The liquid structure of elastin
- The Hospital for Sick Children, Canada
- University of Toronto, Canada
Figures
Figure 1 with 2 supplements
Ensemble-averaged polypeptide chain dimensions.
(a) Probability distribution of the radius of gyration, Rg, for SC (blue) and MC (red). Insets show representative backbone conformations of peptide monomer (left) and aggregate (right). (b) …
Figure 1—figure supplement 1
Formation and collapse of the aggregate.
Running averages of (a) the number of hydrogen bonds per residue, XHB, and (b) the radius of gyration, Rg.
Figure 1—figure supplement 2
Ensemble-averaged polypeptide chain dimensions with the TIP4P-D water model.
Probability distribution of the radius of gyration, Rg, for SC (blue) and MC (red) systems obtained using the charmm-modified TIP3P water model (Jorgensen et al., 1983; MacKerell et al., 1998) (as …
Figure 2 with 4 supplements
Peptide-peptide interactions.
Probabilistic description of hydrogen bonding (top row) and non-polar (bottom row) interactions of SC (a and d) and MC (b and e) systems. Panels (a), (b), (d) and (e) are contact maps for pairwise …
Figure 2—figure supplement 1
Non-polar contacts between residue pairs.
The fraction of non-polar contacts between each of the six possible residue pair combinations (V-G, V-V, V-P, P-P, P-G, G-G) is shown for the single chain (a) and multi-chain (b) systems.
Figure 2—figure supplement 2
Hydrogen bonding contact maps.
A contact map is shown for each of the 33 independent MC simulations. The color scheme is the same as the one used in Figure 2.
Figure 2—figure supplement 3
Non-polar contact maps.
A contact map is shown for each of the 33 independent MC simulations. The color scheme is the same as the one used in Figure 2.
Figure 2—figure supplement 4
Peptide-peptide interactions for the SC ensemble obtained using the TIP4P-D water model.
Probabilistic description of hydrogen bonding and non-polar interactions of the SC system obtained using CHARMM 22* with the charmm-modified TIP3P water model (a and d; these results are the same as …
Figure 3 with 2 supplements
Peptide hydration in the liquid-like aggregate.
(a). Representative conformation of the aggregate with non-polar side chains (yellow), peptide backbone (oxygen, red; carbon, white; nitrogen, blue), and hydrogen-bonded water molecules (cyan). …
Figure 3—figure supplement 1
Conformations after 5 µs of simulation.
The final conformation of 5 of the independent simulations is shown in two representations. The color schemes are the same as in Figure 3a and d.
Figure 3—figure supplement 2
Hydration of blob-sized segments.
(a) The scaling of inter-residue distances is shown within a blob-sized segment of 5 residues (linear fit in red) and outside of a blob-sized segment (linear fit in blue). The scaling exponents …
Figure 4
Radial density profiles.
(a). Density profiles for peptide (red) and water (blue) as a function of the distance from the center of mass (COM) of the peptide is shown for the single chain system. (b) Density profiles for …
Figure 5 with 3 supplements
Intrachain distance scaling and comparison to the ideal, random-coil state.
Root-mean-square distance, <rij2>1/2, between residues i and j as a function of sequence separation, |i-j|, for SC (blue) and MC (red), and for the ideal, random coil state modeled using the SC …
Figure 5—figure supplement 1
Equilibration of chain dimensions in the aggregate.
The mean separation distance is shown as a function of sequence separation for 200 ns time intervals of the simulation. The color scheme is given in the legend: each interval is colored from red to …
Figure 5—figure supplement 2
Temperature dependence of the conformational properties of the monomer.
The scaling of inter-residue distances (the same analysis as shown in Figure 5) is shown for the SC ensemble at a range of temperatures between 298 K and 447 K, covering the entire range of …
Figure 5—figure supplement 3
Intrachain distance scaling for the ensemble obtained using TIP4P-D.
Root-mean-square distance, <rij2>1/2, between residues i and j as a function of sequence separation, |i-j|, for the ensemble obtained using the CHARMM 22* force field with the TIP4P-D water model …
Figure 6 with 1 supplement
Kinetics of end-to-end contact formation.
Survival probability of the open state (without a contact between the chain ends) as a function of time for the single chain (SC) (a) and for the aggregated chains (MC) (b) . The lifetime of the …
Figure 6—figure supplement 1
Chain dynamics within the aggregate.
(a) The mean squared displacement, MSD, of the central residue of the chain is shown as a function of time. This curve is an average over all chains (27 chains per system) and all simulations (33 in …
Figure 7
Structural basis of entropic elasticity in self-assembled elastomeric proteins.
Schematic description of polypeptide main chains (black), non-polar side chains (yellow), solvating water molecules (blue), and peptide-peptide hydrogen bonds (red) in monomeric (SC, top row) and …
Videos
Video 1
In Video 1, the final 95 ns of a 5 microsecond trajectory of an aggregate is shown.
Each of the 27 peptide chains is colored individually. Frames in the movie correspond to conformations separated by 50 ps time intervals. A smoothing window of 2 frames was applied and all …
Tables
Table 1
Populations and lifetimes of hydrogen-bonded turns.
https://doi.org/10.7554/eLife.26526.010| Turn | Population (%) | Lifetime (ns) | ||
|---|---|---|---|---|
| SC | MC | SC | MC | |
| VPGV* | 18 ± 1 | 16 ± 2 | 0.18 ± 0.02 | 0.19 ± 0.01 |
| VPGVG | 5.9 ± 0.9 | 4.6 ± 0.7 | 0.9 ± 0.3 | 0.8 ± 0.1 |
| PGV | 1.5 ± 0.1 | 2.0 ± 0.2 | 0.008 ± 0.002 | 0.009 ± 0.001 |
| PGVG | 2.3 ± 0.2 | 2.9 ± 0.3 | 0.30 ± 0.05 | 0.39 ± 0.03 |
| GVGV | 20 ± 3 | 17 ± 2 | 0.15 ± 0.02 | 0.24 ± 0.07 |
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*A hydrogen-bonded turn refers to a hydrogen bond between the first and last residue in the sequences shown. For example, the VPGV turn has a hydrogen bond between valine 1 and valine 4.
Additional files
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Supplementary file 1
Supplementary information: Supplementary Methods (Method to Compute the Average Dimensions of the Ideal, Random Coil State), Figure S1 and Tables S1 and S2.
- https://doi.org/10.7554/eLife.26526.023
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Supplementary file 2
The supplementary file contains a coordinate file (prot_100ns.gro) and a trajectory file corresponding to the final 100 ns (4_9 ms_to_5 ms.xtc) of one of the aggregate simulations.
A larger trajectory file (4 ms_to_5 ms.xtc) corresponding to the final microsecond of the same simulation can be downloaded from the public repository figshare.com (S. Rauscher and R. Pomès, ‘Microsecond-long molecular dynamics trajectory of an aggregate of elastin-like peptides in water.’ DOI: 10.6084/m9.figshare.5532214).
- https://doi.org/10.7554/eLife.26526.024
