Peptide recognition by the T cell receptor: comparison of binding free energies from thermodynamic integration, Poisson-Boltzmann and linear interaction energy approximations

Shunzhou Wan, Peter V. Coveney, DR Flower

Research output: Contribution to journalArticle

Abstract

The binding to the T cell receptor of wild-type and variant HTLV-1 Tax peptide complexed to the major histocompatibility complex has been investigated by means of molecular dynamics simulations. The binding free energy difference is calculated using the molecular mechanics Poisson–Boltzmann surface area and linear interaction energy methods. These methods extract useful information on the binding energetics from simulations of the physical states of the ligands, which are more computationally expedient than the commonly used thermodynamic integration method. The successful reproduction of the relative binding free energies shows that these methods can be useful for free energy calculations and the rational design of drugs and vaccines
Original languageEnglish
Pages (from-to)2037-2053
Number of pages17
JournalPhilosophical Transactions A
Volume363
Issue number1833
DOIs
Publication statusPublished - Aug 2005

Keywords

  • free energy calculation
  • thermodynamic integration
  • Poisson–Boltzmann
  • inear interaction energy

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