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Structure and sequence analyses of Bacteroides proteins BVU_4064 and BF1687 reveal presence of two novel predominantly-beta domains, predicted to be involved in lipid and cell surface interactions

Overview of attention for article published in BMC Bioinformatics, January 2015
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Title
Structure and sequence analyses of Bacteroides proteins BVU_4064 and BF1687 reveal presence of two novel predominantly-beta domains, predicted to be involved in lipid and cell surface interactions
Published in
BMC Bioinformatics, January 2015
DOI 10.1186/s12859-014-0434-7
Pubmed ID
Authors

Padmaja Natarajan, Marco Punta, Abhinav Kumar, Andrew P Yeh, Adam Godzik, L Aravind

Abstract

BackgroundN-terminal domains of BVU_4064 and BF1687 proteins from Bacteroides vulgatus and Bacteroides fragilis respectively are members of the Pfam family PF12985 (DUF3869). Proteins containing a domain from this family can be found in most Bacteroides species and, in large numbers, in all human gut microbiome samples. Both BVU_4064 and BF1687 proteins have a consensus lipobox motif implying they are anchored to the membrane, but their functions are otherwise unknown. The C-terminal half of BVU_4064 is assigned to protein family PF12986 (DUF3870); the equivalent part of BF1687 was unclassified.ResultsCrystal structures of both BVU_4064 and BF1687 proteins, solved at the JCSG center, show strikingly similar three-dimensional structures. The main difference between the two is that the two domains in the BVU_4064 protein are connected by a short linker, as opposed to a longer insertion made of 4 helices placed linearly along with a strand that is added to the C-terminal domain in the BF1687 protein. The N-terminal domain in both proteins, corresponding to the PF12985 (DUF3869) domain is a ß¿sandwich with pre-albumin-like fold, found in many proteins belonging to the Transthyretin clan of Pfam. The structures of C-terminal domains of both proteins, corresponding to the PF12986 (DUF3870) domain in BVU_4064 protein and an unclassified domain in the BF1687 protein, show significant structural similarity to bacterial pore-forming toxins. A helix in this domain is in an analogous position to a loop connecting the second and third strands in the toxin structures, where this loop is implicated to play a role in the toxin insertion into the host cell membrane. The same helix also points to the groove between the N- and C-terminal domains that are loosely held together by hydrophobic and hydrogen bond interactions. The presence of several conserved residues in this region together with these structural determinants could make it a functionally important region in these proteins.ConclusionsStructural analysis of BVU_4064 and BF1687 points to possible roles in mediating multiple interactions on the cell-surface/extracellular matrix. In particular the N-terminal domain could be involved in adhesive interactions, the C-terminal domain and the inter-domain groove in lipid or carbohydrate interactions.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 19 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Netherlands 1 5%
Unknown 18 95%

Demographic breakdown

Readers by professional status Count As %
Researcher 6 32%
Student > Bachelor 4 21%
Student > Ph. D. Student 2 11%
Professor > Associate Professor 2 11%
Student > Master 1 5%
Other 0 0%
Unknown 4 21%
Readers by discipline Count As %
Agricultural and Biological Sciences 4 21%
Biochemistry, Genetics and Molecular Biology 3 16%
Chemistry 2 11%
Computer Science 2 11%
Philosophy 1 5%
Other 2 11%
Unknown 5 26%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 17 January 2015.
All research outputs
#15,315,142
of 22,778,347 outputs
Outputs from BMC Bioinformatics
#5,371
of 7,276 outputs
Outputs of similar age
#209,086
of 352,360 outputs
Outputs of similar age from BMC Bioinformatics
#96
of 146 outputs
Altmetric has tracked 22,778,347 research outputs across all sources so far. This one is in the 22nd percentile – i.e., 22% of other outputs scored the same or lower than it.
So far Altmetric has tracked 7,276 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.4. This one is in the 18th percentile – i.e., 18% of its peers scored the same or lower than it.
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We're also able to compare this research output to 146 others from the same source and published within six weeks on either side of this one. This one is in the 22nd percentile – i.e., 22% of its contemporaries scored the same or lower than it.