Many biologically critical recognition events involve the specific binding of flexible ligands such as single-stranded (ss) DNA, RNA, peptides and carbohydrates. Structural plasticity, defined as the ability of an interface to adopt alternate conformations when bound to different ligands, has been invoked to explain binding specificity and promiscuity in several protein/ligand systems. Furthermore, an understanding of the malleability of a binding interface is increasingly recognized as key to predicting its binding activity and specificity. Discerning the scope and mechanisms of rearrangements at binding interfaces is essential to understanding the biophysics of molecular recognition events. The focus of this proposal is to investigate the extent of structural plasticity in the recognition of these flexible ligands.
We use the recognition of ssDNA by the telomere end-binding proteins as the predominant model to characterize the contribution of structural plasticity to recognition. The telomere-end binding proteins Pot1 and Cdc13 bind the conserved 3’ ssDNA overhang at telomeres. This binding is required for cellular viability. However, the sequence of the overhang is somewhat variable, meaning that these proteins need to bind divergent ligands while maintaining exquisite specificity. Extensive evidence suggests that the protein/nucleic acid interface adopts altered configurations in the presence of different ligands that bind with similar affinities. We will test the hypothesis that this structural plasticity is important for specificity. Moreover, the malleability of the interface may further contribute to function by providing a way to physically alter the structure and accessibility of the 3’ end.
The Protection of Telomeres 1 (Pot1) protein is a central component of the shelterin complex at telomerase and is conserved from fission yeast to humans. Pot1 binds directly to the 3’ single-stranded telomere ends and regulates a variety of essential functions, including telomere length and end-protection.
Our work has primarily focused on the study of the Pot1 protein fromSchizosaccromyces pombe (fission yeast). Our biochemical and structural studies have revealed many thermodynamically equivalent yet distinct binding modes used by Pot1. Future work in this system aims to understand how this malleability is achieved.
Cdc13 is a single-stranded telomeric DNA-binding protein identified genetically from S. cerevisiae (budding yeast) and is a member of the telomere end-protection (TEP) family of proteins. This essential protein protects the ends of chromosomes from degradation and acts as both a positive and negative regulator of telomerase activity. In addition to interactions with telomerase, Cdc13 is also involved in mediating protein/protein interactions necessary for proper telomere maintenance. These functions are fulfilled by the direct interaction of Cdc13 with the 3' single-stranded telomeric end.
The ssDNA binding activity of Cdc13 is facilitated by its single-stranded DNA (ssDNA) binding domain (Cdc13-DBD), which we have found exhibits an unusually high affinity for ssDNA. Our research in this area focuses on how this high affinity is achieved, what mechanisms underlay specificity, and how these unprecedented activities contribute to function in vivo.