Limits...
The Trigger Factor Chaperone Encapsulates and Stabilizes Partial Folds of Substrate Proteins.

Singhal K, Vreede J, Mashaghi A, Tans SJ, Bolhuis PG - PLoS Comput. Biol. (2015)

Bottom Line: Unfolded chains are kinetically trapped when bound to TF, which suppresses the formation of transient, non-native end-to-end contacts.This encapsulation mechanism is distinct from that of chaperones such as GroEL, and allows folded structures of diverse size and composition to be protected from aggregation and misfolding interactions.The results suggest that an ATP cycle is not required to enable both encapsulation and liberation.

View Article: PubMed Central - PubMed

Affiliation: van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands.

ABSTRACT
How chaperones interact with protein chains to assist in their folding is a central open question in biology. Obtaining atomistic insight is challenging in particular, given the transient nature of the chaperone-substrate complexes and the large system sizes. Recent single-molecule experiments have shown that the chaperone Trigger Factor (TF) not only binds unfolded protein chains, but can also guide protein chains to their native state by interacting with partially folded structures. Here, we used all-atom MD simulations to provide atomistic insights into how Trigger Factor achieves this chaperone function. Our results indicate a crucial role for the tips of the finger-like appendages of TF in the early interactions with both unfolded chains and partially folded structures. Unfolded chains are kinetically trapped when bound to TF, which suppresses the formation of transient, non-native end-to-end contacts. Mechanical flexibility allows TF to hold partially folded structures with two tips (in a pinching configuration), and to stabilize them by wrapping around its appendages. This encapsulation mechanism is distinct from that of chaperones such as GroEL, and allows folded structures of diverse size and composition to be protected from aggregation and misfolding interactions. The results suggest that an ATP cycle is not required to enable both encapsulation and liberation.

No MeSH data available.


Four 200 ns long AA-MD simulations of extended TF each with full MBP and P2.A. Contact probabilities of TF residues with MBP (top panel) and P2 (bottom panel). The barcode plots the standard hydrophobicity map of TF: color-scaled from red (hydrophilic) to green (hydrophobic). B. Distribution of the fraction of hydrophilic contacts in TF-substrate binding for different substrates. The dashed lines plot the distribution in the first 10 ns, while solid lines with circles plot the distribution over the whole trajectory. C. Visualization of the most important interaction sites (blue) on TF for MBP and P2. D. Representative final conformations of TF-MBP and TF-P2 complexes. The substrates are shown in transparent white colored wire-mesh.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4626277&req=5

pcbi.1004444.g005: Four 200 ns long AA-MD simulations of extended TF each with full MBP and P2.A. Contact probabilities of TF residues with MBP (top panel) and P2 (bottom panel). The barcode plots the standard hydrophobicity map of TF: color-scaled from red (hydrophilic) to green (hydrophobic). B. Distribution of the fraction of hydrophilic contacts in TF-substrate binding for different substrates. The dashed lines plot the distribution in the first 10 ns, while solid lines with circles plot the distribution over the whole trajectory. C. Visualization of the most important interaction sites (blue) on TF for MBP and P2. D. Representative final conformations of TF-MBP and TF-P2 complexes. The substrates are shown in transparent white colored wire-mesh.

Mentions: Once the smallest partial-fold (P1) is completely folded, TF further interacts with the larger partial folds (e.g., P2), eventually interacting with full MBP. We simulated these interaction through six MD runs of TF with a larger partial fold P2, and four runs with full native MBP molecule (see S6 and S7 Figs). The contact probability plots in Fig 5A (top panel for MBP, bottom panel for P2) show that for both systems, the tip of N-terminal domain (residues 38–55) is responsible for the majority of the interactions, while other domains play only minor roles. P2 also binds to the tips of Arm1 (residues 320–325). The TF structures in Fig 5B visualize the location of these interaction sites with MBP and P2. Most of them lie at the tips of TF’s appendages, while the PPIase domain again appears to cover P2, like a lid, with its inner surface. The hydrophobicity maps show that the dominant interaction sites for both substrates lie in hydrophilic regions. Fig 5D visualizes the TF-substrate binding with two representations of TF-MBP and TF-P2 complexes.


The Trigger Factor Chaperone Encapsulates and Stabilizes Partial Folds of Substrate Proteins.

Singhal K, Vreede J, Mashaghi A, Tans SJ, Bolhuis PG - PLoS Comput. Biol. (2015)

Four 200 ns long AA-MD simulations of extended TF each with full MBP and P2.A. Contact probabilities of TF residues with MBP (top panel) and P2 (bottom panel). The barcode plots the standard hydrophobicity map of TF: color-scaled from red (hydrophilic) to green (hydrophobic). B. Distribution of the fraction of hydrophilic contacts in TF-substrate binding for different substrates. The dashed lines plot the distribution in the first 10 ns, while solid lines with circles plot the distribution over the whole trajectory. C. Visualization of the most important interaction sites (blue) on TF for MBP and P2. D. Representative final conformations of TF-MBP and TF-P2 complexes. The substrates are shown in transparent white colored wire-mesh.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4626277&req=5

pcbi.1004444.g005: Four 200 ns long AA-MD simulations of extended TF each with full MBP and P2.A. Contact probabilities of TF residues with MBP (top panel) and P2 (bottom panel). The barcode plots the standard hydrophobicity map of TF: color-scaled from red (hydrophilic) to green (hydrophobic). B. Distribution of the fraction of hydrophilic contacts in TF-substrate binding for different substrates. The dashed lines plot the distribution in the first 10 ns, while solid lines with circles plot the distribution over the whole trajectory. C. Visualization of the most important interaction sites (blue) on TF for MBP and P2. D. Representative final conformations of TF-MBP and TF-P2 complexes. The substrates are shown in transparent white colored wire-mesh.
Mentions: Once the smallest partial-fold (P1) is completely folded, TF further interacts with the larger partial folds (e.g., P2), eventually interacting with full MBP. We simulated these interaction through six MD runs of TF with a larger partial fold P2, and four runs with full native MBP molecule (see S6 and S7 Figs). The contact probability plots in Fig 5A (top panel for MBP, bottom panel for P2) show that for both systems, the tip of N-terminal domain (residues 38–55) is responsible for the majority of the interactions, while other domains play only minor roles. P2 also binds to the tips of Arm1 (residues 320–325). The TF structures in Fig 5B visualize the location of these interaction sites with MBP and P2. Most of them lie at the tips of TF’s appendages, while the PPIase domain again appears to cover P2, like a lid, with its inner surface. The hydrophobicity maps show that the dominant interaction sites for both substrates lie in hydrophilic regions. Fig 5D visualizes the TF-substrate binding with two representations of TF-MBP and TF-P2 complexes.

Bottom Line: Unfolded chains are kinetically trapped when bound to TF, which suppresses the formation of transient, non-native end-to-end contacts.This encapsulation mechanism is distinct from that of chaperones such as GroEL, and allows folded structures of diverse size and composition to be protected from aggregation and misfolding interactions.The results suggest that an ATP cycle is not required to enable both encapsulation and liberation.

View Article: PubMed Central - PubMed

Affiliation: van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands.

ABSTRACT
How chaperones interact with protein chains to assist in their folding is a central open question in biology. Obtaining atomistic insight is challenging in particular, given the transient nature of the chaperone-substrate complexes and the large system sizes. Recent single-molecule experiments have shown that the chaperone Trigger Factor (TF) not only binds unfolded protein chains, but can also guide protein chains to their native state by interacting with partially folded structures. Here, we used all-atom MD simulations to provide atomistic insights into how Trigger Factor achieves this chaperone function. Our results indicate a crucial role for the tips of the finger-like appendages of TF in the early interactions with both unfolded chains and partially folded structures. Unfolded chains are kinetically trapped when bound to TF, which suppresses the formation of transient, non-native end-to-end contacts. Mechanical flexibility allows TF to hold partially folded structures with two tips (in a pinching configuration), and to stabilize them by wrapping around its appendages. This encapsulation mechanism is distinct from that of chaperones such as GroEL, and allows folded structures of diverse size and composition to be protected from aggregation and misfolding interactions. The results suggest that an ATP cycle is not required to enable both encapsulation and liberation.

No MeSH data available.