Physical Biology
Physical Biology
4 years ago

Binding Stability of Peptides on Major Histocompatibility Complex Class I Proteins: Role of Entropy and Dynamics.

Ahmet Gul, Burak Erman
Prediction of peptide binding on specific human leukocyte antigens (HLA) has long been studied with successful results. We herein describe the effects of entropy and dynamics by investigating the binding stabilities of 10 nanopeptides on various HLA Class I alleles using a theoretical model based on molecular dynamics simulations. The fluctuational entropies of the peptides are estimated over a temperature range of 310-460 K. The estimated entropies correlate well with experimental binding affinities of the peptides: Peptides that have higher binding affinities have lower entropies compared to non-binders, which have significantly larger entropies. The computation of the entropies is based on a simple model that requires short molecular dynamics trajectories and allows for approximate but rapid determination. The paper invites attention to the long neglected dynamic aspects of peptide binding, and provides a fast computation scheme allowing for rapid scanning of large numbers of peptides on selected HLA antigens, which may be useful in defining right peptides for personal immunotherapy.

Publisher URL: http://doi.org/10.1088/1478-3975/aa93b8

DOI: 10.1088/1478-3975/aa93b8

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