Molecular dynamics simulations of a β-hairpin fragment of protein G: Balance between side-chain and backbone forces

Buyong Ma, Ruth Nussinov

Research output: Contribution to journalArticlepeer-review

Abstract

How is the native structure encoded in the amino acid sequence? For the traditional backbone centric view, the dominant forces are hydrogen bonds (backbone) and φ-ψ propensity. The role of hydrophobicity is non-specific. For the side-chain centric view, the dominant force of protein folding is hydrophobicity. In order to understand the balance between backbone and side-chain forces, we have studied the contributions of three components of a β-hairpin peptide: turn, backbone hydrogen bonding and side-chain interactions, of a 16-residue fragment of protein G. The peptide folds rapidly and cooperatively to a conformation with a defined secondary structure and a packed hydrophobic cluster of aromatic side-chains. Our strategy is to observe the structural stability of the β-hairpin under systematic perturbations of the turn region, backbone hydrogen bonds and the hydrophobic core formed by the side-chains, respectively. In our molecular dynamics simulations, the peptides are solvated with explicit water molecules, and an all-atom force field (CFF91) is used. Starting from the original peptide (G41EWTYDDATKTFTVTE56), we carried out the following MD simulations. (1) unfolding at 350 K; (2) forcing the distance between the C(α) atoms of ASP47 and LYS50 to be 8 Å; (3) deleting two turn residues (Ala48 and Thr49) to form a β-sheet complex of two short peptides, GEWTYDD and KTFTVTE; (4) four hydrophobic residues (W43, Y45, F52 and T53) are replaced by a glycine residue step-by-step; and (5) most importantly, four amide hydrogen atoms (T44, D46, T53, and T55, which are crucial for backbone hydrogen bonding), are substituted by fluorine atoms. The fluorination not only makes it impossible to form attractive hydrogen bonding between the two β-hairpin strands, but also introduces a repulsive force between the two strands due to the negative charges on the fluorine and oxygen atoms. Throughout all simulations, we observe that backbone hydrogen bonds are very sensitive to the perturbations and are easily broken. In contrast, the hydrophobic core survives most perturbations. In the decisive test of fluorination, the fluorinated peptide remains folded under our simulation conditions (5 ns, 278 K). Hydrophobic interactions keep the peptide folded, even with a repulsive force between the β-strands. Thus, our results strongly support a side-chain centric view for protein folding. (C) 2000 Academic Press.

Original languageEnglish
Pages (from-to)1091-1104
Number of pages14
JournalJournal of Molecular Biology
Volume296
Issue number4
DOIs
StatePublished - 3 Mar 2000

Keywords

  • Hydrogen bonding
  • Hydrophobic interactions
  • Protein folding
  • Side-chain interaction
  • β-hairpin
  • β-peptide

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