Water Dynamics around T0 vs. R4 of Hemoglobin from Local Hydrophobicity Analysis

Abstract

The local hydration around tetrameric Hb in its T$_0$ and R$_4$ conformational substates is analyzed based on molecular dynamics simulations. Analysis of the local hydrophobicity (LH) for all residues at the $\alpha_1 \beta_2$ and $\alpha_2 \beta_1$ interfaces, responsible for the quaternary T$\rightarrow$R transition, which is encoded in the MWC model, as well as comparison with earlier computations of the solvent accessible surface area (SASA), makes clear that the two quantities measure different aspects of hydration. Local hydrophobicity quantifies the presence and structure of water molecules at the interface whereas ``buried surface'' reports on the available space for solvent. For simulations with Hb frozen in its T$_0$ and R$_4$ states the correlation coefficient between LH and buried surface is 0.36 and 0.44, respectively, but it increases considerably if the 95 \% confidence interval is used. The LH with Hb frozen and flexible changes little for most residues at the interfaces but is significantly altered for a few select ones, which are Thr41$\alpha$, Tyr42$\alpha$, Tyr140$\alpha$, Trp37$\beta$, Glu101$\beta$ (for T$_0$) and Thr38$\alpha$, Tyr42$\alpha$, Tyr140$\alpha$ (for R$_4$). The number of water molecules at the interface is found to increase by $\sim 25$ \% for T$_0$$\rightarrow$R$_4$ which is consistent with earlier measurements. Since hydration is found to be essential to protein function, it is clear that hydration also plays an essential role in allostery.