Computational Evolution of Beta-2-Microglobulin Binding Peptides for Nanopatterned Surface Sensors

Int J Mol Sci. 2021 Jan 15;22(2):812. doi: 10.3390/ijms22020812.


The bottom-up design of smart nanodevices largely depends on the accuracy by which each of the inherent nanometric components can be functionally designed with predictive methods. Here, we present a rationally designed, self-assembled nanochip capable of capturing a target protein by means of pre-selected binding sites. The sensing elements comprise computationally evolved peptides, designed to target an arbitrarily selected binding site on the surface of beta-2-Microglobulin (β2m), a globular protein that lacks well-defined pockets. The nanopatterned surface was generated by an atomic force microscopy (AFM)-based, tip force-driven nanolithography technique termed nanografting to construct laterally confined self-assembled nanopatches of single stranded (ss)DNA. These were subsequently associated with an ssDNA-peptide conjugate by means of DNA-directed immobilization, therefore allowing control of the peptide's spatial orientation. We characterized the sensitivity of such peptide-containing systems against β2m in solution by means of AFM-based differential topographic imaging and surface plasmon resonance (SPR) spectroscopy. Our results show that the confined peptides are capable of specifically capturing β2m from the surface-liquid interface with micromolar affinity, hence providing a viable proof-of-concept for our approach to peptide design.

Keywords: DNA; atomic force microscopy (AFM); beta-2-Microglobulin; biosensor; computational design; peptides; self-assembly.

MeSH terms

  • Binding Sites / genetics
  • Biosensing Techniques / methods
  • Computational Biology / methods*
  • DNA, Single-Stranded / chemistry
  • DNA, Single-Stranded / genetics
  • DNA, Single-Stranded / metabolism*
  • Humans
  • Kinetics
  • Microscopy, Atomic Force / methods
  • Molecular Dynamics Simulation
  • Peptides / chemistry
  • Peptides / genetics
  • Peptides / metabolism*
  • Protein Binding
  • Surface Plasmon Resonance / methods
  • beta 2-Microglobulin / chemistry
  • beta 2-Microglobulin / genetics
  • beta 2-Microglobulin / metabolism*


  • DNA, Single-Stranded
  • Peptides
  • beta 2-Microglobulin