A new mechanism of voltage-dependent gating exposed by KV10.1 channels interrupted between voltage sensor and pore

Voltage-gated ion channels couple transmembrane potential changes to ion flow. Conformational changes in the voltage-sensing domain (VSD) of the channel are thought to be transmitted to the pore domain (PD) through an α-helical linker between them (S4-S5 linker). However, our recent work on channels disrupted in the S4-S5 linker has challenged this interpretation for the KCNH family. Furthermore, a recent single-particle cryo-electron microscopy structure of KV10.1 revealed that the S4-S5 linker is a short loop in this KCNH family member, confirming the need for an alternative gating model. Here we use "split" channels made by expression of VSD and PD as separate fragments to investigate the mechanism of gating in KV10.1. We find that disruption of the covalent connection within the S4 helix compromises the ability of channels to close at negative voltage, whereas disconnecting the S4-S5 linker from S5 slows down activation and deactivation kinetics. Surprisingly, voltage-clamp fluorometry and MTS accessibility assays show that the motion of the S4 voltage sensor is virtually unaffected when VSD and PD are not covalently bound. Finally, experiments using constitutively open PD mutants suggest that the presence of the VSD is structurally important for the conducting conformation of the pore. Collectively, our observations offer partial support to the gating model that assumes that an inward motion of the C-terminal S4 helix, rather than the S4-S5 linker, closes the channel gate, while also suggesting that control of the pore by the voltage sensor involves more than one mechanism

Voltage-dependent gating of KCNH potassium channels lacking a covalent link between voltage-sensing and pore domains

Voltage-gated channels open paths for ion permeation upon changes in membrane potential, but how voltage changes are coupled to gating is not entirely understood. Two modules can be recognized in voltage-gated potassium channels, one responsible for voltage sensing (transmembrane segments S1 to S4), the other for permeation (S5 and S6). It is generally assumed that the conversion of a conformational change in the voltage sensor into channel gating occurs through the intracellular S4–S5 linker that provides physical continuity between the two regions. Using the pathophysiologically relevant KCNH family, we show that truncated proteins interrupted at, or lacking the S4–S5 linker produce voltage-gated channels in a heterologous model that recapitulate both the voltage-sensing and permeation properties of the complete protein. These observations indicate that voltage sensing by the S4 segment is transduced to the channel gate in the absence of physical continuity between the modules

Mapping genetic variations to three- dimensional protein structures to enhance variant interpretation: a proposed framework

The translation of personal genomics to precision medicine depends on the accurate interpretation of the multitude of genetic variants observed for each individual. However, even when genetic variants are predicted to modify a protein, their functional implications may be unclear. Many diseases are caused by genetic variants affecting important protein features, such as enzyme active sites or interaction interfaces. The scientific community has catalogued millions of genetic variants in genomic databases and thousands of protein structures in the Protein Data Bank. Mapping mutations onto three-dimensional (3D) structures enables atomic-level analyses of protein positions that may be important for the stability or formation of interactions; these may explain the effect of mutations and in some cases even open a path for targeted drug development. To accelerate progress in the integration of these data types, we held a two-day Gene Variation to 3D (GVto3D) workshop to report on the latest advances and to discuss unmet needs. The overarching goal of the workshop was to address the question: what can be done together as a community to advance the integration of genetic variants and 3D protein structures that could not be done by a single investigator or laboratory? Here we describe the workshop outcomes, review the state of the field, and propose the development of a framework with which to promote progress in this arena. The framework will include a set of standard formats, common ontologies, a common application programming interface to enable interoperation of the resources, and a Tool Registry to make it easy to find and apply the tools to specific analysis problems. Interoperability will enable integration of diverse data sources and tools and collaborative development of variant effect prediction methods

ZFIRE: Similar Stellar Growth in Hα-emitting Cluster and Field Galaxies at z ~ 2

We compare galaxy scaling relations as a function of environment at $z\sim2$ with our ZFIRE survey where we have measured H$\alpha$ fluxes for 90 star-forming galaxies selected from a mass-limited [$\log(M_{\star}/M_{\odot})>9$] sample based on ZFOURGE. The cluster galaxies (37) are part of a confirmed system at z=2.095 and the field galaxies (53) are at $1.9<z<2.4$; all are in the COSMOS legacy field. There is no statistical difference between H$\alpha$-emitting cluster and field populations when comparing their star formation rate (SFR), stellar mass ($M_{\star}$), galaxy size ($r_{eff}$), SFR surface density [$\Sigma$(H$\alpha_{star}$)], and stellar age distributions. The only difference is that at fixed stellar mass, the H$\alpha$-emitting cluster galaxies are $\log(r_{eff})\sim0.1$ larger than in the field. Approximately 19% of the H$\alpha$-emitters in the cluster and 26% in the field are IR-luminous ($L_{IR}>2\times10^{11} L_{\odot}$). Because the LIRGs in our combined sample are $\sim5$ times more massive than the low-IR galaxies, their radii are $\sim70$% larger. To track stellar growth, we separate galaxies into those that lie above, on, and below the H$\alpha$ star-forming main sequence (SFMS) using $\Delta$SFR$(M_{\star})=\pm0.2$ dex. Galaxies above the SFMS (starbursts) tend to have higher H$\alpha$ SFR surface densities and younger light-weighted stellar ages compared to galaxies below the SFMS. Our results indicate that starbursts (+SFMS) in the cluster and field at $z\sim2$ are growing their stellar cores. Lastly, we compare to the (SFR-$M_{\star}$) relation from RHAPSODY cluster simulations and find the predicted slope is nominally consistent with the observations. However, the predicted cluster SFRs tend to be too low by a factor of $\sim2$ which seems to be a common problem for simulations across environment.Comment: ApJ in press; full version of Table 1 available from ApJ and upon request. Survey websites are http://zfire.swinburne.edu.au and http://zfourge.tamu.ed

THE SAMI GALAXY SURVEY: REVISITING GALAXY CLASSIFICATION THROUGH HIGH-ORDER STELLAR KINEMATICS

Recent cosmological hydrodynamical simulations suggest that integral field spectroscopy can connect the high-order stellar kinematic moments h3 (~skewness) and h4 (~kurtosis) in galaxies to their cosmological assembly history. Here, we assess these results by measuring the stellar kinematics on a sample of 315 galaxies, without a morphological selection, using 2D integral field data from the SAMI Galaxy Survey. A proxy for the spin parameter ($\lambda_{R_e}$) and ellipticity ($\epsilon_e$) are used to separate fast and slow rotators; there exists a good correspondence to regular and non-regular rotators, respectively, as also seen in earlier studies. We confirm that regular rotators show a strong h3 versus $V/\sigma$ anti-correlation, whereas quasi-regular and non-regular rotators show a more vertical relation in h3 and $V/\sigma$. Motivated by recent cosmological simulations, we develop an alternative approach to kinematically classify galaxies from their individual h3 versus $V/\sigma$ signatures. We identify five classes of high-order stellar kinematic signatures using Gaussian mixture models. Class 1 corresponds to slow rotators, whereas Classes 2-5 correspond to fast rotators. We find that galaxies with similar $\lambda_{R_e}-\epsilon_e$ values can show distinctly different h3-$V/\sigma$ signatures. Class 5 objects are previously unidentified fast rotators that show a weak h3 versus $V/\sigma$ anti-correlation. These objects are predicted to be disk-less galaxies formed by gas-poor mergers. From morphological examination, however, there is evidence for large stellar disks. Instead, Class 5 objects are more likely disturbed galaxies, have counter-rotating bulges, or bars in edge-on galaxies. Finally, we interpret the strong anti-correlation in h3 versus $V/\sigma$ as evidence for disks in most fast rotators, suggesting a dearth of gas-poor mergers among fast rotators.Comment: Accepted for Publication in The Astrophysical Journal. 35 pages and 30 figures, abstract abridged for arXiv submission. The key figures of the paper are: 7, 11, 12 , and 1