Biology subjects

Swanson, J. M.

Publications and source records attributed to Swanson, J. M..

12 recordsLinked to original sources

bioRxiv2026

Voltage versus concentration in ion channels: Physical signatures reveal rate-limiting steps

Within the field of electrophysiology, I-V curves are a primary experimental means of characterizing ion channel behavior. By directly measuring ionic currents across membranes, electrophysiological techniques quantify key properties, including conductance, ion selectivity, and voltage dependence. We demonstrate a method of linking experimentally observed ion flux with microscopic mechanistic properties of channels. Although voltage and chemical potential can provide the same net electrochemical driving force, they perturb ion transport differently: voltage modifies transition rates throughout the permeation pathway, whereas chemical potential primarily alters ion uptake probabilities. Consequently, uptake, transfer, and release respond differently to the two driving forces, producing distinct flux signatures and causing chemical potential-driven flux to plateau while voltage-driven flux continues to increase. These differences encode the rate-limiting step (RLS) in open-channel flux. We propose a protocol based on three standard I-V measurements obtained under symmetric and asymmetric ion concentrations for elucidating the RLS. Application of this analysis to experimental data from the KcsA potassium channel identifies release as the RLS for outward permeation, consistent with available structural and computational evidence. Together, these results reveal how the physics of the electrochemical driving force shapes ion transport and provide an experimentally accessible strategy for connecting macroscopic electrophysiology measurements to microscopic transport mechanisms.

biophysics↗

bioRxiv2026

Asymmetry and Allostery: Insights into the Mechanism of DirectionalPeptide Translocation in AAA+ Unfoldases

Molecular motors convert stochastic ATP chemistry into directional motion. Modern nonequilibrium theories explain this behavior through kinetic asymmetry, yet the molecular mechanisms that generate kinetic asymmetry in AAA+ unfoldases remain unresolved. Cryo-electron microscopy has consistently revealed unfoldases take on an asymmetric helical staircase structure, inspiring the proposed processive hand-over-hand translocation mechanism. In contrast, biochemical and single-molecule studies have reported bursts, slips, and variable step sizes indicative of stochastic behavior. How these observations are reconciled and how directional motion emerges from stochastic ATP hydrolysis remain central questions. Here we use all-atom molecular dynamics simulations of the AAA+ unfoldases Yme1 and Vps4 to explore structural changes induced by hydrolysis, ADP release, and ATP association. The simulations reveal coexisting pre- and post-hydrolysis conformations consistent with experimental cryo- EM densities while also uncovering interconnected allosteric communication networks. One network links the Walker B glutamate to the proximal subunits nucleotide binding pocket (NBP), providing a mechanism for backward propagation of hydrolysis competence around the hexamer. Another network couples NBP and salt bridge rearrangements to pore-loop dynamics, connecting subunit position rather than ATP hydrolysis to substrate release. Simulations of nucleotide exchange intermediates further show that ATP binding before ADP and/or Mg2+ release can induce transient strain leading to alternative hydrolysis-competent configurations that still favor forward progression, providing a structural basis for some of the experimentally observed stochastic behavior. Together, these findings suggest that structural asymmetry creates position-dependent allosteric interactions that generate kinetic asymmetry, biasing a fundamentally stochastic ATPase cycle toward directional substrate translocation while still permitting variation in stepping behavior. Significance StatementAAA+ ATPases play a central role in biology, converting ATP binding, hydrolysis, and release into the directional forces needed to carry out work, such as substrate translocation, remodeling, and degradation. In addition to being important therapeutic targets, understanding how these molecular machines convert stochastic ATP chemistry into persistent mechanical motion is of fundamental interest. Using all-atom molecular dynamics simulations of Yme1 and Vps4, we identify position-responsive conformational changes and allosteric communication networks that propagate hydrolysis competence, coordinate substrate release, and redistribute the relative probabilities of mechanochemical transitions around the ATPase ring. These findings provide molecular insight into how structural asymmetry and kinetic redistribution enable directional substrate translocation.

biophysics↗

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

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↗

bioRxiv2024

Selective binding of MLX to triacylglycerol-rich lipid droplets: Mechanisms of cytosolic localization and proteome regulation

The activation of transcription factor Max-Like Protein x (MLX) is modulated by competition between active dimerization and inactive association with cytosolic lipid droplets (LDs). However, LD association has been shown to depend on the neutral lipid composition. This work explores the mechanism by which MLX specifically targets LDs rich in triacylglycerol (TG) over those with abundant sterol esters (SE). We compare the association ensembles for a potential minimal targeting sequence, an amphipathic helix-loop-helix hairpin, and the full dimerization and cytoplasmic localization domain (DCD), finding the latter requires larger packing defects and quantifiably alters LD membrane properties. Surprisingly, direct interactions with TG neutral lipids are not observed for either sequence. Instead, targeting to SE-rich LDs is blocked for both sequences by insufficient packing defects. We additionally explore the full mechanism of hairpin association, aiming to understand sequence-specific features that enable strong membrane association. We find that there are multiple association pathways, but that each involves a catch, dive, snorkeling, and embedding phase. The combination of multiple catch and dive residues placed on opposing ends of amphipathic helices lengthens the catch phase, greatly enhancing association in a manner that resembles kinetic selection. Once bound, locking interhelical interactions block dissociation. Collectively, our findings suggest that in addition to relative binding affinities, both kinetics and altered surface properties due to protein association could influence competition within the LD proteome. SignificanceThe transcription factor Max-Like Protein x (MLX plays) a central role in metabolic regulation by responding to nutrient status and, simultaneously, neutral lipid composition. This work reveals how MLX selectively targets triacylglycerol-rich lipid droplets (LDs) through sequence-specific interactions with packing defects. We show that LD surface modulates MLX binding and that MLX in turn alters monolayer properties, highlighting a dynamic interplay between protein association and membrane properties. These findings provide new insight into how protein localization and function may be regulated at LD surfaces, with implications for nutrient sensing and, more broadly, transcriptional control relevant to metabolic and disease states.

biophysics↗

bioRxiv2023

Mycolactone A vs. B: Does localization or association explain isomer-specific toxicity?

Mycolactone is an exotoxin produced by Mycobacterium ulcerans that causes the neglected tropical skin disease Buruli ulcer. This toxin inhibits the Sec61 translocon in the endoplasmic reticulum (ER), preventing the host cell from producing many secretory and transmembrane proteins, resulting in cytotoxic and immunomodulatory effects. Interestingly, only one of the two dominant isoforms of mycolactone is cytotoxic. Here, we investigate the origin of this specificity by performing extensive molecular dynamics (MD) simulations with enhanced free energy sampling to query the association trends of the two isoforms with both the Sec61 translocon and the ER membrane, which serves as a toxin reservoir prior to association. Our results suggest that mycolactone B (the cytotoxic isoform) has a stronger association with the ER membrane than mycolactone A due to more favorable interactions with membrane lipids and water molecules. This could increase the reservoir of toxin proximal to the Sec61 translocon. Isomer B also interacts more closely with the lumenal and lateral gates of the translocon, the dynamics of which are essential for protein translocation. These interactions induce a more closed conformation, which has been suggested to block signal peptide insertion and subsequent protein translocation. Collectively, these findings suggest that isomer Bs unique cytotoxicity is a consequence of both increased localization to the ER membrane and channel-locking association with the Sec61 translocon, facets that could be targeted in the development of Buruli Ulcer diagnostics and Sec61-targeted therapeutics.

biophysics↗

bioRxiv2022

Capturing the liquid-crystalline phase transformation: Implications for protein targeting to sterol ester-rich lipid droplets

Lipid droplets are essential organelles that store and traffic neutral lipids. The phospholipid monolayer surrounding their neutral lipid core engages with a highly dynamic proteome that changes according to cellular and metabolic conditions. Recent work has demonstrated that when the abundance of sterol esters increases above a critical concentration, such as under conditions of starvation or high LDL exposure, the lipid droplet core can undergo an amorphous to liquid-crystalline phase transformation. Herein we study the consequences of this transformation on the physical properties of lipid droplets that are thought to regulate protein association. Using simulations of different sterol-ester concentrations we have captured the liquid-crystalline phase transformation at the molecular level, highlighting the alignment of sterol esters in alternating orientations to form concentric layers. We demonstrate how ordering in the core permeates into the neutral lipid/phospholipid interface, changing the magnitude and nature of neutral lipid intercalation and inducing ordering in the phospholipid monolayer. Increased phospholipid packing is concomitate with altered surface properties, including smaller area per phospholipid and substantially reduced packing defects. Additionally, the ordering of sterol esters in the core causes less hydration in more ordered regions. We discuss these findings in the context of their expected consequences for preferential protein recruitment to lipid droplets under different metabolic conditions.

biophysics↗

bioRxiv2022

Can Membrane Composition Traffic Toxins? Mycolactone and Preferential Membrane Interactions

Mycolactone is a cytotoxic and immunosuppressive macrolide produced by Mycobacterium ulcerans and the sole causative agent of the neglected tropical skin disease Buruli ulcer. The toxin acts by invading host cells and interacting with intracellular targets to disrupt multiple fundamental cellular processes. Mycolactones amphiphilic nature enables strong interactions with lipophilic environments, including cellular membranes; however, the specificity of these interactions and the role of membranes in the toxins pathogenicity remain unknown. It is likely that preferential interactions with lipophilic carriers play a key role in the toxins distribution in the host, which, if understood, could provide insights to aid in the development of needed diagnostics for Buruli ulcer disease. In this work, molecular dynamics simulations were combined with enhanced free energy sampling to characterize mycolactones association with and permeation through models of the mammalian endoplasmic reticulum (ER) and plasma membranes (PM). We find that increased order in the PM not only leads to a different permeation mechanism compared to that in the ER membrane, but also an energetic driving force for ER localization. Increased hydration, membrane deformation, and preferential interactions with unsaturated lipid tails stabilize the toxin in the ER membrane, while disruption of lipid packing is a destabilizing force in the PM. STATEMENT OF SIGNIFICANCEMycolactone is sole the causative agent of Buruli ulcer, a neglected tropical disease involving large necrotic lesions that can cause permanent disfigurement if left untreated. Due to its amphiphilic nature, the toxin hides from traditional diagnostic detection and the host immune system by associating with lipophilic carriers, including cellular membranes. Our work uses extensive all-atom simulations to query if the toxin has preferential interactions with different types of membranes. We find a clear preference for more disordered membranes, like the endoplasmic reticulums, via interactions with unsaturated lipid tails and membrane deformation. The revealed insights can be used to predict host cell distribution between different types of lipophilic carriers and to aid in the design of Buruli ulcer diagnostics.

biophysics↗

bioRxiv2019

The Role of Gene Encoding Variation of DRD4 in the Relationship between Inattention and Seasonal Daylight

Daylight is the strongest synchronizer of human circadian rhythms. The circadian pathway hypothesis posits that synchrony between daylight and the circadian system relates to (in)attention. The dopamine neurotransmitter system is implicated in regulating the circadian system as well as in (attention)-deficit hyperactivity disorder [ADHD]. We studied the role of functional genetic variation in the gene encoding of dopamine-receptor-D4 (DRD4) in the relationship between inattention and seasonal daylight (changes). Gene-by-environment (GxE) mega-analyses were performed across eight studies including 3757 adult participants (with and without ADHD). We tested 1) the Spring-focus hypothesis, in which attention in 7R-carriers normalizes with increasing daylight levels preceding measurement, 2) the Summer-born ADHD hypothesis, in which 7R-carriers report more inattention when born in spring/summer than in autumn/winter, 3) the Winter-born ADHD hypothesis, opposing the second hypothesis. The Spring-focus hypothesis was upheld (1386 ADHD, 760 controls; d=-0.16 between periods); 7R-carriers reported even less inattention than 7R-non-carriers after winter solstice (d=0.27 between genotype-groups). Results were diagnosis-independent. Sensitivity analyses at individual study level confirmed the circannual patterns for 7R-carriers. Incorporating geographic changes into the independent measure, we also calculated changes in sunlight levels. This approach likewise showed that inattention correlated negatively with increasing light levels in 7R-carriers (r=-.135). Results emphasize peripheral effects of dopamine and the effects of (seasonal) daylight changes on cognition.

genetics↗

bioRxiv2017

Balancing Strengths and Weaknesses in Dimensional Psychiatry

ObjectiveTo evaluate the feasibility and value of creating an extensible framework for psychiatric phenotyping that indexes both strengths and weaknesses of behavioral dimensions. The Extended Strengths and Weaknesses Assessment of Normal Behavior (E-SWAN) reconceptualizes each diagnostic criterion for selected DSM-5 disorders as a behavior, which can range from high (strengths) to low (weaknesses). Initial efforts have focused on Panic Disorder, Social Anxiety, Major Depression, and Disruptive Mood Dysregulation Disorder.\n\nMethodsData were collected from 523 participants (ages: 5-21 years old) in the Child Mind Institute Healthy Brain Network - an ongoing community-referred study. Parents completed each of the four E-SWAN scales and traditional unidirectional scales addressing the same disorders. Distributional properties, Item Response Theory Analysis (IRT) and Receiver Operating Characteristic (ROC) curves (for diagnostic prediction) were used to assess and compare the performance of E-SWAN and traditional scales.\n\nResultsIn contrast to the traditional scales, which exhibited truncated distributions, all four E-SWAN scales were found to have near-normal distributions. IRT analyses indicate the E-SWAN subscales provided reliable information about respondents throughout the population distribution; in contrast, traditional scales only provided reliable information about respondents at the high end of the distribution. Predictive value for DSM-5 diagnoses was comparable to prior scales.\n\nConclusionE-SWAN bidirectional scales can capture the full spectrum of the population distribution for DSM disorders. The additional information provided can better inform examination of inter-individual variation in population studies, as well as facilitate the identification of factors related to resiliency in clinical samples.

neuroscience↗