Limits...
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.


Persistency of the native secondary structures in each of ten unfolding simulations as a function of time. Trajectories of fractions of native α-helix and β-sheet are shown in red and blue, respectively. Secondary structures were assigned by DSSP42.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC5036653&req=5

f4-3_1: Persistency of the native secondary structures in each of ten unfolding simulations as a function of time. Trajectories of fractions of native α-helix and β-sheet are shown in red and blue, respectively. Secondary structures were assigned by DSSP42.

Mentions: The native structure of barnase has three α-helices and a five-stranded anti-parallel β-sheet (Fig. 1a). Figure 4 shows the persistency of the native secondary structure elements (α-helices and β-sheet) along the time axis for each trajectory. Gradual losses of the native secondary structures, in particular, the β-sheet, were commonly seen although they proceeded in different manners among 10 trajectories. The α-helices were more sustainable than the β-sheet, the reason of which might be partly due to amber 1994 (Cornell et al.) force field28, the force field we used, which is known as an α-helix-favoring force field. We next unified all the trajectories and analyzed them together to extract common properties among trajectories by introducing another progress variable Q, defined as a fraction of residual native contacts. As expected, Q values were gradually decreasing along time axes in our unfolding simulations (data not shown). By classifying all snapshot structures based on their Q values, we can treat all trajectories together on the Q-axis. Following Tsai et al.36, we classified all snapshot structures into four bins based on Q values; 1.0 <=Q< 0.75, 0.75 <=Q<0.5, 0.5 <=Q<0.25, and 0.25 <=Q< 0.0. These four bins were named, by taking medians, Q=0.875, Q=0.625, Q=0.375, and Q≡0.125, respectively. We analyzed average persistency of the native secondary structures for each bin (Fig. 5a). In contrast to the time trajectories illustrated in Figure 4, Figure 5a clearly shows that both native α-helices and β-sheet were gradually lost as unfolding proceeded along the Q axis and that the α-helices were more stable than the β-sheet. At the most native-like ensemble (the bin of Q=0.875), both native secondary structure elements showed similar and high persistencies (α-helices: 0.729, β-sheet: 0.655), and the persistencies gradually decreased as unfolding proceeded. Finally, the most unfolded ensemble (the bin of Q=0.125) has 0.269 of residual native α-helices and almost no native β-sheet (persistency: 0.001) (Fig. 5a). It should be noted that the regions (the C-terminal half of α1 and the turn connecting β3 and β4) which correspond to the residual local structures in urea-denatured barnase observed by an NMR relaxation measurement10, were found to retain their native-like conformations with high persistency even for the most unfolded ensemble (the bin of Q=0.125) in the simulations.


Retention of local conformational compactness in unfolding of barnase; Contribution of end-to-end interactions within quasi-modules
Persistency of the native secondary structures in each of ten unfolding simulations as a function of time. Trajectories of fractions of native α-helix and β-sheet are shown in red and blue, respectively. Secondary structures were assigned by DSSP42.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC5036653&req=5

f4-3_1: Persistency of the native secondary structures in each of ten unfolding simulations as a function of time. Trajectories of fractions of native α-helix and β-sheet are shown in red and blue, respectively. Secondary structures were assigned by DSSP42.
Mentions: The native structure of barnase has three α-helices and a five-stranded anti-parallel β-sheet (Fig. 1a). Figure 4 shows the persistency of the native secondary structure elements (α-helices and β-sheet) along the time axis for each trajectory. Gradual losses of the native secondary structures, in particular, the β-sheet, were commonly seen although they proceeded in different manners among 10 trajectories. The α-helices were more sustainable than the β-sheet, the reason of which might be partly due to amber 1994 (Cornell et al.) force field28, the force field we used, which is known as an α-helix-favoring force field. We next unified all the trajectories and analyzed them together to extract common properties among trajectories by introducing another progress variable Q, defined as a fraction of residual native contacts. As expected, Q values were gradually decreasing along time axes in our unfolding simulations (data not shown). By classifying all snapshot structures based on their Q values, we can treat all trajectories together on the Q-axis. Following Tsai et al.36, we classified all snapshot structures into four bins based on Q values; 1.0 <=Q< 0.75, 0.75 <=Q<0.5, 0.5 <=Q<0.25, and 0.25 <=Q< 0.0. These four bins were named, by taking medians, Q=0.875, Q=0.625, Q=0.375, and Q≡0.125, respectively. We analyzed average persistency of the native secondary structures for each bin (Fig. 5a). In contrast to the time trajectories illustrated in Figure 4, Figure 5a clearly shows that both native α-helices and β-sheet were gradually lost as unfolding proceeded along the Q axis and that the α-helices were more stable than the β-sheet. At the most native-like ensemble (the bin of Q=0.875), both native secondary structure elements showed similar and high persistencies (α-helices: 0.729, β-sheet: 0.655), and the persistencies gradually decreased as unfolding proceeded. Finally, the most unfolded ensemble (the bin of Q=0.125) has 0.269 of residual native α-helices and almost no native β-sheet (persistency: 0.001) (Fig. 5a). It should be noted that the regions (the C-terminal half of α1 and the turn connecting β3 and β4) which correspond to the residual local structures in urea-denatured barnase observed by an NMR relaxation measurement10, were found to retain their native-like conformations with high persistency even for the most unfolded ensemble (the bin of Q=0.125) in the simulations.

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.