key: cord-1037217-d7zsjh4l
authors: Ansari, Narjes; Rizzi, Valerio; Carloni, Paolo; Parrinello, Michele
title: Water-triggered, irreversible conformational change of SARS-CoV-2 main protease on passing from the solid state to aqueous solution
date: 2021-05-21
journal: bioRxiv
DOI: 10.1101/2021.05.21.445090
sha: 1e9eeaf77358a5b2f8cc53247864733a365b5eb2
doc_id: 1037217
cord_uid: d7zsjh4l

The main protease from SARS-CoV-2 is a homodimer. Yet, a recent 0.1 ms long molecular dynamics simulation shows that it readily undergoes a symmetry breaking event on passing from the solid state to the aqueous solution. As a result, the subunits present distinct conformations of the binding pocket. By analysing this long time simulation, here we uncover a previously unrecognised role of water molecules in triggering the transition. Interestingly, each subunit presents a different collection of long-lived water molecules. Enhanced sampling methods performed here, along with machine learning approaches, further establish that the transition to the asymmetric state is essentially irreversible.

stantly emerging new variants of the virus. Thus, it 23 is imperative to advance drug discovery campaigns to 24 identify ligands which may interfere with the disease 5 . Fig. 1 (a) ). The enzymatic reaction is performed by 36 the catalytic His41-Cys145 dyad, located in the S2 site ). The two regions bind to each other via the Glu166@I -and Phe140@I -Ser1@A H-bonds. The intra-subunit interaction is supported by His163@I and Phe140@I π-stacking. (e) One water enters the S1 binding pocket and forms a bridge between His163@I and Tyr161@I. (f) A rotation of Glu166@I leads to a breakage of its H-bond with the N-finger. (g) A water molecule that leaves the S1 binding pocket triggers a disruption of the hydrophobic contact between residues His163@I and Phe140@I, and eventually leads to the inactivation of subunit I.

Could the protein swap from one asymmetric confor-78 mation to the other? Our analysis helps us in identi-79 fying a slow mode of the system that expresses a sub- Let us now describe these results in more detail. We ising the S1 binding pocket ( Fig. 1 (d) ). First, it shows 108 an intra-subunit π-stacking contact between side-chains 109 Phe-140 and His-163 ( Fig. 1 (d) ). Second, it has an inter-110 subunit hydrogen bond between its Glu-166 residue and 111 the Ser-1 residue of the other subunit ( Fig. 1 (d) ).

After 750 ns, a water molecule bridges the imida-113 zole nitrogen atom of His163@I and the hydroxyl oxy-114 gen atom of Tyr161@I (see Fig. 1 (e) ). After about 150 115 ns, Glu166@I rotates. Following that, the N-finger@A 116 changes its conformation, and disrupting the link be-117 tween the m-shaped loop@I and the N-finger@A. Even-118 tually, the water molecule exits from the S1 binding 119 Figure 2 . The average position of (a) medium-and (b) long-lived water molecules (for their definition, see text) inside of the two subunits of a SC-2 M pro after 60.2 µs. In the former case, the distribution of medium-lived water molecules is asymmetric and delocalised, while in the latter case, the distribution is symmetrical in both subunits and consists of 4 hydration sites (W1-W4). The water maximum residency time τ max is shown in µs.

pocket, leaving behind an empty space that probably 120 encourages residues His163@I and Phe140@I to rotate 121 away from one another, breaking the catalytic dyad (see The long-lived water molecules (with a lifetime larger 134 than 5 µs) are located in four spots (W1-W4) whose po-135 sition is symmetrical in the two subunits ( Fig. 2 (b) ).

The lifetime increases on passing from W1 to W4. W1 The medium-lived water molecules (with a lifetime 149 between 0.5 µs and 5 µs) sit preferentially in non-150 symmetry related positions (see Fig. 2 (a) ), thus con-151 tributing to the asymmetry of what appears to be the 152 equilibrium state. They occupy a region that mostly 153 encompasses the S1 binding pocket (see Fig. 3 ). We (Fig. 3 (a) ). This event opens up a path for wa-170 ter molecules to enter, leading to the collapse of the 171 S1 pocket (indicated by label (3) in Fig. 3 (a) ). Be- Fig. 3 (b) ).

To determine whether the symmetry breaking can be 

A new coronavirus associated with human respi

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We acknowledge the Italian Institute of Technology for funding and support. The simulations were performed on the supercomputer CLAIX-2016-GPU at Forschungszentrum Jülich. Part of this work was performed under the auspices of ETH Zürich and Università della Svizzera italiana, Lugano. We thank David Shaw's group for making their long MD trajectory available to the scientific community.