@article{MandlSinelnikovaOestlinetal.,
  author    = {Mandl, Thomas and Sinelnikova, Anna and {\"O}stlin, Christofer and Gr{\aa}n{\"a}s, Oscar and Brodmerkel, Maxim N. and Markl, Erik G. and Caleman, Carl},
  title     = {Reproducibility in the unfolding process of protein induced by an external electric field},
  series = {Chemical Science},
  journal   = {Chemical Science},
  abstract  = {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.},
  subject      = {Reproducibility protein},
  language  = {en}
}
@article{SinelnikovaMandlAgeliietal.,
  author    = {Sinelnikova, Anna and Mandl, Thomas and Agelii, Harald and Gr{\aa}n{\"a}s, Oscar and Marklund, Erik G. and Caleman, Carl and De Santis, Emiliano},
  title     = {Protein orientation in time-dependent electric fields: orientation before destruction},
  series = {Biophysical Journal},
  journal   = {Biophysical Journal},
  number    = {Volume 120, Issue 17},
  pages     = {3709 -- 3717},
  subject      = {Protein},
  language  = {en}
}
@article{KierspelKadekBarranetal.,
  author    = {Kierspel, Thomas and Kadek, Alan and Barran, Perdita and Bellina, Bruno and Bijedic, Adi and Brodmerkel, Maxim N. and Commandeur, Jan and Caleman, Carl and Damjanovic, Tomislav and Dawod, Ibrahim and De Santis, Emiliano and Lekkas, Alexandros and Lorenzen, Kristina and L{\´o}pez Morillo, Luis and Mandl, Thomas and Marklund, Erik G. and Papanastasiou, Dimitris and Ramakers, Lennart A. I. and Schweikhard, Lutz and Simke, Florian and Sinelnikova, Anna and Smyrnakis, Athanasios and Timneanu, Nicusor and Uetrecht, Charlotte},
  title     = {Coherent diffractive imaging of proteins and viral capsids: simulating MS SPIDOC},
  series = {Analytical and Bioanalytical Chemistry},
  volume    = {2023},
  journal   = {Analytical and Bioanalytical Chemistry},
  number    = {415},
  doi       = {https://doi.org/10.1007/s00216-023-04658-y},
  pages     = {4209 -- 4220},
  abstract  = {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.},
  subject      = {SPI},
  language  = {en}
}