disorders of keratinization.

Amino Acid Sequence↗
PubMed1989

An estimate of the mean length of collagen fibrils in rat tail-tendon as a function of age.

A theoretical expression has been derived for the mean collagen fibril length in tendon based on the assumption that collagen fibrils originate in cell surface invaginations and terminate either at some remote cell surface or another collagen fibril bundle. The expression thus determined requires knowledge of the effective lengths of the fibrocytes (or fibrocyte assemblies) and the cellular content of the tendon. Both of these parameters have been measured experimentally as a function of age for rat-tail tendon using a combined light microscope and electron microscope approach. The results obtained for immature tendon suggest that the mean collagen fibril length is at least equal to the critical length required to maintain the appropriate tensile properties. In the most mature tissue studied, however, the mean-collagen fibril length is in excess of 100 times the critical length.

Aging↗
PubMed1988

Detection and determination of common benzodiazepines and their metabolites in blood samples of forensic science interest. Microcolumn cleanup and high-performance liquid chromatography with reductive electrochemical detection at a pendent mercury drop electrode.

Benzodiazepines in the blood samples typical of forensic science work are recovered from 100-250 microliters amounts of blood (diluted with aqueous sodium octyl sulphate to suppress protein binding) onto microcolumns of Porapak-T, and finally eluted into 60-microliters volumes of aqueous acetonitrile. The eluates may be taken directly for analysis by high-performance liquid chromatography (HPLC) with reductive amperometric detection at a pendent mercury drop electrode held at potentials down to -1.2 V vs. Ag/AgCl. For high sensitivity work the electrode is preceded by a coulometric detector fitted with porous carbon electrodes held at 0 V (proprietary reference electrode). The technique detects all of the commonly encountered benzodiazepines and others except clobazam, which contains no azomethine group. The detection limits generally are in the range 1-5 ng/ml (40-200 pg HPLC-injected) in hemolyzed human blood, with recovery values of 84-95%, depending on the actual benzodiazepine, over the range examined (less than or equal to 2.14 micrograms/ml). The respective values for the metabolites of nitrazepam are 8-12 ng/ml and 75-84%. The technique is very much less susceptible to the interferences afflicting other commonly applied techniques, and facilitates considerably the analysis of degraded samples.

Animals↗
PubMed1988

Synthesis, antiviral activity, and conformational characterization of mouse-human alpha-interferon hybrids.

Reciprocal hybrids were constructed between human and mouse interferons (IFNs), and their antiviral activity was examined on different target cells and compared to the activity of the parental molecules. In addition, we used a number of predictive algorithms on a data base of the available alpha-interferon sequences to propose a working model for the overall conformation of the alpha-interferon molecule that is consistent with the structural predictions. Remarkable conservation within the predicted alpha-helical segments of the interferon molecule was observed. We propose that the observed changes in the activity and specificity of the hybrids obtained are largely due to the sequences present in the loops at the ends of the major helical structures; these are less conserved, contain beta-bends, and are generally hydrophilic and flexible. The data on the constructed mouse-human hybrids have shown that the activity on human cells is contributed by determinants present in the N-terminal 122 amino acids of human IFN, thus implicating one or more loops within this region (e.g. loops 1-12, 25-38, 70-74, and 103-113). The activity on bovine cells appears to be localized mainly in sequence 60-121, implicating the role of loops 70-74 and/or 103-113 of the human IFN molecule. The specificity of mouse IFN for mouse cells is in some or all of the loops (70-74, 103-113, 134-139, and 163-166) in the C-terminal sequence. The proposed working model should provide guidelines for the study of the specificity of action in molecular terms.

Amino Acid Sequence↗