Julian Bender
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View article: The yeast peroxisomal proteome at absolute quantitative scale
The yeast peroxisomal proteome at absolute quantitative scale Open
Peroxisomes are dynamic organelles vital for lipid metabolism and redox homeostasis. In Saccharomyces cerevisiae , the expression of peroxisomal proteins is tightly regulated in response to metabolic conditions. Here, we provide the first …
View article: PEX39 facilitates the peroxisomal import of PTS2-containing proteins
PEX39 facilitates the peroxisomal import of PTS2-containing proteins Open
View article: Microtubule anchoring and coupling of CD20 to the RhoA/Rock1 pathway
Microtubule anchoring and coupling of CD20 to the RhoA/Rock1 pathway Open
CD20 is a B cell-specific four-helix transmembrane protein and a prominent target of therapeutic anti-CD20 antibodies. CD20 is localized within a membrane nanocluster harboring the IgD class B cell antigen receptor (IgD-BCR) where it funct…
View article: Silencing mitochondrial gene expression in living cells
Silencing mitochondrial gene expression in living cells Open
Mitochondria fulfill central functions in metabolism and energy supply. They express their own genome, which encodes key subunits of the oxidative phosphorylation system. However, the central mechanisms underlying mitochondrial gene expres…
View article: Ca2+-dependent lipid preferences shape synaptotagmin-1 C2A and C2B dynamics: Insights from experiments and simulations
Ca2+-dependent lipid preferences shape synaptotagmin-1 C2A and C2B dynamics: Insights from experiments and simulations Open
Signal transmission between neurons requires exocytosis of neurotransmitters from the lumen of synaptic vesicles into the synaptic cleft. Following an influx of Ca2+, this process is facilitated by the Ca2+ sensor syn…
View article: Aqueous Ionic Liquid Mixtures as Minimal Models of Lipid Bilayer Membranes
Aqueous Ionic Liquid Mixtures as Minimal Models of Lipid Bilayer Membranes Open
We introduce aqueous ionic liquid (IL) mixtures, specifically mixtures of 1-butyl-3-imidazoliumtetrafluoroborate (BMImBF4), with water as a minimal model of lipid bilayer membranes. Imidazolium-based ILs are known to form cluste…
View article: PEX39 facilitates the peroxisomal import of PTS2 proteins
PEX39 facilitates the peroxisomal import of PTS2 proteins Open
SUMMARY Peroxisomes are metabolic organelles essential for human health. Defects in peroxisomal biogenesis proteins (peroxins/PEXs) cause devastating disease. PEX7 binds newly synthesized proteins containing a type 2 peroxisomal targeting …
View article: Ageing-dependent thiol oxidation reveals early oxidation of proteins with core proteostasis functions
Ageing-dependent thiol oxidation reveals early oxidation of proteins with core proteostasis functions Open
Oxidative post-translational modifications of protein thiols are well recognized as a readily occurring alteration of proteins, which can modify their function and thus control cellular processes. The development of techniques enabling the…
View article: Autoprot: Processing, Analysis and Visualization of Proteomics Data in Python
Autoprot: Processing, Analysis and Visualization of Proteomics Data in Python Open
Motivation The increasing numbers of complex quantitative mass spectrometry-based proteomics data sets demand a standardised and reliable analysis pipeline. For this purpose, Python-based analysis, particularly through Jupyter notebooks, s…
View article: Molecular dynamics trajectories for "Biophysical characterisation of lipid and membrane binding of Calcium-sensor Synaptotagmin-1"
Molecular dynamics trajectories for "Biophysical characterisation of lipid and membrane binding of Calcium-sensor Synaptotagmin-1" Open
Syt-1 MD simulation trajectories Trajectories for the simulation of Synpatotagmin-1 C2 domains C2A and C2B interacting with models of the synaptic vesicle (SV) and plasma membranes. The biological background and motivation are described in…
View article: Molecular dynamics trajectories for "Biophysical characterisation of lipid and membrane binding of Calcium-sensor Synaptotagmin-1"
Molecular dynamics trajectories for "Biophysical characterisation of lipid and membrane binding of Calcium-sensor Synaptotagmin-1" Open
Syt-1 MD simulation trajectories Trajectories for the simulation of Synpatotagmin-1 C2 domains C2A and C2B interacting with models of the synaptic vesicle (SV) and plasma membranes. The biological background and motivation are described in…
View article: Analysis of ageing-dependent thiol oxidation reveals early oxidation of proteins involved in core proteostasis functions
Analysis of ageing-dependent thiol oxidation reveals early oxidation of proteins involved in core proteostasis functions Open
Oxidants have a profound impact on biological systems in physiology and under pathological conditions. Oxidative post-translational modifications of protein thiols are well-recognized as a readily occurring alteration of proteins. Changes …
View article: Lighting up Nobel Prize-winning studies with protein intrinsic disorder
Lighting up Nobel Prize-winning studies with protein intrinsic disorder Open
View article: p166 links membrane and intramitochondrial modules of the trypanosomal tripartite attachment complex
p166 links membrane and intramitochondrial modules of the trypanosomal tripartite attachment complex Open
The protist parasite Trypanosoma brucei has a single mitochondrion with a single unit genome termed kinetoplast DNA (kDNA). Faithfull segregation of replicated kDNA is ensured by a complicated structure termed tripartite attachment complex…
View article: Effects of non-ionic and zwitterionic detergents on soluble proteins during native mass spectrometry experiments
Effects of non-ionic and zwitterionic detergents on soluble proteins during native mass spectrometry experiments Open
Detergents are commonly employed for solubilization and stabilization of integral membrane proteins. Their effects on the charge states of detergent-solubilized membrane proteins in native mass spectrometry measurements have previously bee…
View article: Towards the molecular architecture of the peroxisomal receptor docking complex
Towards the molecular architecture of the peroxisomal receptor docking complex Open
Significance Peroxisomal matrix enzymes are synthesized in the cytosol and carry targeting signals. These are recognized and bound by an import receptor in the cytosol. The cargo-loaded receptor further binds to the “docking” complex at th…
View article: Alternatively spliced isoforms of AUF1 regulate a miRNA–mRNA interaction differentially through their YGG motif
Alternatively spliced isoforms of AUF1 regulate a miRNA–mRNA interaction differentially through their YGG motif Open
Proper base-pairing of a miRNA with its target mRNA is a key step in miRNA-mediated mRNA repression. RNA remodelling by RNA-binding proteins (RBPs) can improve access of miRNAs to their target mRNAs. The largest isoform p45 of the RBP AUF1…
View article: Evaluation of NHS-Acetate and DEPC labelling for determination of solvent accessible amino acid residues in protein complexes
Evaluation of NHS-Acetate and DEPC labelling for determination of solvent accessible amino acid residues in protein complexes Open
The activity of most proteins and protein complexes relies on the formation of defined three-dimensional structures. The analysis of these arrangements is therefore key for understanding their function and regulation in the cell. Besides t…
View article: Towards the molecular architecture of the peroxisomal receptor docking complex
Towards the molecular architecture of the peroxisomal receptor docking complex Open
Import of yeast peroxisomal matrix proteins is initiated by cytosolic receptors, which specifically recognize and bind the respective cargo proteins. At the peroxisomal membrane, the cargo-loaded receptor interacts with the docking protein…
View article: The CroCo cross-link converter: a user-centred tool to convert results from cross-linking mass spectrometry experiments
The CroCo cross-link converter: a user-centred tool to convert results from cross-linking mass spectrometry experiments Open
Motivation A variety of search engines exists for the identification of peptide spectrum matches after cross-linking mass spectrometry experiments. The resulting diversity in output formats complicates data validation and visualization as …
View article: Mass spectrometry of membrane protein complexes
Mass spectrometry of membrane protein complexes Open
Membrane proteins are key players in the cell. Due to their hydrophobic nature they require solubilising agents such as detergents or membrane mimetics during purification and, consequently, are challenging targets in structural biology. I…