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An assembly funnel makes biomolecular complex assembly efficient.

Zenk J, Schulman R - PLoS ONE (2014)

Bottom Line: For typical complexes, an assembly funnel occurs in a narrow window of conditions whose location is highly complex specific.However, by redesigning the components this window can be drastically broadened, so that complexes can form quickly across many conditions.The generality of this approach suggests assembly funnel design as a foundational strategy for robust biomolecular complex synthesis.

View Article: PubMed Central - PubMed

Affiliation: Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America.

ABSTRACT
Like protein folding and crystallization, the self-assembly of complexes is a fundamental form of biomolecular organization. While the number of methods for creating synthetic complexes is growing rapidly, most require empirical tuning of assembly conditions and/or produce low yields. We use coarse-grained simulations of the assembly kinetics of complexes to identify generic limitations on yields that arise because of the many simultaneous interactions allowed between the components and intermediates of a complex. Efficient assembly occurs when nucleation is fast and growth pathways are few, i.e. when there is an assembly "funnel". For typical complexes, an assembly funnel occurs in a narrow window of conditions whose location is highly complex specific. However, by redesigning the components this window can be drastically broadened, so that complexes can form quickly across many conditions. The generality of this approach suggests assembly funnel design as a foundational strategy for robust biomolecular complex synthesis.

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Complexes form rapidly in the assembly funnel regime.Yield of 3×3 square grid complex as a function of reaction time by assembling via annealing and at various isothermal assembly conditions:  (orange, nucleation-limited),  (green, assembly funnel)  (blue, parallel assembly pathways and rearrangement-limited). Inset plot (top left) depicts yield during an anneal as a function of interaction strength for different reaction times:  (salmon),  (beige), and  (purple). Inset diagram (bottom right) depicts the complex.
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pone-0111233-g004: Complexes form rapidly in the assembly funnel regime.Yield of 3×3 square grid complex as a function of reaction time by assembling via annealing and at various isothermal assembly conditions: (orange, nucleation-limited), (green, assembly funnel) (blue, parallel assembly pathways and rearrangement-limited). Inset plot (top left) depicts yield during an anneal as a function of interaction strength for different reaction times: (salmon), (beige), and (purple). Inset diagram (bottom right) depicts the complex.

Mentions: While complexes form quickly in the assembly funnel regime, the specific reaction conditions that generate an assembly funnel depend on the set of possible reaction pathways as well as kinetic and thermodynamic parameters that are generally unknown and difficult to estimate. One solution to this problem is to assemble via annealing. A typical annealing protocol begins at a temperature above the melting temperature of the complex, which is then gradually decreased until effectively irreversible conditions are achieved. To determine how yields using this protocol compare to those during isothermal assembly, we simulated annealing for square grid complexes. We found that yields during an anneal are predominately determined by the amount of the time spent in the assembly funnel regime. As the temperature decreases, few complexes form before the assembly funnel regime is reached. Within the funnel regime, complexes form rapidly, primarily through thermodynamic pathways (Figs. 3, 4 and Figs. S16–S18). After the annealing moves out of the assembly funnel regime, complexes are stabilized, but relatively few new complexes form. Thus, assembly via annealing is relatively efficient even when it is not known which conditions that generate an assembly funnel, which is in agreement to recent computational findings on DNA brick self-assembly [44]. However, to produce high yields, an anneal must be slower than a comparable isothermal assembly process in the assembly funnel regime because complex formation is slow for the majority of the anneal. This effect becomes more pronounced as complex size increases because the range of reaction conditions that produce an assembly funnel decreases. Thus, for very large complexes, it may be important to find ideal isothermal conditions, even when annealing is a practical option for assembly [28].


An assembly funnel makes biomolecular complex assembly efficient.

Zenk J, Schulman R - PLoS ONE (2014)

Complexes form rapidly in the assembly funnel regime.Yield of 3×3 square grid complex as a function of reaction time by assembling via annealing and at various isothermal assembly conditions:  (orange, nucleation-limited),  (green, assembly funnel)  (blue, parallel assembly pathways and rearrangement-limited). Inset plot (top left) depicts yield during an anneal as a function of interaction strength for different reaction times:  (salmon),  (beige), and  (purple). Inset diagram (bottom right) depicts the complex.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4215988&req=5

pone-0111233-g004: Complexes form rapidly in the assembly funnel regime.Yield of 3×3 square grid complex as a function of reaction time by assembling via annealing and at various isothermal assembly conditions: (orange, nucleation-limited), (green, assembly funnel) (blue, parallel assembly pathways and rearrangement-limited). Inset plot (top left) depicts yield during an anneal as a function of interaction strength for different reaction times: (salmon), (beige), and (purple). Inset diagram (bottom right) depicts the complex.
Mentions: While complexes form quickly in the assembly funnel regime, the specific reaction conditions that generate an assembly funnel depend on the set of possible reaction pathways as well as kinetic and thermodynamic parameters that are generally unknown and difficult to estimate. One solution to this problem is to assemble via annealing. A typical annealing protocol begins at a temperature above the melting temperature of the complex, which is then gradually decreased until effectively irreversible conditions are achieved. To determine how yields using this protocol compare to those during isothermal assembly, we simulated annealing for square grid complexes. We found that yields during an anneal are predominately determined by the amount of the time spent in the assembly funnel regime. As the temperature decreases, few complexes form before the assembly funnel regime is reached. Within the funnel regime, complexes form rapidly, primarily through thermodynamic pathways (Figs. 3, 4 and Figs. S16–S18). After the annealing moves out of the assembly funnel regime, complexes are stabilized, but relatively few new complexes form. Thus, assembly via annealing is relatively efficient even when it is not known which conditions that generate an assembly funnel, which is in agreement to recent computational findings on DNA brick self-assembly [44]. However, to produce high yields, an anneal must be slower than a comparable isothermal assembly process in the assembly funnel regime because complex formation is slow for the majority of the anneal. This effect becomes more pronounced as complex size increases because the range of reaction conditions that produce an assembly funnel decreases. Thus, for very large complexes, it may be important to find ideal isothermal conditions, even when annealing is a practical option for assembly [28].

Bottom Line: For typical complexes, an assembly funnel occurs in a narrow window of conditions whose location is highly complex specific.However, by redesigning the components this window can be drastically broadened, so that complexes can form quickly across many conditions.The generality of this approach suggests assembly funnel design as a foundational strategy for robust biomolecular complex synthesis.

View Article: PubMed Central - PubMed

Affiliation: Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America.

ABSTRACT
Like protein folding and crystallization, the self-assembly of complexes is a fundamental form of biomolecular organization. While the number of methods for creating synthetic complexes is growing rapidly, most require empirical tuning of assembly conditions and/or produce low yields. We use coarse-grained simulations of the assembly kinetics of complexes to identify generic limitations on yields that arise because of the many simultaneous interactions allowed between the components and intermediates of a complex. Efficient assembly occurs when nucleation is fast and growth pathways are few, i.e. when there is an assembly "funnel". For typical complexes, an assembly funnel occurs in a narrow window of conditions whose location is highly complex specific. However, by redesigning the components this window can be drastically broadened, so that complexes can form quickly across many conditions. The generality of this approach suggests assembly funnel design as a foundational strategy for robust biomolecular complex synthesis.

Show MeSH