Probing the stability-limiting regions of an antibody single-chain variable fragment: a molecular dynamics simulation study

Protein Eng Des Sel. 2011 Sep;24(9):649-57. doi: 10.1093/protein/gzr029. Epub 2011 Jul 5.


Antibody single-chain variable fragments (scFvs) offer particular advantages over the full-size antibodies, including easy expression, efficient local concentration and fast body clearance. However, scFvs typically show low thermal stability that limits their biomedical and biotechnological applications. In this study, we examined the thermal stability of the human and murine vascular endothelial growth factor antibody scFv fragment by molecular dynamics simulations. A consistent observation was the dissociation of the light-chain (VL) and heavy-chain (VH) domains and loss of the native structures of both domains in the simulations at the elevated temperatures. The stability-limiting structural elements in the protein were revealed from the detailed analyses on the native contacts. We found that dissociation of the VL-VH domains was the first event leading to the unfolding of the native structure of the protein and the disruption of the VL-VH interface was largely due to the break of the interfacial hydrophobic and aromatic interactions while the hydrogen-bonding interaction between Gln38 in VL and Gln39 in VH remained. Within the β-barrel structure of the VL and VH domains, β-strands β6, β2 and β11 appeared to be the least stable. In addition, we found that the VH domain was more thermally resistant than the VL domain. Based on these findings, we discussed potential strategies to improve the stability of this therapeutically important scFv fragment.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Humans
  • Hydrogen Bonding
  • Hydrophobic and Hydrophilic Interactions
  • Immunoglobulin Heavy Chains / chemistry
  • Immunoglobulin Heavy Chains / metabolism
  • Immunoglobulin Light Chains / chemistry
  • Immunoglobulin Light Chains / metabolism
  • Mice
  • Molecular Dynamics Simulation*
  • Protein Folding
  • Protein Stability
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Single-Chain Antibodies / chemistry*
  • Single-Chain Antibodies / metabolism
  • Thermodynamics
  • Vascular Endothelial Growth Factor A / chemistry
  • Vascular Endothelial Growth Factor A / metabolism


  • Immunoglobulin Heavy Chains
  • Immunoglobulin Light Chains
  • Single-Chain Antibodies
  • Vascular Endothelial Growth Factor A