Biology subjects

Goetz, A.

Publications and source records attributed to Goetz, A..

12 recordsLinked to original sources

bioRxiv2026

Chemically tunable permeability of engineered alpha-Hemolysin in synthetic cells

Controlling molecular transport across membranes is a defining feature of living cells, yet replicating this functionality in synthetic systems remains a major challenge. Self-inserting protein nanopores, such as -hemolysin (HL), offer a promising route towards programmable membrane permeability due to their robust assembly, compatibility with diverse membrane systems, and intrinsic permeability for diverse biomolecules. Here, we explored the use of chemically functionalized HL nanopores as tunable transport modules. To quantify translocation of peptide substrates across HL-containing membranes, we developed a high-throughput luminescence-based breakage-controlled assay using large unilamellar vesicles. With this assay we introduce a one-pot nanopore modification and strategy, compatible with scalable workflows. Electrophysiology and molecular simulations demonstrate that the introduction of cysteine residues at defined pore locations, combined with targeted chemical modification, enables controlled tuning of HL-nanopore selectivity based on peptide structure and charge. Together, these findings position engineered protein nanopores as versatile and responsive components for controlling membrane transport in synthetic biology.

synthetic biology↗

bioRxiv2026

Endocytosis shapes extracellular chemical gradients in autonomous cell-cell attraction

Receptor-mediated ligand endocytosis is traditionally viewed as a negative feedback mechanism for signal attenuation. Here we show that ligand removal can paradoxically enhance directional information in autonomous cell-cell attraction. Many cell systems migrate toward one another in the absence of externally imposed gradients, implying that secretion, diffusion, and uptake must themselves generate usable directional cues. We develop a surface-resolved theory of a finite-sized detector exposed to a nearby source and derive analytical expressions for the steady-state ligand field. The resulting concentration profiles are governed by a single dimensionless Damkohler number that compares receptor-mediated endocytosis to diffusive ligand transport. Increasing ligand removal lowers extracellular ligand concentrations and reduces absolute concentration differences across the detector surface, but preferentially enhances relative surface anisotropy. Thus, destroying the signal can increase the usable information encoded in relative gradients. Incorporating nonlinear downstream processing reveals a tradeoff between contrast enhancement and signal depletion that yields a well-defined optimal endocytosis rate, in a regime consistent with experimentally measured receptor internalization kinetics. These results recast receptor-mediated endocytosis as an extracellular information-processing mechanism that reshapes self-generated gradients to enhance directional information.

biophysics↗

bioRxiv2025

Neural CXCR4 contributes to neuroimmune modulation of atherosclerosis in a cardio-metabolic Ldlr-/- mouse model

BackgroundAtherosclerosis is a chronic inflammatory disease characterized by metabolic and immune dysregulation. Emerging evidence suggests that specific central nervous system (CNS) regions modulate its progression via neuroimmune cardiovascular interfaces (NICIs). While the C-X-C motif chemokine receptor 4 (CXCR4) is known to participate in atherogenesis by regulating immune cell dynamics and vascular wall responses, the role of neural CXCR4 in atherosclerotic plaque formation remains unclear. MethodsWe generated a Nestin-Cre-mediated conditional Cxcr4 knockout mouse model on a low-density lipoprotein receptor-deficient (Ldlr-/-) background and fed these mice a western diet (WD) for up to 12 weeks to induce atherosclerosis. To evaluate the impact of neural CXCR4 function, we quantified atherosclerotic plaque burden, systemic metabolic parameters and circulating immune cell profiles, comparing neural Cxcr4-deficient mice with corresponding genetic controls. Spatial transcriptomics and RNAscope were employed to map Cxcr4 mRNA and its non-canonical ligand macrophage migration inhibitory factor (Mif) mRNA in neuroimmune-regulatory brain regions, and to assess diet-induced expression changes in relation to neuroinflammatory responses. ResultsNeural conditional deletion of Cxcr4 in Ldlr-/- mice significantly reduced atherosclerotic plaque formation in the aortic arch and aorta, without affecting body weight, lipid levels, glucose tolerance, or circulating immune cells. Cxcr4 gene expression was found to be uniformly low across hypothalamic subregions implicated in neuroimmune regulation of systemic inflammation and atherogenesis. Importantly, WD feeding did not modify this consistently low expression in male Ldlr-/- mice. In contrast, Mif mRNA expression was significantly upregulated in the PVN after 5-day WD feeding, but not after 8 weeks. Exploratory spatial transcriptomic analysis of PVN-containing coronal brain sections from male Ldlr-/- mice suggested that 5-day WD exposure is associated with MIF-CXCR4 signaling and downstream neuroinflammatory pathways in the PVN. ConclusionsThis study identifies neural CXCR4 as a component of neuroimmune modulation in atherosclerosis, exerting its effect independently of systemic metabolic or inflammatory changes. Short-term WD exposure activated gene expression of the CXCR4 ligand Mif in the PVN, pointing to a neuroimmune axis that may promote vascular inflammation and atherosclerotic plaque development. These findings establish a link between CNS CXCR4 and vascular disease and suggest that MIF-CXCR4-dependent neuroimmune pathways may play a role in cardiometabolic risk. Trial registrationNot applicable.

immunology↗

bioRxiv2024

Receptor polarization through localized activity and global sensitization

Directional sensing enables eukaryotic cells to detect spatial gradients of extracellular ligands by comparing local signaling activity to an internal set point. While this capability is typically attributed to signaling pathways downstream of cell surface receptors, we present a reaction-diffusion model to argue that receptors themselves can perform directional sensing via a mechanism we term Localized Activity and Global Sensitization (LAGS). LAGS integrates common receptor signaling motifs: lateral diffusion, basal activity, and active receptor degradation. Without diffusion, receptor activity locally adapts to a ligand-independent set point via degradation-mediated integral feedback, leading to receptor depletion in ligand-rich regions. The introduction of lateral diffusion redistributes primarily ligand-free receptors across the cell surface, creating a spatial mismatch between local activity and feedback. This mismatch drives polarized receptor activity relative to the set point, while rapid ligand equilibration and receptor degradation protects it from diffusion. The model predicts an optimal diffusion coefficient that maximizes receptor polarization, and shows that cells respond to relative - not absolute - changes in ligand levels. Cooperative receptor interactions further amplify the polarized response. Finally, stochastic analysis identifies an optimal set point that maximizes the signal-to-noise ratio in polarization. A survey of kinetic parameters across diverse receptor systems supports LAGS as a general mechanism for receptor-mediated directional sensing. Significance statementCells navigate their spatially heterogeneous environments by detecting spatial gradients of external signals - a process known as directional sensing. While traditionally attributed to downstream signaling pathways, we argue that cell surface receptors can themselves perform directional sensing by leveraging lateral diffusion, basal activity, and active receptor degradation. Using a reaction-diffusion model, we identify a general mechanism of directional sensing which we call Localized Activity and Global Sensitization (LAGS). In LAGS, degradation-driven integral feedback and receptor diffusion together generate robust, spatially polarized receptor activity. Our results suggest that directional sensing can emerge directly from receptor-level dynamics, revealing a broadly applicable strategy encoded in the biophysics of diverse signaling systems.

biophysics↗

bioRxiv2024

Tunable ligand discrimination via kinetic sorting

Signaling receptors often encounter multiple ligands and haven been shown to respond selectively to generate appropriate, context-specific outcomes. At thermal equilibrium, ligand specificity is limited by the relative affinities of ligands for their receptors. Here, we present a non-equilibrium model in which receptors overcome thermodynamic constraints to preferentially signal from specific ligands while suppressing others. In our model, multi-site phosphorylation and active receptor degradation act in concert to regulate ligand specificity, with receptor degradation providing a previously under-appreciated layer of control. Here, ligand-bound receptors undergo sequential phosphorylation, with progression restarted by ligand unbinding or receptor turnover. High-affinity complexes are kinetically sorted toward degradation-prone states, while low-affinity complexes are sorted towards inactivated states, both limiting signaling. As a result, network activity is maximized for ligands with intermediate affinities. This mechanism explains paradoxical experimental observations in receptor tyrosine kinase (RTK) signaling, including non-monotonic dependence of signaling output on ligand affinity and kinase activity. Given the ubiquity of multi-site phosphorylation and ligand-induced degradation across signaling receptors, we propose that kinetic sorting may be a general non-equilibrium ligand-discrimination strategy used by multiple signaling receptors.

systems biology↗

bioRxiv2024

Computational modeling of drug response identifies mutant-specific constraints for dosing panRAF and MEK inhibitors in melanoma

Purpose: This study explores the potential of preclinical in vitro cell line response data and computational modeling in identifying optimal dosage requirements of pan-RAF (Belvarafenib) and MEK (Cobimetinib) inhibitors in melanoma treatment. Our research is motivated by the critical role of drug combinations in enhancing anti-cancer responses and the need to close the knowledge gap around selecting effective dosing strategies to maximize their potential. Results: In a drug combination screen of 43 melanoma cell lines, we identified unique dosage landscapes of panRAF and MEK inhibitors for NRAS vs BRAF mutant melanomas. Both experienced benefits, but with a notably more synergistic and narrow dosage range for NRAS mutant melanoma. Computational modeling and molecular experiments attributed the difference to a mechanism of adaptive resistance by negative feedback. We validated in vivo translatability of in vitro dose-response maps by accurately predicting tumor growth in xenografts. Then, we analyzed pharmacokinetic and tumor growth data from Phase 1 clinical trials of Belvarafenib with Cobimetinib to show that the synergy requirement imposes stricter precision dose constraints in NRAS mutant melanoma patients. Conclusion: Leveraging pre-clinical data and computational modeling, our approach proposes dosage strategies that can optimize synergy in drug combinations, while also bringing forth the real-world challenges of staying within a precise dose range. Simple SummaryCombining drugs is crucial for enhancing anti-cancer responses. However, the potential of pre-clinical data in identifying suitable combinations and dosage is often underutilized. In this study, we leverage preclinical in vitro cell line drug response data and computational modeling of signal transduction and of pharmacokinetics to elucidate distinct dose requirements for the combination of pan-RAF and MEK inhibitors in melanoma. Our findings reveal a more synergistic, but narrower dosing landscape in NRAS vs BRAF mutant melanoma, which we linked to a mechanism of adaptive resistance through negative feedback. Further, our analysis suggests the importance of drug dosing strategies to optimize synergy based on mutational context, yet highlights the real-world challenges of maintaining a narrow dose range. This approach establishes a framework for translational investigation of drug responses in the refinement of combination therapy, balancing the potential for synergy and practical feasibility in cancer treatment planning.

systems biology↗

bioRxiv2024

Classification of human actin pathological variants using C. elegans CRISPR-generated models

Actin plays a crucial role in diverse physiological processes by forming dynamic networks that determine cellular shape and mechanical properties. Non-Muscle Actinopathies (NMA) are rare diseases caused by de novo variants in human cytoskeletal {beta}-actin (ACTB) and {gamma}-actin (ACTG1) genes, ranging from missense mutations to whole gene deletions. Currently, the high clinical variability and genotype-phenotype correlations in NMA remain largely unresolved. To address this concern, we inserted nine mutations identified in patients in the C. elegans cytoplasmic actin orthologue act-2 and performed a quantitative multiscale characterization of these animal models. We uncovered various perturbations including micro-scale actin network defects, cell-scale abnormalities, morphogenesis failure, and weaker behavioural phenotypes. Notably, the severity of the observed defects correlates with the severity of patients symptoms. Thus, we provide evidence that such C. elegans models are relevant to investigate the mechanisms underlying NMA physiopathology and could ultimately be used to screen for therapeutic strategies.

cell biology↗

bioRxiv2023

The ability to sense the environment is heterogeneously distributed in cell populations

Channel capacity of signaling networks quantifies their fidelity in sensing extracellular inputs. Low estimates of channel capacities for several mammalian signaling networks suggest that cells can barely detect the presence/absence of environmental signals. However, given the extensive heterogeneity and temporal stability of cell state variables, we hypothesize that the sensing ability itself may depend on the state of the cells. In this work, we present an information theoretic framework to quantify the distribution of sensing abilities from single cell data. Using data on two mammalian pathways, we show that sensing abilities are widely distributed in the population and most cells achieve better resolution of inputs compared to an "average cell". We verify these predictions using live cell imaging data on the IGFR/FoxO pathway. Importantly, we identify cell state variables that correlate with cells sensing abilities. This information theoretic framework will significantly improve our understanding of how cells sense in their environment.

systems biology↗

bioRxiv2022

GIP receptor agonism improves dyslipidemia and atherosclerosis independently of body weight in obese mice

Agonism at the receptors for the glucose-dependent insulinotropic polypeptide (GIPR) is a key component of the novel unimolecular co-agonists which are among the most promising drugs in clinical development for the treatment of obesity and diabetes. The therapeutic effect of chronic GIPR agonism to treat dyslipidemia, and thus to reduce the cardiovascular disease risk, has not been explored yet. Herein we found that treatment with a long-acting acylated GIP analog (Acyl-GIP) reduced dyslipidemia and atherogenesis in male LDL receptor knockout mice. Acyl-GIP administration resulted in smaller adipocytes within the inguinal fat depot and RNAseq analysis of the latter revealed that Acyl-GIP may improve dyslipidemia by directly modulating lipid metabolism in this fat depot. This study identified an unanticipated efficacy of chronic GIPR agonist administration to improve dyslipidemia and cardiovascular disease.

pharmacology and toxicology↗

bioRxiv2018

Stabilization / destabilization of the APP transmembrane domain by mutations in the di-glycine hinge alter helical structure and dynamics, and impair cleavage by γ-secretase

Intramembrane cleavage of the {beta}-amyloid precursor protein C99 substrate by {gamma}-secretase is implicated in Alzheimers disease pathogenesis. Since conformational flexibility of a di-glycine hinge in the C99 transmembrane domain (TMD) might be critical for {gamma}-secretase cleavage, we mutated one of the glycine residues, G38, to a helix-stabilizing leucine and to a helix-distorting proline. CD, NMR and hydrogen/deuterium exchange measurements as well as MD simulations showed that the mutations distinctly altered the intrinsic structural and dynamical properties of the TMD. However, although helix destabilization/unfolding was not observed at the initial {varepsilon}-cleavage sites of C99, both mutants impaired {gamma}-secretase cleavage and altered its cleavage specificity. Moreover, helix flexibility enabled by the di-glycine hinge translated to motions of other helix parts. Our data suggest that both local helix stabilization and destabilization in the di-glycine hinge may decrease the occurrence of enzyme-substrate complex conformations required for normal catalysis and that hinge mobility can be conducive for productive substrate-enzyme interactions.

biophysics↗

bioRxiv2018

Increased γ-Site H-Bond Stability Relates to Altered ε-Efficiency and Aβ Levels in the I45T Familial Alzheimer’s Disease Mutant of APP

Cleavage of the amyloid precursor proteins (APP) transmembrane domain (TMD) by {gamma}-secretase is a crucial step in the aetiology of Alzheimers Disease (AD). Mutations in the APP TMD alter cleavage and lead to familial forms of AD (FAD). The majority of FAD mutations shift the preference of initial cleavage from {varepsilon}49 to {varepsilon}48, thus raising the AD-related A{beta}42/A{beta}40 ratio. The I45T mutation is among the few FAD mutations that do not alter {varepsilon}-site preference, while it dramatically reduces the efficiency of {varepsilon}-cleavage. Here, we investigate the impact of the I45T mutation on the backbone dynamics of the substrate TMD. Amide exchange experiments and molecular dynamics simulations in solvent and a lipid bilayer reveal an increased stability of amide hydrogen bonds at the {zeta}-and {gamma}-cleavage sites. Stiffening of the H-bond network is caused by an additional H-bond between the T45 side chain and the TMD backbone, which alters dynamics within the cleavage domain. In particular, the increased H-bond stability inhibits an upward movement of the {varepsilon}-sites in the I45T mutant. Thus, an altered presentation of {varepsilon}-sites to the active site of {gamma}-secretase as a consequence of restricted local flexibility provides a rationale for reduced {varepsilon}-cleavage efficiency of the I45T mutant.

biophysics↗

bioRxiv2018

Dissecting Conformational Changes in APP’s Transmembrane Domain Linked to Altered ε-Efficiency of Familial Alzheimer’s Disease Mutants

The mechanism by which familial Alzheimers disease (FAD) mutations within the transmembrane domain (TMD) of the Amyloid Precursor Protein (APP) affect [a]-endoproteolysis is only poorly understood. Thereby, mutations in the cleavage domain reduce [a]-efficiency of a-secretase cleavage and some even shift entry into production lines. Since cleavage occurs within the TMD, a relationship between processing and TMD structure and dynamics seems obvious. Using molecular dynamic simulations, we dissect the dynamic features of wild type and seven FAD-mutants into local and global components. Mutations consistently enhance hydrogen8 bond fluctuations upstream of the [a]-cleavage sites but maintain strong helicity there. Dynamic perturbation response scanning reveals that FAD-mutants target backbone motions utilized in the bound state. Those motions, obscured by large-scale motions in the pre-bound state, provide (i) a dynamic mechanism underlying the proposedcoupling between binding and [a]-cleavage, (ii) key sites consistent with experimentally determined docking sites, and (iii) the distinction between mutants and wild-type.

biophysics↗