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Nuclear Pore Complex Structure and Dynamics Revealed by Cryoelectron Tomography
The central plug/transporter of nuclear pore complexes was variable in volume and could occupy different positions along the nucleocytoplasmic axis, which supports the notion that it essentially represents cargo in transit. Expand
The quantitative proteome of a human cell line
This work provides a quantitative description of the proteome of a commonly used human cell line in two functional states, interphase and mitosis, and shows that these human cultured cells express at least ∼10 000 proteins and that the quantified proteins span a concentration range of seven orders of magnitude up to 20 000 000 copies per cell. Expand
Integrated Structural Analysis of the Human Nuclear Pore Complex Scaffold
It is shown that 32 copies of the Nup107 subcomplex assemble into two reticulated rings, one each at the cytoplasmic and nuclear face of the NPC, which may explain how changes of the diameter are realized that would accommodate transport of huge cargoes. Expand
Snapshots of nuclear pore complexes in action captured by cryo-electron tomography
Cryo-electron tomography is used to study the structure of nuclear pore complexes in their functional environment, that is, in intact nuclei of Dictyostelium discoideum and a new image-processing strategy compensating for deviations of the asymmetric units from a perfect eight-fold symmetry enabled the structure to be refined and to identify new features. Expand
Probing Native Protein Structures by Chemical Cross-linking, Mass Spectrometry, and Bioinformatics*
The critical steps of chemical cross-linking and its implications for (structural) biology are discussed: reagent design and cross- linking protocols, separation and mass spectrometric analysis of cross-linked samples, dedicated software for data analysis, and the use ofCross-l linking data for computational modeling. Expand
Identification of cross-linked peptides from large sequence databases
It is shown that xQuest can identify cross-linked peptides from a total Escherichia coli lysate with an unrestricted database search and reduces the search space by an upstream candidate-peptide search before the recombination step. Expand
Structure of the 26S proteasome from Schizosaccharomyces pombe at subnanometer resolution
An integrated model is presented which sheds light on the early steps of protein degradation by the 26S complex and a belt of high “activity” surrounding the AAA-ATPase module is tentatively assigned to the reversible association of proteasome interacting proteins and the conformational heterogeneity among the particles. Expand
Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans
This work presents a mass-spectrometry-based strategy to determine the absolute quantity, that is, the average number of protein copies per cell in a cell population, for a large fraction of the proteome in genetically unperturbed cells and expects it to become a cornerstone of quantitative biology and systems biology. Expand
mProphet: automated data processing and statistical validation for large-scale SRM experiments
Selected reaction monitoring (SRM) is a targeted mass spectrometric method that is increasingly used in proteomics for the detection and quantification of sets of preselected proteins at highExpand
Structural Probing of a Protein Phosphatase 2A Network by Chemical Cross-Linking and Mass Spectrometry
This study establishes XL-MS as an integral part of hybrid structural biology approaches for the analysis of endogenous protein complexes by gaining distance restraints on a modular interaction network of protein complexes affinity-purified from human cells by applying an adaptedXL-MS protocol. Expand