Unfolding dynamics of the protein ubiquitin: Insight from simulation

The temperature-induced unfolding pathway of ubiquitin has been investigated by molecular dynamics simulation at four different temperatures. It has been observed that the sequences of the unfolding events are same at all the temperatures. However, the time scale of the dynamics at different temperatures are different. The transition states at various temperatures also possess similar secondary structural elements. The intermediate conformations visited by the protein at different temperatures can help determination of the transition states. The well known “$A$ state” of ubiquitin, hitherto found to be stable only in methanol water mixture, have been observed to be a common transient intermediate conformation in the unfolding path of the protein in water. Our observation about the similarities of the unfolding process at different temperatures strongly recommend for a defined pathway for the unfolding process.

Figure 1

(a) The native structure of ubiquitin. (b) Structure of one representative of the transition state ensemble.

Figure 2

RMSD vs time plot of the backbone of the protein at different temperatures. From left to right: $520\mathrm{K}$ (black), $450\mathrm{K}$ (light gray), at $385\mathrm{K}$ (gray), $300\mathrm{K}$ (black). The temperatures have also been shown in the figure. The increment of the scale for the horizontal axis has been set differently so that the rapid change at $520\mathrm{K}$ could be viewed clearly.

Figure 3

RMSD vs time plot of the different portion of the backbone of the protein: (a) at $520\mathrm{K}$ and (b) at $385\mathrm{K}$. The number within the parentheses indicate the data for a range of residues. The coloring scheme is as follows: residue No. 1–33 (light gray), 34–76 (gray), core residues (black). The definition of the core residues has been mentioned in the text.

Figure 4

Plot of radius of gyration $\left(R_g\right)$ of the protein vs time at different temperatures. The coloring scheme and the increment on the scale in the horizontal axis is similar to that in Fig. 2.

Figure 5

Change of solvent accessible surface area (SASA) of the protein with time at different temperatures. The coloring scheme and the increment on the scale in the horizontal axis is same with the Fig. 2.

Figure 6

Time-dependent variation of the tertiary contact $\left(N_{\mathrm{cont}}\right)$ of the protein at different temperatures. The coloring scheme is similar to the Fig. 2.

Figure 7

$C_{\alpha }\text{‐}{C}_{\alpha }$ contact map of the protein at different temperatures and at different time points. (a) Starting structure, (b) after $4\mathrm{ns}$, at $385\mathrm{K}$, (c) after $8\mathrm{ns}$, at $385\mathrm{K}$, (d) after $12\mathrm{ns}$, at $385\mathrm{K}$, (e) after $2\mathrm{ns}$, at $450\mathrm{K}$, (f) after $4\mathrm{ns}$, at $450\mathrm{K}$, (g) after $6\mathrm{ns}$, at $450\mathrm{K}$, (h) after $8\mathrm{ns}$, $450\mathrm{K}$.

Figure 8

The three-dimensional plot of the protein conformations in the RMSD space. The distance between two points implies the RMS difference between two conformations. The line connects the two conformations evolved sequentially in time. The resolution is of $2\mathrm{ps}$ time interval between the conformations.

Figure 9

Snapshots of the protein structure evolved at different time points at different temperatures. The structures having similar secondary and tertiary interactions but generated at different temperatures have been put in a same column. The first column shows the starting structure, second column shows the initial disruption leading to the transition state (third column). The fourth and fifth column are the steps in the way of complete denaturation. The last column show the final structure generated at the time of truncation of the trajectory. The numbers in the right bottom corner of each structure indicate the time point in nanosecond time scale.