Central Pore
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2021 ◽  
Kyle Tucker ◽  
Savitha Sridharan ◽  
Hillel Adesnik ◽  
Stephen G Brohawn

Microbial channelrhodopsins are light-gated ion channels widely used for optogenetic manipulation of neuronal activity. ChRmine is a bacteriorhodopsin-like cation channelrhodopsin (BCCR) more closely related to ion pump rhodopsins than other channelrhodopsins. ChRmine displays unique properties favorable for optogenetics including high light sensitivity, a red-shifted activation spectrum, cation selectivity, and large photocurrents while its slow closing kinetics impede some applications. The structural basis for ChRmine function, or that of any other BCCR, is unknown. Here, we present cryo-EM structures of ChRmine in lipid nanodiscs in apo (opsin) and retinal-bound (rhodopsin) forms. The structures reveal an unprecedented trimeric architecture with a lipid filled central pore. Large electronegative cavities on either side of the membrane facilitate high conductance and selectivity for cations over protons. The retinal binding pocket structure suggests spectral and kinetic properties could be tuned with mutations and we identify ChRmine variants with two-fold increased and ten-fold decreased closing rates. These results provide insight into structural features that generate an ultra-potent microbial opsin and provide a platform for rational engineering of channelrhodopsins with improved properties that could expand the scale, depth, and precision of optogenetic manipulations.

2021 ◽  
Vol 154 (1) ◽  
Zhuyuan Chen ◽  
Sheng Lin ◽  
Tianze Xie ◽  
Jin-Ming Lin ◽  
Cecilia M. Canessa

Proton-gated ion channels conduct mainly Na+ to induce postsynaptic membrane depolarization. Finding the determinants of ion selectivity requires knowledge of the pore structure in the open conformation, but such information is not yet available. Here, the open conformation of the hASIC1a channel was computationally modeled, and functional effects of pore mutations were analyzed in light of the predicted structures. The open pore structure shows two constrictions of similar diameter formed by the backbone of the GAS belt and, right beneath it, by the side chains of H28 from the reentrant loop. Models of nonselective mutant channels, but not those that maintain ion selectivity, predict enlargement of the GAS belt, suggesting that this motif is quite flexible and that the loss of stabilizing interactions in the central pore leads to changes in size/shape of the belt. Our results are consistent with the “close-fit” mechanism governing selectivity of hASIC1a, wherein the backbone of the GAS substitutes at least part of the hydration shell of a permeant ion to enable crossing the pore constriction.

2021 ◽  
Qian Yu ◽  
Yanxian Wang ◽  
Yuling Shi ◽  
Jun Gu

Abstract Background Epidermal cysts are common skin tumors that are composed of a keratinocytic cyst wall and central keratin material, which can occur anywhere in the body, especially on the face. However, there are no relevant reports of multiple epidermal cysts coexisting at the same location.Case presentation Here, we report one rare case of facial multiple epidermal cysts, who underwent sequential resection of all cysts. A 45-year-old male presented with facial multiple masses for over 2 years. Physical examination showed multiple cysts with varied sizes on the face. All cysts were smooth, dome-shaped, freely movable, and some of them were attached to the skin by a central pore. The histopathology revealed cysts in the dermis, the wall of which were composed of stratified squamous epithelium, and the cavity were filled with keratin. Therefore, the patient was diagnosed as facial multiple epidermal cysts.Conclusions This is the first well-documented case of multiple epidermal cysts on the face. We report this rare case to highlight that although epidermal cysts usually appear single, they may also appear multiple in the same location, especially in those patients with vigorous sebaceous gland function. Surgical excision is the first-line effective treatment for epidermal cysts.

2021 ◽  
Shyamal Mosalaganti ◽  
Agnieszka Obarska-Kosinska ◽  
Marc Siggel ◽  
Beata Turonova ◽  
Christian E Zimmerli ◽  

Nuclear pore complexes (NPCs) mediate nucleocytoplasmic transport. Their intricate 120 MDa architecture remains incompletely understood. Here, we report a near-complete structural model of the human NPC scaffold with explicit membrane and in multiple conformational states. We combined AI-based structure prediction with in situ and in cellulo cryo-electron tomography and integrative modeling. We show that linker Nups spatially organize the scaffold within and across subcomplexes to establish the higher-order structure. Microsecond-long molecular dynamics simulations suggest that the scaffold is not required to stabilize the inner and outer nuclear membrane fusion, but rather widens the central pore. Our work exemplifies how AI-based modeling can be integrated with in situ structural biology to understand subcellular architecture across spatial organization levels.

2021 ◽  
Zhejian Ji ◽  
Hao Li ◽  
Daniele Peterle ◽  
Joao A Paulo ◽  
Scott B Ficarro ◽  

The hexameric Cdc48 ATPase (p97 or VCP in mammals) cooperates with its cofactor Ufd1/Npl4 to extract polyubiquitinated proteins from membranes or macromolecular complexes for degradation by the proteasome. Here, we clarify how the Cdc48 complex unfolds its substrates and translocates polypeptides with branchpoints. The Cdc48 complex recognizes primarily polyubiquitin chains, rather than the attached substrate. Cdc48 and Ufd1/Npl4 cooperatively bind the polyubiquitin chain, resulting in the unfolding of one ubiquitin molecule (initiator). Next, the ATPase pulls on the initiator ubiquitin and moves all ubiquitin molecules linked to its C-terminus through the central pore of the hexameric double-ring, causing transient ubiquitin unfolding. When the ATPase reaches the isopeptide bond of the substrate, it can translocate and unfold both N- and C-terminal segments. Ubiquitins linked to the branchpoint of the initiator dissociate from Ufd1/Npl4 and move outside the central pore, resulting in the release of unfolded, polyubiquitinated substrate from Cdc48.

Processes ◽  
2021 ◽  
Vol 9 (10) ◽  
pp. 1821
Luis Fernando Capa-Cobos ◽  
Ximena Jaramillo-Fierro ◽  
Silvia González

The adsorption of sodium dihydrogen phosphate (NaH2PO4) onto X- and Y-type faujasite zeolites was computationally studied using the Density Functional Theory (DFT) method. The structures were modeled using the Materials Studio software. The Si/Al ratios for the X- and Y-type zeolite models were 1.2 and 2.5, respectively. The central pore of the zeolite provided a more favorable coordination for adsorbing NaH2PO4. Full molecular optimization and adsorption energy calculations were performed using the VASP code. The adsorption was more effective on zeolite Y, with an adsorption energy of 161 kJ/mol, compared to the zeolite X system, with an adsorption energy of 31.64 kJ/mol. This calculated value for X-type faujasite was found in the interval of the adsorption energy of H2PO4− on hydrated Fe oxide (94.4 kJ/mol) and modified polyether sulfone (22.5 kJ/mol), and the calculated adsorption energy of the molecule on Y-type faujasite coincides with the reported value for this adsorbate on Mg/Ca-modified biochar structures. The molecular conformations of the adsorbate on the two studied models are very different, so the difference between the adsorption energy values of each type of zeolite model is comprehensible. On the one hand, the oxygen atoms of the molecule formed a bidentate complex with the hydrogen atoms of the pore in the X-type faujasite model, and the O-H distance was 1.5 Ǻ. On the other hand, an adsorbed oxygen atom of the phosphate was placed on a hydrogen atom at site II of the Y-type faujasite zeolite, and two of the hydrogen atoms of the phosphate were placed on the oxygen atoms. The Bader analysis results indicated that the negative charge of the phosphate anions was delocalized on the zeolites protons. The hydroxy groups of the phosphate form bonds between their hydrogen atoms and the oxygen atoms of the zeolite porous structure; therefore, we concluded that these sites have an alkaline character. The aim of this study was to include a computational analysis of possible phosphate adsorption mechanisms in faujasite zeolites that can be confirmed by experimental tests, and hence contribute to the generation of new technologies for capturing pollutant molecules in wastewater. The results are in agreement with the experimental information concerning the influence of pH on the adsorption activity of phosphate adsorption on zeolites.

2021 ◽  
Vol 14 (10) ◽  
pp. 988
Balázs Zoltán Zsidó ◽  
Rita Börzsei ◽  
Erika Pintér ◽  
Csaba Hetényi

Transient receptor potential ankyrin 1 (TRPA1) is a transmembrane protein channeling the influx of calcium ions. As a polymodal nocisensor, TRPA1 can be activated by thermal, mechanical stimuli and a wide range of chemically damaging molecules including small volatile environmental toxicants and endogenous algogenic lipids. After activation by such compounds, the ion channel opens up, its central pore widens allowing calcium influx into the cytosol inducing signal transduction pathways. Afterwards, the calcium influx desensitizes irritant evoked responses and results in an inactive state of the ion channel. Recent experimental determination of structures of apo and holo forms of TRPA1 opened the way towards the design of new agonists, which can activate the ion channel. The present study is aimed at the elucidation of binding dynamics of agonists using experimental structures of TRPA1-agonist complexes at the atomic level applying molecular docking and dynamics methods accounting for covalent and non-covalent interactions. Following a test of docking methods focused on the final, holo structures, prerequisite binding modes were detected involving the apo forms. It was shown how reversible interactions with prerequisite binding sites contribute to structural changes of TRPA1 leading to covalent bonding of agonists. The proposed dynamics of action allowed a mechanism-based forecast of new, druggable binding sites of potent agonists.

2021 ◽  
Lan Wang ◽  
Hannah Toutkoushian ◽  
Claire Y Kokontis ◽  
Peter Walter ◽  
Vladislav Belyy

The mitochondrial AAA protein ATAD1 (in humans; Msp1 in yeast) removes mislocalized membrane proteins, as well as stuck import substrates from the mitochondrial outer membrane, facilitating their re-insertion into their cognate organelles and maintaining mitochondria's protein import capacity. In doing so, it helps to maintain proteostasis in mitochondria. How ATAD1 tackles the energetic challenge to extract hydrophobic membrane proteins from the lipid bilayer and what structural features adapt ATAD1 for its particular function has remained a mystery. Previously, we determined the structure of Msp1 in complex with a peptide substrate (Wang et al., 2020). The structure showed that Msp1's mechanism follows the general principle established for AAA proteins while adopting several structural features that specialize it for its function. We used the yeast growth assay to test the function of key amino acids within these structural elements. In this work, we determined the cryo-EM structures of the human ATAD1 in complex with a peptide substrate at near atomic resolution. The structures show that phylogenetically conserved structural elements adapt ATAD1 for its function while generally adopting a conserved mechanism shared by many AAA proteins. ATAD1's distinguishing features include an abundance of aromatic amino acids that line the central pore proposed to give ATAD1 a firm grip on its substrate and a short a-helix at the C-terminus that strongly facilitates ATAD1's oligomerization. We also developed a microscopy-based assay reporting on protein mislocalization, with which we directly assessed ATAD1's activity in live cells.

2021 ◽  
Sanket Walujkar ◽  
Jeffrey M Lotthammer ◽  
Collin R Nisler ◽  
Joseph C Sudar ◽  
Angela Ballesteros ◽  

Inner-ear sensory hair cells convert mechanical stimuli from sound and head movements into electrical signals during mechanotransduction. Identification of all molecular components of the inner-ear mechanotransduction apparatus is ongoing; however, there is strong evidence that TMC1 and TMC2 are pore-forming subunits of the complex. We present molecular dynamics simulations that probe ion conduction of TMC1 models built based on two different structures of related TMEM16 proteins. Unlike most channels, the TMC1 models do not show a central pore. Instead, simulations of these models in a membrane environment at various voltages reveal a peripheral permeation pathway that is exposed to lipids and that shows cation permeation at rates comparable to those measured in hair cells. Furthermore, our analyses suggest that TMC1 gating mechanisms involve protein conformational changes and tension-induced lipid-mediated pore widening. These results provide insights into ion conduction and activation mechanisms of hair-cell mechanotransduction channels essential for hearing and balance.

2021 ◽  
I-Shan Chen ◽  
Jodene Eldstrom ◽  
David Fedida ◽  
Yoshihiro Kubo

G-protein-gated inwardly rectifying K+ (GIRK; Kir3.x) channels play important physiological roles in various organs. Some of the disease-associated mutations of GIRK channels are known to induce loss of K+ selectivity but their structural changes remain unclear. In this study, we investigated the mechanisms underlying the abnormal ion selectivity of inherited GIRK mutants. By the two-electrode voltage-clamp analysis of GIRK mutants heterologously expressed in Xenopus oocytes, we observed that Kir3.2 G156S permeates Li+ better than Rb+, while T154del or L173R of Kir3.2 and T158A of Kir3.4 permeate Rb+ better than Li+, suggesting a unique conformational change in the G156S mutant. Applications of blockers of the selectivity filter (SF) pathway, Ba2+ or Tertiapin-Q (TPN-Q), remarkably increased the Li+-selectivity of Kir3.2 G156S but did not alter those of the other mutants. In single-channel recordings of Kir3.2 G156S expressed in mouse fibroblasts, two types of events were observed, one attributable to a TPN-Q sensitive K+ current and the second a TPN-Q resistant Li+ current. The results show that a novel Li+ permeable and blocker-resistant pathway exists in G156S in addition to the SF pathway. Mutations in the pore helix (PH), S148F and T151A, also induced high Li+ permeation. Our results demonstrate that the mechanism underlying the loss of K+ selectivity of Kir3.2 G156S involves formation of a novel ion permeation pathway besides the SF pathway, which allows permeation of various species of cations.

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