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Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approach
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10.1063/1.3010881
/content/aip/journal/jcp/129/21/10.1063/1.3010881
http://aip.metastore.ingenta.com/content/aip/journal/jcp/129/21/10.1063/1.3010881
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Figures

Image of FIG. 1.
FIG. 1.

(a) Oligomer distribution at the simulated concentration . The line represents fractions of each oligomer that were directly obtained from the ensemble of simulations, the crosses are fractions predicted by a simple 5-state SCMSM, and the circles are fractions predicted by a 30-state SCMSM. The 5-state SCMSM agrees well with the raw data at longer timescales, but we needed a more detailed model (e.g., 30-state SCMSM) to pick up complete quantitative agreement at short timescales. (b) Analytic extensions to the Markov model for low concentrations allow the prediction of oligomer formation from the microsecond timescale (dimer) to the timescale (tetramer).

Image of FIG. 2.
FIG. 2.

The autocorrelation of the interchain contact maps shows a nonsingle exponential behavior with a rapid early phase and a slow second phase (a). The slope of the slow phase indicates the time scale for tertiary structure formation for each oligomer (b). The data suggest that the time scale for tertiary structure formation in the dimer and trimers is in the hundreds of nanoseconds. The corresponding figures for intrachain contacts are similar and not shown here.

Image of FIG. 3.
FIG. 3.

Timescale of oligomer species formation vs concentration (log-log.) The simulated monomer concentration was iteratively varied using the analytic component of the ACMSM, bridging the simulations with experimental and biological concentrations. Time scales are represented as mean first passage times for the resultant transition matrices. Note that for an monomer concentration of tetramer formation is on the order of , in contrast to the nanosecond time scales when concentration is closer to that of the simulation box.

Image of FIG. 4.
FIG. 4.

Markovian model for oligomerization. Our model was built using the different aggregation states as the Markov states; in a system with four chains, there are five such states: four monomers (MMMM), two monomers and one dimer (MMD), two dimers (DD), one monomer and one trimer (MT), and finally, one tetramer (Q). In addition, to include the effects of low concentration found experimentally, we discriminate EC states (in which states are close) from separated states. The rate limiting steps in the aggregation process are shown as dotted lines. The numbers associated with the transitions are transition probabilities. The significant figures were determined from the uncertainties in the transition probabilities. Some transitions with very low probability have not been shown for the sake of clarity.

Image of FIG. 5.
FIG. 5.

The top tetramer clusters do not show the formation of a single hydrophobic core comprising all four chains. Instead the cores seemed to be of the form of monomers (a) or (b) or (c). This suggests that trimers might be the preferred oligomer for this system. The observed tetramers are possibly loosely associated lower order oligomers. The N-terminus is shown as brown spheres, residues M35-V36 are shown as blue spheres, G37-G38 are shown as light blue spheres, and the C-terminus is shown as slate sticks. All pictures were rendered using PYMOL (Ref. 26).

Image of FIG. 6.
FIG. 6.

Contact maps for monomers, dimers, trimers, and tetramers. The high density region in the upper left corner corresponds to the hydrophobic core formed by C-terminal association. The contact maps for the other aggregation states are very similar. Note that the fraction of contacts formed is per oligomeric species rather than per chain.

Image of FIG. 7.
FIG. 7.

Secondary structure profiles in each aggregation state. There is some tendency to form a helix near the N-terminus and a very slight formation of a hairpin near the C-terminus. In each case, there is little or no correlation between the secondary structure and the aggregation state.

Image of FIG. 8.
FIG. 8.

trimer structural properties, as shown by (a) representative cluster center and (b) an alignment of six representative trimer structures. The N-terminal residues are shown in red, and residues M35-V40 which correspond to the darkest regions in the contact map are shown in blue and cyan. The oligomers are stabilized by a hydrophobic core formed by the C-terminal regions of the chains while the N-terminal segments are solvent exposed and unstructured.

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/content/aip/journal/jcp/129/21/10.1063/1.3010881
2008-12-04
2014-04-20
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approach
http://aip.metastore.ingenta.com/content/aip/journal/jcp/129/21/10.1063/1.3010881
10.1063/1.3010881
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