scholarly journals Identification and Analysis of Novel Tandem Repeats in the Cell Surface Proteins of Archaeal and Bacterial Genomes Using Computational Tools

2004 ◽  
Vol 5 (1) ◽  
pp. 2-16 ◽  
Author(s):  
S. Adindla ◽  
K. K. Inampudi ◽  
K. Guruprasad ◽  
L. Guruprasad
Keyword(s):  
Amino Acid ◽  
Cell Surface ◽  
Protein Sequence ◽  
Tandem Repeats ◽  
Surface Proteins ◽  
Sequence Motifs ◽  
Methanosarcina Acetivorans ◽  
Bacterial Genomes ◽  
Cell Surface Proteins ◽  
Conserved Sequence

We have identified four novel repeats and two domains in cell surface proteins encoded by theMethanosarcina acetivoransgenome and in some archaeal and bacterial genomes. The repeats correspond to a certain number of amino acid residues present in tandem in a protein sequence and each repeat is characterized by conserved sequence motifs. These correspond to: (a) a 42 amino acid (aa) residue RIVW repeat; (b) a 45 aa residue LGxL repeat; (c) a 42 aa residue LVIVD repeat; and (d) a 54 aa residue LGFP repeat. The domains correspond to a certain number of aa residues in a protein sequence that do not comprise internal repeats. These correspond to: (a) a 200 aa residue DNRLRE domain; and (b) a 70 aa residue PEGA domain. We discuss the occurrence of these repeats and domains in the different proteins and genomes analysed in this work.

scholarly journals Identification and Analysis of Novel Amino-Acid Sequence Repeats inBacillus anthracisstr.AmesProteome Using Computational Tools

2007 ◽  
Vol 2007 ◽  
pp. 1-23 ◽  
Author(s):  
G. R. Hemalatha ◽  
D. Satyanarayana Rao ◽  
L. Guruprasad
Keyword(s):  
Amino Acid ◽  
Amino Acid Residue ◽  
Protein Sequence ◽  
Amino Acid Residues ◽  
Sequence Motifs ◽  
Computational Tools ◽  
Conserved Sequence ◽  
Conserved Sequence Motifs ◽  
Multiple Copies ◽  
Domain 3

We have identified four repeats and ten domains that are novel in proteins encoded by theBacillus anthracisstr.Amesproteome using automated in silico methods. A “repeat” corresponds to a region comprising less than 55-amino-acid residues that occur more than once in the protein sequence and sometimes present in tandem. A “domain” corresponds to a conserved region with greater than 55-amino-acid residues and may be present as single or multiple copies in the protein sequence. These correspond to (1) 57-amino-acid-residue PxV domain, (2) 122-amino-acid-residue FxF domain, (3) 111-amino-acid-residue YEFF domain, (4) 109-amino-acid-residue IMxxH domain, (5) 103-amino-acid-residue VxxT domain, (6) 84-amino-acid-residue ExW domain, (7) 104-amino-acid-residue NTGFIG domain, (8) 36-amino-acid-residue NxGK repeat, (9) 95-amino-acid-residue VYV domain, (10) 75-amino-acid-residue KEWE domain, (11) 59-amino-acid-residue AFL domain, (12) 53-amino-acid-residue RIDVK repeat, (13) (a) 41-amino-acid-residue AGQF repeat and (b) 42-amino-acid-residue GSAL repeat. A repeat or domain type is characterized by specific conserved sequence motifs. We discuss the presence of these repeats and domains in proteins from other genomes and their probable secondary structure.

Identification of immunoglobulins using Chou's pseudo amino acid composition with feature selection technique

2016 ◽  
Vol 12 (4) ◽  
pp. 1269-1275 ◽  
Author(s):  
Hua Tang ◽  
Wei Chen ◽  
Hao Lin
Keyword(s):  
Feature Selection ◽  
Immune System ◽  
Amino Acid ◽  
Cell Surface ◽  
Surface Proteins ◽  
Pseudo Amino Acid Composition ◽  
Feature Selection Technique ◽  
Cell Surface Proteins ◽  
Selection Technique ◽  
Foreign Substance

Immunoglobulins, also called antibodies, are a group of cell surface proteins which are produced by the immune system in response to the presence of a foreign substance (called antigen).

scholarly journals Coding Tandem Repeats Generate Diversity in Aspergillus fumigatus Genes

2007 ◽  
Vol 6 (8) ◽  
pp. 1380-1391 ◽  
Author(s):  
Emma Levdansky ◽  
Jacob Romano ◽  
Yona Shadkchan ◽  
Haim Sharon ◽  
Kevin J. Verstrepen ◽  
...  
Keyword(s):  
Cell Wall ◽  
Amino Acid ◽  
Cell Surface ◽  
Aspergillus Fumigatus ◽  
Tandem Repeats ◽  
Size Variation ◽  
Surface Proteins ◽  
Host Immune System ◽  
Cell Wall Proteins ◽  
Cell Surface Antigens

ABSTRACT Genes containing multiple coding mini- and microsatellite repeats are highly dynamic components of genomes. Frequent recombination events within these tandem repeats lead to changes in repeat numbers, which in turn alters the amino acid sequence of the corresponding protein. In bacteria and yeasts, the expansion of such coding repeats in cell wall proteins is associated with alterations in immunogenicity, adhesion, and pathogenesis. We hypothesized that identification of repeat-containing putative cell wall proteins in the human pathogen Aspergillus fumigatus may reveal novel pathogenesis-related elements. Here, we report that the genome of A. fumigatus contains as many as 292 genes with internal repeats. Fourteen of 30 selected genes showed size variation of their repeat-containing regions among 11 clinical A. fumigatus isolates. Four of these genes, Afu3g08990, Afu2g05150 (MP-2), Afu4g09600, and Afu6g14090, encode putative cell wall proteins containing a leader sequence and a glycosylphosphatidylinositol anchor motif. All four genes are expressed and produce variable-size mRNA encoding a discrete number of repeat amino acid units. Their expression was altered during development and in response to cell wall-disrupting agents. Deletion of one of these genes, Afu3g08990, resulted in a phenotype characterized by rapid conidial germination and reduced adherence to extracellular matrix suggestive of an alteration in cell wall characteristics. The Afu3g08990 protein was localized to the cell walls of dormant and germinating conidia. Our findings suggest that a subset of the A. fumigatus cell surface proteins may be hypervariable due to recombination events in their internal tandem repeats. This variation may provide the functional diversity in cell surface antigens which allows rapid adaptation to the environment and/or elusion of the host immune system.

What do nanometer molecular trajectories tell us about heterogeneous cell surface domaines?

1995 ◽  
Vol 53 ◽  
pp. 786-787
Author(s):  
Watt W. Webb
Keyword(s):  
Cell Surface ◽  
Lipid Membranes ◽  
Surface Proteins ◽  
Protein Diffusion ◽  
Coated Pits ◽  
Cell Surface Proteins ◽  
Membrane Heterogeneity ◽  
Fluorescence Photobleaching Recovery ◽  
Photobleaching Recovery ◽  
Plasma Membrane Heterogeneity

Plasma membrane heterogeneity is implicit in the existence of specialized cell surface organelles which are necessary for cellular function; coated pits, post and pre-synaptic terminals, microvillae, caveolae, tight junctions, focal contacts and endothelial polarization are examples. The persistence of these discrete molecular aggregates depends on localized restraint of the constituent molecules within specific domaines in the cell surface by strong intermolecular bonds and/or anchorage to extended cytoskeleton. The observed plasticity of many of organelles and the dynamical modulation of domaines induced by cellular signaling evidence evanescent intermolecular interactions even in conspicuous aggregates. There is also strong evidence that universal restraints on the mobility of cell surface proteins persist virtually everywhere in cell surfaces, not only in the discrete organelles. Diffusion of cell surface proteins is slowed by several orders of magnitude relative to corresponding protein diffusion coefficients in isolated lipid membranes as has been determined by various ensemble average methods of measurement such as fluorescence photobleaching recovery(FPR).

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