| 1. |
- Brodmerkel, Maxim, et al.
(författare)
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Molecular dynamics simulations reveal barrel opening during the unfolding of the outer membrane protein FhaC
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Many membrane proteins carry out gatekeeping and transport functions across the membrane, which makes them tremendously important for the control of what passes into or out from the cell. Their underlying dynamics can be very challenging to capture for structural biology techniques, for which structural heterogeneity often is problematic. Native ion mobility mass spectrometry (IM-MS) is capable of maintaining non-covalent interactions between biomolecules in vacuo, allowing for intact protein complexes from heterogeneous mixtures to be analysed with respect to their masses and structures, making it a powerful tool for structural biology. Recent collision induced unfolding (CIU) experiments, where IM-MS is used to track the unfolding of proteins after activation, were used to investigate the dynamics of the membrane protein FhaC from Bordetella pertussis. FhaC is a β-barrel transmembrane protein found in the outer membrane, where it secretes virulence factors to the outside of the bacterium, requiring notable changes to its structure. CIU cannot on its own provide detailed information about the structural changes along the unfolding pathway. Here, we use MD simulations to mimic the CIU experiments to see if the unfolding proceeds as expected, with cytoplasm-facing domains leading the unfolding, or if other parts of the structure breaks first. By separating our simulation data according to experimental CIU data from literature, we match the structures in the former to the unfolding states identified in the latter, and find that FhaC instead unfolds from a “seam” in the β-barrel. In a wider context, our investigation provides insights into the structural stability and unfolding dynamics of β-barrel membrane proteins and how they can be studied using a combination of CIU and MD.
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| 2. |
- Brodmerkel, Maxim N., et al.
(författare)
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Collision induced unfolding and molecular dynamics simulations of norovirus capsid dimers reveal strain-specific stability profiles
- 2024
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084.
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Tidskriftsartikel (refereegranskat)abstract
- Collision induced unfolding is method used with ion mobility mass spectrometry to examine protein structures and their stability. Such experiments yield information about higher order protein structures, yet are unable to provide details about the underlying processes. That information can however be provided using molecular dynamics simulations. Here, we investigate the collision induced unfolding of norovirus capsid dimers from the Norwalk and Kawasaki strains by employing molecular dynamics simulations over a range of temperatures, representing different levels of activation. The dimers have highly similar structures, but the activation reveals differences in the dynamics that arises in response to the activation.
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| 3. |
- Brodmerkel, Maxim N., et al.
(författare)
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Rehydration Post-orientation : Investigating Field-Induced Structural Changes via Computational Rehydration
- 2023
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Ingår i: The Protein Journal. - : Springer Nature. - 1572-3887 .- 1875-8355. ; 42:3, s. 205-218
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Tidskriftsartikel (refereegranskat)abstract
- Proteins can be oriented in the gas phase using strong electric fields, which brings advantages for structure determination using X-ray free electron lasers. Both the vacuum conditions and the electric-field exposure risk damaging the protein structures. Here, we employ molecular dynamics simulations to rehydrate and relax vacuum and electric-field exposed proteins in aqueous solution, which simulates a refinement of structure models derived from oriented gas-phase proteins. We find that the impact of the strong electric fields on the protein structures is of minor importance after rehydration, compared to that of vacuum exposure and ionization in electrospraying. The structures did not fully relax back to their native structure in solution on the simulated timescales of 200 ns, but they recover several features, including native-like intra-protein contacts, which suggests that the structures remain in a state from which the fully native structure is accessible. Our fndings imply that the electric fields used in native mass spectrometry are well below a destructive level, and suggest that structures inferred from X-ray difraction from gas-phase proteins are relevant for solution and in vivo conditions, at least after in silico rehydration.
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| 4. |
- Brodmerkel, Maxim N., et al.
(författare)
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Stability and conformational memory of electrosprayed and rehydrated bacteriophage MS2 virus coat proteins
- 2022
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Ingår i: Current Research in Structural Biology. - : Elsevier. - 2665-928X. ; 4, s. 338-348
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Tidskriftsartikel (refereegranskat)abstract
- Proteins are innately dynamic, which is important for their functions, but which also poses significant challenges when studying their structures. Gas-phase techniques can utilise separation and a range of sample manipulations to transcend some of the limitations of conventional techniques for structural biology in crystalline or solution phase, and isolate different states for separate interrogation. However, the transfer from solution to the gas phase risks affecting the structures, and it is unclear to what extent different conformations remain distinct in the gas phase, and if resolution in silico can recover the native conformations and their differences. Here, we use extensive molecular dynamics simulations to study the two distinct conformations of dimeric capsid protein of the MS2 bacteriophage. The protein undergoes notable restructuring of its peripheral parts in the gas phase, but subsequent simulation in solvent largely recovers the native structure. Our results suggest that despite some structural loss due to the experimental conditions, gas-phase structural biology techniques provide meaningful data that inform not only about the structures but also conformational dynamics of proteins.
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| 5. |
- Dawod, Ibrahim, et al.
(författare)
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MolDStruct : modelling the dynamics and structure of matter exposed to ultrafast X-ray lasers with hybrid collisional-radiative/molecular dynamics
- 2024
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Ingår i: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 160:18
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Tidskriftsartikel (refereegranskat)abstract
- We describe a method to compute photon–matter interaction and atomic dynamics with x-ray lasers using a hybrid code based on classical molecular dynamics and collisional-radiative calculations. The forces between the atoms are dynamically determined based on changes to their electronic occupations and the formation of a free electron cloud created from the irradiation of photons in the x-ray spectrum. The rapid transition from neutral solid matter to dense plasma phase allows the use of screened potentials, reducing the number of non-bonded interactions. In combination with parallelization through domain decomposition, the hybrid code handles large-scale molecular dynamics and ionization. This method is applicable for large enough samples (solids, liquids, proteins, viruses, atomic clusters, and crystals) that, when exposed to an x-ray laser pulse, turn into a plasma in the first few femtoseconds of the interaction. We present four examples demonstrating the applicability of the method. We investigate the non-thermal heating and scattering of bulk water and damage-induced dynamics of a protein crystal using an x-ray pump–probe scheme. In both cases, we compare to the experimental data. For single particle imaging, we simulate the ultrafast dynamics of a methane cluster exposed to a femtosecond x-ray laser. In the context of coherent diffractive imaging, we study the fragmentation as given by an x-ray pump–probe setup to understand the evolution of radiation damage in the time range of hundreds of femtoseconds.
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| 6. |
- De Santis, Emiliano, PhD, et al.
(författare)
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Is styrene competitive for dopamine receptor binding?
- 2022
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Ingår i: Biomolecular Concepts. - : Walter de Gruyter. - 1868-503X. ; 13:1, s. 200-206
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Tidskriftsartikel (refereegranskat)abstract
- The potential role of styrene oxide in altering the dopaminergic pathway in the ear is investigated by means of molecular docking and molecular dynamics simulations. We estimate the binding affinity of both styrene oxide and dopamine to the dopaminergic receptor DrD2 by computing the free-energy difference, ∆G, between the configuration where the ligand is bound to the receptor and the situation in which it is “infinitely” far away from it. The results show that the styrene oxide has a somewhat lower affinity for binding with respect to dopamine, which, however, may not be enough to prevent exogenous high concentration styrene oxide to compete with endogenous dopamine for DrD2 binding.
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| 7. |
- Galchenkova, Marina, et al.
(författare)
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Radiation damage in a hemoglobin crystal studied with an X-ray free-electron laser
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Radiation damage is a topic since the dawn of X-ray crystallography, and has gained new importance in the era of X-ray free-electron lasers (XFELs), due to their unprecedented brilliance and pulse duration. One of the driving questions has been how short the XFEL pulse has to be for the structural information to be ”damage free”. Here we compare data from Serial Femtosecond Crystallography (SFX) experiments conducted with a 3 fs and a 10 fs X-ray pulse. We conclude that even if the estimated displacement of atoms in the sample is an order of magnitude larger in the case of the 10 fs experiment, the displacement is still too small to affect the experimental data at a resolution relevant for structural determination.
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| 8. |
- Kierspel, Thomas, et al.
(författare)
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Coherent diffractive imaging of proteins and viral capsids : simulating MS SPIDOC
- 2023
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Ingår i: Analytical and Bioanalytical Chemistry. - : Springer Nature. - 1618-2642 .- 1618-2650. ; 415:18 SI, s. 4209-4220
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Tidskriftsartikel (refereegranskat)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.
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| 9. |
- Lindblad, Rebecka, Dr, 1984-, et al.
(författare)
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Experimental and theoretical near-edge x-ray-absorption fine-structure studies of NO
- 2022
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Ingår i: Physical Review A: covering atomic, molecular, and optical physics and quantum information. - : American Physical Society. - 2469-9926 .- 2469-9934. ; 106:4
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Tidskriftsartikel (refereegranskat)abstract
- Experimental near-edge x-ray-absorption fine-structure (NEXAFS) spectra of the nitrosonium NO+ ion are presented and theoretically analyzed. While neutral NO has an open shell, the cation is a closed-shell species, which for NEXAFS leads to the simplicity of a closed-shell spectrum. Compared to neutral NO, the electrons in the cation experience a stronger Coulomb potential, which introduces a shift of the ionization potential towards higher energies, a depletion of intensity in a large interval above the pi* resonance, and a shift of the sigma* resonance from the continuum to below the ionization threshold. NEXAFS features at the nitrogen and oxygen K edges of NO+ are compared, as well as NEXAFS features at the nitrogen edges of the isoelectronic closed-shell species NO+, N2, and N2H+.
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| 10. |
- Pihlava, Lassi, et al.
(författare)
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Shell-dependent photofragmentation dynamics of a heavy-atom-containing bifunctional nitroimidazole radiosensitizer
- 2024
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 26:11, s. 8879-8890
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Tidskriftsartikel (refereegranskat)abstract
- Radiation therapy uses ionizing radiation to break chemical bonds in cancer cells, thereby causing DNA damage and leading to cell death. The therapeutic effectiveness can be further increased by making the tumor cells more sensitive to radiation. Here, we investigate the role of the initial halogen atom core hole on the photofragmentation dynamics of 2-bromo-5-iodo-4-nitroimidazole, a potential bifunctional radiosensitizer. Bromine and iodine atoms were included in the molecule to increase the photoionization cross-section of the radiosensitizer at higher photon energies. The fragmentation dynamics of the molecule was studied experimentally in the gas phase using photoelectron-photoion-photoion coincidence spectroscopy and computationally using Born-Oppenheimer molecular dynamics. We observed significant changes between shallow core (I 4d, Br 3d) and deep core (I 3d) ionization in fragment formation and their kinetic energies. Despite the fact, that the ions ejected after deep core ionization have higher kinetic energies, we show that in a cellular environment, the ion spread is not much larger, keeping the damage well-localized. A study on photodissociation dynamics of 2-bromo-5-iodo-nitroimidazole - a model radiosensitizer - using coincidence spectroscopy and computational methods.
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