Analysis of the strength of interfacial hydrogen bonds between tubulin dimers using quantum theory of atoms in molecules

Abstract

Microtubules are key structural elements that, among numerous biological functions, maintain the cytoskeleton of the cell and have a major role in cell division, which makes them important cancer chemotherapy targets. Understanding the energy balance that brings tubulin dimers, the building blocks of microtubules, together to form a microtubule is especially important for revealing the mechanism of their dynamic instability. Several studies have been conducted to estimate various contributions to the free energy of microtubule formation. However, the hydrogen-bond contribution was not studied before as a separate component. In this work, we use concepts such as the quantum theory of atoms in molecules to estimate the per-residue strength of hydrogen bonds contributing to the overall stability that brings subunits together in pair of tubulin heterodimers, across both the longitudinal and lateral interfaces. Our study shows that hydrogen bonding plays a major role in the stability of tubulin systems. Several residues that are crucial to the binding of vinca alkaloids are shown to be strongly involved in longitudinal microtubule stabilization. This indicates a direct relation between the binding of these agents and the effect on the interfacial hydrogen-bonding network, and explains the mechanism of their action. Lateral contacts showed much higher stability than longitudinal ones (-462 ± 70 vs. -392 ± 59 kJ/mol), which suggests a dramatic lateral stabilization effect of the GTP cap in the β-subunit. The role of the M-loop in lateral stability in absence of taxol was shown to be minor. The B-lattice lateral hydrogen bonds are shown to be comparable in strength to the A-lattice ones (-462 ± 70 vs. -472 ± 46 kJ/mol). These findings establish the importance of hydrogen bonds to the stability of tubulin systems.

Figure 1

Microtubule lattice and interfaces, with (dark blue) α-subunits and (cyan) β-subunits. (a) A model of a microtubule cylinder. (b) A model of the B-lattice configuration showing only nine tubulin dimers. (c) A model for the A-lattice configuration showing only seven tubulin dimers. In panels b and c, the three different interfaces between tubulin dimers that we studied are highlighted. These are 1), the longitudinal interdimer interfaces, LongAB; 2), the lateral interprotofilament interfaces in B-configuration, LatB; and 3), the lateral interprotofilament interfaces in A-configuration, LatA. (d) A more detailed model of the αβ-tubulin heterodimer showing the domains that make lateral contacts (red) and the domains that make longitudinal contacts (green). To see this figure in color, go online.

Figure 2

The major hydrogen bonds at the longitudinal interface. It is clear that they are distributed over the entire width and length of the interface to provide stronger support to the protofilament structure. To see this figure in color, go online.

Figure 3

Relative orientation of the two adjacent heterodimers in the LatB system before the simulation (orange) and after 25 ns of the simulation (cyan). To see this figure in color, go online.

Figure 4

Major hydrogen bonds in the LatB system at the (a) β-β interface and (b) α-α interface. To see this figure in color, go online.

Figure 5

Major hydrogen bonds at the (a) α-β interface and (b) β-α interface of the LatA system. To see this figure in color, go online.