A Perspective on Molecular Structure and Bond-Breaking in Radiation Damage in Serial Femtosecond Crystallography

SARS-CoV-2 Mpro responds to oxidation by forming disulfide and NOS/SONOS bonds

The main protease (Mpro) of SARS-CoV-2 is critical for viral function and a key drug target. Mpro is only active when reduced; turnover ceases upon oxidation but is restored by re-reduction. This suggests the system has evolved to survive periods in an oxidative environment, but the mechanism of this protection has not been confirmed. Here, we report a crystal structure of oxidized Mpro showing a disulfide bond between the active site cysteine, C145, and a distal cysteine, C117. Previous work proposed this disulfide provides the mechanism of protection from irreversible oxidation. Mpro forms an obligate homodimer, and the C117-C145 structure shows disruption of interactions bridging the dimer interface, implying a correlation between oxidation and dimerization. We confirm dimer stability is weakened in solution upon oxidation. Finally, we observe the protein's crystallization behavior is linked to its redox state. Oxidized Mpro spontaneously forms a distinct, more loosely packed lattice. Seeding with crystals of this lattice yields a structure with an oxidation pattern incorporating one cysteine-lysine-cysteine (SONOS) and two lysine-cysteine (NOS) bridges. These structures further our understanding of the oxidative regulation of Mpro and the crystallization conditions necessary to study this structurally.

Heavy element incorporation in nitroimidazole radiosensitizers: molecular-level insights into fragmentation dynamics

The present study investigates the photofragmentation behavior of iodine-enhanced nitroimidazole-based radiosensitizer model compounds in their protonated form using near-edge X-ray absorption mass spectrometry and quantum mechanical calculations. These molecules possess dual functionality: improved photoabsorption capabilities and the ability to generate species that are relevant to cancer sensitization upon photofragmentation. Four samples were investigated by scanning the generated fragments in the energy regions around C 1s, N 1s, O 1s, and I 3d-edges with a particular focus on NO2+ production. The experimental summed ion yield spectra are explained using the theoretical near-edge X-ray absorption fine structure spectrum based on density functional theory. Born-Oppenheimer-based molecular dynamics simulations were performed to investigate the fragmentation processes.

Time-Resolved Crystallography

This Special Issue on ‘Time-Resolved Crystallography’ is a collection of eight original articles providing interesting results that give insight into the processes involved in generating and analysing time-resolved data [...]

Imaging of femtosecond bond breaking and charge dynamics in ultracharged peptides

X-ray free-electrons lasers have revolutionized the method of imaging biological macromolecules such as proteins, viruses and cells by opening the door to structural determination of both single particles and crystals at room temperature. By utilizing high intensity X-ray pulses on femtosecond timescales, the effects of radiation damage can be reduced. Achieving high resolution structures will likely require knowledge of how radiation damage affects the structure on an atomic scale, since the experimentally obtained electron densities will be reconstructed in the presence of radiation damage. Detailed understanding of the expected damage scenarios provides further information, in addition to guiding possible corrections that may need to be made to obtain a damage free reconstruction. In this work, we have quantified the effects of ionizing photon-matter interactions using first principles molecular dynamics. We utilize density functional theory to calculate bond breaking and charge dynamics in three ultracharged molecules and two different structural conformations that are important to the structural integrity of biological macromolecules, comparing to our previous studies on amino acids. The effects of the ultracharged states and subsequent bond breaking in real space are studied in reciprocal space using coherent diffractive imaging of an ensemble of aligned biomolecules in the gas phase.

Ultrafast dynamics and scattering of protic ionic liquids induced by XFEL pulses

X-rays are routinely used for structural studies through scattering, and femtosecond X-ray lasers can probe ultrafast dynamics. We aim to capture the femtosecond dynamics of liquid samples using simulations and deconstruct the interplay of ionization and atomic motion within the X-ray laser pulse. This deconstruction is resolution dependent, as ionization influences the low momentum transfers through changes in scattering form factors, while atomic motion has a greater effect at high momentum transfers through loss of coherence. Our methodology uses a combination of classical molecular dynamics and plasma simulation on a protic ionic liquid to quantify the contributions to the scattering signal and how these evolve with time during the X-ray laser pulse. Our method is relevant for studies of organic liquids, biomolecules in solution or any low-Z materials at liquid densities that quickly turn into a plasma while probed with X-rays.

Serial synchrotron and XFEL crystallography for studies of metalloprotein catalysis

An estimated half of all proteins contain a metal, with these being essential for a tremendous variety of biological functions. X-ray crystallography is the major method for obtaining structures at high resolution of these metalloproteins, but there are considerable challenges to obtain intact structures due to the effects of radiation damage. Serial crystallography offers the prospect of determining low-dose synchrotron or effectively damage free XFEL structures at room temperature and enables time-resolved or dose-resolved approaches. Complementary spectroscopic data can validate redox and or ligand states within metalloprotein crystals. In this opinion, we discuss developments in the application of serial crystallographic approaches to metalloproteins and comment on future directions.

Recovery of undamaged electron-density maps in the presence of damage-induced partial coherence in single-particle imaging

Resolving the electronic structure of single biological molecules in their native state was among the primary motivations behind X-ray free-electron lasers. The ultra-short pulses they produce can outrun the atomic motion induced by radiation damage, but the electronic structure of the sample is still significantly modified from its original state. This paper explores the decoherence of the scattered signal induced by temporal evolution of the electronic structure in the sample molecule. It is shown that the undamaged electron density of a single-molecule sample can often be retrieved using only the two most occupied modes from the coherent mode decomposition of the partially coherent diffraction fluence.