Biology subjects

Miller, B. R.

Publications and source records attributed to Miller, B. R..

5 recordsLinked to original sources

bioRxiv2025

Molecular dynamics of the pathogenic KCNQ2 variant G256W reveal mechanisms of channel dysfunction in epileptic encephalopathy

Brain voltage-gated potassium channels containing the subunit KCNQ2 are essential for regulating electrical signals contributing to sensation, learning, memory, and motor control. De novo KCNQ2 variants are among the more common Mendelian causes of early life epilepsy and neurodevelopmental impairment. Some patients with KCNQ2 variants are affected with KCNQ2 developmental and epileptic encephalopathy (KCNQ2 DEE) characterized by seizures and developmental delays. Children with KCNQ2 DEE exhibit a range of impairment patterns that appear to be correlated with specific consequences of the variant for protein function. Here, we used all-atom molecular dynamics to analyze a pathogenic missense variant KCNQ2 G256W, located in the pore turret. G256W subunit simulations showed migration of the hydrophobic W256 sidechain towards the lipid membrane. This movement affected turret structure and mobility prominently involving K255. We identified novel hydrogen bonding interactions in the wild type KCNQ2 turret region which formed a network that extended to the selectivity filter and identified N258, H260P, and K283 as key residues. Simulations comparing WT and G256W tetrameric channels exhibited more conformationally unstable ion selectivity filters for G256W. We analyzed how different stoichiometries of wild type and G256W subunits, as expected in heterozygous individuals, impacted dynamics and compared the G256W results to three additional variants of the turret-selectivity filter network. Our results provide additional support for an integral role of the KCNQ2 turret selectivity filter stability. The majority of severe KCNQ2 DEE variants are clustered near the selectivity filter in the pore domain. Our study provides insights that may be broadly applicable to this clinically important allele subgroup. Broader audience statementA serious childhood illness, called KCNQ2 developmental and epileptic encephalopathy, usually arises from single amino acid substitutions, or missense variants. This paper provides insight into how such a local change can profoundly disrupt the function of a large oligomeric protein containing over 3,400 residues. Molecular dynamics simulations of the pathogenic KCNQ2 pore domain variant, G256W, revealed that W256 changed the structure and flexibility of the pore domain turret and altered the ion selectivity filter. These findings shed light on the functional impact of KCNQ2 pathogenic variants and may help illuminate general mechanisms underlying severe KCNQ2 variants that occur commonly near the ion pore.

neuroscience↗

bioRxiv2022

A Photonic Biosensor-Integrated Tissue Chip Platform for Real-Time Sensing of Lung Epithelial Inflammatory Markers

Tissue chip (TC) devices seek to mimic human physiology on a small scale. They are intended to improve upon animal models in terms of reproducibility and human relevance, at a lower monetary and ethical cost. Virtually all TC systems are analyzed at an endpoint, leading to widespread recognition that new methods are needed to enable sensing of specific biomolecules in real time, as they are being produced by the cells. To address this need, we incorporated photonic biosensors for inflammatory cytokines into a model TC. Human bronchial epithelial cells seeded in a microfluidic device were stimulated with lipopolysaccharide, and the cytokines secreted in response sensed in real time. Sensing analyte transport through the TC in response to disruption of tissue barrier was also demonstrated. This work demonstrates the first application of photonic sensors to a human TC device, and will enable new applications in drug development and disease modeling.

bioengineering↗

bioRxiv2020

Mechanisms of allosteric and mixed mode aromatase inhibitors

Aromatase (Cyp19) catalyzes the last biosynthetic step of estrogens in mammals and is a primary drug target for hormone-related breast cancer. However, treatment with aromatase inhibitors is often associated with adverse effects and drug resistance. In this study, we used virtual screening targeting a predicted cytochrome P450 reductase binding site on aromatase to discover four novel non-steroidal aromatase inhibitors. The inhibitors have potencies comparable to the noncompetitive tamoxifen metabolite, endoxifen. Our two most potent inhibitors, AR11 and AR13, exhibit both mixed-type and competitive-type inhibition. The cytochrome P450 reductase-Cyp19 coupling interface likely acts as a transient binding site. Our modeling shows that our inhibitors bind better at different sites near the catalytic site. Our results predict the location of multiple ligand binding sites on aromatase. The combination of modeling and experimental results supports the important role of the reductase binding interface as a low affinity, promiscuous ligand binding site. Our new inhibitors may be useful as alternative chemical scaffolds that may show different adverse effects profiles than current clinically used aromatase inhibitors.

biochemistry↗

bioRxiv2019

Methyl-Metabolite Depletion Elicits Adaptive Responses to Support Heterochromatin Stability and Epigenetic Persistence

S-adenosylmethionine (SAM) is the methyl-donor substrate for DNA and histone methyltransferases that regulate cellular epigenetic states. This metabolism-epigenome link enables the sensitization of chromatin methylation to altered SAM abundance. However, a chromatin-wide understanding of the adaptive/responsive mechanisms that allow cells to actively protect epigenetic information during life-experienced fluctuations in SAM availability are unknown. We identified a robust response to SAM depletion that is highlighted by preferential cytoplasmic and nuclear de novo mono-methylation of H3 Lys 9 (H3K9) at the expense of global losses in histone di- and tri-methylation. Under SAM-depleted conditions, de novo H3K9 mono-methylation preserves heterochromatin stability and supports global epigenetic persistence upon metabolic recovery. This unique chromatin response was robust across the mouse lifespan and correlated with improved metabolic health, supporting a significant role for epigenetic adaptation to SAM depletion in vivo. Together, these studies provide the first evidence for active epigenetic adaptation and persistence to metabolic stress.

biochemistry↗

bioRxiv2018

An increase in spontaneous activity mediates visual habituation

The cerebral cortex is spontaneously active1,2, but the function of this ongoing activity remains unclear3, 4. One possibility is that spontaneous activity provides contextual information in cortical computations, replaying previously learned patterns of activity5-8 that conditions the cortex to respond more efficiently, based on past experience. To test this, we measured the response of neuronal populations in mouse primary visual cortex with chronic two-photon calcium imaging during a visual habituation to a specific oriented stimulus. We unexpectedly found that, during habituation, spontaneous activity increased in neurons across the full range of orientation selectivity, eventually matching that of evoked levels. The increase in spontaneous activity strongly correlated with the degree of habituation. In fact, boosting spontaneous activity with two-photon optogenetic stimulation to the levels of stimulus-evoked activity induced habituation in naive animals. Our study shows that cortical spontaneous activity is causally linked to habituation, which unfolds by minimizing the difference between spontaneous and stimulus-evoked activity levels, rendering the cortex less responsive. We also show how manipulating spontaneous activity can accelerate this type of learning. We hypothesize that spontaneous activity in visual cortex gates incoming sensory information.

neuroscience↗