Folding thermodynamics of β‐hairpins studied by replica‐exchange molecular dynamics simulations

Abstract

We study the differences in folding stability of β-hairpin peptides, including GB1 hairpin and a point mutant GB1 K10G, as well as tryptophan zippers (TrpZips): TrpZip1, TrpZip2, TrpZip3-1, and TrpZip4. By performing replica-exchange molecular dynamics simulations with Amber03* force field (a modified version of Amber ff03) in explicit solvent, we observe ab initio folding of all the peptides except TrpZip3-1, which is experimentally known to be the least stable among the peptides studied here. By calculating the free energies of unfolding of the peptides at room temperature and folding midpoint temperatures for thermal unfolding of peptides, we find that TrpZip4 and GB1 K10G peptides are the most stable β-hairpins followed by TrpZip1, GB1, and TrpZip2 in the given order. Hence, the proposed K10G mutation of GB1 peptide results in enhanced stability compared to wild-type GB1. An important goal of our study is to test whether simulations with Amber 03* model can reproduce experimentally predicted folding stability differences between these peptides. While the stabilities of GB1 and TrpZip1 yield close agreement with experiment, TrpZip2 is found to be less stable than predicted by experiment. However, as heterogenous folding of TrpZip2 may yield divergent thermodynamic parameters by different spectroscopic methods, mismatching of results with previous experimental values are not conclusive of model shortcomings. For most of the cases, molecular simulations with Amber03* can successfully reproduce experimentally known differences between the mutated peptides, further highlighting the predictive capabilities of current state-of-the-art all-atom protein force fields.

Effect of heterochiral inversions on the structure of a β‐hairpin peptide

“…Adoption of an α L configuration in this position has been found to be strictly correlated with folding in atomistic simulations and has accordingly been suggested to be one of the key events in the GB1 hairpin's folding. Moreover, replacing the L ‐lysine residue in this position with glycine has been found to increase the stability of the hairpin . This increased stability has been explained as follows.…”

“…Peptides are modeled using the Amber03* protein force field and water is modeled using the TIP3P model . This particular protein/water model combination has been successfully used to infer the folding mechanisms and thermodynamic properties of hairpins, yielding close agreement with experiments …”

“…58 This particular protein/ water model combination has been successfully used to infer the folding mechanisms and thermodynamic properties of hairpins, yielding close agreement with experiments. 46,52 The force field contains an asymmetric dihedral angle term. 57 We simply adjust this term for D-amino acids by inverting the sign of the phase shift angle of the term and we generate the D-configuration internal coordinates as an initial condition for mutated residues.…”

“…For glycine, an achiral amino acid, positive and negative backbone torsion angles of the same magnitude are equally favorable, and it is therefore one of the preferred mutations in such a position when the goal is to increase the stability of the protein folds . The glycine mutation approach has been shown to work for the turn of GB1 . The positive ϕ angles being more favorable for D ‐amino acids, they have also, accordingly, been suggested as possible candidates for mutations in such positions in order to increase the folding stability .…”

“…[49][50][51] The glycine mutation approach has been shown to work for the turn of GB1. 34,52 The positive ϕ angles being more favorable for D-amino acids, they have also, accordingly, been suggested as possible candidates for mutations in such positions in order to increase the folding stability. 53,54 One of the many chiral inversions that we investigate in this work addresses specifically the effect of mutated chirality at the i + 3 turn position.…”