Role of cotranslational folding for β-sheet-enriched proteins: A perspective from molecular dynamics simulations

The formations of correct three-dimensional structures of proteins are essential to their functions. Cotranslational folding is vital for proteins to form correct structures in vivo. Although some experiments have shown that cotranslational folding can improve the efficiency of folding, its microscopic mechanism is not yet clear. Previously, we built a model of the ribosomal exit tunnel and investigated the cotranslational folding of a three-helix protein by using all-atom molecular dynamics simulations. Here we study the cotranslational folding of three β-sheet-enriched proteins using the same method. The results show that cotranslational folding can enhance the helical population in most cases and reduce non-native long-range contacts before emerging from the ribosomal exit tunnel. After exiting the tunnel, all proteins fall into local minimal states and the structural ensembles of cotranslational folding show more helical conformations than those of free folding. In particular, for one of the three proteins, the GTT WW domain, we find that one local minimum state of the cotranslational folding is the known folding intermediate, which is not found in free folding. This result suggests that the cotranslational folding may increase the folding efficiency by accelerating the sampling more than by avoiding the misfolded state, which is presently a mainstream viewpoint.

Figure 1

Cartoon representation of three proteins studied in this work. These figures were created by the vmd program [36].

Figure 2

(a) Schematic diagram of the model of the ribosomal exit tunnel. The green lines represent the rigid wall of the tunnel model. (b) Four geometric parameters of the tunnel model. (c) Flow chart of cotranslational folding simulation; residues with and without constraints are shown as red and blue lines, respectively.

Figure 3

The population where each residue is in a helical or β-sheet structure in cotranslational folding (orange dashed line) and free folding (blue solid line) for (a)–(d) GTT, (e)–(h) SH3, and (i)–(l) CI2 before exiting from the ribosomal tunnel. The corresponding shadows represent 95% confidence intervals of eight to ten independent trajectories. The numbers outside and inside the brackets represent the average and standard deviation of the cumulative probability of all residues, respectively. The coloring scheme for numbers is the same as for lines.

Figure 4

At a translation speed of residue/10 ns, the relationship between the helix tendency (a)–(d) or the hydropathic index (e)–(h) of amino acids and the increment of the helical population. The increment is calculated by subtracting the helical population in cotranslational folding and free folding in Fig. 3. Each dot represents one kind of amino acid, and the dotted line represents the average value of the helical increment. The amino acids with the top six highest increments, namely, Met, Glu, Trp, Asn, Lys, and Ser are marked by red, orange, blue, cyan, green, and purple, respectively.

Figure 5

The numbers of native contacts ($Q_{\mathrm{nat}}$) and non-native contacts ($Q_{\mathrm{non}}$) of (a)–(d) GTT, (e)–(h) SH3, and (i)–(l) CI2 change with time before exiting from the ribosomal exit tunnel. The meaning of the shadow is the same as in Fig. 3.

Figure 6

The cumulative numbers of (a), (c) native contacts (${\mathrm{AQ}}_{\mathrm{nat}}$) and (b), (d) non-native contacts (${\mathrm{AQ}}_{\mathrm{non}}$) before exiting from the ribosomal exit tunnel. The labeled percentage represents the ratio of ${\mathrm{AQ}}_{\mathrm{non}}$ in CTF to ${\mathrm{AQ}}_{\mathrm{non}}$ in FF.

Figure 7

The structural ensembles of the nascent peptides in the simulations at the specific time $N\mathrm{\Delta }t$, where $\mathrm{\Delta }t$ is the translation speed and $N$ is the residue number.

Figure 8

The contact maps of the structural ensembles of (a), (b) GTT, (c), (d) SH3, and (e), (f) CI2 under free folding (blue, upper triangle) and cotranslational folding (red, lower triangle) when all the residues completely enter the tunnel (that is, the simulation time equals the translation speed multiplied by the number of residues). The darker the color, the higher the proportion of the contact in the ensemble.

Figure 9

After exiting from the ribosome tunnel, the population of Helix and Sheet of each residue of (a), (b) GTT, (c), (d) SH3, and (e), (f) CI2 under free folding (blue dots) and cotranslational folding at the speed of residue/2 ns (orange crosses) and residue/10 ns (green squares). The first-microsecond trajectory is not used in the analysis, and the subsequent analysis is also the same.

Figure 10

After exiting the ribosome tunnel, the distribution of $Q_{\mathrm{nat}}$ and $Q_{\mathrm{non}}$ of (a), (b) GTT, (c), (d) SH3, and (e), (f) CI2 in free folding (blue) and cotranslational folding at the speeds of residual/2 ns (red) and residual/10 ns (green).

Figure 11

After exiting from the ribosome exit tunnel, the distribution of root-mean-square deviation (RMSD) and radius of gyration (ROG) of (a), (b) GTT, (c), (d) SH3, and (e), (f) CI2 in free folding (blue) and cotranslational folding at the speeds of residual/2 ns (red) and residual/10 ns (green).

Figure 12

After exiting from the ribosome exit tunnel, the representative structures of the five largest clusters of three proteins in three types of simulations. The RMSD values of the representative structures and the population of clusters are summarized in Table S2 [41]. This figure was prepared with pymol [53].

Figure 13

(a) The fifth cluster C5 in CTF-10 has a native hairpin, which is the feature of the on-pathway folding intermediate. The RMSD of the alignment of the hairpin is 0.99 Å. (b) A short free folding simulation trajectory of GTT at 350 K, where GTT is successfully folded to its native state (defined by RMSD < 2 Å). The inset shows the structural alignment between the structure obtained by simulation (RMSD is 1.68 Å) and the native structure. Simulated and native structures are colored in red and blue, respectively.