Abstract
Proline cis-trans isomerisation is a regulatory mechanism used in a range of biological processes, and is related to various diseases such as Alzheimers disease and cancer. However, the details of the exact molecular mechanism by which it occurs are not known. Using X-ray crystallography, proline isomerisation has been shown to occur following formation of an antigen-antibody complex between the target epiregulin (EPR) and the antibody 9E5, at proline (Pro103), located in the third complementarity-determining region (CDR) of the heavy chain of 9E5. To obtain an accurate description of the pathway involved in cis-trans isomerisation in this system, we performed ten independent long molecular dynamics (MD) simulations starting at a stable transient bound structure obtained from many short binding MD simulations. As a result, we were able to describe the process by which cis-trans isomerisation is initiated, and suggest a catalysis mechanism for cis-trans isomerization in this antigen-antibody system. We found that Asp102, which is immediately adjacent to Pro103, rotates while changing its interacting partner residues in the light chain of 9E5, and at the same time EPR polar residues help to stabilise the intermediate states in the isomerisation process by interacting strongly with Asp102.
Highlights
Among the 20 amino acids, proline is unique because both the cis and trans conformers of the prolyl peptide bond are thermodynamically feasible, in contrast to non-prolyl peptide bonds that strongly favour remaining in the trans conformation
The 9E5 fragment antigen-binding portion (Fab) has a proline at residue 103 (Pro103) in the complementary determining regions (CDR)-H3 loop, which was found to be in the cis conformation for EPR-free apo 9E5 and in the trans conformation in the EPR-9E5 complex
We performed extensive molecular dynamics (MD) simulations to investigate the mechanism of peptidyl prolyl cis-trans isomerization of the antigen-antibody complex of EPR and 9E5, which was intensively explored for use in cancer therapy[55,56]
Summary
Among the 20 amino acids, proline is unique because both the cis and trans conformers of the prolyl peptide bond are thermodynamically feasible, in contrast to non-prolyl peptide bonds that strongly favour remaining in the trans conformation. Kado et al found that prolyl cis-trans isomerisation occurred in the CDR-H3 loop (Arg98-Gly99-Gly100-Gly101-Asp102-Pro103-Val104-Phe105-Val 106-Tyr107-Trp108) of the fragment antigen-binding portion (Fab) of 9E5 in the X-ray crystal structure[55].
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