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Ligand-binding prediction in the resistance-nodulation-cell division (RND) proteins

Paper ID Volume ID Publish Year Pages File Format Full-Text
15492 1417 2007 9 PDF Available
Title
Ligand-binding prediction in the resistance-nodulation-cell division (RND) proteins
Abstract

The resistance-nodulation-cell division (RND) protein family is a ubiquitous group of proteins primarily present in bacteria. These proteins, involved in the transport of multiple drugs across the cell envelope in bacteria, exhibit broad substrate specificity and act like efflux pumps. In this work, a protein belonging to the RND protein family, AcrB of Escherichia coli was used as a working model to predict in silico the compounds transported by 47 RND proteins. From AcrB we extracted and clustered 14 amino acids directly involved in substrate interactions. This clustering provides enough information to identify 16 groups that correlates with the ligand they extrude, such as proteins expelling aromatic hydrocarbons (SrpB cluster) or proteins expelling heavy metals (CnrA cluster). The relationship between conserved, cluster-specific and variable residues indicates that although the ligand-binding domain is conserved in structure, it has enough flexibility to recognize specifically a diversity of molecules.

Keywords
RND-proteins; AcrB; Ligand binding prediction
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Ligand-binding prediction in the resistance-nodulation-cell division (RND) proteins
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 31, Issue 2, April 2007, Pages 115–123
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us