Biology subjects

Eriksson, L.

Publications and source records attributed to Eriksson, L..

5 recordsLinked to original sources

bioRxiv2026

Membrane proteins retain native architecture through native ESI and soft-landing

Native MS offers a clear picture of membrane protein stoichiometry and interactions, but it lacks direct structural insights at high resolution. Here, we examine the extent to which solution-phase structure and architecture can be retained after native, soft-landing electrospray ion beam deposition (ESIBD) by interrogating several membrane-protein complexes of diverse folds and oligomeric states by cryoEM. The overall protein architectures with secondary structure motifs can be observed after gas-phase transfer, soft landing, and embedding in amorphous ice. Notably, we determined the structure of the ammonium transporter AmtB at sub-3 [A] resolution. It is nearly identical to the structure of the plunge-frozen control and even shows an extended C-terminal segment of AmtB, a dynamic region absent in the solution-phase structure. Our analysis shows that detergent adducts preserve membrane protein structure in vacuum by minimising destabilization of solvent-exposed regions and stabilization through additional polar contacts in vacuo. Molecular dynamics (MD) simulations support these results, suggesting that a monolayer shell of surfactant adducts avoids destabilization driven by unshielded polar residues and disruption of hydrogen bond networks. Overall, our findings provide a structural framework for integrating native MS with cryo-EM showing that gas-phase transfer and surfactant stabilisation preserves key architectural features and high-resolution structure of membrane proteins.

biophysics↗

bioRxiv2025

Sensitive detection of copy number alterations in low-pass liquid biopsy sequencing data

Liquid biopsies, coupled with analysis of copy number alterations (CNAs), have emerged as a promising tool for non-invasive monitoring of cancer progression and tumor composition. However, methods utilizing CNA data from liquid biopsies are limited by the low signal in the samples, caused by a low percentage of cancer DNA in the blood, and inherent noise introduced in the sequencing. To address this challenge, we developed BayesCNA, a method designed to improve signal extraction from low-pass liquid biopsy sequencing data, by utilizing a Bayesian changepoint detection algorithm. We use information of the posterior changepoint probabilities to identify likely changepoints, where a changepoint indicates a shift in the copy number state. The signal is then reconstructed using the identified partition. We show the effectiveness of the method on synthetically generated datasets and compare the method with state-of-the-art bioinformatics tools under noisy conditions. Our results show that this novel approach increases sensitivity in detecting CNAs, particularly in low-quality cases.

bioinformatics↗

bioRxiv2025

Cryo-EM Sample Preparation with Soft-Landing and Laser Flash Melting

The preparation of cryo-EM samples by soft-landing mass spectrometry promises to significantly simplify sample optimization, which has remained an important bottleneck in single-particle cryo-electron microscopy (cryo-EM). However, only compacted configurations are observed after soft-landing since the proteins are dehydrated in the process. Here, we demonstrate that proteins can be returned to their native state by depositing a layer of amorphous ice and briefly flash melting the sample to rehydrate the soft-landed proteins. Melting with a 30 {micro}s laser pulse creates a broad ensemble of partially rehydrated conformations. However, a subset of particles recovers their native configuration. This allows us to propose strategies to fully rehydrate the entire ensemble and brings routine sample preparation by soft-landing mass spectrometry within reach. Finally, the experiments also expand the toolbox of microsecond time-resolved cryo-EM for initiating a broader range of protein dynamics.

biophysics↗

bioRxiv2023

An experimental target-based platform in yeast for screening Plasmodium vivax deoxyhypusine synthase inhibitors

The enzyme deoxyhypusine synthase (DHS) catalyzes the first step in the post-translational modification of the eukaryotic translation factor 5A (eIF5A). This is the only protein known to contain the amino acid hypusine, which results from this modification. Both eIF5A and DHS are essential for cell viability in eukaryotes, and inhibiting DHS can be a promising strategy for the development of new therapeutic alternatives. The human and parasitic orthologous proteins are different enough to render selective targeting against infectious diseases; however, no DHS inhibitor selective for the parasite ortholog has previously been reported. Here, we established a yeast surrogate genetics platform to identify inhibitors of DHS from Plasmodium vivax, one of the major causative agents of malaria. We constructed genetically modified Saccharomyces cerevisiae strains expressing DHS genes from Homo sapiens (HsDHS) or P. vivax (PvDHS) in place of the endogenous DHS gene from S. cerevisiae. This new strain background was [~]60-fold more sensitive to an inhibitor of human DHS than the one previously used. Initially, a virtual screen using datasets from the ChEMBL-NTD database was performed. Candidate ligands were tested in growth assays using the newly generated yeast strains expressing heterologous DHS genes. Among these, two showed promise by preferentially reducing the growth of the PvDHS-expressing strain. Further, in a robotized assay, we screened 400 compounds from the Pathogen Box library using the same S. cerevisiae strains, and one compound preferentially reduced the growth of the PvDHS-expressing yeast strain. Western blot revealed that these compounds significantly reduced eIF5A hypusination in yeast. Our study demonstrates that this yeast-based platform is suitable for identifying and verifying candidate small molecule DHS inhibitors, selective for the parasite over the human ortholog.

synthetic biology↗

bioRxiv2023

Cryo-EM of soft-landed β-galactosidase: Gas-phase and native structures are remarkably similar

Native mass spectrometry (native MS) is a powerful technique that provides information on stoichiometry, interactions, homogeneity and shape of protein complexes. However, the extent of deviation between protein structures in the mass spectrometer and in solution remains a matter of debate. Here, we uncover the gas-phase structure of {beta}-galactosidase using single particle electron cryomicroscopy (cryo-EM) down to 2.6 [A] resolution, enabled by soft-landing of mass-selected protein complexes onto cold TEM grids and in-situ ice coating. We find that large parts of the secondary and tertiary structure are retained from solution, with dehydration-driven subunit reorientation leading to consistent compaction in the gas phase. Our work enables visualizing the structure of gas-phase protein com-plexes from numerous experimental scenarios at side-chain resolution and demonstrates the possibility of more controlled cryo-EM sample preparation. One Sentence SummaryElectrospray ion-beam deposition on cold grids and in-vacuum ice growth enable cryo-EM of mass-selected proteins at 2.6 [A].

biochemistry↗