Free Energies, Transition Mechanisms, and Structural Characteristics of Proline-Rich Peptides

Proline is the only natural amino acid in which the side chain is cyclized to the backbone, restricting proline's conformational freedom considerably, as compared to other amino acids. Traditionally, the relative rigid structure of Polyproline type II (PPII) has been used as a "molecular ruler" in structural biology. However, recent experimental and theoritical studies have called this traditional picture of polyproline peptide as a rigid rod into question. We have used classical molecular dynamics simulations, with state-of-the-art force fields and novel sampling methodology to study the free energy landscapes and conformational characteristics of polyproline peptides. Our results indicate that there exist many minima being associated with several stable or metastable polyproline structures which are characterized in terms of the cis or trans nature of the prolyl bonds.;In addition to pure polyproline peptides, we have studied several other proline-rich systems in the so-called host-guest setting. There has been considerable debate about the intrinsic PPII propensity of amino acid residues in denatured polypeptides. We carried out a comprehensive analysis of the conformational equilibria of the proline-based host oligopeptides with single guests. We found no evidence for an intrinsic PPII propensity in any of the guest amino acids other than proline. Instead, the PPII content as derived from experiments may be explained in terms of: (i) a local correlation between the dihedral angles of the guest amino acid and the proline residue immediately preceding it; and (ii) a non-local correlation between the cis/trans states of the peptide bonds. In terms of the latter, we find that the presence of a guest (other than proline, tyrosine or tryptophan) increases the trans content of most of the prolyl bonds, which results in an effective increase of the peptide PPII content.;From a computational point of view, the characterization of the conformations of proline-based peptides is rather difficult, since the cis/trans isomerization is much slower than the formation and rupture of hydrogen bonds in an alpha-helix coil transition. Indeed, characteristic time scales for prolyl isomerization range in tens to hundreds of seconds at room temperature. Therefore, traditional MD simulations cannot explore the relevant conformational space, and the whole range of cis/trans transitions. In order to explore the configurational space of these systems, we combined three complementary methods: a non-equilibrium umbrella sampling method (adaptively biased MD, or ABMD), replica-exchange molecular dynamics (REMD) and steered molecular dynamics (SMD).