Radiation Damage in XFEL: Case study from the oxygen-evolving complex of Photosystem II.

Muhamed Amin,S S Obayya,Ashraf Badawi

doi:10.1038/srep36492

Muhamed Amin, S S Obayya + Show 1 more

Open Access

https://doi.org/10.1038/srep36492

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Abstract

Structural changes induced by radiation damage in X-ray crystallography hinder the ability to understand the structure/function relationship in chemical reactions. Serial femtosecond crystallography overcomes this problem by exposing the sample to very short and intense laser pulse leading to measurement before destruction. Here we use molecular modeling to map the radiation damage during the 10–50 fs to the intensity, the energy and the time duration of the laser pulse on the oxygen-evolving complex (OEC) of photosystem II. In the model, the nuclei move classically in a fully quantum potential created by electron density under the effect of strong laser pulse in the Ehrenfest dynamics regime. The results show that the Mn-Mn and Mn-Ca distances are less affected by radiation damage due to the their heavy masses, while one μ-oxo bridge (O5) moves significantly. The radiation damage may induce conformational changes of the water ligands but only bond elongation for the amino acids ligands. These effects are relatively intensity independent from 1016 to 1017 W/cm2, but changes increase dramatically if the beam intensity is increased to 1018 W/cm2. In addition, the self amplified spontaneous emission (SASE) nature of the laser beam does not affect the dynamics of the ions.

Highlights

In serial femtosecond crystallography randomly oriented crystals are exposed to very intense, ultra short laser pulses that produce one diffraction pattern in the tens of femtoseconds before it destroys the crystal[1]
The reported Mn-Mn distances in the 3.1 Å structure were not fully consistence with those found via Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy and the differences were attributed to the radiation damage, which reduced the Mn in the oxygen-evolving center (OEC) distorting the cluster[16]
We study how the beam intensity and energy correlate with the evolution of the root mean square deviation (RMSD) of the nuclei and the energy of the system by applying laser pulses at different intensities and energies for 10 femtoseconds

Summary

Introduction

In serial femtosecond crystallography randomly oriented crystals are exposed to very intense, ultra short laser pulses that produce one diffraction pattern in the tens of femtoseconds before it destroys the crystal[1]. Calculations, which suggested that the Mn centers are reduced because of the free electrons generated due to the radiation damage[17]. Suga and coworkers obtained a radiation-damage-free structure by collecting still diffraction images of highly isomorphous crystals using the 10 KeV XFEL beam at a cryogenic temperature[20].

Results

Conclusion