Orientation before destruction. A multiscale molecular dynamics study

TL;DR

This study investigates how external electric fields can orient proteins prior to destruction, using multiscale molecular dynamics simulations to determine optimal field strengths for protein orientation without structural damage.

Contribution

It demonstrates the feasibility of protein orientation with electric fields below destructive levels, providing insights for experimental design in X-ray imaging.

Findings

Protein orientation achieved with fields as low as 0.5 V/nm within 10 ns.

Protein structure remains intact during orientation process.

Estimated bond-breaking threshold at 45 V/nm for Trp-cage protein.

Abstract

The emergence of ultra-fast X-ray free-electron lasers opens the possibility of imaging single molecules in the gas phase at atomic resolution. The main disadvantage of this imaging technique is the unknown orientation of the sample exposed to the X-ray beam, making the three dimensional reconstruction not trivial. Induced orientation of molecules prior to X-ray exposure can be highly beneficial, as it significantly reduces the number of collected diffraction patterns whilst improving the quality of the reconstructed structure. We present here the possibility of protein orientation using a time-dependent external electric field. We used ab initio simulations on Trp-cage protein to provide a qualitative estimation of the field strength required to break protein bonds, with 45 V/nm as a breaking point value. Furthermore, we simulated, in a classical molecular dynamics approach, the orientation of ubiquitin protein by exposing it to different time-dependent electric fields. The protein structure was preserved for all samples at the moment orientation was achieved, which we denote `orientation before destruction'. Moreover, we find that the minimal field strength required to induce orientation within ten ns of electric field exposure, was of the order of 0.5 V/nm. Our results help explain the process of field orientation of proteins and can support the design of instruments for protein orientation.