Indigo, a rich blue dye, is an incredibly photostable molecule that has survived in ancient art for centuries. It is also unique in that it can undergo both an excited-state hydrogen and proton transfer on the picosecond timescale followed by a ground-state back transfer. Previously, we performed gas phase excited-state lifetime studies on indigo to study these processes in a solvent-free environment, combined with excited-state calculations. We found two decay pathways, a fast sub-nanosecond decay and a slow decay on the order of 10 ns. Calculations of the excited-state potential energy surface found that both hydrogen and proton transfer are nearly isoenergetic separated by a 0.1 eV barrier. To further elucidate these dynamics, we now report a study with deuterated indigo, using resonance-enhanced multi-photon ionization and pump-probe spectroscopy with mass spectrometric isotopomer selection. From new calculations of the excited-state potential energy surface, we find sequential double-proton or hydrogen transfer, whereby the trajectory to the second transfer passes a second barrier and then encounters a conical intersection that leads back to the ground state. We find that deuteration only increases the excited-state lifetimes of the fast decay channel, suggesting tunneling through the first barrier, while the slower channel is not affected and may involve a different intermediate state.
Hv1 is a voltage-gated proton channel whose main function is to facilitate extrusion of protons from the cell. The development of effective channel blockers for Hv1 can lead to new therapeutics for the treatment of maladies related to Hv1 dysfunction. Although the mechanism of proton permeation in Hv1 remains to be elucidated, a series of small molecules have been discovered to inhibit Hv1. Here, we computed relative binding free energies of a prototypical Hv1 blocker on a model of human Hv1 in an open state. We used alchemical free energy perturbation techniques based on atomistic molecular dynamics simulations. The results support our proposed open state model and shed light on the preferred tautomeric state of the channel blocker. This work lays the groundwork for future studies on adapting the blocker molecule for more effective inhibition of Hv1.
more » « less- NSF-PAR ID:
- 10183257
- Publisher / Repository:
- Nature Publishing Group
- Date Published:
- Journal Name:
- Scientific Reports
- Volume:
- 10
- Issue:
- 1
- ISSN:
- 2045-2322
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Graphical abstract -
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Voltage-gated sodium, potassium, and calcium channels consist of four voltage-sensing domains (VSDs) that surround a central pore domain and transition from a down state to an up state in response to membrane depolarization. While many types of drugs bind pore domains, the number of organic molecules known to bind VSDs is limited. The Hv1 voltage-gated proton channel is made of two VSDs and does not contain a pore domain, providing a simplified model for studying how small ligands interact with VSDs. Here, we describe a ligand, named HIF, that interacts with the Hv1 VSD in the up and down states. We find that HIF rapidly inhibits proton conduction in the up state by blocking the open channel, as previously described for 2-guanidinobenzimidazole and its derivatives. HIF, however, interacts with a site slowly accessible in the down state. Functional studies and MD simulations suggest that this interaction traps the compound in a narrow pocket lined with charged residues within the VSD intracellular vestibule, which results in slow recovery from inhibition. Our findings point to a “wrench in gears” mechanism whereby side chains within the binding pocket trap the compound as the teeth of interlocking gears. We propose that the use of screening strategies designed to target binding sites with slow accessibility, similar to the one identified here, could lead to the discovery of new ligands capable of interacting with VSDs of other voltage-gated ion channels in the down state.
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Abstract Pentameric ligand-gated ion channels (pLGICs) mediate synaptic transmission and are sensitive to their lipid environment. The mechanism of phospholipid modulation of any pLGIC is not well understood. We demonstrate that the model pLGIC, ELIC (
Erwinia ligand-gated ion channel), is positively modulated by the anionic phospholipid, phosphatidylglycerol, from the outer leaflet of the membrane. To explore the mechanism of phosphatidylglycerol modulation, we determine a structure of ELIC in an open-channel conformation. The structure shows a bound phospholipid in an outer leaflet site, and structural changes in the phospholipid binding site unique to the open-channel. In combination with streamlined alchemical free energy perturbation calculations and functional measurements in asymmetric liposomes, the data support a mechanism by which an anionic phospholipid stabilizes the activated, open-channel state of a pLGIC by specific, state-dependent binding to this site. -
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Key points Gap junctions formed by different connexins are expressed throughout the body and harbour unique channel properties that have not been fully defined mechanistically.
Recent structural studies by cryo‐electron microscopy have produced high‐resolution models of the related but functionally distinct lens connexins (Cx50 and Cx46) captured in a stable open state, opening the door for structure–function comparison.
Here, we conducted comparative molecular dynamics simulation and electrophysiology studies to dissect the isoform‐specific differences in Cx46 and Cx50 intercellular channel function.
We show that key determinants Cx46 and Cx50 gap junction channel open stability and unitary conductance are shaped by structural and dynamic features of their N‐terminal domains, in particular the residue at the 9th position and differences in hydrophobic anchoring sites.
The results of this study establish the open state Cx46/50 structural models as archetypes for structure–function studies targeted at elucidating the mechanism of gap junction channels and the molecular basis of disease‐causing variants.
Abstract Connexins form intercellular communication channels, known as gap junctions (GJs), that facilitate diverse physiological roles, from long‐range electrical and chemical coupling to coordinating development and nutrient exchange. GJs formed by different connexin isoforms harbour unique channel properties that have not been fully defined mechanistically. Recent structural studies on Cx46 and Cx50 defined a novel and stable open state and implicated the amino‐terminal (NT) domain as a major contributor for isoform‐specific functional differences between these closely related lens connexins. To better understand these differences, we constructed models corresponding to wildtype Cx50 and Cx46 GJs, NT domain swapped chimeras, and point variants at the 9th residue for comparative molecular dynamics (MD) simulation and electrophysiology studies. All constructs formed functional GJ channels, except the chimeric Cx46‐50NT variant, which correlated with an introduced steric clash and increased dynamical behaviour (instability) of the NT domain observed by MD simulation. Single channel conductance correlated well with free‐energy landscapes predicted by MD, but resulted in a surprisingly greater degree of effect. Additionally, we observed significant effects on transjunctional voltage‐dependent gating (
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Study of the doubly charmed tetraquark $${{{{{{\rm{T}}}}}}}_{{{{{{\rm{c}}}}}}{{{{{\rm{c}}}}}}}^{+}$$Abstract Quantum chromodynamics, the theory of the strong force, describes interactions of coloured quarks and gluons and the formation of hadronic matter. Conventional hadronic matter consists of baryons and mesons made of three quarks and quark-antiquark pairs, respectively. Particles with an alternative quark content are known as exotic states. Here a study is reported of an exotic narrow state in the D 0 D 0 π + mass spectrum just below the D *+ D 0 mass threshold produced in proton-proton collisions collected with the LHCb detector at the Large Hadron Collider. The state is consistent with the ground isoscalar $${{{{{{\rm{T}}}}}}}_{{{{{{\rm{c}}}}}}{{{{{\rm{c}}}}}}}^{+}$$ T c c + tetraquark with a quark content of $${{{{{\rm{c}}}}}}{{{{{\rm{c}}}}}}\overline{{{{{{\rm{u}}}}}}}\overline{{{{{{\rm{d}}}}}}}$$ c c u ¯ d ¯ and spin-parity quantum numbers J P = 1 + . Study of the DD mass spectra disfavours interpretation of the resonance as the isovector state. The decay structure via intermediate off-shell D *+ mesons is consistent with the observed D 0 π + mass distribution. To analyse the mass of the resonance and its coupling to the D * D system, a dedicated model is developed under the assumption of an isoscalar axial-vector $${{{{{{\rm{T}}}}}}}_{{{{{{\rm{c}}}}}}{{{{{\rm{c}}}}}}}^{+}$$ T c c + state decaying to the D * D channel. Using this model, resonance parameters including the pole position, scattering length, effective range and compositeness are determined to reveal important information about the nature of the $${{{{{{\rm{T}}}}}}}_{{{{{{\rm{c}}}}}}{{{{{\rm{c}}}}}}}^{+}$$ T c c + state. In addition, an unexpected dependence of the production rate on track multiplicity is observed.more » « less
