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Role of tryptophan side chain dynamics on the Trp-cage mini-protein folding studied by molecular dynamics simulations.

Kannan S, Zacharias M - PLoS ONE (2014)

Bottom Line: Whereas the majority of intermediate start structures with the central Trp side chain in a near-native rotameric state folded successfully within less than 100 ns only a fraction of start structures reached near-native folded states with an initially non-native Trp side chain rotamer state.Weak restraining of the Trp side chain dihedral angles to the state in the folded protein resulted in significant acceleration of the folding both starting from fully extended or intermediate conformations.The results indicate that the side chain conformation of the central Trp residue can create a significant barrier for controlling transitions to a near native folded structure.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Institute, Agency for Science Technology and Research, Singapore, Singapore ; Experimental Therapeutics Centre, Agency for Science Technology and Research, Singapore, Singapore.

ABSTRACT
The 20 residue Trp-cage mini-protein is one of smallest proteins that adopt a stable folded structure containing also well-defined secondary structure elements. The hydrophobic core is arranged around a single central Trp residue. Despite several experimental and simulation studies the detailed folding mechanism of the Trp-cage protein is still not completely understood. Starting from fully extended as well as from partially folded Trp-cage structures a series of molecular dynamics simulations in explicit solvent and using four different force fields was performed. All simulations resulted in rapid collapse of the protein to on average relatively compact states. The simulations indicate a significant dependence of the speed of folding to near-native states on the side chain rotamer state of the central Trp residue. Whereas the majority of intermediate start structures with the central Trp side chain in a near-native rotameric state folded successfully within less than 100 ns only a fraction of start structures reached near-native folded states with an initially non-native Trp side chain rotamer state. Weak restraining of the Trp side chain dihedral angles to the state in the folded protein resulted in significant acceleration of the folding both starting from fully extended or intermediate conformations. The results indicate that the side chain conformation of the central Trp residue can create a significant barrier for controlling transitions to a near native folded structure. Similar mechanisms might be of importance for the folding of other protein structures.

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MD simulations of intermediate Trp-cage structures.RMSDCα of sampled Trp-cage conformations in explicit solvent starting from a set of intermediate structures (a subset of intermediate structures of set2 shown in Figure 5B,) vs. simulation time with different Amber force fields (A) ff03 (B) ff99SB, (C) ff99SB_ILDN, (D) ff99SB_NMR. All these examples eventually reached a near-native conformation with RMSDCα <2 Å from the native Trp-cage structure.
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pone-0088383-g005: MD simulations of intermediate Trp-cage structures.RMSDCα of sampled Trp-cage conformations in explicit solvent starting from a set of intermediate structures (a subset of intermediate structures of set2 shown in Figure 5B,) vs. simulation time with different Amber force fields (A) ff03 (B) ff99SB, (C) ff99SB_ILDN, (D) ff99SB_NMR. All these examples eventually reached a near-native conformation with RMSDCα <2 Å from the native Trp-cage structure.

Mentions: In another set of intermediate structures (set 2) only the N-terminal α-helix was already partially formed, but the rest of the protein differed significantly from the native structure missing the 310 helix, part of the PPII helix and proper native tertiary contacts (Figure 4B, Table 2). These intermediate structures had an RMSDCα of 3.5–6.0 Å from the experimental structure and in most cases Trp6 was in a non-native rotameric state (Figure 4B, Table 2). In contrast to the first set only a part of the start structures from the second set of intermediate conformations reached the folded state of the Trp-cage protein within 100 ns MD simulation time (Figure 5, Table 2). In some of the simulations the Trp-cage conformation remained close to the start structure and also unfolding of the protein was observed (Figure S4, Table 2). Detailed analysis of simulation trajectories that reached the folded state of the protein revealed some interesting key events that occurred along the folding pathway. Interestingly, in most of the simulations that resulted in folding to near-native conformations the protein eventually started to move away from its compact start state (Figure 5, 6). The final transition to the folded conformation was typically associated with a sudden drop of the RMSDCα from ∼3–7 Å down to ∼<1.5 Å. A prerequisite for successful collapse to the native structure was either the presence of a near-native rotameric state of the Trp6 side chain or the transition of the Trp6 side chain to the native rotameric state typically several nanoseconds before the successful collapse to the near-native conformation (indicated for one case per force field in Figure 6 and in Figures S5, S6, S7). In the majority of successful folding events, the Trp6 first establishes interaction with the Pro12 residue (in the middle 310 helix segment). Subsequently, contacts of Trp6 with Pro18 or Pro17 from the PPII motif at the C-terminus are established to complete the process (Figure 6E, and Figure 7). Successful folding to low final RMSDCα is especially tightly coupled to contacts between Trp6 and Pro12 as well as Pro18 (there are no near-native Trp-cage structures without close Trp6-Pro12 and Trp6-Pro18 contacts, Figure 7). There is no such tight coupling between the Tyr3-Pro19 distance and occurrence of near –native Trp-cage structures. Even for sampled conformations with RMSDCα <2 Å from the native structure the Tyr3-Pro19 distance can vary between 5–12 Å (Figure 7A).


Role of tryptophan side chain dynamics on the Trp-cage mini-protein folding studied by molecular dynamics simulations.

Kannan S, Zacharias M - PLoS ONE (2014)

MD simulations of intermediate Trp-cage structures.RMSDCα of sampled Trp-cage conformations in explicit solvent starting from a set of intermediate structures (a subset of intermediate structures of set2 shown in Figure 5B,) vs. simulation time with different Amber force fields (A) ff03 (B) ff99SB, (C) ff99SB_ILDN, (D) ff99SB_NMR. All these examples eventually reached a near-native conformation with RMSDCα <2 Å from the native Trp-cage structure.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3921895&req=5

pone-0088383-g005: MD simulations of intermediate Trp-cage structures.RMSDCα of sampled Trp-cage conformations in explicit solvent starting from a set of intermediate structures (a subset of intermediate structures of set2 shown in Figure 5B,) vs. simulation time with different Amber force fields (A) ff03 (B) ff99SB, (C) ff99SB_ILDN, (D) ff99SB_NMR. All these examples eventually reached a near-native conformation with RMSDCα <2 Å from the native Trp-cage structure.
Mentions: In another set of intermediate structures (set 2) only the N-terminal α-helix was already partially formed, but the rest of the protein differed significantly from the native structure missing the 310 helix, part of the PPII helix and proper native tertiary contacts (Figure 4B, Table 2). These intermediate structures had an RMSDCα of 3.5–6.0 Å from the experimental structure and in most cases Trp6 was in a non-native rotameric state (Figure 4B, Table 2). In contrast to the first set only a part of the start structures from the second set of intermediate conformations reached the folded state of the Trp-cage protein within 100 ns MD simulation time (Figure 5, Table 2). In some of the simulations the Trp-cage conformation remained close to the start structure and also unfolding of the protein was observed (Figure S4, Table 2). Detailed analysis of simulation trajectories that reached the folded state of the protein revealed some interesting key events that occurred along the folding pathway. Interestingly, in most of the simulations that resulted in folding to near-native conformations the protein eventually started to move away from its compact start state (Figure 5, 6). The final transition to the folded conformation was typically associated with a sudden drop of the RMSDCα from ∼3–7 Å down to ∼<1.5 Å. A prerequisite for successful collapse to the native structure was either the presence of a near-native rotameric state of the Trp6 side chain or the transition of the Trp6 side chain to the native rotameric state typically several nanoseconds before the successful collapse to the near-native conformation (indicated for one case per force field in Figure 6 and in Figures S5, S6, S7). In the majority of successful folding events, the Trp6 first establishes interaction with the Pro12 residue (in the middle 310 helix segment). Subsequently, contacts of Trp6 with Pro18 or Pro17 from the PPII motif at the C-terminus are established to complete the process (Figure 6E, and Figure 7). Successful folding to low final RMSDCα is especially tightly coupled to contacts between Trp6 and Pro12 as well as Pro18 (there are no near-native Trp-cage structures without close Trp6-Pro12 and Trp6-Pro18 contacts, Figure 7). There is no such tight coupling between the Tyr3-Pro19 distance and occurrence of near –native Trp-cage structures. Even for sampled conformations with RMSDCα <2 Å from the native structure the Tyr3-Pro19 distance can vary between 5–12 Å (Figure 7A).

Bottom Line: Whereas the majority of intermediate start structures with the central Trp side chain in a near-native rotameric state folded successfully within less than 100 ns only a fraction of start structures reached near-native folded states with an initially non-native Trp side chain rotamer state.Weak restraining of the Trp side chain dihedral angles to the state in the folded protein resulted in significant acceleration of the folding both starting from fully extended or intermediate conformations.The results indicate that the side chain conformation of the central Trp residue can create a significant barrier for controlling transitions to a near native folded structure.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Institute, Agency for Science Technology and Research, Singapore, Singapore ; Experimental Therapeutics Centre, Agency for Science Technology and Research, Singapore, Singapore.

ABSTRACT
The 20 residue Trp-cage mini-protein is one of smallest proteins that adopt a stable folded structure containing also well-defined secondary structure elements. The hydrophobic core is arranged around a single central Trp residue. Despite several experimental and simulation studies the detailed folding mechanism of the Trp-cage protein is still not completely understood. Starting from fully extended as well as from partially folded Trp-cage structures a series of molecular dynamics simulations in explicit solvent and using four different force fields was performed. All simulations resulted in rapid collapse of the protein to on average relatively compact states. The simulations indicate a significant dependence of the speed of folding to near-native states on the side chain rotamer state of the central Trp residue. Whereas the majority of intermediate start structures with the central Trp side chain in a near-native rotameric state folded successfully within less than 100 ns only a fraction of start structures reached near-native folded states with an initially non-native Trp side chain rotamer state. Weak restraining of the Trp side chain dihedral angles to the state in the folded protein resulted in significant acceleration of the folding both starting from fully extended or intermediate conformations. The results indicate that the side chain conformation of the central Trp residue can create a significant barrier for controlling transitions to a near native folded structure. Similar mechanisms might be of importance for the folding of other protein structures.

Show MeSH
Related in: MedlinePlus