Biology subjects

Habeck, M.

Publications and source records attributed to Habeck, M..

8 recordsLinked to original sources

bioRxiv2025

Active Conformations of Neuronal Na+,K+-ATPase isoforms and a Disease-Causing Mutant

Na+,K+-ATPases establish and maintain the vital electrochemical gradients for Na+ and K+ across animal cell membranes. The protein is a ternary complex composed of , {beta} and FXYD subunits, of which isoforms that fine-tune transport properties are expressed in a tissue-specific fashion. Here we report cryo-EM structures under active ATPase turn-over conditions of the ubiquitously expressed human 1{beta}1FXYD1 and neuron-specific 3{beta}1FXYD1 isoform complexes and probe their specific functional and biophysical properties. The data provides an extensive insight into Na+-transport of ATP-activated enzyme through four distinct conformational states, including a long-sought sodium-bound phosphoenzyme intermediate, denoted [Na3]E2P. This hitherto elusive conformation reveals a crucial structural change that precedes Na+ release in the inward to outward (E1P-E2P) transition, within the general context of the sequential, active transport mechanism. We investigated and discuss the mechanism of the physiologically important differentiation in Na+ affinity of 3 compared to 1, the co-operative Na+ binding at the ion-binding sites, and the mechanistic aspects of cytoplasmic ion gating and extracellular Na+ release. Finally we present the first structures of a disease-causing mutant form of 3, associated with Alternating Hemiplegia of Childhood (Q140L). The mutation compromises a specific phospholipid-binding pocket and impedes polyunsaturated phospholipid-mediated stimulation of Na+,K+-ATPase activity.

biochemistry↗

bioRxiv2025

Sarcomere analysis in human cardiomyocytes by computing radial frequency spectra

In cardiomyocytes, the basic contractile unit are sarcomeres, which are organized in a regular manner facilitating their function. Here, we present a new computational approach to assess the functional properties of sarcomeres at the nanoscale level in human cardiac cells, induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs). We combined our analysis to different types of high-resolution imaging data, structured illumination microscopy (SIM), stimulated emission depletion (STED) microscopy-based imaging, as well as confocal microscopy data. We show that the radially averaged magnitude spectrum (RAMS) revealed sarcomere properties in a human cardiomyocyte model, iPSC-CMs, and compared our RAMS-based analysis to a real-space approach based on manually selected regions of interest. Moreover, we found the RAMS method suitable to quantify molecular differences of sarcomeres such as present in severe cardiac diseases, such as dilated cardiomyopathy (DCM). Defects in the sarcomere organization that occur in the presence of inherited DCM mutations in sarcomere proteins were efficiently recapitulated by our analysis. This new approach may facilitate streamlined analysis of molecular disease-specific phenotypic imaging data of cardiac cells, aiding our deeper understanding of the molecular basis of cardiac diseases.

bioinformatics↗

bioRxiv2024

Minimally and vaguely informative priors to combat practical parameter non-identifiability of hidden Markov models exemplified by ion channel data

Hidden Markov models (HMMs) for biomolecules suffer from various forms of parameter non-identifiability. This poses severe challenges to both maximum likelihood and Bayesian inference. However, Bayesian inference offers effective means of overcoming these pathologies. We study the role of prior distributions in the face of practical parameter non-identifiability in Bayesian inference applied to prototypical patch clamp data of ligand-gated ion channels. We advocate the use of minimally informative priors, as they increase the accuracy and decrease the uncertainty of the inference. For complex HMMs, stronger prior assumptions are needed to render the posterior sufficiently proper. This can be achieved by confining the parameter space to physically motivated limits. Another beneficial assumption is finite cooperativity of ligand-binding and unbinding events, which introduces a bias towards non-cooperativity but still allows for a non-vanishing degree of cooperativity that is inferred from the data. Despite its vagueness, our prior renders the posterior sufficiently proper for all datasets that we considered without imposing the assumption of non-cooperativity. Combining all prior factors allows for meaningful inferences with a dataset of a thousand times lower quality.

bioinformatics↗

bioRxiv2023

Bayesian Maximum Entropy Ensemble Refinement

The principle of maximum entropy provides a canonical way to include measurement results into a thermodynamic ensemble. Observable features of a thermodynamic system, which are measured as averages over an ensemble are included into the partition function by using Lagrange multipliers. Applying this principle to the systems energy leads to the well-known exponential form of the Boltzmann probability density. Here, we present a Bayesian approach to the estimation of maximum entropy parameters from nuclear Overhauser effect measurements in order to achieve a refined ensemble in molecular dynamics simulations. To achieve this goal, we leverage advances in the treatment of doubly intractable Bayesian inference problems by adaptive Markov Chain Monte Carlo methods. We illustrate the properties and viability of our method for alanine dipeptide as a simple model system and trp-cage as an example for a more complex peptide.

bioinformatics↗

bioRxiv2021

Cryo-EM structure of the human NKCC1 transporter reveals mechanisms of ion coupling and specificity

The sodium-potassium-chloride transporter NKCC1 (SLC12A2) performs Na+-dependent Cl- and K+ ion uptake across plasma membranes. NKCC1 is important for regulating e.g. cell volume, hearing, blood pressure, and chloride gradients defining GABAergic and glycinergic signaling in brain. Here, we present a 2.6 [A] resolution cryo-electron microscopy (cryo-EM) structure of human NKCC1 in the substrate-loaded (Na+, K+, 2 Cl-) and inward-facing conformation adopting an occluded state that has also been observed for the SLC6 type transporters MhsT and LeuT. Cl- binding at the Cl1 site together with the nearby K+ ion provide a crucial bridge between the LeuT-fold scaffold and bundle domains. Cl- ion binding at the Cl2 site seems to undertake a structural role similar to a conserved glutamate of SLC6 transporters and may allow for chloride-sensitive regulation of transport. Supported by functional studies in mammalian cells and computational simulations we describe the Na+ binding site and a putative Na+ release pathway along transmembrane helix 5. The results provide insight into the structure-function relationship of NKCC1 with broader implications for other SLC12 family members.

biochemistry↗

bioRxiv2020

Spinal Column Architecture of the Flexible SPP1 Bacteriophage Tail Tube

Phage therapy has recently regained attention at combating multidrug-resistant bacteria. In 2019, tailed bacteriophages of the Siphoviridae family were engineered to successfully treat a disseminated bacterial infection after all other drugs had failed.(1) This family of phages features a long, flexible, non-contractile tail that has been difficult to characterize structurally. Here, we present the atomic structure of the tail-tube of the bacteriophage SPP1 - a member of this family. Our hybrid structure is based on the integration of structural restraints from solid-state NMR and a density map from cryo-EM. We show that the tail tube protein (TTP) gp17.1 organizes into hexameric rings that are stacked by flexible linker domains and, thus, form a hollow flexible tube with a negatively charged lumen suitable for the transport of DNA. One sentence summaryIntegrative structural biology by solid-state NMR and cryo-EM enables structure determination of the flexible tail of the bacteriophage SPP1.

biophysics↗

bioRxiv2019

Allosteric structural alterations and auto-regulation of Rab5 GEF activity in Rabex5

Intracellular trafficking depends on the function of Rab GTPases, whose activation is regulated by guanine exchange factors (GEFs). The Rab5 GEF, Rabex5, was previously proposed to be autoinhibited by its C-terminus. Here, we studied full-length Rabex5 and Rabaptin5 proteins as well as domain deletion Rabex5 mutants using hydrogen deuterium exchange mass spectrometry. We generated a structural model of Rabex5, using chemical crosslinking mass spectrometry and integrative modeling techniques. Our results are inconsistent with the previous model of autoinhibition. By correlating structural changes with nucleotide exchange activity for each construct, we uncovered new auto-regulatory roles for the Ubiquitin binding domains and the Linker connecting those domains to the catalytic core of Rabex5. Our results suggest a more complex auto-regulation mechanism than previously thought and imply that Ubiquitin binding serves not only to position Rabex5 but to also control its Rab5 GEF activity through allosteric structural alterations.

biophysics↗

bioRxiv2018

Bayesian inference of chromatin structure ensembles from population Hi-C data

High-throughput chromosome conformation capture (Hi-C) experiments are typically performed on a large population of cells and therefore only yield average numbers of genomic contacts. Nevertheless population Hi-C data are often interpreted in terms of a single genomic structure, which ignores all cell-to-cell variability. We propose a probabilistic, statistically rigorous method to infer chromatin structure ensembles from population Hi-C data that takes the ensemble nature of the data explicitly into account and allows us to infer the number of structures required to explain the data.

bioinformatics↗