Cardiac cell modelling: Observations from the heart of the cardiac physiome project

In this manuscript we review the state of cardiac cell modelling in the context of international initiatives such as the IUPS Physiome and Virtual Physiological Human Projects, which aim to integrate computational models across scales and physics. In particular we focus on the relationship between experimental data and model parameterisation across a range of model types and cellular physiological systems. Finally, in the context of parameter identification and model reuse within the Cardiac Physiome, we suggest some future priority areas for this field

Structural basis for KCNE3 modulation of potassium recycling in epithelia

abstract: The single-span membrane protein KCNE3 modulates a variety of voltage-gated ion channels in diverse biological contexts. In epithelial cells, KCNE3 regulates the function of the KCNQ1 potassium ion (K[superscript +]) channel to enable K[superscript +] recycling coupled to transepithelial chloride ion (Cl[superscript −]) secretion, a physiologically critical cellular transport process in various organs and whose malfunction causes diseases, such as cystic fibrosis (CF), cholera, and pulmonary edema. Structural, computational, biochemical, and electrophysiological studies lead to an atomically explicit integrative structural model of the KCNE3-KCNQ1 complex that explains how KCNE3 induces the constitutive activation of KCNQ1 channel activity, a crucial component in K[superscript +] recycling. Central to this mechanism are direct interactions of KCNE3 residues at both ends of its transmembrane domain with residues on the intra- and extracellular ends of the KCNQ1 voltage-sensing domain S4 helix. These interactions appear to stabilize the activated “up” state configuration of S4, a prerequisite for full opening of the KCNQ1 channel gate. In addition, the integrative structural model was used to guide electrophysiological studies that illuminate the molecular basis for how estrogen exacerbates CF lung disease in female patients, a phenomenon known as the “CF gender gap.

Bioengineering models of cell signaling

Strategies for rationally manipulating cell behavior in cell-based technologies and molecular therapeutics and understanding effects of environmental agents on physiological systems may be derived from a mechanistic understanding of underlying signaling mechanisms that regulate cell functions. Three crucial attributes of signal transduction necessitate modeling approaches for analyzing these systems: an ever-expanding plethora of signaling molecules and interactions, a highly interconnected biochemical scheme, and concurrent biophysical regulation. Because signal flow is tightly regulated with positive and negative feedbacks and is bidirectional with commands traveling both from outside-in and inside-out, dynamic models that couple biophysical and biochemical elements are required to consider information processing both during transient and steady-state conditions. Unique mathematical frameworks will be needed to obtain an integrated perspective on these complex systems, which operate over wide length and time scales. These may involve a two-level hierarchical approach wherein the overall signaling network is modeled in terms of effective "circuit" or "algorithm" modules, and then each module is correspondingly modeled with more detailed incorporation of its actual underlying biochemical/biophysical molecular interactions

Molecular Dynamics Simulations to Probe Effects of Ultra-Short, Very-High Voltage Pulses on Cells

The use of very high electric fields (∼ 100kV/cm or higher) with pulse durations in the nanosecond range (Ultra-short) has been a very recent development in bioelectrics. Traditionally, the electric field effects have mostly been confined to: (a) low field, long-duration pulses, and (b) focused mainly on electroporation studies. Thus, aspects such as possible field-induced DNA damage, calcium release, alterations in neuro-transmitters, or voltage-gating have generally been overlooked. Ultra-short, high-field pulses open the way to targeted and deliberate apoptotic cell killing (e.g., of tumor cells). Though experimental data is very useful, it usually yields information on macroscopic variables that is inherently an average over time and/or space. Measurements often do not provide the molecular level information or details, as might be possible through numerical simulations. Also, the relevance and relative role of underlying physical mechanisms cannot be probed. With developments in computer technology, rapid advances in numerical algorithms for parallel computing, and with increasing computational resources, computer simulations of cellular dynamics and biological phenomena is gaining increasing popularity. A range of simulation methods exist that span the macroscopic continuum approaches (e.g. the Smoluchowski equation), to those based on the semi-classical retarded Langevin and Green\u27s functions, to microscopic-kinetic analyses based on Brownian dynamics or Molecular Dynamics (MD). Here we focus on the MD technique, as it provides the most comprehensive, time-dependent, three-dimensional nanoscale analyses with inclusion of the many-body aspects. This dissertation research presents simulations and analyses of lipid membrane poration and its dynamics, predictions of transport parameters under high-field, non-equilibrium conditions, electric fields effects on DNA, micelle disintegration, protein unfolding and intra-cellular calcium release. The following results have been found as a result of the application of external electric fields on cells: (a) Poration due to the re-orientation of the lipid molecules within the lipid bilayer, (b) Externalization of charged molecules such as Phosphotidyl Serine (PS), (c) Dramatic lowering of permittivity and diffusion coefficient with spatially structured layering of the membrane nanopore, (d) DNA alignment in the direction of electric field and eventual fragmentation, (e) Calcium release from the endoplasmic reticulum (ER) leading to time-dependent oscillatory waves and (f) Membrane fragmentation upon the application of high external fields

How do metalloenzymes propagate and control chemical reactions?

Enzymes control and propagate a dizzying array of chemical reactions, including radical reactions and reactions cleaving carbon-carbon bonds. Metalloenzymes, which contain a metal cofactor, are particularly adept at propagating these reactions. This thesis focuses on several metalloenzymes; each an example of a different unique reaction control strategy. Both experimental and computational methodologies have been employed in order to identify specific residues or features which contribute to each enzyme\u27s ability to control the reaction. Emphasis is made on special properties of the metal Manganese. Controlling residues include not only first shell or active site residues, but also residues more distant from the active-site. Further, manipulation of such residues can be used to alter reactivity at non -active-sites, or to alter the apparent electrostatics of the protein (in the case of substitution of hydrogen with fluorine). Electron Paramagnetic Resonance (EPR) and other forms of magnetic spectroscopy can be used to evaluate subtle differences imposed by substitution for controlling residues to a metal center, which gives further insight into the electronic contributions of given residues, as well as the electronic properties of metal cofactors. In summary, the catalysis by Mn-dependent and other metal-dependent metalloenzymes can be investigated through multiple kinetic and spectroscopic avenues, unveiling suprising and novel themes in enzymatic catalysis, such as mechano-chemical switches and super long-distance metallo-interactions

Theoretical and computational studies of the correlated ionic motion in narrow ion channels

An ion channel is a protein with a hole down its middle embedded into the cytoplasmic membrane of a living biological cells. Ion channels facilitate ionic transport across the membrane, thus bridging the intra- and extra-cellular compartments. Properly functioning channels contribute to the healthy state of an organism, making them one of the main targets for pharmaceutical applications. The description and prediction of a channel’s performance --conductivity, selectivity, blocking etc., -- under arbitrary experimental conditions starting from its crystal structure thus appears as an important challenge in contemporary theoretical research. The main obstacle for such description arises from the presence of the multiple non-negligible interactions in the system. These include ion-ion, ion-water, ion-ligands, ion-pore, and other interactions. Their self-consistent consideration is essential in narrow ion channels, where due to inter-ion interactions and atomic confinement, the ions move in a single-file highly-correlated manner. Molecular dynamics, the most detailed computational tool to date, does not allow one routinely to evaluate the properties of such channels, while continuous methods overlook the ion-ion interactions. Therefore, one needs a method that combines atomic details with the ability to estimate ionic currents. This thesis focuses on the classical treatment of ion channels. Namely, a Brownian Dynamics simulation is described where the interactions of the ion with other ions and the channel are incorporated via the multi-ion potential of the mean force (PMF). This allows one to model the channel’s behaviour under various experimental conditions, while preserving the details of the structure and nanoscale interactions with atomic precision. Secondly, we use the concept of a quasiparticle to describe the highly-correlated ionic motion in the selectivity filter of the KcsA channel. We derive the quasiparticle’s effective potential from the multi-ion atomic PMF, thus connecting the quasiparticle’s properties with the nanoscale features of the channel. We also evaluate the rates of transition between different quasiparticles by virtue of the BD simulation. These ingredients comprehensively describe the quasiparticle’s dynamics which hence serves as an intermediary between the crystal structure and the experimentally observed properties of a narrow ion channel. Lastly, an analytical method to describe the ion-solvent interaction is proposed. It incorporates the ion-solvent and ion-lattice radial density functions, and hence automatically accounts for the pore shape, the type of atoms comprising the lattice, the type of solvent, and the ion’s location near the pore entrance. This method paves the way to an analytical decomposition of single-ion PMFs, what is of fundamental importance in predicting the conductive and selective properties of mutated biological ion channels. This method can also find application in designing functionalized artificial nanopores with on-demand transport properties for efficient water desalination

Self-restoration of cardiac excitation rhythm by anti-arrhythmic ion channel gating

Homeostatic regulation protects organisms against hazardous physiological changes. However, such regulation is limited in certain organs and associated biological processes. For example, the heart fails to self-restore its normal electrical activity once disturbed, as with sustained arrhythmias. Here we present proof-of-concept of a biological self-restoring system that allows automatic detection and correction of such abnormal excitation rhythms. For the heart, its realization involves the integration of ion channels with newly designed gating properties into cardiomyocytes. This allows cardiac tissue to i) discriminate between normal rhythm and arrhythmia based on frequency-dependent gating and ii) generate an ionic current for termination of the detected arrhythmia. We show in silico, that for both human atrial and ventricular arrhythmias, activation of these channels leads to rapid and repeated restoration of normal excitation rhythm. Experimental validation is provided by injecting the designed channel current for arrhythmia termination in human atrial myocytes using dynamic clamp