Biology subjects

Damjanovic, A.

Publications and source records attributed to Damjanovic, A..

4 recordsLinked to original sources

bioRxiv2025

From Atoms to Neuronal Spikes: A Multi-Scale Simulation Framework

Understanding how molecular events in ion channels impact neuronal excitability, as derived from the calculation of the time course of the membrane potentials, can help elucidate the mechanisms of neurological disease-linked mutations and support neuroactive drug design. Here, we propose a multi-scale simulation approach which couples molecular simulations with neuronal simulations to predict the variations in membrane potential and neural spikes. We illustrate this through two examples. First, molecular dynamics simulations predict changes in current and conductance through the AMPAR neuroreceptor when transitioning from the wild-type protein to certain disease-associated variants. The results of these simulations inform morphologically detailed models of cortical pyramidal neurons, which are simulated using the Arbor framework to determine neural spike activity. Based on these multiscale simulations, we suggest that disease associated AMPAR variants may significantly impact neuronal excitability. In the second example, the Arbor model is coupled with coarse-grained Monte Carlo gating simulations of voltage-gated (K+ and Na+) channels. The pre-dicted current from these ion channels altered the membrane potential and, in turn, the excitation state of the neuron was updated in Arbor. The resulting membrane potential was then fed back into the Monte Carlo simulations of the voltage-gated ion channels, resulting in a bidirectional coupling of current and membrane potential. This allowed the transitions of the states of the ion channels to influence the membrane potentials and vice versa. Our simulations also included the crucial -- so far unexplored -- effects of the composition of the lipid membrane embedding the ion channels on the membrane potential and revealed a significant impact of temperature on the neuronal excitability. Our combined approaches predicted membrane potentials consistent with electrophysiological recordings and established a multi-scale framework linking the atomistic perturbations to neuronal excitability.

neuroscience↗

bioRxiv2025

Characterizing the Ion-Conductive State of the α7-Nicotinic Acetylcholine Receptor via Single-Channel Measurements and Molecular Dynamics Simulations

The 7-nicotinic acetylcholine receptor (7-nAChR) is a cation-selective Cys-loop receptor involved in diverse physiological processes and is an important therapeutic target. Multiple cryo-EM structures of putative open states are now available and their functional relevance is under active investigation. Here, we combined single-channel patch-clamp recordings with atomistic molecular dynamics (MD) simulations to assess the conductive properties of several 7-nAChR structures solved with different ligands. Simulations restrained to the respective cryo-EM structures produced only modest ion flux for all models, inconsistent with experiment, whereas fully unrestrained simulations revealed marked differences in their ability to relax into physiologically conductive ensembles. Two structures, 7KOX and ligand-bound 8V82, consistently stabilized into conductive states whose permeation properties matched our measured inward single-channel conductance. The conduction of 8V82 nearly stopped upon removing the modeled ligands. 8V80 showed only intermittent conduction with ligands and remained non-conductive without them. 7EKT collapsed into a non-conductive conformation upon relaxation, irrespective of whether the modeled ligands were retained or removed. 9LH5, despite having a transmembrane pore nearly identical to 7KOXs, exhibited approximately twofold higher conductance, likely due to a widened extracellular vestibule. Across models, permeation events followed Poissonian statistics with a characteristic entry lag captured by a double-Poisson model. Simulations of outward currents consistently overestimated the conductance compared to experiments, perhaps reflecting the absence of the full intracellular domain in available structural models and/or the presence of current-blocking concentrations of cytosolic Mg2+ in patch-clamp cell-attached recordings. These results identify the conformations most compatible with the physiological open state and underscore the importance of unrestrained MD, ligand stabilization, and extracellular-vestibule geometry in shaping 7-nAChR conduction.

biophysics↗

bioRxiv2024

Quantitating SARS-CoV-2 Neutralizing Antibodies from Human Dried Blood Spots

BackgroundIn the earliest days of COVID-19 pandemic, the collection of dried blood spots (DBS) enabled public health laboratories to undertake population-scale seroprevalence studies to estimate rates of SARS-CoV-2 exposure. With SARS-CoV-2 seropositivity levels now estimated to exceed 94% in the United States, attention has turned to using DBS to assess functional (neutralizing) antibodies within cohorts of interest. MethodsContrived DBS eluates from convalescent, fully vaccinated and pre-COVID-19 serum samples were evaluated in SARS-CoV-2 plaque reduction neutralization titer (PRNT) assays, a SARS-CoV-2 specific 8-plex microsphere immunoassay, a cell-based pseudovirus assay, and two different spike-ACE2 inhibition assays, an in-house Luminex-based RBD-ACE2 inhibition assay and a commercial real-time PCR-based inhibition assay (NAB-Sure). ResultsDBS eluates from convalescent individuals were compatible with the spike-ACE2 inhibition assays, but not cell-based pseudovirus assays or PRNT. However, the insensitivity of cell-based pseudovirus assays was overcome with DBS eluates from vaccinated individuals with high SARS-CoV-2 antibody titers. ConclusionSARS-CoV-2 neutralizing titers can be derived with confidence from DBS eluates, thereby opening the door to the use of these biospecimens for the analysis of vulnerable populations and normally hard to reach communities.

immunology↗

bioRxiv2022

Intrinsically disordered interaction network in an RNA chaperone revealed by native mass spectrometry

RNA-binding proteins contain intrinsically disordered regions whose functions in RNA recognition are poorly understood. The RNA chaperone Hfq is a homohexamer that contains six flexible C-terminal domains (CTDs). The effect of the CTDs on Hfqs integrity and RNA binding has been challenging to study because of their sequence identity and inherent disorder. We used native mass spectrometry (nMS) coupled with surface-induced dissociation (SID) and molecular dynamics (MD) simulations to disentangle the arrangement of the CTDs and their impact on the stability of E. coli Hfq with and without RNA. The results show that the CTDs stabilize the Hfq hexamer through multiple interactions with the core and between CTDs. RNA binding perturbs this network of CTD interactions, destabilizing the Hfq ring. This destabilization is partially compensated by binding of RNAs that contact multiple surfaces of Hfq. By contrast, binding of short RNAs that only contact one or two subunits results in net destabilization of the complex. Together, the results show that a network of intrinsically disordered interactions integrate RNA contacts with the six subunits of Hfq. We propose that this CTD network raises the selectivity of RNA binding. Significance StatementHfq is a protein hexamer necessary for gene regulation by non-coding RNA in bacteria, during infection or under stress. In the cell, Hfq must distinguish its RNA partners from many similar nucleic acids. Mass spectrometry dissociation patterns, together with molecular dynamics simulations, showed that flexible extensions of each Hfq subunit form a dense network that interconnects the entire hexamer. This network is disrupted by RNA binding, but the lost interactions are compensated by RNAs that contact multiple Hfq subunits. By measuring interactions that are too irregular to be counted by other methods, mass spectrometry shows how flexible protein extensions help chaperones like Hfq recognize their RNA partners in the messy interior of the cell.

biophysics↗