Evidence of functional protein dynamics from X-ray crystallographic ensembles

Abstract

It is widely recognized that representing a protein as a single static conformation is inadequate to describe the dynamics essential to the performance of its biological function. We contrast the amino acid displacements below and above the protein dynamical transition temperature, T(D)∼215K, of hen egg white lysozyme using X-ray crystallography ensembles that are analyzed by molecular dynamics simulations as a function of temperature. We show that measuring structural variations across an ensemble of X-ray derived models captures the activation of conformational states that are of functional importance just above T(D), and they remain virtually identical to structural motions measured at 300K. Our results highlight the ability to observe functional structural variations across an ensemble of X-ray crystallographic data, and that residue fluctuations measured in MD simulations at room temperature are in quantitative agreement with the experimental observable.

Figure 1. Local density correlations for P1 and non-P1 X-ray ensembles.

The P1 space group ensemble and the non-P1 space group ensembles compared to the 3LZT-MSSA ensemble. This defines the experimentally allowed regions of disorder on a residue-by-residue basis. The largest deviations measured between the P1 and non-P1 ensemble captures the functional motions corresponding to the β-turn connecting the first two strands of the β-sheet (residues 44–50) and the central portion of long loop (residues 67–73) in the β-domain, and the enhanced fluctuations in the N-terminus and C-terminus in the α-domain, around a central hinge .

Figure 2. Molecular dynamics trajectory data of RMSD (against the 3LZT reference) at different temperatures.

200K (black), 210K (red), 220K (green), 230K (blue) and 300K (yellow).

Figure 3. Local density correlations for X-ray ensemble and MD ensemble <215K.

The values of LDC<0.75 seen in the X-ray ensemble measures captures the functional motions of the protein at a residue level (see text and Figure 1). It is apparent that below 215K, no functional motions have been activated.

Figure 4. Local density correlations for X-ray ensemble and MD ensemble >215K and at 300K.

The values of LDC<0.75 seen in the X-ray ensemble measures captures the functional motions of the protein at a residue level (see text and Figure 1). It is apparent that above 215K, the functional motions have been activated.