Investigation of the interactions between the EphB2 receptor and SNEW peptide variants
Open accessAbstract
EphB2 interacts with cell surface-bound ephrin ligands to relay bidirectional signals. Overexpression of the EphB2 receptor protein has been linked to different types of cancer. The SNEW (SNEWIQPRLPQH) peptide binds with high selectivity and moderate affinity to EphB2, inhibiting Eph-ephrin interactions by competing with ephrin ligands for the EphB2 high-affinity pocket. We used rigorous free energy perturbation (FEP) calculations to re-evaluate the binding interactions of SNEW peptide with the EphB2 receptor, followed by experimental testing of the computational results. Our results provide insight into dynamic interactions of EphB2 with SNEW peptide. While the first four residues of the SNEW peptide are already highly optimized, change of the C-terminal end of the peptide has the potential to improve SNEW-binding affinity. We identified a PXSPY motif that can be similarly aligned with several other EphB2-binding peptides.
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Conformational dynamics and the distribution of the conformational ensemble are important in Eph-ephrin recognition.
“Conformational dynamics and the distribution of the conformational ensemble are important in Eph-Ephrin recognition.9,475,513–516”
From Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell (2016) · cites this paper as [515]
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References 54 · Cited by 10
- Authors
- Ma, B., Kolb, S., Diprima, M., Karna, M., Tosato, G., Yang, Q., Huang, Q., & Nussinov, R.
- Affiliations
- National Cancer Institute (US)
- Fudan University (CN)
- Tel Aviv University (IL)
- Corresponding author
- Ma, Buyong
- Nussinov, Ruth
- Venue
- Growth Factors
- Publisher
- Informa UK Limited
- Published
- 2014-11-20
- Volume
- 32
- Issue
- 6
- Pages
- 236-246
- ISSN
- 0897-7194 (ISSN-L)
- 1029-2292
- PMC
- PMC4627370
- OpenAlex
- W1997271876
- Cited by
- 10
- References
- 54
- Citations by year
- 2026: 1 · 2023: 1 · 2022: 1 · 2020: 3 · 2017: 1 · 2016: 1 · 2015: 2
- FWCI
- 0.61
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Growth Factors (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Frederick National Laboratory for Cancer Research
- National Institutes of Health (HHSN261200800001C)
- National Cancer Institute (HHSN261200800001E))
- Topics
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Axon Guidance and Neuronal Signaling
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
- Keywords
- EphB2, binding pocket, peptide variants, free energy perturbation
- MeSH terms
- Amino Acid Sequence, Binding Sites, Humans, Molecular Sequence Data, Peptide Fragments, Protein Binding, Receptor, EphB2, Molecular Docking Simulation
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