Functional understanding of solvent structure in GroEL cavity through dipole field analysis

Abstract

Solvent plays a ubiquitous role in all biophysical phenomena. Yet, just how the molecular nature of water impacts processes in biology remains an important question. While one can simulate the behavior of water near biomolecules such as proteins, it is challenging to gauge the potential structural role solvent plays in mediating both kinetic and equilibrium processes. Here, we propose an analysis scheme for understanding the nature of solvent structure at a local level. We first calculate coarse-grained dipole vector fields for an explicitly solvated system simulated through molecular dynamics. We then analyze correlations between these vector fields to characterize water structure under biologically relevant conditions. In applying our method to the interior of the wild type chaperonin complex GroEL+ES, along with nine additional mutant GroEL complexes, we find that dipole field correlations are strongly related to chaperonin function.

Figure 1

GroEL/GroES chaperonin complex in its closed state (PDB 1PCQ), viewed from the side (left) and bottom (right). The bioactive complex consists of two stacked GroEL subunits, the cavities of which are capped by GroES during portions of the catalytic cycle. The above images were generated using MacPyMOL.

Figure 2

Refolding rates of various mutant GroEL complexes, as reported in the literature.

Figure 3

Close-up view of chaperonin (red, bold) and water (blue) dipole vector fields near the interior chaperonin wall. Cross-correlations were computed between these two vector fields.

Figure 4

Dipole vector field representation of GroEL/GroES chaperonin complex. The dipole field corresponding to the system's water molecules is omitted for clarity. Cross-correlation functions were computed over the area surrounded by the black box at increments of one grid spacing in the vertical direction. The two interior horizontal lines mark the approximate locations of mutations carried out in the nine mutant GroEL complexes. The plot at left illustrates how the relative correlation length would be projected onto the vertical coordinate.

Figure 5

Mean chaperonin/water cross-correlation length as a function of the vertical coordinate for the wild-type complex. Error bars represent 95%-confidence intervals estimated using a bootstrapping method over the all frames analyzed. The grey boxes (placed at ±6 Å from the two interior horizontal lines shown in Figure 4) indicate the full “mutation regions” used for later analysis.

Figure 6

Schematic representation of chaperonin-solvent correlation functions from Figure S2. Correlations below 1% were deemed insignificant and are indicated by dashes. Blue arrows indicate, on average, the relative orientation of the solvent dipole field to that of the chaperonin. As is clear from the illustration, these mutations act to both decrease the chaperonin/solvent correlation length and change the local structure of the water dipole field.

Figure 7

Correlation plots indicating the relationship between refolding rate and two different properties. Top: Correlation between refolding rate and the root mean square difference of the chaperonin/solvent correlation length, from wild type. Colors indicate the net cavity surface charge, and standard error bars for both theory and experiment are displayed. Bottom: Correlation between refolding rate and number of orientation differences from wild type in the water dipole field, as counted from Figure 6. Both quantities exhibit a strong anti-correlation with refolding rate, suggesting such differences can serve as predictors of conserved chaperonin function.