Changes at the floor of the peptide-binding groove induce a strong preference for proline at position 3 of the bound peptide: Molecular dynamics simulations of HLA-A*0217

Hidehiro Toh, Christopher J. Savoie, Nobuhiro Kamikawaji, Shigeru Muta, Takehiko Sasazuki, Satoru Kuhara

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

We report on molecular dynamics simulations of major histocompatibility complex (MHC)-peptide complexes. Class I MHC molecules play an important role in cellular immunity by presenting antigenic peptides to cytotoxic T cells. Pockets in the peptide-binding groove of MHC molecules accommodate anchor side chains of the bound peptide. Amino acid substitutions in MHC affect differences in the peptide-anchor motifs. HLA-A*0217, human MHC class I molecule, differs from HLA-A*0201 only by three amino acid residues substitutions (positions 95, 97, and 99) at the floor of the peptide-binding groove. A*0217 showed a strong preference for Pro at position 3 (p3) and accepted Phe at p9 of its peptide ligands, but these preferences have not been found in other HLA-A2 ligands. To reveal the structural mechanism of these observations, the A*0217-peptide complexes were simulated by 1000 ps molecular dynamics at 300 K with explicit solvent molecules and compared with those of the A*0201-peptide complexes. We examined the distances between the anchor side chain of the bound peptide and the pocket, and the rms fluctuations of the bound peptides and the HLA molecules. On the basis of the results from our simulations, we propose that Pro at p3 serves as an optimum residue to lock the dominant anchor residue (p9) tightly into pocket F and to hold the peptide in the binding groove, rather than a secondary anchor residue fitting optimally the complementary pocket. We also found that Phe at p9 is used to occupy the space created by replacements of three amino acid residues at the floor within the groove. These findings would provide a novel understanding in the peptide-binding motifs of class I MHC molecules. (C) 2000 John Wiley and Sons, Inc.

Original languageEnglish
Pages (from-to)318-327
Number of pages10
JournalBiopolymers
Volume54
Issue number5
DOIs
Publication statusPublished - Oct 15 2000

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HLA-A Antigens
Molecular Dynamics Simulation
Proline
Peptides
Molecular dynamics
Computer simulation
Major Histocompatibility Complex
Anchors
Molecules
Amino acids
Amino Acid Substitution
Amino Acids
Substitution reactions
Ligands
HLA-A2 Antigen
T-cells
Cellular Immunity

All Science Journal Classification (ASJC) codes

  • Biophysics
  • Biochemistry
  • Biomaterials
  • Organic Chemistry

Cite this

Changes at the floor of the peptide-binding groove induce a strong preference for proline at position 3 of the bound peptide : Molecular dynamics simulations of HLA-A*0217. / Toh, Hidehiro; Savoie, Christopher J.; Kamikawaji, Nobuhiro; Muta, Shigeru; Sasazuki, Takehiko; Kuhara, Satoru.

In: Biopolymers, Vol. 54, No. 5, 15.10.2000, p. 318-327.

Research output: Contribution to journalArticle

Toh, Hidehiro ; Savoie, Christopher J. ; Kamikawaji, Nobuhiro ; Muta, Shigeru ; Sasazuki, Takehiko ; Kuhara, Satoru. / Changes at the floor of the peptide-binding groove induce a strong preference for proline at position 3 of the bound peptide : Molecular dynamics simulations of HLA-A*0217. In: Biopolymers. 2000 ; Vol. 54, No. 5. pp. 318-327.
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