Molecular Dynamics Characterization of Protein Crystal Contacts in Aqueous Solutions

We employ nonequilibrium molecular dynamics simulation to characterize the effective interactions between lysozyme molecules involved in the formation of two hydrophobic crystal contacts. We show that the effective interactions between crystal contacts do not exceed a few $kT$, the range of the attractive part of the potential is less than 4 Å, and, within this range, there is a significant depletion of water density between two protein contacts. Our findings highlight the different natures of protein crystallization and protein recognition processes.

Figure 1

Potential of mean force calculated for two crystal contacts $A$ and $B$ averaged over 25 ($A$) and 100 ($B$) forward and reverse trajectories. The process of convergence as the trajectories are accumulated is also shown.

Figure 2

Reduced concentration $C/C_{\mathrm{bulk}}$ profiles for water and ions (the insets) as a function of proteins separation $z(\AA )$ averaged over forward pullings (similar trends are observed for reverse pullings and are not shown for clarity). The left graph corresponds to contact $A$, and the right graph corresponds to contact $B$. Water is shown in black circles, whereas chloride ion concentration is shown in blue triangles and sodium ion concentration in red squares.