Biology subjects

Michaelis, J.

Publications and source records attributed to Michaelis, J..

8 recordsLinked to original sources

bioRxiv2022

Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins

Single-molecule FRET (smFRET) has become an established tool to study biomolecular structure and dynamics in vitro and in live cells. We performed a worldwide blind study involving 19 labs to assess the uncertainty of FRET experiments for proteins with respect to the measured FRET efficiency histograms, determination of distances, and the detection and quantification of structural dynamics. Using two protein systems that undergo distinct conformational changes, we obtained an uncertainty of the FRET efficiency of less than {+/-} 0.06, corresponding to an interdye distance precision of [≤] 0.2 nm and accuracy of [≤] 0.5 nm. We further discuss the limits for detecting distance fluctuations with sensitivity down to [lsim] 10% of the Forster distance and provide guidelines on how to detect potential dye perturbations. The ability of smFRET experiments to simultaneously measure distances and avoid averaging of conformational dynamics slower than the fluorescence lifetime is unique for dynamic structural biology.

biophysics↗

bioRxiv2022

CLARITY increases sensitivity and specificity of fluorescence immunostaining in long-term archived human brain tissue

Immunohistochemistry on archival human brains is often limited because several conditions arise that complicate the use for high-resolution fluorescence microscopy. In this study, we developed a novel clearing approach for immunofluorescence-based analysis of perfusion- and immersion-fixed post mortem human brain tissue, termed hCLARITY. hCLARITY is optimized for specificity by reducing off-target labeling and yields very sensitive stainings in human brain sections allowing for super-resolution microscopy with unprecedented imaging of pre- and postsynaptic compartments. Moreover, hallmarks of the Alzheimers disease were preserved with hCLARITY, and importantly classical DAB or Nissl stainings are compatible with this protocol. hCLARITY is extremely versatile as demonstrated by the use of more than 30 well performing antibodies and allows for de- and subsequent re-staining of the same tissue section, which is important for multi-labelling approaches, e.g., in super-resolution microscopy. Taken together, hCLARITY enables research of the human brain with highest sensitivity and down to sub-diffraction resolution and therefore has enormous potential for the investigation of local morphological changes, e.g., in neurodegenerative diseases. Striking Image / Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/489700v1_ufig1.gif" ALT="Figure 1"> View larger version (79K): org.highwire.dtl.DTLVardef@1732df2org.highwire.dtl.DTLVardef@cda615org.highwire.dtl.DTLVardef@152b44aorg.highwire.dtl.DTLVardef@ba972a_HPS_FORMAT_FIGEXP M_FIG Summary of the main advantages of hCLARITY. CLARITY was applied on human post mortem brain tissue in direct comparison to untreated sections (minus CLARITY). Owing to removal of lipids during the clearing with SDS and the resulting reduction in light scattering, cleared sections were less opaque. The denaturing effect of the detergent SDS most likely results in better accessibility of certain epitopes. The major benefits of hCLARITY were found in an increased sensitivity and specificity of antibodies for neuronal cells. The adapted hCLARITY protocol is compatible with staining techniques for confocal microscopy, super-resolution microscopy, and light microscopy. C_FIG

neuroscience↗

bioRxiv2022

Stress induced TDP-43 mobility loss independent of stress granules

TAR DNA binding protein 43 (TDP-43) is closely related to the pathogenesis of amyotrophic lateral sclerosis (ALS) and translocates to stress granules (SGs). The role of SGs as aggregation-promoting "bioreactors" for TDP-43, however, is still under debate. We analyzed TDP-43 mobility and localization under different stress and recovery conditions using live cell single-molecule tracking and super-resolution microscopy. Besides reduced mobility within SGs, a stress induced decrease of TDP-43 mobility in the cytoplasm and the nucleus was observed. Stress removal led to a recovery of TDP-43 mobility, which strongly depended on the stress duration. Stimulated-emission depletion microscopy (STED) and tracking and localization microscopy (TALM) revealed not only TDP-43 substructures within stress granules but also numerous patches of slow TDP-43 species throughout the cytoplasm. The data provide new insights into the aggregation of TDP-43 in living cells and provide evidence suggesting that TDP-43 oligomerization takes place in the cytoplasm separate from SGs.

biophysics↗

bioRxiv2022

Structural dynamics of DNA strand break sensing by PARP-1 at a single-molecule level

Single stranded breaks (SSBs) are the most frequent DNA lesions threatening genomic integrity. A highly kinked DNA structure in complex with human PARP-1 led to the proposal that SSB sensing in Eukaryotes relies on dynamics of both the broken DNA double helix and PARP-1s multi-domain organization. Here, we directly probe this fundamental yet poorly understood process at the single-molecule level. Quantitative SM-FRET and structural ensemble calculations reveal how PARP-1 binding converts DNA SSBs from a largely unperturbed conformation into the highly kinked state. Binding of the second N-terminal zinc finger yields an intermediate DNA conformation that can be recognized by the first zinc finger. Thus, the data is inconsistent with a conformational selection model, instead an induced fit mechanism via a multi-domain assembly cascade drives SSBs sensing. Interestingly, a clinically used PARP-1 inhibitor niraparib shifts the equilibrium towards the unkinked state, whereas the inhibitor EB47 stabilizes the kinked state.

biophysics↗

bioRxiv2020

Nucleolar TFIIE plays a role in ribosomal biogenesis and performance

Ribosome biogenesis is a highly energy-demanding process in eukaryotes which requires the concerted action of all three RNA polymerases. In RNA polymerase II transcription, the general transcription factor TFIIH is recruited by TFIIE to the initiation site of protein-coding genes. Distinct mutations in TFIIH and TFIIE give rise to the degenerative disorder trichothiodystrophy (TTD). Here we uncovered an unexpected role of TFIIE in ribosomal RNA synthesis by RNA polymerase I. With high resolution microscopy we detected TFIIE in the nucleolus where TFIIE binds to actively transcribed rDNA. Mutations in TFIIE affects gene-occupancy of RNA polymerase I, rRNA maturation, ribosomal assembly and performance. In consequence, the elevated translational error rate with imbalanced protein synthesis and turnover results in an increase in heat-sensitive proteins. Collectively, mutations in TFIIE - due to impaired ribosomal biogenesis and translational accuracy - lead to a loss of protein homeostasis (proteostasis) which can partly explain the clinical phenotype in TTD.

cell biology↗

bioRxiv2020

Shank2 expression identifies a subpopulation of glycinergic interneurons involved in nociception and altered in an autism mouse model

Patients suffering from Autism Spectrum Disorders (ASD) experience disturbed nociception in form of either hyposensitivity to pain or hypersensitivity and allodynia. We have determined that Shank2-KO mice, which recapitulate the genetic and behavioural disturbances of ASD, display increased sensitivity to formalin pain and thermal, but not mechanical allodynia. We demonstrate that high levels of Shank2 expression identifies a subpopulation of neurons in murine and human dorsal spinal cord, composed mainly by glycinergic interneurons and that loss of Shank2 causes the decrease in NMDAR in excitatory synapses on these inhibitory interneurons. In fact, in the subacute phase of the formalin test, glycinergic interneurons are strongly activated in WT mice but not in Shank2-KO mice. As consequence, nociception projection neurons in lamina I are activated in larger numbers in Shank2-KO mice. Our findings prove that Shank2 expression identifies a new subset of inhibitory interneurons involved in reducing the transmission of nociceptive stimuli and whose unchecked activation is associated with pain hypersensitivity. Thus, we provide evidence that dysfunction of spinal cord pain processing circuits may underlie the nociceptive phenotypes in ASD patients and mouse models.

neuroscience↗

bioRxiv2019

Artifact Formation in Single Molecule Localization Microscopy

We investigate the influence of different accuracy-detection rate trade-offs on image reconstruction in single molecule localization microscopy. Our main focus is the investigation of image artifacts experienced when using low localization accuracy, especially in the presence of sample drift and inhomogeneous background. In this context we present a newly developed SMLM software termed FIRESTORM which is optimized for high accuracy reconstruction. For our analysis we used in silico SMLM data and compared the reconstructed images to the ground truth data. We observe two discriminable reconstruction populations of which only one shows the desired localization behavior.

biophysics↗

bioRxiv2016

Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes.

The yeast Chd1 protein acts to position nucleosomes across genomes. Here we model the structure of the Chd1 protein in solution and when bound to nucleosomes. In the apo state the DNA binding domain contacts the edge of the nucleosome while in the presence of the non-hydrolyzable ATP analog, ADP-beryllium fluoride, we observe additional interactions between the ATPase domain and the adjacent DNA gyre 1.5 helical turns from the dyad axis of symmetry. Binding in this conformation involves unravelling the outer turn of nucleosomal DNA and requires substantial reorientation of the DNA binding domain with respect to the ATPase domains. The orientation of the DNA-binding domain is mediated by sequences in the N-terminus and mutations to this part of the protein have positive and negative effects on Chd1 activity. These observations indicate that the unfavourable alignment of C-terminal DNA binding region in solution contributes to an auto-inhibited state.

molecular biology↗