A5043755661- Immunotherapy and Immune Responses
- Protein Structure and Dynamics
- Monoclonal and Polyclonal Antibodies Research
- Cellular transport and secretion
- SARS-CoV-2 and COVID-19 Research
- Glycosylation and Glycoproteins Research
- Virus-based gene therapy research
- T-cell and B-cell Immunology
- Computational Drug Discovery Methods
- RNA modifications and cancer
- Lipid Membrane Structure and Behavior
- Ubiquitin and proteasome pathways
- Cervical Cancer and HPV Research
- Enzyme Structure and Function
- Advanced Proteomics Techniques and Applications
- Protein purification and stability
- Immune Cell Function and Interaction
- RNA and protein synthesis mechanisms
- Peptidase Inhibition and Analysis
- Metabolomics and Mass Spectrometry Studies
- Cancer-related gene regulation
- vaccines and immunoinformatics approaches
- Alzheimer's disease research and treatments
- Field-Flow Fractionation Techniques
- Microbial Metabolic Engineering and Bioproduction
Centre for Structural Systems Biology
2020-2025
European Molecular Biology Laboratory
2017-2025
European Molecular Biology Laboratory
2018-2024
European Bioinformatics Institute
2020
Constructor University
2019
Technical University of Munich
2019
Technical University of Denmark
2019
Lundbeck Foundation
2014
Aarhus University
2014
Hutchison/MRC Research Centre
2010
The coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous human suffering. To date, no effective drug available to directly treat the disease. In a search for against COVID-19, we have performed high-throughput x-ray crystallographic screen of two repurposing libraries main protease (M
Lysine methylation is an important post-translational modification of histone proteins that defines epigenetic status and controls heterochromatin formation, X-chromosome inactivation, genome imprinting, DNA repair, transcriptional regulation. Despite considerable efforts by chemical biologists to synthesize modified histones for use in deciphering the molecular role these phenomena, no general method exists bearing quantitative site-specific methylation. Here we demonstrate a installation...
Abstract Protein stability in detergent or membrane-like environments is the bottleneck for structural studies on integral membrane proteins (IMP). Irrespective of method to study structure an IMP, solubilization from usually first step workflow. Here, we establish a simple, high-throughput screening identify optimal conditions protein stabilization. We apply differential scanning fluorimetry combination with scattering upon thermal denaturation unfolding proteins. Nine different prokaryotic...
Disulfide-stabilized MHC class I are empty peptide-receptive molecules that rapidly load peptide and improve T cell detection. See the related Research Article by Moritz et al . in this issue.
Protein stability is a key factor in successful structural and biochemical research. However, the approaches for systematic comparison of protein are limited by sample consumption or compatibility with buffer components. Here we describe how miniaturized measurement intrinsic tryptophan fluorescence (NanoDSF assay) combination simplified description unfolding can be used to interrogate sample. We demonstrate that improved measures, such as apparent Gibbs free energy unfolding, rather than...
Abstract Differential scanning fluorimetry (DSF) using the inherent fluorescence of proteins (nDSF) is a popular technique to evaluate thermal protein stability in different conditions (e.g. buffer, pH). In many cases, ligand binding increases and often this can be detected as clear shift nDSF experiments. Here, we affinity quantification based on shifts. We present four systems with ligands, ranging from nM high μM. Our study suggests that affinities determined by isothermal analysis are...
SARS-CoV-2 papain-like protease (PLpro) covers multiple functions. Beside the cysteine-protease activity, facilitating cleavage of viral polypeptide chain, PLpro has additional and vital function removing ubiquitin ISG15 (Interferon-stimulated gene 15) from host-cell proteins to support coronaviruses in evading host's innate immune responses. We identified three phenolic compounds bound PLpro, preventing essential molecular interactions by screening a natural compound library. The X-ray...
The main protease (M
Abstract Circular dichroism (CD) spectroscopy is an established biophysical technique to study chiral molecules. CD allows investigating conformational changes under varying experimental conditions and has been used understand secondary structure, folding binding of proteins nucleic acids. Here, we present ChiraKit, a user-friendly, online, open-source tool process raw data perform advanced analysis. ChiraKit features include the calculation protein structure with SELCON3 SESCA algorithms,...
In clathrin-mediated endocytosis, adapter proteins assemble together with clathrin through interactions specific lipids on the plasma membrane. However, precise mechanism of protein assembly at cell membrane is still unknown. Here, we show that membrane-proximal domains ENTH epsin and ANTH Sla2 form complexes phosphatidylinositol 4,5-bisphosphate (PIP2) lipid interfaces. Native mass spectrometry reveals how assemblies by sharing PIP2 molecules. Furthermore, crystal structures Ent2 domain...
Abstract Major Histocompatibility Complex (MHC) class I molecules selectively bind peptides for presentation to cytotoxic T cells. The peptide-free state of these is not well understood. Here, we characterize a disulfide-stabilized version the human molecule HLA-A*02:01 that stable in absence peptide and can readily exchange cognate peptides. We present X-ray crystal structures HLA-A*02:01, together with have dipeptides bound A F pockets. These structural snapshots reveal amino acid side...
All biological processes rely on the formation of protein-ligand, protein-peptide and protein-protein complexes. Studying affinity, kinetics thermodynamics binding between these pairs is critical for understanding basic cellular mechanisms. Many different technologies have been designed probing interactions biomolecules, each based measuring signals (fluorescence, heat, thermophoresis, scattering interference, among others). Evaluation data from experiments their fitting an essential step...
Proteins and peptides are amongst the most widely used research reagents but often their quality is inadequate can result in poor data reproducibility. Here we propose a simple set of guidelines that, when correctly applied to protein should provide more reliable experimental data.
Abstract The amyloid-antimicrobial link hypothesis is based on antimicrobial properties found in human amyloids involved neurodegenerative and systemic diseases, along with amyloidal structural peptides (AMPs). Supporting this hypothesis, we here determined the fibril structure of two AMPs from amphibians, uperin 3.5 aurein 3.3, by cryogenic electron microscopy (cryo-EM), revealing amyloid cross-β fibrils mated β-sheets at atomic resolution. Uperin formed a 3-blade symmetrical propeller nine...
Drug discovery starts with the identification of a ‘hit’ compound that, following long and expensive optimization process, evolves into drug candidate. Bigger screening collections increase odds finding more better hits. For this reason, large pharmaceutical companies have invested heavily in high-throughput (HTS) that can contain several million compounds. However, figure pales comparison emergent on-demand chemical collections, which recently reached trillion scale. These are potentially...
ABSTRACT Mitochondrial respiratory complexes are organized into supercomplexes (SC) to regulate electron flow and mitigate oxidative stress. Alterations in SC organization the brain may affect energy expenditure, stress, neuronal survival. In this report, we investigated amount, activity of mitochondrial complex I (CI) hippocampus 12‐month‐old McGill‐R‐Thy1‐APP transgenic (Tg) rats, an animal model Alzheimer's‐like cerebral amyloidosis. By means BN‐PAGE, found that did not differ between...
Microbialites are organosedimentary structures dating to the Precambrian that serve as archives of Earth s environmental evolution. Today, they persist in only a few environments markedly different from those which first arose. Here, we report modern microbialite reef Laguna Pozo Bravo (Puna region, Argentina), exposed high radiation, low oxygen pressure, and volcanic inputs reminiscent early Earth. Through physicochemical, mineralogical, spectroscopic, electron microscopy, metagenomic...
Functionally empty and peptide-receptive soluble HLA-A*02:01 enables high-throughput analysis of TCR binding to peptide-MHCs. See the related Research Article by Saini et al . in this issue.
Successful sample preparation is the foundation to any structural biology technique. Membrane proteins are of particular interest as these important targets for drug design, but also notoriously difficult work with. For electron cryo-microscopy (cryo-EM), biophysical characterization purity, homogeneity, and integrity well biochemical activity prerequisite good quality cryo-EM grids factors impact result computational reconstruction. Here, we present a control pipeline prior single particle...
The HPV16 E7 oncoprotein is an extended dimer, with a stable and cooperative fold, but that displays properties of "natively unfolded" proteins. Two regions conserved sequence are found in proteins, where the N-terminus (1-40) includes retinoblastoma tumor suppressor binding casein kinase II phosphorylation sites. A fragment containing highly acidic N-terminal half shows apparently disordered conformation by far-UV-circular dichroism (CD) at neutral pH, its hydrodynamic radius much larger...
The major phosphorylation sites of the bovine papillomavirus E2 transactivator protein are two serine residues, 298 and 301, that located in a flexible hinge region between DNA binding transactivation domains. Phosphorylation residue 301 promotes ubiquitination rapid degradation by proteasome pathway. To understand mechanism through which regulates intracellular levels this unique regulatory protein, we have carried out an extensive mutational analysis surrounding protein. Our results...