The stability of cylindrin β-barrel amyloid oligomer models-a molecular dynamics study

Abstract

Small-soluble amyloid oligomers are believed to play a significant role in the pathology of amyloid diseases. Recently, the atomic structure of a toxic oligomer formed by an 11 residue and its tandem repeat was found to have an out-off register antiparallel β-strands in the shape of a β-barrel. In the present article we investigate the effect of mutations in the hydrophobic cores on the structure and dynamic of the β-barrels using all atom multiple molecular dynamics simulations with an explicit solvent. Extending previous experiments with molecular dynamics simulations we systematically test how stability and formation of cylindrin depends on the interplay between hydrophobicity and steric effects of the core residues. We find that strong hydrophobic interactions between geometrically fitting residues keep the strands (both in register and out-off-register interface) in close proximity, which in turn stabilizes the side-chain and main-chain hydrogen bonds, and the salt bridges on the outer surface along the weak out-of-register interface. Our simulations also indicate presence of water molecules in the hydrophobic interior of the cylindrin β-barrel.Proteins 2013.

Keywords: amyloid fibrils; cylindrin; molecular dynamics; soluble oligomers; αB-crystalline.

Figure 1

Residues involved in the salt bridge interactions (A) and hydrophobic interactions (B) are labeled and shown in sphere in the initial structure of the tandem repeat cylindrin.

Figure 2

Snapshots of wild type and mutants of tandem repeat cylindrin at the beginning and end of 300 ns simulation.

Figure 3

The fraction of native contacts and average backbone RMS fluctuations (RMSF) per residue as function of time. The average fraction of native contacts (A) and the average RMSF (B) of the tandem repeat cylindrin simulations. Red for wild-type (WT-TR), magenta for V4GV8G-TR, brown for V4AV8A-TR, blue V2L-TR, and green for VTL-TR. The average fraction of native contacts (C) and the average RMSF (D) of the single chain cylindrin simulations. Red for wild-type (WT), magenta for V4GV8G, brown for V4AV8A, blue V2L-TR, and green for VTL. The results are calculated by using the three 300 ns trajectories for each model.

Figure 4

Hydrophobic contacts Cα-Cα distances between the pair of residue 4 from each strand (St) in the dry interior of tandem repeat cylindrin as function of time. Red for wild-type (WT-TR), magenta for V4GV8G-TR, brown for V4AV8A-TR, blue V2L-TR, and green for VTL-TR. Shown are the averages over three independent 300 ns trajectories. For each model, the standard deviations are calculated from the three values obtained by averaging over each of the 300 ns trajectories.

Figure 5

Average numbers of main chain hydrogen bonds and side chain-side chain as function of time. For tandem repeat cylindrin, the average main chain hydrogen bonds are shown in (A) and side chain-side chain in (B). Red for wild-type (WT-TR), magenta for V4GV8G-TR, brown for V4AV8A-TR, blue V2L-TR, and green for VTL-TR. For single chain cylindrin, the average main chain hydrogen bonds are displayed in (C) and side chain-side chain in (D). Red for wild-type (WT), magenta for V4GV8G, brown for V4AV8A, blue V2L-TR, and green for VTL. The results are the averages of three independent 300ns trajectories. Here, a stands for strand number and b for residue number in _aSt^b-_aSt^b designation of the Cα-Cα distance of the hydrophobic core residues Val of the wild type tandem repeat and mutants.

Figure 6

Comparison of the average salt bridge interactions distances between Lys (K) and Asp (D) along the 300 ns simulation of the wild-type and its mutants of tandem repeat cylindrin along the three out of register interfaces. Red for wild-type (WT-TR), magenta for V4GV8G-TR, brown for V4AV8A-TR, blue V2L-TR, and green for VTL-TR. The results are the average of three independent 300 ns simulations of each system. Here, a stands for strand number and b for residue number in _aK^b- _aD^b designation of the salt bridge distance of the wild type tandem repeat cylindrin and mutants.

Figure 7

Number of water molecules in the interior central hydrophobic region of the cylindrin pore as a function of time for the three independent simulations (red, blue and green, respectively) of WT-TR (A) and V2L-TR(B)

Figure 8

Snapshots of the tandem repeat β-barrel models with water molecules in the interior for WT-TR (A) and V2L-TR(B).