Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2020.03.31.016170

Periprotein lipidomes of Saccharomyces cerevisiae provide a flexible environment for conformational changes of membrane proteins

van't Klooster, J.·Cheng, T.-Y.·Sikkema, H. R.·Jeucken, A.·Moody, B.·Poolman, B.
View original source ↗Export metadata ↓

Abstract

Yeast tolerates a low pH and high solvent concentrations. The permeability of the plasma membrane (PM) for small molecules is low and lateral diffusion of proteins is slow. These findings suggest a high degree of lipid order, which raises the question of how membrane proteins function in such an environment. The yeast PM is segregated into the Micro-Compartment-of-Can1 (MCC) and Pma1 (MCP), which have different lipid compositions. We extracted proteins from these microdomains via stoichiometric capture of lipids and proteins in styrene-maleic-acid-lipid-particles (SMALPs). We purified SMALP-lipid-protein complexes by chromatography and quantitatively analyzed periprotein lipids located within the diameter defined by one SMALP. Phospholipid and sterol concentrations are similar for MCC and MCP, but sphingolipids are enriched in MCP. Ergosterol is depleted from this periprotein lipidome, whereas phosphatidylserine is enriched relative to the bulk of the plasma membrane. Direct detection of PM lipids in the periprotein space supports the conclusion that proteins function in the presence of a locally disordered lipid state.

Source connections

Explore related subjects

biochemistryPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

van't Klooster, J., Cheng, T.-Y., Sikkema, H. R., Jeucken, A., Moody, B., Poolman, B.. 2020-04-01. Periprotein lipidomes of Saccharomyces cerevisiae provide a flexible environment for conformational changes of membrane proteins. https://doi.org/10.1101/2020.03.31.016170

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Structure of influenza D virus NS1 reveals a novel Zn-binding site and ssRNA-binding activity

Influenza D virus (IDV) is an emerging pathogen associated with bovine respiratory disease and has potential for zoonotic transmission. Although nonstructural protein 1 (NS1) is a major virulence factor in influenza A and B viruses, the structure and function of IDV NS1 remain poorly defined. Here, we determined crystal structures of the IDV NS1 N-terminal RNA-binding domain (NTD) and C-terminal effector domain (CTD). The NTD retains the conserved homodimeric six-helix fold, whereas the CTD adopts a distinct architecture containing a novel Zn2+-binding site. IDV NS1 CTD preferentially binds single-stranded RNA, and mutagenesis identified lysine and arginine residues critical for this activity. Single-residue substitutions disrupting either the Zn2+-binding site or RNA-binding interface prevented recovery of infectious recombinant IDV. These findings reveal distinct structural and functional features of IDV NS1 and establish the importance of CTD integrity for viral replication. Conservation of key CTD residues in influenza C virus NS1 suggests shared structural features that distinguish influenza C and D virus NS1 proteins from their influenza A and B counterparts.

biochemistry↗
bioRxiv2026

Recognition of the centromere-binding protein Ndc10 by Scm3HJURP directs Cse4CENP-A deposition at native centromeres

Kinetochores connect centromeres to spindle microtubules, ensuring accurate chromosome segregation. Kinetochore assembly at centromeres depends on deposition of CENP-A, a histone H3 variant. Despite considerable progress, how CENP-A is specifically assembled on native centromeres remains an open question. Centromere-specific assembly of CENP-A occurs spontaneously in a cell-free extract system from the yeast Saccharomyces cerevisiae, but with low efficiency, suggesting that one or more factors are limiting. Here, we show Scm3HJURP, a specific chaperone for the centromeric histone Cse4CENP-A, is one such limiting component. The addition of a complex of Scm3, Cse4 and histone H4 strongly stimulates Cse4 assembly in a centromeric DNA sequence- and dose-dependent manner; in addition, improvements in both Cse4 and kinetochore assembly were more prominent in mitotic versus interphase (G1) extracts. Using the complemented cell-free reconstitution system, we show that distinct Scm3 interfaces with Cse4 and with the Ndc10 subunit of the yeast centromere DNA sequence-recognizing CBF3 complex are essential for centromere-specific Cse4 assembly and cell viability. Thus, recognition of Ndc10 directs Scm3-dependent and locus-specific centromeric histone deposition.

biochemistry↗
bioRxiv2026

Heterogeneous primary nucleation determines Aβ42 fibrilstructure.

The current developments in the field of amyloid fibril structure determination has revealed multiple structures for peptides of identical sequence. This may reflect variations in sample environment or similar nucleation barriers for multiple folds. Here we investigate the influence of aggregating surface and during fibril formation from monomeric amyloid {beta} peptide (A{beta}42). The fibril structures formed in identical solutions in glass vials / bottles and PEGylated polystyrene 96-well plates display very different monomer fold within the fibrils. This is a clear indication of extremely slow homogeneous primary nucleation. Instead, heterogeneous primary nucleation at vessel walls or at the three-line interface between air, water and vessel wall dictate the outcome in each solution, where the initially formed structure is propagated through elongation and secondary nucleation. The results further imply that the conversion towards the thermodynamically stable fibril structure one is slow for A{beta}42.

biochemistry↗