Biology subjects

Burghardt, T. P.

Publications and source records attributed to Burghardt, T. P..

8 recordsLinked to original sources

bioRxiv2024

Neural-symbolic hybrid model for myosin complex in cardiac ventriculum decodes structural bases for inheritable heart disease from its genetic encoding

BackgroundHuman ventriculum myosin ({beta}mys) powers contraction sometimes in complex with myosin binding protein C (MYBPC3). The latter regulates {beta}mys activity and impacts overall cardiac function. Nonsynonymous single nucleotide variants (SNVs) change protein sequence in {beta}mys or MYBPC3 causing inheritable heart diseases by affecting the {beta}mys/MYBPC3 complex. Muscle genetics encode instructions for contraction informing native protein construction, functional integration, and inheritable disease impairment. A digital model decodes these instructions and evolves by continuously processing new information content from diverse data modalities in partnership with the human agent. MethodsA general neural-network contraction model characterizes SNV impacts on human health. It rationalizes phenotype and pathogenicity assignment given the SNVs genetic characteristics and in this sense decodes {beta}mys/MYBPC3 complex genetics and implicitly captures ventricular muscle functionality. When a SNV modified domain locates to an inter-protein contact in {beta}mys/MYBPC3 it affects complex coordination. Domains involved, one in {beta}mys and the other in MYBPC3, form coordinated domains (co-domains). Co-domains are bilateral implying potential for their SNV modification probabilities to respond jointly to a common perturbation to reveal their location. Human genetic diversity from the serial founder effect is the common systemic perturbation coupling co-domains that are mapped by a methodology called 2-dimensional correlation genetics (2D-CG). ResultsInterpreting the general neural-network contraction model output involves 2D-CG co-domain mapping that provides natural language expressed structural insights. It aligns machine-learned intelligence from the neural network model with human provided structural insight from the 2D-CG map, and other data from the literature, to form a neural-symbolic hybrid model integrating genetic and protein interaction data into a nascent digital twin. This process is the template for combining new information content from diverse data modalities into a digital model that can evolve. The nascent digital twin interprets SNV implications to discover disease mechanism, can evaluate potential remedies for efficacy, and does so without animal models. HighlightsNeural-symbolic hybrid model decodes muscle genetics into contraction mechanisms And evolves in virtuous cycle Optimize-Interpret-Revise-Repeat aided by human partner Nascent digital twin unravels inheritable disease mechanism without animal models And estimates cardiac phenotype coupling strength to myosin thick-filament structures

bioinformatics↗

bioRxiv2022

Variants identify sarcomere inter-protein contacts distinguishing inheritable cardiac muscle diseases

Human ventriculum myosin ({beta}mys) powers contraction sometimes while complexed with myosin binding protein C (MYBPC3) on the myosin thick filament. The latter regulates {beta}mys activity through inter-protein contacts. Single nucleotide variants (SNVs) change protein sequence in {beta}mys or MYBPC3. They cause inheritable heart disease. When a SNV modified domain locates to an inter-protein contact it affects complex coordination. Domains involved, one in {beta}mys and the other in MYBPC3, form coordinated domains called co-domains. Co-domains are bilateral implying the potential for a shared impact from SNV modification in either domain suggesting their joint response to a common perturbation assigns location. Human population genetic divergence is the common systemic perturbation. A general contraction model with a neural/Bayes network design reveals SNV probabilities specifying correlations between domain members using 2D correlation genetics (2D-CG). It reveals co-domain locations in three common human heart diseases caused by SNVs, familial hypertrophic cardiomyopathy (FHC), dilated cardiomyopathy (DCM), and left ventricle non-compaction (LVN). Co-domain maps for DCM and LVN link MYBPC3 with two levels of myosin heads on the myosin thick filament surface implying these myosin dimers form the super-relaxed state (SRX). The FHC co-domain map involves just one myosin dimer implying the myosins do not form SRX. Comparing co-domain maps for FHC, DCM, and LVN phenotypes suggests SRX disruption involves a co-domain between MYBPC3 regulatory domain and the myosin regulatory light chain (RLC) N-terminus. The general contraction model scenarios, constructed from feed-forward neural networks, were explored with the purpose to understand how to interpret them mechanistically with basic natural language characteristics. These characteristics emerge from dependencies among inputs coded in hidden layer width and depth when they are deciphered using 2D-CG. In this application, the thick filament structural states emerge for FHC, DCM, and LVN phenotypes defining thick filament structural state joining the other standard characteristics of phenotype and pathogenicity. Emergent natural language interpretations for general network contraction models are on the horizon.

bioinformatics↗

bioRxiv2021

Natural variants with 2D correlation genetics identify domains coordinating sarcomere proteins during contraction

Muscle proteins assemble in a sarcomere then by coordinated action produce contraction force to shorten muscle. In the human heart ventriculum, cardiac myosin motor ({beta}mys) repetitively converts ATP free energy into work. Cardiac myosin binding protein C (MYBPC3) in complex with {beta}mys regulates contraction power generation. Their bimolecular complex {beta}mys/MYBPC3 models the contractile system and is used here to study protein coupling. The database for single nucleotide variants (SNVs) in {beta}mys and MYBPC3 surveys human populations worldwide. It consistently records SNV physical characteristics including substituted residue location in the protein functional domain, the side chain substitution, substitution frequency, and human population group, but inconsistently records SNV implicated phenotype and pathology outcomes. A selected consistent subset of the data trains and validates a feed-forward neural network modeling the contraction mechanism. The full database is completed using the model then interpreted probabilistically with a discrete Bayes network to give the SNV probability for a functional domain location given pathogenicity and human population. Co-domains, intra-protein domains coupling {beta}mys and MYBPC3, are identified by their population correlated SNV probability product for given pathogenicity. Divergent genetics in human populations identify co-domain correlates in this method called 2D correlation genetics. Pathogenic and benign SNV data identify three critical regulatory sites, two in MYBPC3 with links to several domains across the {beta}mys motor, and, one in {beta}mys with links to the known MYBPC3 regulatory domain. Critical sites in MYBPC3 are hinges (one known another proposed) sterically enabling regulatory interactions with {beta}mys. The critical site in {beta}mys is the actin binding C-loop, a contact sensor triggering actin-activated myosin ATPase and contraction velocity modulator coordinating also with actin bound tropomyosin. C-loop and MYBPC3 regulatory domain linkage potentially impacts multiple functions across the contractile system. Identification of co-domains in a binary protein complex implies a capacity to estimate spatial proximity constraints for specific dynamic protein interactions in vivo opening another avenue for protein complex structure/function determination.

biochemistry↗

bioRxiv2020

The frequency-dependent effect of electrical fields on the mobility of intracellular vesicles in astrocytes

Slow-wave sleep, defined by low frequency (<4 Hz) electrical brain activity, is a basic brain function affecting metabolite clearance and memory consolidation. Although the origin of low-frequency activity is related to cortical up and down states, the underlying cellular mechanism of how low-frequency activity becomes effective has remained elusive. We applied electrical stimulation to cultured glial astrocytes while monitored the trafficking of GFP-tagged intracellular vesicles using TIRFM. We found a frequency-dependent effect of electrical stimulation that electrical stimulation in low frequency elevates the mobility of astrocytic intracellular vesicles. We suggest a novel mechanism of brain modulation that electrical signals in the lower range frequencies embedded in brainwaves modulate the functionality of astrocytes for brain homeostasis and memory consolidation. This finding suggests a physiological mechanism whereby endogenous low-frequency brain oscillations enhance astrocytic function that may underlie some of the benefits of slow-wave sleep and highlights possible medical device approach for treating neurological diseases.

neuroscience↗

bioRxiv2019

Demographic Model for Inheritable Cardiac Disease

The cardiac muscle proteins, generating and regulating energy transduction during a heartbeat, assemble in the sarcomere into a cyclical machine repetitively translating actin relative to myosin filaments. Myosin is the motor transducing ATP free energy into actin movement against resisting force. Cardiac myosin binding protein C (mybpc3) regulates shortening velocity probably by transient N-terminus binding to actin while its C-terminus strongly binds the myosin filament. Inheritable heart disease associated mutants frequently modify these proteins involving them in disease mechanisms. Nonsynonymous single nucleotide polymorphisms (SNPs) cause single residue substitutions with independent characteristics (sequence location, residue substitution, human demographic, and allele frequency) hypothesized to decide dependent phenotype and pathogenicity characteristics in a feed-forward Neural network model. Trial models train and validate on a dynamic worldwide SNP database for cardiac muscle proteins then predict phenotype and pathogenicity for any single residue substitution in myosin, mybpc3, or actin. A separate Bayesian model formulates conditional probabilities for phenotype or pathogenicity given independent SNP characteristics. Neural/Bayes forecasting tests SNP pathogenicity vs (in)dependent SNP characteristics to assess individualized disease risk and in particular to elucidate gender and human subpopulation bias in disease. Evident subpopulation bias in myosin SNP pathogenicities imply myosin normally engages other sarcomere proteins functionally. Consistent with this observation, mybpc3 forms a third actomyosin interaction competing with myosin essential light chain N-terminus suggesting a novel strain-dependent mechanism adapting myosin force-velocity to load dynamics. The working models, and the integral myosin/mybpc3 motor concept, portends the wider considerations involved in understanding heart disease as a systemic maladaptation.

bioinformatics↗

bioRxiv2018

Uncured PDMS Inhibits Myosin In Vitro Motility in a Microfluidic Flow Cell

The myosin motor powers cardiac contraction and is frequently implicated in hereditary heart disease by its mutation. Principal motor function characteristics include myosin unitary step size, duty cycle, and force-velocity relationship for translating actin under load. These characteristics are sometimes measured in vitro with a motility assay detecting fluorescent labeled actin filament gliding velocity over a planar array of surface immobilized myosin. Assay miniaturization in a polydimethylsiloxane/glass (PDMS/glass) hybrid microfluidic flow channel is an essential component to a small sample volume assay applicable to costly protein samples however the PDMS substrate dramatically inhibits myosin motility. Myosin in vitro motility in a PDMS/glass hybrid microfluidic flow cell was tested under a variety of conditions to identify and mitigate the effect of PDMS on myosin. Substantial contamination by the monomeric species in polymerized PDMS flow cells is shown to be the cause of myosin motility inhibition. Normal myosin motility recovers by either extended cell aging ([~]20 days) to allow more complete polymerization or by direct chemical extraction of the free monomers from the polymer substrate. PDMS flow cell aging is the low cost alternative compatible with the other PDMS and glass modifications needed for in vitro myosin motility assaying.

biophysics↗

bioRxiv2018

Cardiac and Skeletal Actin Substrates Uniquely Tune Cardiac Myosin Strain-Dependent Mechanics

Native cardiac ventricular myosin ({beta}mys) translates actin under load by transducing ATP free energy into mechanical work on actin during muscle contraction. Unitary {beta}mys translation of actin is the myosin step-size. In vitro and in vivo {beta}mys regulates contractile force and velocity by remixing 3 different step-sizes with stepping frequencies autonomously adapted to workload. Cardiac and skeletal actin isoforms have a specific 1:4 stoichiometry in normal adult human ventriculum. Human adults with inheritable hypertrophic cardiomyopathy (HCM) up-regulate skeletal actin in ventriculum suggesting that increasing skeletal/cardiac actin stoichiometry also adapts myosin force-velocity to respond to the muscles inability to meet demand.\n\nNanometer scale displacement of quantum dot (Qdot) labeled actin under resistive load when impelled by {beta}mys measures single myosin force-velocity in vitro in the Qdot assay. Unitary displacement classification constraints introduced here better separates myosin based signal from background upgrading step-size spatial resolution to the sub-nanometer range. Single {beta}mys force-velocity for skeletal vs cardiac actin substrates was compared using the Qdot assay.\n\nTwo competing myosin strain-sensitive mechanisms regulate step-size choices dividing mechanical characteristics into low- and high-force regimes. The actin isoforms alter myosin strain-sensitive regulation such that onset of the high-force regime, where a short step-size is a large or major contributor, is offset to higher loads by a unique cardiac ELC N-terminus/cardiac-actin contact at Glu6/Ser358. It modifies {beta}mys force-velocity by stabilizing the ELC N-terminus/cardiac-actin association. Uneven onset of the high-force regime for skeletal vs cardiac actin dynamically changes force-velocity characteristics as skeletal/cardiac actin fractional content increases in diseased muscle.

biophysics↗

bioRxiv2017

Single Cardiac Ventricular Myosins Change Step-Size with Loading

The cardiac myosin motor powers the beating heart by catalyzed ATPase free energy conversion to contractile work. Transgenic mouse models for heart disease express mouse -cardiac myosin heavy chain with human essential light chain (ELC) in wild type (WT), or hypertrophic cardiomyopathy linked mutant forms, A57G or E143K. Mutants modify the ELC actin binding N-terminus or C-terminus regions. Motility and single myosin mechanical characteristics show stark contrasts between the motors related to their average force, power, and displacement while all indicate the ability to down-shift ensemble step-size with increasing load. A57G and E143K consume more ATP than control WT in the presence of actin with A57G upregulating and E143K downregulating power compared with WT. Higher ATP consumption and downregulated power in E143K implies a lower unitary force. Effects on power are consistent with an A57G that impairs the ELC N-terminus actin binding and an E143K that reduces lever-arm rigidity.

biophysics↗