Sensitive detection of sequence similarity using combinatorial pattern discovery: A challenging study of two distantly related protein families

2005 ◽  
Vol 61 (4) ◽  
pp. 926-937 ◽  
Author(s):  
Nikos Darzentas ◽  
Isidore Rigoutsos ◽  
Christos A. Ouzounis
Keyword(s):  
Sequence Similarity ◽  
Pattern Discovery ◽  
Sensitive Detection ◽  
Related Protein ◽  
Protein Families ◽  
Combinatorial Pattern

scholarly journals Evolution of polymer formation within the actin superfamily

2017 ◽  
Vol 28 (19) ◽  
pp. 2461-2469 ◽  
Author(s):  
Patrick R. Stoddard ◽  
Tom A. Williams ◽  
Ethan Garner ◽  
Buzz Baum
Keyword(s):  
Convergent Evolution ◽  
Atp Hydrolysis ◽  
Linear Polymers ◽  
Related Protein ◽  
Protein Families ◽  
Structure And Dynamics ◽  
Polymer Formation ◽  
Filament Structure ◽  
Related Proteins ◽  
Actin Superfamily

While many are familiar with actin as a well-conserved component of the eukaryotic cytoskeleton, it is less often appreciated that actin is a member of a large superfamily of structurally related protein families found throughout the tree of life. Actin-related proteins include chaperones, carbohydrate kinases, and other enzymes, as well as a staggeringly diverse set of proteins that use the energy from ATP hydrolysis to form dynamic, linear polymers. Despite differing widely from one another in filament structure and dynamics, these polymers play important roles in ordering cell space in bacteria, archaea, and eukaryotes. It is not known whether these polymers descended from a single ancestral polymer or arose multiple times by convergent evolution from monomeric actin-like proteins. In this work, we provide an overview of the structures, dynamics, and functions of this diverse set. Then, using a phylogenetic analysis to examine actin evolution, we show that the actin-related protein families that form polymers are more closely related to one another than they are to other nonpolymerizing members of the actin superfamily. Thus all the known actin-like polymers are likely to be the descendants of a single, ancestral, polymer-forming actin-like protein.

scholarly journals Utilizing Whole Fusobacterium Genomes To Identify, Correct, and Characterize Potential Virulence Protein Families

2019 ◽  
Vol 201 (23) ◽  
Author(s):  
Ariana Umaña ◽  
Blake E. Sanders ◽  
Christopher C. Yoo ◽  
Michael A. Casasanta ◽  
Barath Udayasuryan ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Virulence Factors ◽  
Serine Proteases ◽  
Sequence Similarity ◽  
Protein Families ◽  
Emerging Pathogens ◽  
Content Type ◽  
Virulence Protein ◽  
Similarity Networks ◽  
Sequence Similarity Networks

ABSTRACT Fusobacterium spp. are Gram-negative, anaerobic, opportunistic pathogens involved in multiple diseases, including a link between the oral pathogen Fusobacterium nucleatum and the progression and severity of colorectal cancer. The identification and characterization of virulence factors in the genus Fusobacterium has been greatly hindered by a lack of properly assembled and annotated genomes. Using newly completed genomes from nine strains and seven species of Fusobacterium, we report the identification and corrected annotation of verified and potential virulence factors from the type 5 secreted autotransporter, FadA, and MORN2 protein families, with a focus on the genetically tractable strain F. nucleatum subsp. nucleatum ATCC 23726 and type strain F. nucleatum subsp. nucleatum ATCC 25586. Within the autotransporters, we used sequence similarity networks to identify protein subsets and show a clear differentiation between the prediction of outer membrane adhesins, serine proteases, and proteins with unknown function. These data have identified unique subsets of type 5a autotransporters, which are key proteins associated with virulence in F. nucleatum. However, we coupled our bioinformatic data with bacterial binding assays to show that a predicted weakly invasive strain of F. necrophorum that lacks a Fap2 autotransporter adhesin strongly binds human colonocytes. These analyses confirm a gap in our understanding of how autotransporters, MORN2 domain proteins, and FadA adhesins contribute to host interactions and invasion. In summary, we identify candidate virulence genes in Fusobacterium, and caution that experimental validation of host-microbe interactions should complement bioinformatic predictions to increase our understanding of virulence protein contributions in Fusobacterium infections and disease. IMPORTANCE Fusobacterium spp. are emerging pathogens that contribute to mammalian and human diseases, including colorectal cancer. Despite a validated connection with disease, few proteins have been characterized that define a direct molecular mechanism for Fusobacterium pathogenesis. We report a comprehensive examination of virulence-associated protein families in multiple Fusobacterium species and show that complete genomes facilitate the correction and identification of multiple, large type 5a secreted autotransporter genes in previously misannotated or fragmented genomes. In addition, we use protein sequence similarity networks and human cell interaction experiments to show that previously predicted noninvasive strains can indeed bind to and potentially invade human cells and that this could be due to the expansion of specific virulence proteins that drive Fusobacterium infections and disease.

scholarly journals Prediction of Protein–Ligand Interaction Based on the Positional Similarity Scores Derived from Amino Acid Sequences

2019 ◽  
Vol 21 (1) ◽  
pp. 24 ◽  
Author(s):  
Dmitry Karasev ◽  
Boris Sobolev ◽  
Alexey Lagunin ◽  
Dmitry Filimonov ◽  
Vladimir Poroikov
Keyword(s):  
Prediction Accuracy ◽  
Sequence Similarity ◽  
Amino Acid Sequences ◽  
Protein Families ◽  
Pairwise Sequence Alignment ◽  
Ligand Interaction ◽  
Protein Ligand Interactions ◽  
General Chemical ◽  
Local Sequence ◽  
Ligand Interactions

The affinity of different drug-like ligands to multiple protein targets reflects general chemical–biological interactions. Computational methods estimating such interactions analyze the available information about the structure of the targets, ligands, or both. Prediction of protein–ligand interactions based on pairwise sequence alignment provides reasonable accuracy if the ligands’ specificity well coincides with the phylogenic taxonomy of the proteins. Methods using multiple alignment require an accurate match of functionally significant residues. Such conditions may not be met in the case of diverged protein families. To overcome these limitations, we propose an approach based on the analysis of local sequence similarity within the set of analyzed proteins. The positional scores, calculated by sequence fragment comparisons, are used as input data for the Bayesian classifier. Our approach provides a prediction accuracy comparable or exceeding those of other methods. It was demonstrated on the popular Gold Standard test sets, presenting different sequence heterogeneity and varying from the group, including different protein families to the more specific groups. A reasonable prediction accuracy was also found for protein kinases, displaying weak relationships between sequence phylogeny and inhibitor specificity. Thus, our method can be applied to the broad area of protein–ligand interactions.

scholarly journals A combinatorial pattern discovery approach for the prediction of membrane dipping (re-entrant) loops

2006 ◽  
Vol 22 (14) ◽  
pp. e290-e297 ◽  
Author(s):  
G. Lasso ◽  
J. F. Antoniw ◽  
J. G.L. Mullins
Keyword(s):  
Pattern Discovery ◽  
Combinatorial Pattern

scholarly journals Identification of Novel Salmonella enterica Serovar Typhimurium DT104-Specific Prophage and Nonprophage Chromosomal Sequences among Serovar Typhimurium Isolates by Genomic Subtractive Hybridization

2005 ◽  
Vol 71 (9) ◽  
pp. 4979-4985 ◽  
Author(s):  
Armand P. H. M. Hermans ◽  
Tjakko Abee ◽  
Marcel H. Zwietering ◽  
Henk J. M. Aarts
Keyword(s):  
Salmonella Enterica ◽  
Salmonella Enterica Serovar Typhimurium ◽  
Sequence Similarity ◽  
Subtractive Hybridization ◽  
The Other ◽  
Dna Fragments ◽  
Related Protein ◽  
Serovar Typhimurium ◽  
Chromosomal Sequences ◽  
Specific Sequences

ABSTRACT Genomic subtractive hybridization was performed between Salmonella enterica serovar Typhimurium LT2 and DT104 to search for novel Salmonella serovar Typhimurium DT104-specific sequences. The subtraction resulted mainly in the isolation of DNA fragments with sequence similarity to phages. Two fragments identified were associated with possible virulence factors. One fragment was identical to irsA of Salmonella serovar Typhimurium ATCC 14028, which is suggested to be involved in macrophage survival. The other fragment was homologous to HldD, an Escherichia coli O157:H7 lipopolysaccharide assembly-related protein. Five selected DNA fragments—irsA, the HldD homologue, and three fragments with sequence similarity to prophages—were tested for their presence in 17 Salmonella serovar Typhimurium DT104 isolates and 27 non-DT104 isolates by PCR. All five selected DNA fragments were Salmonella serovar Typhimurium DT104 specific among the serovar Typhimurium isolates tested. These DNA fragments can be useful for better detection and typing of Salmonella serovar Typhimurium DT104.

scholarly journals Adipocyte differentiation-related protein is secreted into milk as a constituent of milk lipid globule membrane

1996 ◽  
Vol 320 (3) ◽  
pp. 1025-1030 ◽  
Author(s):  
Hans W. HEID ◽  
Martina SCHNÖLZER ◽  
Thomas W. KEENAN
Keyword(s):  
Adipocyte Differentiation ◽  
Sequence Similarity ◽  
Surface Membrane ◽  
Major Constituent ◽  
Milk Lipid ◽  
Related Protein ◽  
Membrane Material ◽  
Lipid Globule ◽  
Lactating Mammary Gland

Milk lipid globules from humans, cows and rats contained a protein identified as adipocyte differentiation-related protein (ADRP) associated with the globule surface membrane material. This protein, previously believed to be specific to adipocytes, was a major constituent of the globule surface and was present in a detergent-insoluble complex that contained stoichiometric amounts of butyrophilin and xanthine oxidase. Identification of ADRP was by sequence similarity of tryptic peptides from cow and human proteins with the sequence inferred from the cDNA for mouse ADRP. The putative ADRP of lipid globules from cow, human and rat milk was recognized specifically by antisera raised against a peptide synthesized to duplicate the N-terminal 26 residues of the mouse protein. In homogenates of lactating mammary gland, ADRP was found only in endoplasmic reticulum and in lipid droplet fractions. ADRP was modified, apparently post-translationally, and one modification apparently was acylation, primarily with C14, C16 and C18 fatty acids. Two isoelectric variants of ADRP were present in cow globule membrane material. In vitro, ADRP served as a substrate for protein kinases associated with milk lipid globule membrane, but this protein did not seem to become phosphorylated intracellularly.

Combinatorial pattern discovery for scientific data

1994 ◽  
Vol 23 (2) ◽  
pp. 115-125 ◽  
Author(s):  
Jason Tsong-Li Wang ◽  
Gung-Wei Chirn ◽  
Thomas G. Marr ◽  
Bruce Shapiro ◽  
Dennis Shasha ◽  
...  
Keyword(s):  
Pattern Discovery ◽  
Scientific Data ◽  
Combinatorial Pattern
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