TY - JOUR A1 - Mandl, Thomas A1 - Östlin, Christofer A1 - Dawod, Ibrahim E. A1 - Brodmerkel, Maxim N. A1 - Marklund, Erik G. A1 - Martin, Andrew V. A1 - Timneanu, Nicusor A1 - Caleman, Carl T1 - Structural Heterogeneity in Single Particle Imaging Using X-ray Lasers JF - The Journal of Physical Chemistry Letters N2 - One of the challenges facing single particle imaging with ultrafast X-ray pulses is the structural heterogeneity of the sample to be imaged. For the method to succeed with weakly scattering samples, the diffracted images from a large number of individual proteins need to be averaged. The more the individual proteins differ in structure, the lower the achievable resolution in the final reconstructed image. We use molecular dynamics to simulate two globular proteins in vacuum, fully desolvated as well as with two different solvation layers, at various temperatures. We calculate the diffraction patterns based on the simulations and evaluate the noise in the averaged patterns arising from the structural differences and the surrounding water. Our simulations show that the presence of a minimal water coverage with an average 3 Å thickness will stabilize the protein, reducing the noise associated with structural heterogeneity, whereas additional water will generate more background noise. KW - Protein structure KW - Physical and chemical processes KW - Peptides and proteins KW - Physical and chemical properties KW - Layers Y1 - 2020 VL - 2020 IS - Volume 11, Issue 15 SP - 6077 EP - 6083 ER - TY - JOUR A1 - Mandl, Thomas A1 - Sinelnikova, Anna A1 - Östlin, Christofer A1 - Grånäs, Oscar A1 - Brodmerkel, Maxim N. A1 - Markl, Erik G. A1 - Caleman, Carl T1 - Reproducibility in the unfolding process of protein induced by an external electric field JF - Chemical Science N2 - The dynamics of proteins are crucial for their function. However, commonly used techniques for studying protein structures are limited in monitoring time-resolved dynamics at high resolution. Combining electric fields with existing techniques to study gas-phase proteins, such as single particle imaging using free-electron lasers and gas-phase small angle X-ray scattering, has the potential to open up a new era in time-resolved studies of gas-phase protein dynamics. Using molecular dynamics simulations, we identify well-defined unfolding pathways of a protein, induced by experimentally achievable external electric fields. Our simulations show that strong electric fields in conjunction with short-pulsed X-ray sources such as free-electron lasers can be a new path for imaging dynamics of gas-phase proteins at high spatial and temporal resolution. KW - Reproducibility protein Y1 - ER - TY - JOUR A1 - Kierspel, Thomas A1 - Kadek, Alan A1 - Barran, Perdita A1 - Bellina, Bruno A1 - Bijedic, Adi A1 - Brodmerkel, Maxim N. A1 - Commandeur, Jan A1 - Caleman, Carl A1 - Damjanovic, Tomislav A1 - Dawod, Ibrahim A1 - De Santis, Emiliano A1 - Lekkas, Alexandros A1 - Lorenzen, Kristina A1 - López Morillo, Luis A1 - Mandl, Thomas A1 - Marklund, Erik G. A1 - Papanastasiou, Dimitris A1 - Ramakers, Lennart A. I. A1 - Schweikhard, Lutz A1 - Simke, Florian A1 - Sinelnikova, Anna A1 - Smyrnakis, Athanasios A1 - Timneanu, Nicusor A1 - Uetrecht, Charlotte T1 - Coherent diffractive imaging of proteins and viral capsids: simulating MS SPIDOC JF - Analytical and Bioanalytical Chemistry N2 - MS SPIDOC is a novel sample delivery system designed for single (isolated) particle imaging at X-ray Free-Electron Lasers that is adaptable towards most large-scale facility beamlines. Biological samples can range from small proteins to MDa particles. Following nano-electrospray ionization, ionic samples can be m/z-filtered and structurally separated before being oriented at the interaction zone. Here, we present the simulation package developed alongside this prototype. The first part describes how the front-to-end ion trajectory simulations have been conducted. Highlighted is a quadrant lens; a simple but efficient device that steers the ion beam within the vicinity of the strong DC orientation field in the interaction zone to ensure spatial overlap with the X-rays. The second part focuses on protein orientation and discusses its potential with respect to diffractive imaging methods. Last, coherent diffractive imaging of prototypical T = 1 and T = 3 norovirus capsids is shown. We use realistic experimental parameters from the SPB/SFX instrument at the European XFEL to demonstrate that low- resolution diffractive imaging data (q < 0.3 nm −1 ) can be collected with only a few X-ray pulses. Such low-resolution data are sufficient to distinguish between both symmetries of the capsids, allowing to probe low abundant species in a beam if MS SPIDOC is used as sample delivery. KW - SPI KW - X-ray KW - Native MS KW - Protein complex structure KW - Simulation Y1 - U6 - http://dx.doi.org/https://doi.org/10.1007/s00216-023-04658-y VL - 2023 IS - 415 SP - 4209 EP - 4220 ER -