Reactive molecular dynamics simulations of lysozyme desorption under Ar cluster impact

Bertolini, Samuel; Delcorte, Arnaud

doi:10.1016/j.apsusc.2023.157487

Cited by 7 publications

(26 citation statements)

References 76 publications

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“…In a recent investigation, our group conducted an experiment to explore the desorption and transfer of Lyz using argon GCIB . To gain a deeper understanding of how the cluster parameters (size and E / n ) influence the process, we modeled the bombardment of a gold substrate decorated by one or more Lyz using Ar clusters . Our simulations were consistent with experimental findings, revealing the desorption of intact Lyz.…”

Section: Introductionsupporting

confidence: 57%

“…53 Our previous simulations showed the desorption of agglomerates of Lyz molecules by a similar soft emission process, when bombarding a bilayer made of pure Lyz. 37 In both cases, the organic layer plays a significant role by mitigating fragmentation and denaturation processes while facilitating the desorption of large proteins and agglomerates. Experimentally, protein denaturation could be directly probed using ion mobility 54 but unfortunately this option is not available on commercial SIMS instruments.…”

Section: Discussionmentioning

confidence: 99%

“…Finally, the optimized ReaxFF parameters were employed to carry out the bombardment simulations described in this study (Figure 1, Results). As was justified in detail previously, 37 we made the choice not to modify the low interdistance region of the force field using a ZBL repulsive potential function. The main reason is that the energy of the projectile atoms in these simulations remains very limited, and we could demonstrate that implementing such a repulsive wall had a negligible effect on the final results.…”

Section: Methodsmentioning

confidence: 99%

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Unraveling the Molecular Dynamics of Glucose Oxidase Desorption Induced by Argon Cluster Collision

Bertolini,

Delcorte

2023

J. Phys. Chem. B

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The bombardment of a protein multilayer target by an energetic argon cluster ion beam enables protein transfer onto a collector in the vacuum while preserving their bioactivity (iBEAM method). In parallel to this new soft-landing variant, protein transfer in the gas phase is a prerequisite for their characterization by mass spectrometry. The successful transfer of bioactive lysozymes (14 kDa) by cluster-induced soft landing and its mechanistic explanation by molecular dynamics (MD) simulations have sparked an important inquiry: Can heavier biomolecules be desorbed while maintaining their tridimensional structure and hence their bioactivity? To address this question, we employed MD simulations using a reactive force field (ReaxFF). Specifically, the Ar cluster-induced desorption of glucose oxidase from either a gold substrate or a lysozyme underlayer was modeled using the LAMMPS code. First, the force field parameters were trained by computing the dissociation energetics of a series of organic molecules with ReaxFF and DFT, in order to realistically describe N–S and O–S interactions in the bombarded glucose oxidase molecule. Second, bombardment simulations investigated the effects of cluster size (ranging from 1000 to 10000 Ar atoms) and kinetic energy (1.5 and 3.0 eV/atom) on the structural features and energetics of the desorbing glucose oxidase. Our results show that large argon clusters (≥7000) are needed to desorb glucose oxidase from a gold surface, yet protein fragmentation and/or pronounced denaturation occur. However, the transfer of structurally preserved glucose oxidase in the gas phase is predicted by the simulations when an organic layer is used as a substrate.

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Section: Introductionsupporting

confidence: 57%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Unraveling the Molecular Dynamics of Glucose Oxidase Desorption Induced by Argon Cluster Collision

Bertolini,

Delcorte

2023

J. Phys. Chem. B

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“…There is a slight increase when the PC is transferred on Si and the increasing factor rises to 79-fold when the lipid is transferred with Ar 5000 + to 34-fold when transferred with Ar 3000 + . The more intense signal obtained with Ar 5000 + can be explained by the fact that the fragmentation induced during the sputtering is a function of the energy per atom ratio ( E / n ) in the cluster projectiles. − Therefore, a higher abundance of intact PC ions compared to the fragments can be expected on the collector.…”

Section: Resultsmentioning

confidence: 99%

“…Interestingly, large argon clusters are able to desorb and transfer larger intact molecules than those that can be ionized and detected by ToF-SIMS, such as lysozyme. , Therefore, the ability of MALDI to ionize larger molecules than SIMS could be very beneficial to uncover a larger spectrum of transferred biomolecules than those visible in SIMS. The other advantage is that, per the size of the interaction volume, MALDI can ablate the entire thickness of the matrix layer and therefore readily take advantage of all the molecular signals available on the collector and not just the surface like static SIMS analyses (see the diffusion profiles of Figure ).…”

Section: Conclusion and Future Prospectsmentioning

confidence: 99%

Enhancing Ion Signals and Improving Matrix Selection in Time-of-Flight Secondary Ion Mass Spectrometry with Microvolume Expansion Using Large Argon Clusters

Tomasetti,

Lauzin,

Delcorte

2023

Anal. Chem.

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The molecular environment has an important impact on the ionization mechanism in time-of-flight secondary ion mass spectrometry (ToF-SIMS). In complex samples, desorption/ionization, and thus the detection of a molecular signal, can be hampered by molecular entanglement, ionizationsuppressive neighbors, or even an unfavorable sample substrate. Here, a method called microvolume expansion is developed to overcome these negative effects. Large argon clusters are able to transfer biomolecules from a target to a collector in vacuum. In this study, argon gas cluster ion beams (Ar n + -GCIB with n centered around 3000 or 5000) are used to expand a microvolume from the sample to a collector, which is a material ideally enhancing the ionization yield. The collector is then analyzed using a liquid metal ion gun. The signal amplification factor corresponding to the expansion of phosphatidylcholine (PC) lipid on collectors partially covered with acidic matrices was evaluated as an initial proof of concept. In one experiment, the PC expansion on a pattern of four drop-casted matrixassisted laser desorption/ionization matrices led to the selection of α-cyano-4-hydroxycinnamic (CHCA) as the optimal candidate for cationic PC detection. The ion signal is increased by at least three orders of magnitude when PC was expanded using 10 keV Ar 3000+ and Ar 5000 + on a sublimated layer of CHCA. Finally, the expansion of the gray matter of a mouse on different materials (Si, Au-coated Si, CHCA, and polyethylene) was achieved with varying degrees of success, demonstrating the potential of the method to further analyze complex and fragile biological assemblies.

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Modification of a ReaxFF potential at short range for energetic materials

Li,

Wang,

et al. 2024

Defence Technology

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Reactive molecular dynamics simulations of lysozyme desorption under Ar cluster impact

Cited by 7 publications

References 76 publications

Unraveling the Molecular Dynamics of Glucose Oxidase Desorption Induced by Argon Cluster Collision

Unraveling the Molecular Dynamics of Glucose Oxidase Desorption Induced by Argon Cluster Collision

Enhancing Ion Signals and Improving Matrix Selection in Time-of-Flight Secondary Ion Mass Spectrometry with Microvolume Expansion Using Large Argon Clusters

Modification of a ReaxFF potential at short range for energetic materials

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