Ali Nekouzadeh

A multiscale model linking ion-channel molecular dynamics and electrostatics to the cardiac action potential

Ion-channel function is determined by its gating movement. Yet, molecular dynamics and electrophysiological simulations were never combined to link molecular structure to function. We performed multiscale molecular dynamics and continuum electrostatics calculations to simulate a cardiac K+ channel (IKs) gating and its alteration by mutations that cause arrhythmias and sudden death. An all-atom model of the IKs α-subunit KCNQ1, based on the recent Kv1.2 structure, is used to calculate electrostatic energies during gating. Simulations are compared with experiments where varying degrees of positive charge—added via point mutation—progressively reduce current. Whole-cell simulations show that mutations cause action potential and ECG QT interval prolongation, consistent with clinical phenotypes. This framework allows integration of multiscale observations to study the molecular basis of excitation and its alteration by disease.

Incremental mechanics of collagen gels: new experiments and a new viscoelastic model.

AbstractPaired incremental uniaxial step (i.e., relaxation) and ramp tests were conducted simultaneously on four (nominally) identical samples of type I collagen gel, over a direct strain range 0 < ɛ < 0.2. The paired step and ramp responses could not both be predicted by a simple viscoelastic constitutive relation (either linear or Fung-type), but could be predicted reasonably accurately by a general nonlinear viscoelastic relation with a strain-dependent relaxation spectrum, of the form

Physically-Induced Cytoskeleton Remodeling of Cells in Three-Dimensional Culture

\sigma (t){} = \int {_{ - \infty}^t g(t - \tau ;\varepsilon )} [d\varepsilon (\tau )/d\tau ]d\tau .

Wave motion in relaxation-testing of nonlinear elastic media

Based on a four-term exponential-series approximation, we measured the stiffness moduli and time constants of the relaxation function, g(t,\varepsilon ), for the four gel samples that we tested, and found that the time constants were independent of strain but the moduli increased strongly with strain. Further, we found that the time constants did not vary across the four gels, but the moduli varied by a factor of about 2 across the gels. Some additional tests show features of the response of collagen gels to cycles of application and removal of loading.

A cost model for optimizing the take back phase of used product recovery

The voltage-sensing domain of voltage-gated channels is comprised of four transmembrane helices (S1–S4), with conserved positively charged residues in S4 moving across the membrane in response to changes in transmembrane voltage. Although it has been shown that positive charges in S4 interact with negative countercharges in S2 and S3 to facilitate protein maturation, how these electrostatic interactions participate in channel gating remains unclear. We studied a mutation in Kv7.1 (also known as KCNQ1 or KvLQT1) channels associated with long QT syndrome (E1K in S2) and found that reversal of the charge at E1 eliminates macroscopic current without inhibiting protein trafficking to the membrane. Pairing E1R with individual charge reversal mutations of arginines in S4 (R1–R4) can restore current, demonstrating that R1–R4 interact with E1. After mutating E1 to cysteine, we probed E1C with charged methanethiosulfonate (MTS) reagents. MTS reagents could not modify E1C in the absence of KCNE1. With KCNE1, (2-sulfonatoethyl) MTS (MTSES)− could modify E1C, but [2-(trimethylammonium)ethyl] MTS (MTSET)+ could not, confirming the presence of a positively charged environment around E1C that allows approach by MTSES− but repels MTSET+. We could change the local electrostatic environment of E1C by making charge reversal and/or neutralization mutations of R1 and R4, such that MTSET+ modified these constructs depending on activation states of the voltage sensor. Our results confirm the interaction between E1 and the fourth arginine in S4 (R4) predicted from open-state crystal structures of Kv channels and reveal an E1–R1 interaction in the resting state. Thus, E1 engages in electrostatic interactions with arginines in S4 sequentially during the gating movement of S4. These electrostatic interactions contribute energetically to voltage-dependent gating and are important in setting the limits for S4 movement.

Continuum Molecular Simulation of Large Conformational Changes during Ion–Channel Gating

Characterizing how cells in three-dimensional (3D) environments or natural tissues respond to biophysical stimuli is a longstanding challenge in biology and tissue engineering. We demonstrate a strategy to monitor morphological and mechanical responses of contractile fibroblasts in a 3D environment. Cells responded to stretch through specific, cell-wide mechanisms involving staged retraction and reinforcement. Retraction responses occurred for all orientations of stress fibers and cellular protrusions relative to the stretch direction, while reinforcement responses, including extension of cellular processes and stress fiber formation, occurred predominantly in the stretch direction. A previously unreported role of F-actin clumps was observed, with clumps possibly acting as F-actin reservoirs for retraction and reinforcement responses during stretch. Responses were consistent with a model of cellular sensitivity to local physical cues. These findings suggest mechanisms for global actin cytoskeleton remodeling in non-muscle cells and provide insight into cellular responses important in pathologies such as fibrosis and hypertension.

Quantification of fibre polymerization through Fourier space image analysis.

Most potassium channels are tetramers of four homologous polypeptides (subunits). During channel gating, each subunit undergoes several conformational changes independent of the state of other subunits before reaching a permissive state, from which the channel can open. However, transition from the permissive states to the open state involves a concerted movement of all subunits. This cooperative transition must be included in Markov models of channel gating. Previously, it was implemented by considering all possible combinations of four subunit states in a much larger expanded model of channel states (e.g., 27,405 channel states versus 64 subunit states), which complicates modeling and is computationally intense, especially when accurate modeling requires a large number of subunit states. To overcome these complexities and retain the tetrameric molecular structure, a modeling approach was developed to incorporate the cooperative transition directly from the subunit models. In this approach, the open state is separated from the subunit models and represented by the net flux between the open state and the permissive states. Dynamic variations of the probability of state residencies computed using this direct approach and the expanded model were identical. Implementation of the direct approach is simple and its computational time is orders-of-magnitude shorter than the equivalent expanded model.

Adaptive Quasi-Linear Viscoelastic Modeling

Relaxation testing is a fundamental tool for mechanical characterization of viscoelastic materials. Inertial effects are usually neglected when analysing these tests. However, relaxation tests involve sudden stretching of specimens, which causes propagation of waves whose effects may be significant. We study wave motion in a nonlinear elastic model specimen and derive expressions for the conditions under which loading may be considered to be quasi-static. Additionally, we derive expressions for wave properties such as wave speed and the time needed to reach a steady-state wave pattern. These expressions can be used to deduce nonlinear elastic material properties from dynamic experiments.