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Updated: Jul 10, 2026
Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
Published on: January 26, 2024
On the benefit of bivalency in peptide ligand/pin1 interactions
Sebastian Daum1, Christian Lücke, Dirk Wildemann
1Max Planck Research Unit for Enzymology of Protein Folding, Weinbergweg 22, 06120 Halle/Saale, Germany.
Abstract:
The human peptidyl prolyl cis/trans isomerase (PPIase) Pin1 has a key role in developmental processes and cell proliferation. Pin1 consists of an N-terminal WW domain and a C-terminal catalytic PPIase domain both targeted specifically to Ser(PO(3)H(2))/Thr(PO(3)H(2))-Pro sequences. Here, we report the enhanced affinity originating from bivalent binding of ligands toward Pin1 compared to monovalent binding. We developed composite peptides where an N-terminal segment represents a catalytic site-directed motif and a C-terminal segment exhibits a predominant affinity to the WW domain of Pin1 tethered by polyproline linkers of different chain length. We used NMR shift perturbation experiments to obtain information on the specific interaction of a bivalent ligand to both targeted sites of Pin1. The bivalent ligands allowed a considerable range of thermodynamic investigations using isothermal titration calorimetry and PPIase activity assays. They expressed up to 350-fold improved affinity toward Pin1 in the nanomolar range in comparison to the monovalent peptides. The distance between the two binding motifs was highly relevant for affinity. The optimum in affinity manifested by a linker length of five prolyl residues between active site- and WW domain-directed peptide fragments suggests that the corresponding domains in Pin1 are allowed to adopt preferred spatial arrangement upon ligand binding.
Insights
Researchers developed bivalent ligands that bind to both the catalytic and WW domains of human peptidyl prolyl cis/trans isomerase (PPIase) Pin1. These ligands show significantly enhanced affinity, up to 350-fold, compared to monovalent versions.
Area of Science:
- Biochemistry
- Molecular Biology
- Structural Biology
Background:
- Human peptidyl prolyl cis/trans isomerase (PPIase) Pin1 regulates crucial cellular processes like development and proliferation.
- Pin1 features an N-terminal WW domain and a C-terminal catalytic PPIase domain, both targeting specific phosphorylated Ser/Thr-Pro motifs.
Purpose of the Study:
- To investigate the enhanced binding affinity of bivalent ligands to Pin1 compared to monovalent ligands.
- To characterize the interaction of composite peptides with Pin1's distinct domains using biophysical methods.
Main Methods:
- Development of composite peptides with separate catalytic site- and WW domain-binding motifs linked by polyproline chains.
- Utilized NMR shift perturbation, isothermal titration calorimetry, and PPIase activity assays to study ligand-Pin1 interactions.
- Investigated the impact of linker length on binding affinity and domain interaction.
Main Results:
- Bivalent ligands demonstrated up to 350-fold improved affinity for Pin1, reaching nanomolar ranges.
- NMR and thermodynamic data confirmed specific binding to both Pin1 domains.
- Optimal affinity was observed with a five-prolyl residue linker, indicating a preferred spatial arrangement for bivalent binding.
Conclusions:
- Bivalent ligand design significantly enhances Pin1 affinity by engaging both catalytic and WW domains.
- The linker length is critical for optimizing the spatial orientation of binding motifs for maximal affinity.
- This strategy offers a promising approach for developing potent Pin1 inhibitors for therapeutic applications.
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