Un trabajo impoluto de los Tedax

To fully elucidate the role of these transiently populated relaxed structures, and to clarify the nature of various residues and functional groups implicated in the catalytic mechanism of the hairpin ribozyme, we used an extensive set of WExplore simulations to exhaustively map out the conformations along two reaction coordinates: (i) the A38(N1)…G+1(P) distance, and (ii) the G8(N1)…G+1(P) distance. In addition, 8 permutations of protonation states of A38, G8 and the 2’OH functional group were subjected to 2D WExplore sampling (Table 4.2.3.1). In the default WExplore simulation setup, the 2’OH retains its canonical protonated state. Low, medium, and high pH conditions were simulated by fixing the protonation states of A38 and G8 at their expected values as illustrated in Table 4.2.3.1. In addition, a transient state that corresponds to the A38H+ and G8- protonation states, which represent the active species in the reaction mechanism, was included even though the population of this state is likely going to be extremely low. Apart from the 4 default WExplore simulations, an additional 4 alternative WExplore simulations were performed, where the 2’OH was adjusted to its negatively charged deprotonated state, which better represents a later stage of the reaction pathway.

Table 4.2.3.1: Permutation of fixed protonation states used in 2D WExplore sampling

Permutation 2’OH A38 G8

def_transient 2’OH A38H(+) G8(-)

def_high 2’OH A38 G8(-)

def_med 2’OH A38 G8H

def_low 2’OH A38H(+) G8H

alt_transient 2’O(-) A38H(+) G8(-)

alt_high 2’O(-) A38 G8(-)

alt_med 2’O(-) A38 G8H

alt_low 2’O(-) A38H(+) G8H

From the collective results of the 8 WEXplore simulations, the identified conformations were clustered using the RMSD of all heavy atoms near the active site, which includes residues

G8, A38, and the two residues flanking the scissile phosphate (G1 and A-1). A total of 11 clusters were identified, and their medoid structures were extracted. Clusters that had G8 or A38 greater than 10 Å away from the center of the active site were excluded from further analysis, as in these structures partial unfolding of the active site was observed. The resulting 5 clusters contributed to 95.5% of all conformations sampled in the 8 WExplore simulations, which ensures that the loss of data from excluding the partially unfolded structures should have little effect on the overall analysis. Separate pH-REX CPHMDMSλD simulations were initiated from the medoid of each of the 5 clusters. The resulting pKa values, which should correspond to the

microscopic pKaare summarized in Table 4.2.3.2.

Table 4.2.3.2: Microscopic pKa calculated from pH-REX CPHMDMSλD simulations of the 5

dominant clusters as identified from 2D WExplore sampling.

Cluster G8 A9 A10 A38 Phos 2'OH Weight

0 13.0 2.0 2.0 13.0 2.0 9.4 0.3642

4 6.0 2.7 7.1 9.5 5.0 11.3 0.0953

5 7.4 2.0 2.3 2.9 6.3 11.7 0.0938

7 9.3 3.1 5.5 3.6 5.9 11.2 0.2204

9 10.7 4.4 3.1 5.6 5.9 5.8 0.1817

We observed that the microscopic pKa of A38 follows a bimodal distribution that

encompasses the apparent pKaof 6.5 measured, with 3 clusters with a pKa of less than ~6.5 and 2

clusters with a pKahigher than ~6.5. This observation is consistent with our earlier 1D WExplore

sampling and reinforces our hypothesis that the hairpin ribozyme undergoes considerable conformational fluctuations between two distinct microenvironments around A38, which alternately favor and disfavor protonation. Similarly, the pKaof G8 shows a bimodal distribution

about the apparent measured pKaof ~10.6, with 3 clusters possessing a lower pKa, and 2 clusters

having a higher pKa. For the 2’OH group, the pKa was downshifted from its reference value of

downshift in pKa value is not unexpected since the proton of the 2’OH is removed during the

first step of the reaction mechanism. As for residues A9 and A10, it was noted that the pKaof A9

is near its reference pKa of 3.5 in all clusters, however for A10, the pKa is elevated to between

~5.5 and ~7 in 2 clusters. Lastly, the non-bridging oxygens on the scissile phosphate are observed to have a pKathat is upshifted from 1.3 to ~5 to 6 in all but the first cluster.

To reconcile our simulation results on the microscopic pKa of the 5 clusters with

experimentally inferred apparent pKa values, we derived a relationship between microscopic

pKa, macroscopic apparent pKa and the free energy difference (or weights) between the various

conformations. From each permutation of 2D WExplore simulations, the weights of the 11 clusters can be obtained. In order to consolidate information from all 8 permutations of protonation states (see Table 4.2.3.1), we averaged the weights across all 8 simulations, and used equation 2.2.5.1 to calculate the apparent pKa. The results as summarized in Table 4.2.3.3 indicate that the calculated apparent pKa of G8 is within 0.5 pKa units from the experimentally

suggested value of 10.6. Based on pKaconsiderations alone, the calculated apparent pKa of A10

at 6.1 and the backbone phosphate at 5.9 would suggest that these residues may play a role in the catalytic mechanism as well. Interestingly, we observed that the apparent pKa of A38 is much

higher than anticipated at 10.5. We attribute this discrepancy relative to our prior results by noting that cluster 0 had a pKa >13 for A38, which is anomalously high. To determine if the

additional 6 excluded clusters would have any effect on the predicted apparent pKa, we

recalculated the apparent pKa using all states, and as shown in Table 4.2.3.3, the values are

Table 4.2.3.3: Reconstructed apparent pKa using microscopic pKa from CPHMD simulations

using average weights and modified weights targeted to experimental pKaof 6.5 and 10.6.

Residue Exp pKa Apparent Calc pKa (11-states) Apparent Calc pKa (5-states)

G8 10.6 10.3 10.8 A9 - 3.9 4.2 A10 - 5.6 6.1 A38 6.5 10.1 10.5 Phos - 5.8 5.9 2’OH - 10.4 10.9

Figure 4.2.3.1: Representative conformation of each cluster as identified from 2D Explore sampling. Relevant distances to the approach of the reaction coordinate, notably A38(N1)…O5’, A38(N1)…O2P, O2P…O2’ and G8(N1)…O2’ are illustrated in the figures.

Next, we examined the structural features of each of the 5 clusters identified, notably the distance between A38(N1)…O5’, to describe the proton transfer between A38 and the active site, A38(N1)…O2P, to describe the proton transfer between A38 and the backbone phosphate,

O2P…O2’ to describe proton transfer between the backbone phosphate and the 2’OH group, and and G8(N1)…O2’ to describe the proton transfer between G8 and the active site. Cluster 0 (Figure 4.2.3.1a) was populated 36.4% in all 8 2D WExplore simulations, and based on RMSD, it most resembles the ground state crystallographic structure. However, we note that in this medoid structure, A38 is positioned in-line (3.3 Å) for a proton transfer to the non-bridging oxygen on the scissile phosphate, which would be a catalytically incompetent structure. In addition, the high charge on the non-bridging oxygen would explain its elevated microscopic pKa

of >13. Further analysis of the structures within cluster 0 indicates that it may not be representative of the local environment around A38, and it can be positioned next to O5’ or O2P, which suggests that this cluster would need to be further divided into sub-clusters to deconvolute mild structural differences that can have a substantially large effect on the microscopic pKa

calculated. As for residue G8, it is positioned in-line for a proton transfer (2.9 Å) to the O2’ oxygen on the ribose sugar. Cluster 4 (Figure 4.2.3.1b) is populated 9.5% of the time, and may be viewed as a hybrid ground/transient conformation. Specifically, A38 is in the proper catalytically competent conformation, in-line (3 Å) for a proton transfer to the O5’ oxygen on the scissile phosphate. This conformation around A38 corresponds to the crystallographic structure, and its pKa is 9.5, which is consistent with our earlier calculations, and it also highlights the

sensitivity of A38 with its interacting atom. In this cluster, the pKa of A10 is also upshifted to

7.1, but it is not close enough to the active site to participate catalytically (>6 Å), and instead we suggest that it provides electronic stabilization of intermediate. G8 is positioned 8.2 Å away from the 2’OH group, and has a reduced pKa of 6.0, which is more representative of a transiently

populated relaxed structure. Cluster 5 (Figure 4.2.3.1c) is populated 9.4% of the time, and may be viewed as a transient relaxed structure, where both A38 and G8 are positioned away from the

reaction site at 6.4 Å and 9.8 Å respectively. Not surprisingly, the microscopic pKa of both

residues are lowered to 7.4 and 2.9 respectively. It is interesting that in this fully relaxed conformation, where both residues are away from the active site, the phosphate group pKa

reaches 6.3, which is the highest observed amongst all the states we simulated. This suggests that the phosphate group may participate in the proton transfer, in situations where the general base and acid are absent from the active site, for example in an A38 abasic mutant. Cluster 7 (Figure 4.2.3.1d), which is populated 22% of the time, has A38 in a relaxed conformation (8.1 Å), but G8 is positioned at a pre-catalytic position at 5.4 Å away from the O2’ atom. Here, G8 has a calculated pKa of 9.3 and the pKa of A10 is also elevated to 5.5. Lastly, cluster 9 (Figure

4.2.3.1e), which is populated 18% of the time, represents a possible catalytically competent state for the non-bridging oxygens on the phosphate group. Here, the O2P non-bridging oxygen is positioned in-line (2.9 Å) for a proton transfer to the O2’ atom on the 2’OH group, and it has an elevated pKaof 5.9. Notably, A38 is relaxed from the active site (6.8 Å) with a lowered pKa of

5.6, and G8 is pre-catalytic at 4.5 Å away with a pKaof 10.6.