Secondary Structure of Rat and Human Amylin across Force Fields

<div><p>The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin was determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states enable dynamic pathways that facilitate the formation of aggregates and, eventually, amyloid fibrils.</p></div

Sequence and charges used for the simulation of rat and human amylin.

<p>Differences in sequence are bolded.</p><p>Sequence and charges used for the simulation of rat and human amylin.</p

Reported biases for selected force fields.

<p>A value of low for α-helix bias indicates that the force field failed to form the experimentally expected α-helically structure or failed to remain stable when experiments suggested that an α-helix was stable. A high value for α-helix bias indicates that the force field formed an α-helix when experimental evidence suggests that an α-helix is disfavored. Similarly, β-Bias indicates biases related to forming parallel and anti-parallel β-sheets.</p><p>Reported biases for selected force fields.</p

Force field and water combinations used to simulate human and rat amylin.

<p>Force field and water combinations used to simulate human and rat amylin.</p

Fraction of structures with a helix (α-helix, 3₁₀ Helix or π Helix) or a strand (β-sheet or β-Bridge) for rIAPP (black symbols) and hIAPP (red symbols) as predicted with various force fields.

<p>Force field and solvent model combinations where the force field was optimized with that solvent model are shown with a filled symbol; otherwise an unfilled symbol is shown.</p

Free energy difference with coil for fraction of residues in a secondary structure predicted for rIAPP vs. time for Amberff99sb*-ILDN with TIP3P.

<p>The secondary structure of each residue was determined using DSSP.</p

Free energy of rat amylin as a function of α_RMSD and β_RMSD for various force fields.

<p>The darker regions indicate regions of lower free energy.</p

Free energy of human amylin as a function of α_RMSD and β_RMSD for various force fields.

<p>The darker regions indicate regions of lower free energy.</p

Predicted C_α secondary chemical shifts for Amberff99sb*-ILDN with TIP3P, Amberff03w with TIP4P2005, CHARMM22* with TIPS3P, CHARMM22/CMAP with TIPS3P, Gromos96 53a6 with SPC, and OPLS-AA/L with TIP4P.

<p>The predictions were made using SPARTA+.</p

Free energy of secondary structure appearing in a residue in rIAPP relative to the coil secondary structure in units of kT at 310 K.

<p>Free energy of secondary structure appearing in a residue in rIAPP relative to the coil secondary structure in units of kT at 310 K.</p