Computational Evolution of Beta-2-Microglobulin Binding Peptides for Nanopatterned Surface Sensors
Abstract
:1. Introduction
2. Results and Discussion
2.1. Biding Site Selection
2.2. Peptides Generation
2.3. Peptides Screening
2.4. Affinity Measures
2.5. Self-Assembly of Functional dsDNA–peptide Nanopatch
2.6. Surface Density Controls the Hybridization Efficiency of ssDNA Nanopatch
2.7. Recognition of β2m by dsDNA–peptide Conjugate Nanopatches
2.8. Competition Assay
3. Materials and Methods
3.1. Binding Site Selection
3.2. Peptide Design
3.3. Molecular Dynamics Simulations
3.4. Materials
3.5. Surface Plasmon Resonance
3.6. ssDNA–peptide Conjugates Preparation
3.7. Preparation of Ultra-Flat Gold Substrate
3.8. Preparation of Top-Oligo-Ethylene-Glycol SAM (TOEGSAM) on the Ultra-Flat Gold Substrate
3.9. Nanografting of Thiol-Modified ssDNA in Contact Mode
3.10. Hybridization with Complementary ssDNA–Peptide Conjugates
3.11. Beta-2-Microglobulin Binding Assay
3.12. AFM Imaging of dsDNA–peptide Assemblages before and after the β2m Recognition Assay
3.13. Competition Assay
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
ß2m | Beta-2-microglobulin |
DNA | Deoxyribonucleic acid |
ss | Single stranded |
ds | Double stranded |
AFM | Atomic force microscopy |
SPR | Surface plasmon resonance |
DDI | DNA-directed immobilization |
MD | Molecular dynamics |
REMD | Replica-exchange molecular dynamics |
RMSD | Root mean square deviation |
KD | Dissociation constant |
S/A | Surface density parameter |
BS | Binding site |
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ID | Sequence | Remark | KD (SPR) |
---|---|---|---|
pep381 | [CRRYSHQHYRHC] | cyclic with S-S bridge | 38 ± 9 µM (Ref. [18]) |
pep331 | [CFETAWRQNEWC] | cyclic with S-S bridge | 300.0 µM (χ2 = 4.5) |
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Adedeji Olulana, A.F.; Soler, M.A.; Lotteri, M.; Vondracek, H.; Casalis, L.; Marasco, D.; Castronovo, M.; Fortuna, S. Computational Evolution of Beta-2-Microglobulin Binding Peptides for Nanopatterned Surface Sensors. Int. J. Mol. Sci. 2021, 22, 812. https://doi.org/10.3390/ijms22020812
Adedeji Olulana AF, Soler MA, Lotteri M, Vondracek H, Casalis L, Marasco D, Castronovo M, Fortuna S. Computational Evolution of Beta-2-Microglobulin Binding Peptides for Nanopatterned Surface Sensors. International Journal of Molecular Sciences. 2021; 22(2):812. https://doi.org/10.3390/ijms22020812
Chicago/Turabian StyleAdedeji Olulana, Abimbola Feyisara, Miguel A. Soler, Martina Lotteri, Hendrik Vondracek, Loredana Casalis, Daniela Marasco, Matteo Castronovo, and Sara Fortuna. 2021. "Computational Evolution of Beta-2-Microglobulin Binding Peptides for Nanopatterned Surface Sensors" International Journal of Molecular Sciences 22, no. 2: 812. https://doi.org/10.3390/ijms22020812