Proteins regulate a wide range of biological processes inside and outside cells by binding to specific molecular partners. In recent years, short peptides that can selectively recognize disease-related proteins have attracted attention as compact molecular tools for biosensors, diagnostic technologies, and drug discovery. However, how such small peptides recognize different proteins depending on their surrounding chemical environment has not yet been fully understood.
Calmodulin-binding peptide (CBP) is a short peptide derived from skeletal muscle myosin light chain kinase and is known to bind calmodulin in the presence of calcium ions. Calmodulin is an important regulatory protein involved in muscle contraction, neurotransmission, cell-cycle control, and other biological processes. Human midkine, on the other hand, is expressed at low levels in normal adult tissues but is upregulated in many cancers, making it an emerging cancer biomarker and therapeutic target.
A research team led by Special Appointment Professor Naoto Nemoto and Professor Koji Matsuoka of the Graduate School of Science and Engineering, Saitama University, focused on the possibility that CBP may recognize proteins other than calmodulin and investigated its interaction with human midkine. The team used wild-type CBP and a mutant CBP with a single amino-acid substitution, and compared their binding to human midkine, bovine serum albumin, GFP, and immunoglobulin G using surface plasmon resonance. They also used AlphaFold 3 to predict how differences in metal ions affect the binding structures between CBP and proteins. As a result, the team revealed that CBP binds calmodulin in the presence of calcium ions, while it binds human midkine in the presence of sodium ions.
The paper, titled "Calmodulin-binding peptide is a natural peptide aptamer that binds to human midkine in a metal ion–dependent manner," was published online in Biochemical and Biophysical Research Communications on July 8, 2026.
Key findings
- The team discovered that calmodulin-binding peptide (CBP) binds human midkine in the presence of sodium ions.
- The results suggest that CBP may bind calmodulin in the presence of calcium ions and human midkine in the presence of sodium ions.
- Surface plasmon resonance experiments confirmed the interaction between CBP and human midkine.
- AlphaFold 3 structural prediction suggested that metal ions may alter the interaction mode between peptides and proteins.
- The study showed that a short, naturally derived peptide may function as a "natural peptide aptamer" that switches its target protein depending on the surrounding ion environment.
Special Appointment Professor Nemoto, the corresponding author of the paper, commented on the significance of the findings: "CBP has long been known as a peptide that binds to calmodulin. In this study, however, we found that in the presence of sodium ions, CBP recognizes human midkine, a protein with a completely different structure. We were surprised to find that the same short peptide can recognize structurally distinct proteins under different ion conditions. This suggests that naturally occurring peptides may possess a previously unrecognized level of adaptability in molecular recognition."
Looking ahead, Professor Matsuoka, a co-author of the study, said: "Midkine is implicated in cancer, inflammation and neurodegenerative disorders. Short peptides capable of selective protein recognition may provide a foundation for future diagnostic and therapeutic technologies. In the future, we expect this work to contribute to medical and biotechnology applications using smaller and more easily designable peptide molecules."
