Exploring the structurial diversity and engineering potential of thermophilic periplasmic binding proteins
Date
2007-05-02
Author
Advisors
Hellinga, Homme W.
Richardson, Jane
York, John
Fitzgerald, Michael
Raetz, Chris
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Abstract
The periplasmic binding protein (PBP) superfamily is found throughout the genosphere
of both prokaryotic and eukaryotic organisms. PBPs function as receptors in bacterial
solute transport and chemotaxis systems; however the same fold is also used in transcriptional
regulators, enzymes, and eukaryotic neurotransmitter receptors. This versatility has
been exploited for structure-based computational protein design experiments where
PBPs have been engineered to bind novel ligands and serve as biosensors for the detection
of small-molecule ligands relevant to biomedical or defense-related interests. In
order to further understand functional adaptation from a structural biology perspective,
and to provide a set of robust starting points for engineering novel biosensors by
structure-based design, I have characterized the ligand-binding properties and solved
the structure of nine PBPs from various thermophilic bacteria. Analysis of these structures
reveals a variety of mechanisms by which diverse function can be encoded in a common
fold. It is observed that re-modeling of secondary structure elements (such as insertions,
deletions, and loop movements), and re-decoration of amino acid side-chains are common
diversification mechanisms in PBPs. Furthermore, the relationship between hinge-bending
motion and ligand binding is critical to understanding the function of natural or
engineered adaptations in PBPs. Three of these proteins were solved in both the presence
and absence of ligand which allowed for the first time the observation and analysis
of ligand-induced structural rearrangements in thermophilic PBPs. This work revealed
that the magnitude and transduction of local and global ligand-induced motions are
diverse throughout the PBP superfamily. Through the analysis of the open-to-closed
transition, and the identification of natural structural adaptations in thermophilic
members of the PBP superfamily, I reveal strategies which can be applied to computational
protein design to significantly improve current strategies.
Type
DissertationDepartment
BiochemistrySubject
periplasmic binding protein (PBP)ligand-binding properties
thermophilic bacteria
computational biology
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https://hdl.handle.net/10161/176Citation
Cuneo, Matthew Joseph (2007). Exploring the structurial diversity and engineering potential of thermophilic periplasmic
binding proteins. Dissertation, Duke University. Retrieved from https://hdl.handle.net/10161/176.Collections
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