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Retention of local conformational compactness in unfolding of barnase; Contribution of end-to-end interactions within quasi-modules

View Article: PubMed Central - PubMed

ABSTRACT

To understand how protein reduces the conformational space to be searched for the native structure, it is crucial to characterize ensembles of conformations on the way of folding processes, in particular ensembles of relatively long-range structures connecting between an extensively unfolded state and a state with a native-like overall chain topology. To analyze such intermediate conformations, we performed multiple unfolding molecular dynamics simulations of barnase at 498K. Some short-range structures such as part of helix and turn were well sustained while most of the secondary structures and the hydrophobic cores were eventually lost, which is consistent with the results by other experimental and computational studies. The most important novel findings were persistence of long-range relatively compact substructures, which was captured by exploiting the concept of module. Module is originally introduced to describe the hierarchical structure of a globular protein in the native state. Modules are conceptually such relatively compact substructures that are resulted from partitioning the native structure of a globular protein completely into several contiguous segments with the least extended conformations. We applied this concept of module to detect a possible hierarchical structure of each snapshot structure in unfolding processes as well. Along with this conceptual extension, such detected relatively compact substructures are named quasi-modules. We found almost perfect persistence of quasi-module boundaries that are positioned close to the native module boundaries throughout the unfolding trajectories. Relatively compact conformations of the quasi-modules seemed to be retained mainly by hydrophobic interactions formed between residues located at both terminal regions within each module. From these results, we propose a hypothesis that hierarchical folding with the early formation of quasi-modules effectively reduces search space for the native structure.

No MeSH data available.


Comparison between native module boundaries and quasi-module boundaries (black dots) plotted as a function of time. Quasi-module boundaries were identified for each snapshot conformation in each trajectory of 10 unfolding simulations (a–j). Regions no more than 2 residues away from the native module boundaries are shaded in pink.
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f6-3_1: Comparison between native module boundaries and quasi-module boundaries (black dots) plotted as a function of time. Quasi-module boundaries were identified for each snapshot conformation in each trajectory of 10 unfolding simulations (a–j). Regions no more than 2 residues away from the native module boundaries are shaded in pink.

Mentions: The native 3D structure of barnase is decomposed into at least six modules, M1–M6; M1 (amino acid residues 1–24), M2 (25–52), M3 (53–73), M4 (74–88), M5 (89–98), and M6 (99–110) (Fig. 1c)20. We decomposed all simulation snapshot conformations into quasi-modules by our automatic module-identification method. In the control simulation at 300 K, barnase retained its native structure throughout 3 ns of simulation time; the Cα-RMSD rose to only around 2 angstrom (Fig. 2). Therefore, the modules of barnase also kept their compact native conformations so that the module boundaries were completely retained in this control simulation (data not shown). In the case of the unfolding simulations, Figure 6 shows quasi-module boundaries along the time axis for each of 10 unfolding trajectories. The native module boundaries are indicated by pink bars with a width of 2 residues at both sides. The most surprising result of this analysis is that the positions corresponding to the native module boundaries were identified nearly perfectly as quasi-module boundaries throughout all the trajectories (Fig. 6). Only one exception is that the quasi-module boundary corresponding to the module boundary between modules M4 and M5 disappeared during last 500 ps of the trajectory D9 (Fig. 6i). On the other hand, there are many residues that are identified as quasi-module boundaries but not close to the native module boundaries. To examine whether these quasi-module boundaries away from the native module boundaries appear as often as those close to the native module boundaries, we plotted a frequency for each residue to be identified as a quasi-module boundary over all trajectories (Fig. 7). From the plot, it is apparent that residues close to the native module boundaries have much higher frequencies to be identified as quasi-module boundaries than other residues.


Retention of local conformational compactness in unfolding of barnase; Contribution of end-to-end interactions within quasi-modules
Comparison between native module boundaries and quasi-module boundaries (black dots) plotted as a function of time. Quasi-module boundaries were identified for each snapshot conformation in each trajectory of 10 unfolding simulations (a–j). Regions no more than 2 residues away from the native module boundaries are shaded in pink.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC5036653&req=5

f6-3_1: Comparison between native module boundaries and quasi-module boundaries (black dots) plotted as a function of time. Quasi-module boundaries were identified for each snapshot conformation in each trajectory of 10 unfolding simulations (a–j). Regions no more than 2 residues away from the native module boundaries are shaded in pink.
Mentions: The native 3D structure of barnase is decomposed into at least six modules, M1–M6; M1 (amino acid residues 1–24), M2 (25–52), M3 (53–73), M4 (74–88), M5 (89–98), and M6 (99–110) (Fig. 1c)20. We decomposed all simulation snapshot conformations into quasi-modules by our automatic module-identification method. In the control simulation at 300 K, barnase retained its native structure throughout 3 ns of simulation time; the Cα-RMSD rose to only around 2 angstrom (Fig. 2). Therefore, the modules of barnase also kept their compact native conformations so that the module boundaries were completely retained in this control simulation (data not shown). In the case of the unfolding simulations, Figure 6 shows quasi-module boundaries along the time axis for each of 10 unfolding trajectories. The native module boundaries are indicated by pink bars with a width of 2 residues at both sides. The most surprising result of this analysis is that the positions corresponding to the native module boundaries were identified nearly perfectly as quasi-module boundaries throughout all the trajectories (Fig. 6). Only one exception is that the quasi-module boundary corresponding to the module boundary between modules M4 and M5 disappeared during last 500 ps of the trajectory D9 (Fig. 6i). On the other hand, there are many residues that are identified as quasi-module boundaries but not close to the native module boundaries. To examine whether these quasi-module boundaries away from the native module boundaries appear as often as those close to the native module boundaries, we plotted a frequency for each residue to be identified as a quasi-module boundary over all trajectories (Fig. 7). From the plot, it is apparent that residues close to the native module boundaries have much higher frequencies to be identified as quasi-module boundaries than other residues.

View Article: PubMed Central - PubMed

ABSTRACT

To understand how protein reduces the conformational space to be searched for the native structure, it is crucial to characterize ensembles of conformations on the way of folding processes, in particular ensembles of relatively long-range structures connecting between an extensively unfolded state and a state with a native-like overall chain topology. To analyze such intermediate conformations, we performed multiple unfolding molecular dynamics simulations of barnase at 498K. Some short-range structures such as part of helix and turn were well sustained while most of the secondary structures and the hydrophobic cores were eventually lost, which is consistent with the results by other experimental and computational studies. The most important novel findings were persistence of long-range relatively compact substructures, which was captured by exploiting the concept of module. Module is originally introduced to describe the hierarchical structure of a globular protein in the native state. Modules are conceptually such relatively compact substructures that are resulted from partitioning the native structure of a globular protein completely into several contiguous segments with the least extended conformations. We applied this concept of module to detect a possible hierarchical structure of each snapshot structure in unfolding processes as well. Along with this conceptual extension, such detected relatively compact substructures are named quasi-modules. We found almost perfect persistence of quasi-module boundaries that are positioned close to the native module boundaries throughout the unfolding trajectories. Relatively compact conformations of the quasi-modules seemed to be retained mainly by hydrophobic interactions formed between residues located at both terminal regions within each module. From these results, we propose a hypothesis that hierarchical folding with the early formation of quasi-modules effectively reduces search space for the native structure.

No MeSH data available.