Biology subjects

Carlsen, R.

Publications and source records attributed to Carlsen, R..

5 recordsLinked to original sources

bioRxiv2025

From Flux to Function: Extracting Mechanistic Insights from Ion Channels via I-V and I-μ Analyses

The molecular origins of ion channel current-voltage (I-V) relationships are often unclear, obscured by ensemble averaging in experimental analysis and persistent underestimation of single-channel ion currents in simulations. Here, we present a mathematical framework that relates ion channel properties to experimentally measured I-V and current-concentration (I-) relationships. By accounting for how rates change in response to electrochemical conditions in a multistate kinetic model of systems with sequential binding sites, this approach demonstrates how the spatial arrangement of sites and transition states, together with rate asymmetries in ion uptake, transfer, and release, manifest in distinct open-channel current and conductance profiles. Varying these properties in model systems reveals a molecular basis for understanding rectification and non-ohmic open-channel flux. Application to more realistic models fit to I-V curves for the Shaker Kv channel demonstrates that these mechanistic trends hold in heterogeneous systems, suggesting a (potentially) transferable paradigm for open channel flux in channels and transporters with two or more sequential binding sites. Together, these results establish a theoretical framework for open channel current and foundation for mechanistically interpreting experimental I-V and I- assays.

biochemistry↗

bioRxiv2025

Metabolic Flexibility of Microglia: Energy Substrate Utilization and Impact on Neuronal Metabolism

Microglia, the main resident immune cells of the brain, play critical roles in maintaining neuronal function and homeostasis. Microglia metabolic flexibility enables rapid adaptation to environmental changes, yet the full extent of their metabolic capabilities and influence on neuronal metabolism remains unclear. While microglia predominantly rely on glucose oxidative metabolism under homeostatic conditions, they shift toward glycolysis upon proinflammatory activation. In this study, we investigated microglial metabolism and its impact on neuronal metabolic homeostasis using isotope tracing with stable carbon 13C-enriched substrates and gas chromatography-mass spectrometry (GC-MS) analysis. Primary microglia were incubated with 13C-labeled glucose, glutamine, or GABA in the presence or absence of lipopolysaccharide (LPS) to assess metabolic adaptations upon an inflammatory challenge. Additionally, neurons co-cultured with quiescent or activated microglia (either with LPS or amyloid-{beta}) were incubated with 13C-enriched glucose to examine microglia-neuron metabolic interactions. Our findings confirm that microglia readily metabolize glucose and glutamine, with LPS stimulation slightly changing the glycolytic activity, as indicated by subtle changes in extracellular lactate. Importantly, we demonstrate for the first time that microglia take up and metabolize the inhibitory neurotransmitter GABA, suggesting a novel metabolic function. Furthermore, microglial presence directly influences neuronal metabolism and neurotransmitter homeostasis, highlighting a previously unrecognized aspect of neuron-microglia metabolic crosstalk. Collectively, these findings provide new insights into microglial metabolism and its role in neuronal function, with implications for neuroinflammatory and neurodegenerative diseases in which microglial metabolism is dysregulated.

neuroscience↗

bioRxiv2025

Ion Channel Reaction Networks: Dielectric Screening and the Importance of Off-Pathway Flux

The transport of ions through channels involves multiple rare-event transitions through a web of interconnected intermediates. Extracting open channel mechanisms generally requires quantifying the relative flux through these intermediates in response to a range of electrochemical gradients. Although this is ideally suited to network-based representations like Markov state models (MSMs), the relative contributions from different pathways and the importance of network resolution remain open areas of research. Herein, we use a complementary approach called multiscale responsive kinetic modeling (MsRKM) to explore how the screening of ionic interactions and the competition between multiple mechanistic pathways contribute to channel mechanisms and current profiles of ion channels. We find that explicitly optimizing screened ionic interactions in the MsRKM framework vastly reduces the solution search space, enabling more efficient identification of physically robust solutions. Using a model of the Shaker Kv channel, we demonstrate that even when systems are well described by a single dominant flux pathway, the remaining contributing pathways and off-pathway flux play multiple essential roles, including shifting current profiles and mechanisms in response to different electrochemical gradients. We additionally discover that current continues to change above the experimentally predicted saturation point. Model systems explain how the degree of dielectric screening influences channel occupancy, the number of contributing pathways, and why current increases or decreases above its experimental saturation point. Our findings emphasize the importance of retaining a full network description to identify and understand ion channel mechanisms. Toc O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/637869v1_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@1144eaaorg.highwire.dtl.DTLVardef@387f8eorg.highwire.dtl.DTLVardef@13e4e01org.highwire.dtl.DTLVardef@1732864_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2024

Nernst Equilibrium, Rectification, and Saturation: Insights into Ion Channel Behavior

The dissipation of electrochemical gradients through ion channels plays a central role in biology. Herein we use voltage responsive kinetic models of ion channels to explore how electrical and chemical potentials differentially influence ion transport properties. These models demonstrate how electrically driven flux is greater than the Nernstian equivalent chemically driven flux, yet still perfectly cancels when the two gradients oppose each other. We find that the location and relative stability of ion binding sites dictates rectification properties by shifting the location of the most voltage sensitive transitions. However, these rectification properties invert when bulk concentrations increase relative to the binding site stabilities, moving the rate limiting steps from uptake into a relatively empty channel to release from an ion-blocked full channel. Additionally, the origin of channel saturation is shown to depend on the free energy of uptake relative to bulk concentrations. Collectively these insights provide framework for interpreting and predicting how channel properties manifest in electrochemical transport behavior. SIGNIFICANCEUnderstanding how electrochemical potentials, such as the proton motive force, drive ion transport is a complex challenge due to the intricate coupling between electrical and chemical gradients, which can have seemingly equivalent effects. This study investigates how channel properties are differentially influenced by these driving forces to enhance or decrease directional flux. Using model systems, we demonstrate how voltage induces greater flux than the Nernstian equivalent chemical gradient yet is still perfectly balanced when the two forces oppose each other. Our findings reveal how binding site locations dictate rectification properties that flip under low and high bulk concentrations. These insights enhance our understanding of channels and transporters, providing foundational relationships between protein properties and electrochemical outcomes.

biochemistry↗

bioRxiv2024

Multiscale Responsive Kinetic Modeling: Quantifying Biomolecular Reaction Flux under Varying Electrochemical Conditions

Attaining a complete thermodynamic and kinetic characterization for processes involving multiple interconnected rare-event transitions remains a central challenge in molecular biophysics. This challenge is amplified when the process must be understood under a range of reaction conditions. Herein, we present a condition-responsive kinetic modeling framework that can combine the strengths of bottom-up rate quantification from multiscale simulations with top-down solution refinement using experimental data. Although this framework can be applied to any process, we demonstrate its use for electrochemically driven transport through channels and transporters. Using the Cl- /H+ antiporter ClC-ec1 as a model system, we show how robust and predictive kinetic solutions can be obtained when the solution space is grounded by thermodynamic constraints, seeded through multiscale rate quantification, and further refined with experimental data, such as electrophysiology assays. Turning to the Shaker K+ channel, we demonstrate that robust solutions and biophysical insights can also be obtained with sufficient experimental data. This multi-pathway method proves capable of identifying single-pathway dominant mechanisms but also highlights that competing and off-pathway flux is still essential to replicate experimental findings and to describe concentration-dependent channel rectification.

biophysics↗