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Conformational Ensembles Exhibit Extensive Molecular Recognition Features

Authors: Robert I. Cukier;

Conformational Ensembles Exhibit Extensive Molecular Recognition Features

Abstract

Intrinsically disordered proteins (IDPs) are important for signaling and regulatory pathways. In contrast to folded proteins, they sample a diverse conformational space. IDPs have residue ranges within a sequence that have been referred to as molecular recognition features (MoRFs). A MoRF can be viewed as contiguous residues exhibiting a conformational disorder that become ordered upon binding to another protein or ligand. In this work, we introduce a structural characterization of MoRFs based on entropy and mutual information (MI). In this view, a MoRF is a set of contiguous residues that exhibit a large entropy (from rotameric residue sampling) and large MI, the latter indicating a dependence among the residues' rotameric sampling comprising the MoRF. The methodology is first applied to a number of ubiquitin ensembles that were obtained based on nuclear magnetic resonance experiments. One is a denatured Ub ensemble that has a large entropy for various unitSizes (number of contiguous residues) but essentially zero MI, indicting no dependence among the residue rotamer sampling. Another ensemble does exhibit extensive regions along the sequence where there are MoRFs centered on nonsecondary structure regions. The MoRFs are present for unitSizes 2-10. That a substantial number of MoRFs are present in Ub strongly suggests a conformational selection mechanism for this protein. Two additional ensembles for the cyclin-dependent kinase inhibitor Sic1 and for the amyloid protein α-synuclein, which have been shown to be IDPs, are also analyzed. Both exhibit MoRF-like character.

Related Organizations
Keywords

Chemistry, QD1-999

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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
2
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Average
Average
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