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Structure-based classification of 45 FK506-binding proteins.

J A Somarelli¹, S Y Lee, J Skolnick

¹Department of Biological Sciences, OE304, Florida International University, Miami, Florida 33199, USA.

|January 25, 2008

Summary

FK506-binding proteins (FKBPs) are crucial chaperones with diverse roles. Computational modeling revealed evolutionary changes and potential new functions, including drug interactions and nucleic acid binding.

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Area of Science:

Biochemistry
Structural Biology
Evolutionary Biology

Background:

FK506-binding proteins (FKBPs) are conserved chaperones involved in numerous cellular processes.
Their functions are linked to specific tertiary structures and domains.
Understanding FKBP structure-function relationships is key to deciphering their roles.

Purpose of the Study:

To predict and analyze the tertiary structures of a diverse set of FKBP proteins.
To classify FKBP homologs based on structural predictions.
To investigate potential evolutionary modifications and novel functional interactions of FKBPs.

Main Methods:

Tertiary structure prediction using the Threading/ASSEmbly/Refinement (TASSER) approach for 45 FKBP proteins across 23 species.
Comparison of predicted models with existing FKBP solution structures.
Identification of homologous protein groups and evolutionary sequence modifications.
Molecular docking simulations to explore drug binding and protein-protein interactions.

Main Results:

Successfully predicted tertiary structures for 45 FKBP proteins, enabling homology-based classification.
Identified significant evolutionary modifications within the FKBP family, including domain losses, duplications, and motif insertions.
Docking simulations suggested that extrachain segments influence drug binding affinity.
Revealed a potential helix-loop-helix (HLH) region in some FKBPs, implicating them in nucleic acid interactions.

Conclusions:

The structural classification of FKBPs aids in inferring functions of newly identified members.
FKBP evolution involves substantial structural diversification.
FKBPs possess uncharacterized regions and domains that influence their interactions with drugs and nucleic acids, expanding their known functional repertoire.