Biology subjects

Fakharzadeh, A.

Publications and source records attributed to Fakharzadeh, A..

3 recordsLinked to original sources

bioRxiv2026

One high-order ion-coupling mechanism generates multiple SLC1A stoichiometries

Human excitatory amino acid transporter 2 (hEAAT2) is a glial transporter that clears glutamate and aspartate from the extracellular space to terminate neurotransmission. When this essential role is disrupted, excess extracellular glutamate causes excitotoxicity and neurological disease. hEAAT2 transports amino acids into cells against their concentration gradients by coupling uptake to the co-transport of Na+ and H+, and counter-transport of K+. Substrate transport also activates a thermodynamically uncoupled Cl- conductance, whose significance is unknown. Here, to dissect the molecular mechanisms underlying coupled and uncoupled ion transport by EAATs, we leverage the tractable Drosophila melanogaster homologue dEAAT2, which transports taurine as well as glutamate and aspartate. By functionally characterising dEAAT2, we confirmed it has features of a canonical EAAT transport cycle, including an uncoupled Cl- conductance. However, it functions an ion-independent electroneutral exchanger, in stark contrast to its ion-coupled electrogenic human counterpart. Cryo-electron microscopy (cryo-EM) and computational simulations confirmed the inability of dEAAT2 to transport cations, but just two point mutations conferred Na+, H+, and K+ dependence, reconstituting the complex ion coupling profile of human transporters in the Drosophila exchanger. We also showed that dEAAT2 transports taurine in a complex with Cl-, bestowing a unique Cl--dependence on taurine transport, independent of uncoupled Cl- flux. Our findings show that ancestral exchangers in the EAAT family preserve the machinery to achieve complex ion-coupled transport, revealing the molecular basis of high-order ion coupling in hEAATs.

biophysics↗

bioRxiv2026

Characterizing the Conformational Dynamics of an Intrinsically Disordered Localization Sequence

Mitochondrial localization peptides (MLPs) play a critical role in directing proteins to mitochondria, yet how subtle sequence variations influence their conformational behavior remains poorly understood. Here, we investigate the conformational dynamics of a 15-residue MLP derived from the androgen receptor, together with a comprehensive panel of single-residue variants generated by systematic substitution at the second position. Across all variants, the peptide remains intrinsically disordered, exhibiting broad conformational heterogeneity and no stable folded state. Global measures of compactness show that single-residue substitutions induce only modest changes to overall peptide dimensions. In contrast, residue-level analysis reveals that the identity of the second residue subtly reshapes local structural preferences, particularly near the N-terminus. Small or hydrophobic substitutions enhance transient -helical sampling, whereas polar or charged substitutions favor increased disorder and {beta}- or polyprolinelike conformations. Comparison across variants further distinguishes mutations that preserve wild-type-like structural behavior from those that produce more pronounced deviations in the conformational ensemble. Enhanced sampling simulations highlight the complexity and ruggedness of the underlying free-energy landscape and demonstrate the challenges associated with achieving convergence for short intrinsically disordered peptides. Collectively, these results show that even minimal sequence changes can bias the dynamic structural ensemble of mitochondrial localization peptides, suggesting a potential mechanism by which targeting efficiency may be modulated. More broadly, this work underscores the importance of advanced sampling strategies for accurately characterizing intrinsically disordered localization signals and provides a framework for connecting sequence variation to functional targeting behavior.

biophysics↗

bioRxiv2019

Thermodynamic and Kinetic Characterization of Protein Conformational Dynamics within a Riemannian Diffusion Formalism

We have formulated a Riemannian framework for describing the geometry of collective variable spaces of biomolecules within the context of collective variable based molecular dynamics simulations. The formalism provides a theoretical framework to develop enhanced sampling techniques, path-finding algorithms, and transition rate estimators consistent with a Riemannian treatment of the collective variable space, where the quantities of interest such as the potential of the mean force, minimum free energy path, the diffusion constant, and the transition rate remain invariant under coordinate transformation due to the Riemannian treatment of the collective variable space. Specific algorithms within this framework are discussed such as the Riemannian umbrella sampling, the Riemannian string method, and a Riemannian-Bayesian estimator of free energy and diffusion constant, which can be used to estimate the transition rate along a minimum free energy path.

biophysics↗