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Generalized iterative annealing model for the action of RNA chaperones
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10.1063/1.4818594
/content/aip/journal/jcp/139/12/10.1063/1.4818594
http://aip.metastore.ingenta.com/content/aip/journal/jcp/139/12/10.1063/1.4818594
View: Figures

Figures

Image of FIG. 1.
FIG. 1.

(a) On the left is shown the secondary structure map of ribozyme, a natural substrate for RNA chaperones. The schematic structure on the right is the three dimensional structure of ribozyme with P4-P5-P6 and P7-P3-P8 domains highlighted. (b) A model for passive assistance of RNA folding by protein cofactor, which generalizes tertiary capture model proposed by Garcia and Weeks. Rapidly collapsed RNA intermediate upon addition of multivalent counter ions forms with a protein cofactor (blue spheres) an intermediate ensemble of RNP complex, which fluctuates between { } and { }. { } is an ensemble of transiently unbound intermediate. Binding and transient release anneal the misfolded RNA, leading to the assembly competent RNP containing the folded RNA. The final step is the release of the native RNA.

Image of FIG. 2.
FIG. 2.

Numerical solution of [], [], [], [], and [] (a) when chaperone does not recognizes the native state, λ = 0.0 min and (b) when chaperone recognizes the native state, λ = 1.0 min with = 1.0, = 0.1, [] = 0, [] = , ϕ = 0.1, = 1 min, = 0.01 min, λ = 30.0 min.

Image of FIG. 3.
FIG. 3.

Kinetics of chaperonin assisted RNA folding on a model folding landscape. (a) Rugged folding landscape of RNA, depicting the native basin of attraction (NBA) and competing basins of attraction (CBAs), and multiple folding routes illustrating the kinetic partitioning mechanism. Reprinted with permission from D. Thirumalai and C. Hyeon, Biochemistry44, 4957 (Year: 2005)10.1021/bi047314+. . (b) A model folding landscape with 1 native ( = 0) and 5 misfolded states corresponding to the CBAs in (a) ( = 1, 2…, 5). The free energy value of each state is assigned as β = 0.00, β = 2.30, β = 3.00, β = 5.00, β = 7.50, and β = 9.00, which leads to λ = 1.66. (c) The plot of (black solid lines), graphically showing the solutions of () = 1, i.e., the pole structure of due to (1 − ()): = 0, = −4.22, = −6.84, = −19.34, = −69.49, = −148.15. (d) The time evolution of the fraction of native state ( ()) with different initial conditions (i) = 0, = = ⋯ = 0.2 (black, solid line), (ii) = 1, = = ⋯ = = 0 (red, dashed line), and (iii) = 0.5, = = ⋯ = , = 0.2, = 0.3 (blue, dotted-dashed line). Note that the fraction of native state in the steady state is ( → ∞) ≠ 1 due to the flux out of native to non-native states. The steady state value is independent of the initial conditions, suggesting that the RNA chaperones redistribute the population of folded and misfolded states till equilibrium is reached.

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/content/aip/journal/jcp/139/12/10.1063/1.4818594
2013-08-21
2014-04-18
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Generalized iterative annealing model for the action of RNA chaperones
http://aip.metastore.ingenta.com/content/aip/journal/jcp/139/12/10.1063/1.4818594
10.1063/1.4818594
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