Rational Design and Biophysical Characterization of Thioredoxin-Based Aptamers: Insights into Peptide Grafting

Institute of Molecular Cellular Biology (A-STAR), Proteos, Biopolis, Singapore 138673, Singapore.
Journal of Molecular Biology (Impact Factor: 4.33). 11/2009; 395(4):871-83. DOI: 10.1016/j.jmb.2009.10.069
Source: PubMed


Peptide aptamers are simple structures, often made up of a single-variable peptide loop constrained within a constant scaffold protein. Aptamers were rationally designed by inserting peptides into a solvent-exposed loop on thioredoxin (Trx). They were designed to interact with the proteins elongation initiation factor 4E (eIF4E) and mouse double minute 2 (MDM2) and were then validated by competitive fluorescence anisotropy experiments. The constructed aptamers interacted with eIF4E and MDM2 with apparent K(d) values of 1.25+/-0.06 microM and 0.09+/-0.01 microM, respectively, as determined by isothermal titration calorimetry (ITC). The MDM2 aptamer (SuperTIP) interacted approximately 2-fold more tightly with MDM2 than the free linear peptide (12.1 peptide), while the eIF4E aptamer elongation initiation factor 4GI-SG interacted approximately 5-fold less strongly than the free linear peptide (elongation initiation factor 4GI). These differences in binding with respect to each aptamer's free peptide reveal that there are more factors involved than just constraining a peptide in a scaffold that lead to tighter binding. ITC studies of aptamer interactions reveal an enthalpic component more favorable than that for the free linear peptides, as well as a larger unfavorable entropic component. These results indicated that stapling of the free peptide in the scaffold increases the favorable enthalpy of the interaction with the target protein. Thermostability studies also revealed that peptide insertion significantly destabilized the Trx scaffold by approximately 27 degrees C. It is this destabilization that leads to an increase in the flexibility of the Trx scaffold, which presumably is lost upon the aptamer's interaction with the target protein and is the cause of the increase in unfavorable entropy in the ITC studies. The precise origin of the enthalpic effect was further studied using molecular dynamics for the MDM2-SuperTIP system, which revealed that there were also favorable electrostatic interactions between the Trx scaffold and the MDM2 protein itself, as well as with the inserted peptide. This work reveals that any increase in the binding affinity of an aptamer over a free peptide is dependent on the increase in the favorable enthalpy of binding, which is ideally caused by stapling of the peptide or by additional interactions between the aptamer protein and its target. These need to be sufficient to compensate for the destabilization of the scaffold by peptide insertion. These observations will be useful in future aptamer designs.

26 Reads
  • Source
    • "These ASOs cause p53 stabilization and activation of the p53 pathway in cancer cells in tumor xenograft as well as cell culture in both p53 wild-type and mutant cells, possibly via the resulting p21 upregulation due to MDM2 inhibition[141]. Other gene targeting strategies include the use of MDM2 ribozymes, MDM2 aptamers, and RNA interference techniques[27],[147],[148]. All these techniques had antiproliferative and pro-apoptotic effects in the in vitro systems tested. "
    [Show abstract] [Hide abstract]
    ABSTRACT: The p53 tumor suppressor is a key transcription factor regulating cellular pathways such as DNA repair, cell cycle, apoptosis, angiogenesis, and senescence. It acts as an important defense mechanism against cancer onset and progression, and is negatively regulated by interaction with the oncoprotein MDM2. In human cancers, the TP53 gene is frequently mutated or deleted, or the wild-type p53 function is inhibited by high levels of MDM2, leading to downregulation of tumor suppressive p53 pathways. Thus, the inhibition of MDM2-p53 interaction presents an appealing therapeutic strategy for the treatment of cancer. However, recent studies have revealed the MDM2-p53 interaction to be more complex involving multiple levels of regulation by numerous cellular proteins and epigenetic mechanisms, making it imperative to reexamine this intricate interplay from a holistic viewpoint. This review aims to highlight the multifaceted network of molecules regulating the MDM2-p53 axis to better understand the pathway and exploit it for anticancer therapy.
    Full-text · Article · Jul 2013
  • Source
    • "Another limitation was the difficulty in translating library diversity, contained in ligation reactions, into corresponding numbers of colonies on selection plates, which is a function of transformation efficiency [21]. Finally, random peptide sequence insertions frequently destabilized the Thioredoxin scaffold and might create molecules that are prone to aggregation [22], [23]. In this work, we successfully addressed these problems and developed a robust method for constructing a Combinatorial Library of Improved Peptide aptamers (CLIPs). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Peptide aptamers are small proteins containing a randomized peptide sequence embedded into a stable protein scaffold, such as Thioredoxin. We developed a robust method for building a Combinatorial Library of Improved Peptide aptamers (CLIPs) of high complexity, containing ≥3×10(10) independent clones, to be used as a molecular tool in the study of biological pathways. The Thioredoxin scaffold was modified to increase solubility and eliminate aggregation of the peptide aptamers. The CLIPs was used in a yeast two-hybrid screen to identify peptide aptamers that bind to various domains of the Receptor for Advanced Glycation End products (RAGE). NMR spectroscopy was used to identify interaction surfaces between the peptide aptamers and RAGE domains. Cellular functional assays revealed that in addition to directly interfering with known binding sites, peptide aptamer binding distal to ligand sites also inhibits RAGE ligand-induced signal transduction. This finding underscores the potential of using CLIPs to select allosteric inhibitors of biological targets.
    Full-text · Article · Jun 2013 · PLoS ONE
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Protein-protein interactions (PPIs) govern all aspects of cell function and, as such, are a major target for research and therapeutic intervention. A major rate-limiting step in PPI research is the expression and purification of full-length proteins. The use of peptides to study PPIs significantly facilitates the structural and biophysical characterization of PPIs as well as the effort to develop drugs to control PPIs. Here we describe examples for the use of peptides to study PPI and some of the important experimental methods that are used in the field. Peptides have proved to be excellent tools to study PPIs and have been contributing both for understanding mechanisms of PPIs as well as for drug design for PPI modulation.
    Preview · Article · Jun 2010 · Future medicinal chemistry
Show more