Distinct interfacial biclique patterns between ssDNA-binding proteins and those with dsDNAs

Zeng, T; Li, J; Liu, J

Distinct interfacial biclique patterns between ssDNA-binding proteins and those with dsDNAs

Zeng, T Li, J

Liu, J

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Publication Type:: Journal Article
Citation:: Proteins: Structure, Function and Bioinformatics, 2011, 79 (2), pp. 598 - 610
Issue Date:: 2011-02-01

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Field	Value	Language
dc.contributor.author	Zeng, T	en_US
dc.contributor.author	Li, J https://orcid.org/0000-0003-1833-7413	en_US
dc.contributor.author	Liu, J	en_US
dc.date.issued	2011-02-01	en_US
dc.identifier.citation	Proteins: Structure, Function and Bioinformatics, 2011, 79 (2), pp. 598 - 610	en_US
dc.identifier.issn	0887-3585	en_US
dc.identifier.uri	http://hdl.handle.net/10453/31227
dc.description.abstract	We introduce a new motif called interfacial biclique pattern to study the difference between double-stranded DNA-binding proteins (DSBs, most of them also known to play the role as transcriptional factors) and single-stranded DNA-binding proteins (SSBs) which are found to involve in many applications recently. An interfacial biclique pattern in a protein-DNA complex usually consists of a group of residues and a group of nucleotides such that every residue has a contact to all of the bases. The proposal of this idea is based on a biological redundancy mechanism that: a site mutation has little influence on the other residues to recognize the target nucleotides and vice versa. The distribution of the residues on the interfacial motifs is investigated to identify distinct stable preferred residues, stable un-preferred residues and unstable preferred residues between SSBs and DSBs. We also examine residue co-occurrence and residue-base association rules in the interfacial motifs to uncover the different choices of residue combinations by SSBs and DSBs that have contacts with one or more bases. We found that DSBs and SSBs have their own right residues at the right places for the binding preference and association with nucleotides. Some of our results can be supported by literature work. © 2010 Wiley-Liss, Inc.	en_US
dc.relation.ispartof	Proteins: Structure, Function and Bioinformatics	en_US
dc.relation.isbasedon	10.1002/prot.22908	en_US
dc.subject.classification	Bioinformatics	en_US
dc.subject.mesh	Nucleotides	en_US
dc.subject.mesh	Amino Acids	en_US
dc.subject.mesh	DNA-Binding Proteins	en_US
dc.subject.mesh	DNA	en_US
dc.subject.mesh	DNA, Single-Stranded	en_US
dc.subject.mesh	Binding Sites	en_US
dc.subject.mesh	Amino Acid Sequence	en_US
dc.subject.mesh	Protein Structure, Tertiary	en_US
dc.subject.mesh	Protein Binding	en_US
dc.subject.mesh	Surface Properties	en_US
dc.subject.mesh	Molecular Sequence Data	en_US
dc.subject.mesh	Propensity Score	en_US
dc.title	Distinct interfacial biclique patterns between ssDNA-binding proteins and those with dsDNAs	en_US
dc.type	Journal Article
utslib.citation.volume	2	en_US
utslib.citation.volume	79	en_US
utslib.for	060499 Genetics not elsewhere classified	en_US
utslib.for	01 Mathematical Sciences	en_US
utslib.for	06 Biological Sciences	en_US
utslib.for	08 Information and Computing Sciences	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Engineering and Information Technology
pubs.organisational-group	/University of Technology Sydney/Strength - AAI - Advanced Analytics Institute Research Centre
pubs.organisational-group	/University of Technology Sydney/Strength - CHT - Health Technologies
utslib.copyright.status	closed_access
pubs.issue	2	en_US
pubs.publication-status	Published	en_US
pubs.volume	79	en_US

Abstract:

We introduce a new motif called interfacial biclique pattern to study the difference between double-stranded DNA-binding proteins (DSBs, most of them also known to play the role as transcriptional factors) and single-stranded DNA-binding proteins (SSBs) which are found to involve in many applications recently. An interfacial biclique pattern in a protein-DNA complex usually consists of a group of residues and a group of nucleotides such that every residue has a contact to all of the bases. The proposal of this idea is based on a biological redundancy mechanism that: a site mutation has little influence on the other residues to recognize the target nucleotides and vice versa. The distribution of the residues on the interfacial motifs is investigated to identify distinct stable preferred residues, stable un-preferred residues and unstable preferred residues between SSBs and DSBs. We also examine residue co-occurrence and residue-base association rules in the interfacial motifs to uncover the different choices of residue combinations by SSBs and DSBs that have contacts with one or more bases. We found that DSBs and SSBs have their own right residues at the right places for the binding preference and association with nucleotides. Some of our results can be supported by literature work. © 2010 Wiley-Liss, Inc.

Please use this identifier to cite or link to this item:

http://hdl.handle.net/10453/31227