Tomas Perez-Acle

Molecular Basis of Ligand Dissociation in β-Adrenergic Receptors

The important and diverse biological functions of β-adrenergic receptors (βARs) have promoted the search for compounds to stimulate or inhibit their activity. In this regard, unraveling the molecular basis of ligand binding/unbinding events is essential to understand the pharmacological properties of these G protein-coupled receptors. In this study, we use the steered molecular dynamics simulation method to describe, in atomic detail, the unbinding process of two inverse agonists, which have been recently co-crystallized with β1 and β2ARs subtypes, along four different channels. Our results indicate that this type of compounds likely accesses the orthosteric binding site of βARs from the extracellular water environment. Importantly, reconstruction of forces and energies from the simulations of the dissociation process suggests, for the first time, the presence of secondary binding sites located in the extracellular loops 2 and 3 and transmembrane helix 7, where ligands are transiently retained by electrostatic and Van der Waals interactions. Comparison of the residues that form these new transient allosteric binding sites in both βARs subtypes reveals the importance of non-conserved electrostatic interactions as well as conserved aromatic contacts in the early steps of the binding process.

Keratitis-ichthyosis-deafness syndrome-associated Cx26 mutants produce nonfunctional gap junctions but hyperactive hemichannels when co-expressed with wild type Cx43.

Mutations in Cx26 gene are found in most cases of human genetic deafness. Some mutations produce syndromic deafness associated with skin disorders, like Keratitis Ichthyosis Deafness syndrome (KID). Because in the human skin Cx26 is co-expressed with other connexins, like Cx43 and Cx30, and since KID syndrome is inherited as autosomal dominant condition, it is possible that KID mutations change the way Cx26 interacts with other co-expressed connexins. Indeed, some Cx26 syndromic mutations showed gap junction dominant negative effect when co-expressed with wild type connexins, including Cx26 and Cx43. The nature of these interactions and the consequences on hemichannels and gap junction channels functions remain unknown. In this study we demonstrate that syndromic mutations at the N-terminus segment of Cx26, change connexin oligomerization compatibility, allowing aberrant interactions with Cx43. Strikingly, heteromeric oligomer formed by Cx43/Cx26 (syndromic mutants) show exacerbated hemichannel activity, but nonfunctional gap junction channels; this also occurs for those Cx26 KID mutants that do not show functional homomeric hemichannels. Heterologous expression of these hyperactive heteromeric hemichannels increases cell membrane permeability, favoring ATP release and Ca2+ overload. The functional paradox produced by oligomerization of Cx43 and Cx26 KID mutants could underlie the severe syndromic phenotype in human skin.

Exploring the Membrane Potential of Simple Dual-Membrane Systems as Models for Gap-Junction Channels

The conductance of ion channels can be modulated by a transmembrane potential difference, due to alterations on ion-mobility and also by changes in the pore structure. Despite the vast knowledge regarding the influence of voltage on transport properties of ion channels, little attention has been paid to describe, with atomic detail, the modulation of ionic transport in gap-junction channels (GJCs). Hence, molecular dynamics simulations were performed to explore the conductance of simple dual-membrane systems that account for the very basic features of GJCs. In doing so, we studied the influence of different charge distributions in the channel surface on these idealized systems under external electric fields, paying attention to the behavior of the electrostatic potential, ion density, ion currents, and equilibrium properties. Our results demonstrate that the incorporation of a charge distribution akin GJCs decreased anionic currents, favoring the transport of cationic species. Moreover, a thermodynamic characterization of ionic transport in these systems demonstrate the existence of a kinetic barrier that hinders anionic currents, reinforcing the role played by the internal arrangement of charges in GJCs. Overall, our results provide insights at the atomic scale on the effects of charge distributions over ionic transport, constituting a step forward into a better understanding of GJCs.

On Biophysical Properties and Sensitivity to Gap Junction Blockers of Connexin 39 Hemichannels Expressed in HeLa Cells

Although connexins (Cxs) are broadly expressed by cells of mammalian organisms, Cx39 has a very restricted pattern of expression and the biophysical properties of Cx39-based channels [hemichannels (HCs) and gap junction channels (GJCs)] remain largely unknown. Here, we used HeLa cells transfected with Cx39 (HeLa-Cx39 cells) in which intercellular electrical coupling was not detected, indicating the absence of GJCs. However, functional HCs were found on the surface of cells exposed to conditions known to increase the open probability of other Cx HCs (e.g., extracellular divalent cationic-free solution (DCFS), extracellular alkaline pH, mechanical stimulus and depolarization to positive membrane potentials). Cx39 HCs were blocked by some traditional Cx HC blockers, but not by others or a pannexin1 channel blocker. HeLa-Cx39 cells showed similar resting membrane potentials (RMPs) to those of parental cells, and exposure to DCFS reduced RMPs in Cx39 transfectants, but not in parental cells. Under these conditions, unitary events of ~75 pS were frequent in HeLa-Cx39 cells and absent in parental cells. Real-time cellular uptake experiments of dyes with different physicochemical features, as well as the application of a machine-learning approach revealed that Cx39 HCs are preferentially permeable to molecules characterized by six categories of descriptors, namely: (1) electronegativity, (2) ionization potential, (3) polarizability, (4) size and geometry, (5) topological flexibility and (6) valence. However, Cx39 HCs opened by mechanical stimulation or alkaline pH were impermeable to Ca2+. Molecular modeling of Cx39-based channels suggest that a constriction present at the intracellular portion of the para helix region co-localizes with an electronegative patch, imposing an energetic and steric barrier, which in the case of GJCs may hinder channel function. Results reported here demonstrate that Cx39 form HCs and add to our understanding of the functional roles of Cx39 HCs under physiological and pathological conditions in cells that express them.

From dimers to collective dipoles: Structure and dynamics of methanol/ethanol partition by narrow carbon nanotubes

Alcohol partitioning by narrow single-walled carbon nanotubes (SWCNTs) holds the promise for the development of novel nanodevices for diverse applications. Consequently, in this work, the partition of small alcohols by narrow tubes was kinetically and structurally quantified via molecular dynamics simulations. Alcohol partitioning is a fast process in the order of 10 ns for diluted solutions but the axial-diffusivity within SWCNT is greatly diminished being two to three orders of magnitude lower with respect to bulk conditions. Structurally, alcohols form a single-file conformation under confinement and more interestingly, they exhibit a pore-width dependent transition from dipole dimers to a single collective dipole, for both methanol and ethanol. Energetic analyses demonstrate that this transition is the result of a detailed balance between dispersion and electrostatics interactions, with the latter being more pronounced for collective dipoles. This transition fully modifies the reorientational dynamics of the loaded particles, generating stable collective dipoles that could find usage in signal-amplification devices. Overall, the results herein have shown distinct physico-chemical features of confined alcohols and are a further step towards the understanding and development of novel nanofluidics within SWCNTs.

Tryptophan Scanning Reveals Dense Packing of Connexin Transmembrane Domains in Gap Junction Channels Composed of Connexin32

Background: Transmembrane domain interactions in gap junction channels are poorly understood. Results: Tryptophan substitution experiments involving all four TM domains of Cx32 revealed tight packing. Conclusion: After modeling, tight packing was found to occur in the midregion. Pore-facing residues were highly sensitive to substitution, whereas lipid-facing residues were variably tolerant. Significance: Connexin-based channels are more densely packed than their innexin-based counterparts. Tryptophan was substituted for residues in all four transmembrane domains of connexin32. Function was assayed using dual cell two-electrode voltage clamp after expression in Xenopus oocytes. Tryptophan substitution was poorly tolerated in all domains, with the greatest impact in TM1 and TM4. For instance, in TM1, 15 substitutions were made, six abolished coupling and five others significantly reduced function. Only TM2 and TM3 included a distinct helical face that lacked sensitivity to tryptophan substitution. Results were visualized on a comparative model of Cx32 hemichannel. In this model, a region midway through the membrane appears highly sensitive to tryptophan substitution and includes residues Arg-32, Ile-33, Met-34, and Val-35. In the modeled channel, pore-facing regions of TM1 and TM2 were highly sensitive to tryptophan substitution, whereas the lipid-facing regions of TM3 and TM4 were variably tolerant. Residues facing a putative intracellular water pocket (the IC pocket) were also highly sensitive to tryptophan substitution. Although future studies will be required to separate trafficking-defective mutants from those that alter channel function, a subset of interactions important for voltage gating was identified. Interactions important for voltage gating occurred mainly in the mid-region of the channel and focused on TM1. To determine whether results could be extrapolated to other connexins, TM1 of Cx43 was scanned revealing similar but not identical sensitivity to TM1 of Cx32.

Towards bio-silicon interfaces: formation of an ultra-thin self-hydrated artificial membrane composed of dipalmitoylphosphatidylcholine (DPPC) and chitosan deposited in high vacuum from the gas-phase.

The recent combination of nanoscale developments with biological molecules for biotechnological research has opened a wide field related to the area of biosensors. In the last years, device manufacturing for medical applications adapted the so-called bottom-up approach, from nanostructures to larger devices. Preparation and characterization of artificial biological membranes is a necessary step for the formation of nano-devices or sensors. In this paper, we describe the formation and characterization of a phospholipid bilayer (dipalmitoylphosphatidylcholine, DPPC) on a mattress of a polysaccharide (Chitosan) that keeps the membrane hydrated. The deposition of Chitosan (~25 Å) and DPPC (~60 Å) was performed from the gas phase in high vacuum onto a substrate of Si(100) covered with its native oxide layer. The layer thickness was controlled in situ using Very High Resolution Ellipsometry (VHRE). Raman spectroscopy studies show that neither Chitosan nor DPPC molecules decompose during evaporation. With VHRE and Atomic Force Microscopy we have been able to detect phase transitions in the membrane. The presence of the Chitosan interlayer as a water reservoir is essential for both DPPC bilayer formation and stability, favoring the appearance of phase transitions. Our experiments show that the proposed sample preparation from the gas phase is reproducible and provides a natural environment for the DPPC bilayer. In future work, different Chitosan thicknesses should be studied to achieve a complete and homogeneous interlayer.

The syndromic deafness mutation G12R impairs fast and slow gating in Cx26 hemichannels

Mutations in connexin 26 (Cx26) hemichannels can lead to syndromic deafness that affects the cochlea and skin. These mutations lead to gain-of-function hemichannel phenotypes by unknown molecular mechanisms. In this study, we investigate the biophysical properties of the syndromic mutant Cx26G12R (G12R). Unlike wild-type Cx26, G12R macroscopic hemichannel currents do not saturate upon depolarization, and deactivation is faster during hyperpolarization, suggesting that these channels have impaired fast and slow gating. Single G12R hemichannels show a large increase in open probability, and transitions to the subconductance state are rare and short-lived, demonstrating an inoperative fast gating mechanism. Molecular dynamics simulations indicate that G12R causes a displacement of the N terminus toward the cytoplasm, favoring an interaction between R12 in the N terminus and R99 in the intracellular loop. Disruption of this interaction recovers the fast and slow voltage-dependent gating mechanisms. These results suggest that the mechanisms of fast and slow gating in connexin hemichannels are coupled and provide a molecular mechanism for the gain-of-function phenotype displayed by the syndromic G12R mutation.

Changes in Olfactory Receptor Expression Are Correlated With Odor Exposure During Early Development in the zebrafish ( Danio rerio )

We have previously shown that exposure to phenyl ethyl alcohol (PEA) causes an increase in the expression of the transcription factor otx2 in the olfactory epithelium (OE) of juvenile zebrafish, and this change is correlated with the formation of an odor memory of PEA. Here, we show that the changes in otx2 expression are specific to βPEA: exposure to αPEA did not affect otx2 expression. We identified 34 olfactory receptors (ORs) representing 16 families on 4 different chromosomes as candidates for direct regulation of OR expression via Otx2. Subsequent in silico analysis uncovered Hnf3b binding sites closely associated with Otx2 binding sites in the regions flanking the ORs. Analysis by quantitative polymerase chain reaction and RNA-seq of OR expression in developing zebrafish exposed to different isoforms of PEA showed that a subset of ORs containing both Otx2/Hnf3b binding sites were downregulated only in βPEA-exposed juveniles and this change persisted through adult life. Localization of OR expression by in situ hybridization indicates the downregulation occurs at the level of RNA and not the number of cells expressing a given receptor. Finally, analysis of immediate early gene expression in the OE did not reveal changes in c-fos expression in response to either αPEA or βPEA.

Stochastic simulation of multiscale complex systems with PISKaS: A rule-based approach

Computational simulation is a widely employed methodology to study the dynamic behavior of complex systems. Although common approaches are based either on ordinary differential equations or stochastic differential equations, these techniques make several assumptions which, when it comes to biological processes, could often lead to unrealistic models. Among others, model approaches based on differential equations entangle kinetics and causality, failing when complexity increases, separating knowledge from models, and assuming that the average behavior of the population encompasses any individual deviation. To overcome these limitations, simulations based on the Stochastic Simulation Algorithm (SSA) appear as a suitable approach to model complex biological systems. In this work, we review three different models executed in PISKaS: a rule-based framework to produce multiscale stochastic simulations of complex systems. These models span multiple time and spatial scales ranging from gene regulation up to Game Theory. In the first example, we describe a model of the core regulatory network of gene expression in Escherichia coli highlighting the continuous model improvement capacities of PISKaS. The second example describes a hypothetical outbreak of the Ebola virus occurring in a compartmentalized environment resembling cities and highways. Finally, in the last example, we illustrate a stochastic model for the prisoners dilemma; a common approach from social sciences describing complex interactions involving trust within human populations. As whole, these models demonstrate the capabilities of PISKaS providing fertile scenarios where to explore the dynamics of complex systems.