scholarly journals Global alignment and assessment of TRP channel transmembrane domain structures to explore functional mechanisms

2020 ◽  
Author(s):  
Katherine E. Huffer ◽  
Antoniya A. Aleksandrova ◽  
Andrés Jara-Oseguera ◽  
Lucy R. Forrest ◽  
Kenton J. Swartz
Keyword(s):  
Transmembrane Domain ◽  
Ion Selectivity ◽  
Structural Data ◽  
Trp Channel ◽  
Structural Basis ◽  
Global Alignment ◽  
Functional Studies ◽  
Domain Structures ◽  
Mechanistic Basis ◽  
Channel Structures

AbstractThe recent proliferation of published TRP channel structures provides a foundation for understanding the diverse functional properties of this important family of ion channel proteins. To facilitate mechanistic investigations, we constructed a structure-based alignment of the transmembrane domains of 120 TRP channel structures. Comparison of structures determined in the absence or presence of activating stimuli reveals similar constrictions in the central ion permeation pathway near the intracellular end of the S6 helices, pointing to a conserved cytoplasmic gate and suggesting that most available structures represent non-conducting states. Comparison of the ion selectivity filters towards the extracellular end of the pore supports existing hypotheses for mechanisms of ion selectivity. Also conserved to varying extents are hot spots for interactions with hydrophobic ligands, lipids and ions, as well as discrete alterations in helix conformations. This analysis therefore provides a framework for investigating the structural basis of TRP channel gating mechanisms and pharmacology, and, despite the large number of structures included, reveals the need for additional structural data and for more functional studies to establish the mechanistic basis of TRP channel function.

scholarly journals Global alignment and assessment of TRP channel transmembrane domain structures to explore functional mechanisms

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Katherine E Huffer ◽  
Antoniya A Aleksandrova ◽  
Andrés Jara-Oseguera ◽  
Lucy R Forrest ◽  
Kenton J Swartz
Keyword(s):  
Transmembrane Domain ◽  
Ion Selectivity ◽  
Structural Data ◽  
Trp Channel ◽  
Structural Basis ◽  
Global Alignment ◽  
Functional Studies ◽  
Domain Structures ◽  
Mechanistic Basis ◽  
Channel Structures

The recent proliferation of published TRP channel structures provides a foundation for understanding the diverse functional properties of this important family of ion channel proteins. To facilitate mechanistic investigations, we constructed a structure-based alignment of the transmembrane domains of 120 TRP channel structures. Comparison of structures determined in the absence or presence of activating stimuli reveals similar constrictions in the central ion permeation pathway near the intracellular end of the S6 helices, pointing to a conserved cytoplasmic gate and suggesting that most available structures represent non-conducting states. Comparison of the ion selectivity filters toward the extracellular end of the pore supports existing hypotheses for mechanisms of ion selectivity. Also conserved to varying extents are hot spots for interactions with hydrophobic ligands, lipids and ions, as well as discrete alterations in helix conformations. This analysis therefore provides a framework for investigating the structural basis of TRP channel gating mechanisms and pharmacology, and, despite the large number of structures included, reveals the need for additional structural data and for more functional studies to establish the mechanistic basis of TRP channel function.

scholarly journals Author response: Global alignment and assessment of TRP channel transmembrane domain structures to explore functional mechanisms

2020 ◽  
Author(s):  
Katherine E Huffer ◽  
Antoniya A Aleksandrova ◽  
Andrés Jara-Oseguera ◽  
Lucy R Forrest ◽  
Kenton J Swartz
Keyword(s):  
Transmembrane Domain ◽  
Trp Channel ◽  
Author Response ◽  
Global Alignment ◽  
Domain Structures ◽  
Functional Mechanisms

scholarly journals Structural basis for substrate specificity of an amino acid ABC transporter

2015 ◽  
Vol 112 (16) ◽  
pp. 5243-5248 ◽  
Author(s):  
Jie Yu ◽  
Jingpeng Ge ◽  
Johanna Heuveling ◽  
Erwin Schneider ◽  
Maojun Yang
Keyword(s):  
Amino Acid ◽  
Abc Transporters ◽  
Transmembrane Domain ◽  
Structural Basis ◽  
Common Mechanism ◽  
Nucleotide Binding Domain ◽  
Functional Studies ◽  
Thermoanaerobacter Tengcongensis ◽  
Pass Through ◽  
Positively Charged

ATP-binding cassette (ABC) transporters are ubiquitous integral membrane proteins that translocate a variety of substrates, ranging from ions to macromolecules, either out of or into the cytosol (hence defined as importers or exporters, respectively). It has been demonstrated that ABC exporters and importers function through a common mechanism involving conformational switches between inward-facing and outward-facing states; however, the mechanism underlying their functions, particularly substrate recognition, remains elusive. Here we report the structures of an amino acid ABC importer Art(QN)2 from Thermoanaerobacter tengcongensis composed of homodimers each of the transmembrane domain ArtQ and the nucleotide-binding domain ArtN, either in its apo form or in complex with substrates (Arg, His) and/or ATPs. The structures reveal that the straddling of the TMDs around the twofold axis forms a substrate translocation pathway across the membrane. Interestingly, each TMD has a negatively charged pocket that together create a negatively charged internal tunnel allowing amino acids carrying positively charged groups to pass through. Our structural and functional studies provide a better understanding of how ABC transporters select and translocate their substrates.

Thermodynamic and structural basis of temperature-dependent gating in TRP channels

2021 ◽  
Author(s):  
Ignacio Diaz-Franulic ◽  
Christian Verdugo ◽  
Felipe Gonzalez ◽  
Fernando Gonzalez-Nilo ◽  
Ramon Latorre
Keyword(s):  
Transient Receptor Potential ◽  
Trp Channels ◽  
Receptor Potential ◽  
Structural Data ◽  
Structural Basis ◽  
Functional Studies ◽  
Structural Framework ◽  
Transient Receptor ◽  
Living Organisms ◽  
Open Question

Living organisms require detecting the environmental thermal clues for survival, allowing them to avoid noxious stimuli or find prey moving in the dark. In mammals, the Transient Receptor Potential ion channels superfamily is constituted by 27 polymodal receptors whose activity is controlled by small ligands, peptide toxins, protons and voltage. The thermoTRP channels subgroup exhibits unparalleled temperature dependence -behaving as heat and cold sensors. Functional studies have dissected their biophysical features in detail, and the advances of single-particle Cryogenic Electron microscopy provided the structural framework required to propose detailed channel gating mechanisms. However, merging structural and functional evidence for temperature-driven gating of thermoTRP channels has been a hard nut to crack, remaining an open question nowadays. Here we revisit the highlights on the study of heat and cold sensing in thermoTRP channels in the light of the structural data that has emerged during recent years.

scholarly journals The structural basis of odorant recognition in insect olfactory receptors

2021 ◽  
Author(s):  
Josefina del Mármol ◽  
Mackenzie Yedlin ◽  
Vanessa Ruta
Keyword(s):  
Olfactory Receptors ◽  
Binding Pocket ◽  
Structural Basis ◽  
Structural Determinants ◽  
Functional Studies ◽  
Chemical Recognition ◽  
Common Strategy ◽  
Olfactory Systems ◽  
Mechanistic Basis ◽  
Insight Into

AbstractOlfactory systems must detect and discriminate an enormous diversity of chemicals in the environment. To contend with this challenge, diverse species have converged on a common strategy in which odorant identity is encoded through the combinatorial activation of large families of olfactory receptors (ORs), thus allowing a finite number of receptors to detect an almost infinite chemical world. Although most individual ORs are sensitive to a variety of odorants, the structural basis for such flexible chemical recognition remains unknown. Here, we combine cryo-electron microscopy with functional studies of receptor tuning to gain insight into the structural and mechanistic basis of promiscuous odorant recognition. We show that OR5 from the jumping bristletail, Machilis hrabei, assembles as a homo-tetrameric odorant-gated ion channel with broad chemical tuning. We elucidated the structure of OR5 in multiple gating states, alone and in complex with two of its agonists—the odorant eugenol and the insect repellent DEET. Both ligands bind to a common binding site located in the transmembrane region of each subunit, composed of a simple geometric arrangement of aromatic and hydrophobic residues. We reveal that binding is mediated by hydrophobic, non-directional interactions with residues distributed throughout the binding pocket, enabling the flexible recognition of structurally distinct odorants. Mutation of individual residues lining the binding pocket predictably altered OR5’s sensitivity to eugenol and DEET and broadly reconfigured the receptor’s tuning, supporting a model in which diverse odorants share the same structural determinants for binding. Together, these studies provide structural insight into odorant detection, shedding light onto the molecular recognition mechanisms that ultimately endow the olfactory system with its immense discriminatory capacity.

scholarly journals Structural studies of Cardiovirus 2A protein reveal the molecular basis for RNA recognition and translational control

2020 ◽  
Author(s):  
Chris H. Hill ◽  
Sawsan Napthine ◽  
Lukas Pekarek ◽  
Anuja Kibe ◽  
Andrew E. Firth ◽  
...  
Keyword(s):  
Translational Control ◽  
Ribosomal Subunit ◽  
Structural Data ◽  
Encephalomyocarditis Virus ◽  
Structural Basis ◽  
Rna Recognition ◽  
Folding Energy ◽  
Translational Initiation ◽  
Infected Cells ◽  
Mechanistic Basis

AbstractEncephalomyocarditis virus 2A protein is a multi-functional virulence factor essential for efficient virus replication with roles in stimulating programmed −1 ribosomal frameshifting (PRF), inhibiting cap-dependent translational initiation, interfering with nuclear import and export and preventing apoptosis of infected cells. The mechanistic basis for many of these activities is unclear and a lack of structural data has hampered our understanding. Here we present the X-ray crystal structure of 2A, revealing a novel “beta-shell” fold. We show that 2A selectively binds to and stabilises a specific conformation of the stimulatory RNA element in the viral genome that directs PRF at the 2A/2B* junction. We dissect the folding energy landscape of this stimulatory RNA element, revealing multiple conformers, and measure changes in unfolding pathways arising from mutation and 2A binding. Furthermore, we demonstrate a strong interaction between 2A and the small ribosomal subunit and present a high-resolution cryo-EM structure of 2A bound to initiated 70S ribosomes. In this complex, three copies of 2A bind directly to 16S ribosomal RNA at the factor binding site, where they may compete for binding with initiation and elongation factors. Together, these results provide an integrated view of the structural basis for RNA recognition by 2A, expand our understanding of PRF, and provide unexpected insights into how a multifunctional viral protein may shut down translation during virus infection.

scholarly journals Structural implications of weak Ca2+ block in Drosophila cyclic nucleotide–gated channels

2015 ◽  
Vol 146 (3) ◽  
pp. 255-263 ◽  
Author(s):  
Yee Ling Lam ◽  
Weizhong Zeng ◽  
Mehabaw Getahun Derebe ◽  
Youxing Jiang
Keyword(s):  
Cyclic Nucleotide ◽  
Ion Selectivity ◽  
Structural Difference ◽  
Selectivity Filter ◽  
Structural Basis ◽  
Functional Studies ◽  
Cyclic Nucleotide Gated Channels ◽  
Cng Channel ◽  
High Resolution Structure ◽  
Calcium Permeability

Calcium permeability and the concomitant calcium block of monovalent ion current (“Ca2+ block”) are properties of cyclic nucleotide–gated (CNG) channel fundamental to visual and olfactory signal transduction. Although most CNG channels bear a conserved glutamate residue crucial for Ca2+ block, the degree of block displayed by different CNG channels varies greatly. For instance, the Drosophila melanogaster CNG channel shows only weak Ca2+ block despite the presence of this glutamate. We previously constructed a series of chimeric channels in which we replaced the selectivity filter of the bacterial nonselective cation channel NaK with a set of CNG channel filter sequences and determined that the resulting NaK2CNG chimeras displayed the ion selectivity and Ca2+ block properties of the parent CNG channels. Here, we used the same strategy to determine the structural basis of the weak Ca2+ block observed in the Drosophila CNG channel. The selectivity filter of the Drosophila CNG channel is similar to that of most other CNG channels except that it has a threonine at residue 318 instead of a proline. We constructed a NaK chimera, which we called NaK2CNG-Dm, which contained the Drosophila selectivity filter sequence. The high resolution structure of NaK2CNG-Dm revealed a filter structure different from those of NaK and all other previously investigated NaK2CNG chimeric channels. Consistent with this structural difference, functional studies of the NaK2CNG-Dm chimeric channel demonstrated a loss of Ca2+ block compared with other NaK2CNG chimeras. Moreover, mutating the corresponding threonine (T318) to proline in Drosophila CNG channels increased Ca2+ block by 16 times. These results imply that a simple replacement of a threonine for a proline in Drosophila CNG channels has likely given rise to a distinct selectivity filter conformation that results in weak Ca2+ block.

scholarly journals Structure and function of stator units of the bacterial flagellar motor

2020 ◽  
Author(s):  
Mònica Santiveri ◽  
Aritz Roa-Eguiara ◽  
Caroline Kühne ◽  
Navish Wadhwa ◽  
Howard C. Berg ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Mechanistic Model ◽  
Structural Data ◽  
Structural Basis ◽  
Flagellar Motor ◽  
Functional Studies ◽  
Torque Generation ◽  
Bacterial Flagellar Motor ◽  
And Function ◽  
Key Residues

AbstractMany bacteria use the flagellum for locomotion and chemotaxis. Its bi-directional rotation is driven by the membrane-embedded motor, which uses energy from the transmembrane ion gradient to generate torque at the interface between stator units and rotor. The structural organization of the stator unit (MotAB), its conformational changes upon ion transport and how these changes power rotation of the flagellum, remain unknown. Here we present ~3 Å-resolution cryo-electron microscopy reconstructions of the stator unit in different functional states. We show that the stator unit consists of a dimer of MotB surrounded by a pentamer of MotA. Combining structural data with mutagenesis and functional studies, we identify key residues involved in torque generation and present a mechanistic model for motor function and switching of rotational direction.One Sentence SummaryStructural basis of torque generation in the bidirectional bacterial flagellar motor

scholarly journals Structural basis of GIRK2 channel modulation by cholesterol and PIP2

2020 ◽  
Author(s):  
Yamuna Kalyani Mathiharan ◽  
Ian W. Glaaser ◽  
Yulin Zhao ◽  
Michael J. Robertson ◽  
Georgios Skiniotis ◽  
...  
Keyword(s):  
G Protein ◽  
Transmembrane Domain ◽  
Structural Data ◽  
Structural Basis ◽  
Girk Channels ◽  
Channel Modulation ◽  
Cryo Electron Microscopy ◽  
Cellular Excitability ◽  
Cholesteryl Hemisuccinate ◽  
Inwardly Rectifying

ABSTRACTG protein-gated inwardly rectifying potassium (GIRK) channels play important roles in controlling cellular excitability in the heart and brain. While structural data begin to unravel the molecular basis for G protein and alcohol dependent activation of GIRK channels, little is known about the modulation by cholesterol. Here, we present cryo-electron microscopy (cryoEM) structures of GIRK2 in the presence and absence of the cholesterol analog cholesteryl hemisuccinate (CHS), and PIP2. The structures and their comparison reveal that CHS binds near PIP2 in lipid-facing hydrophobic pockets of the transmembrane domain (TMD). CHS potentiates the effects of PIP2, which stabilizes the inter-domain region and promotes the engagement of the cytoplasmic domain (CTD) onto the transmembrane region. The results suggest that CHS acts as a positive allosteric modulator and identify novel therapeutic sites for modulating GIRK channels in the brain.

Sign in / Sign up

Export Citation Format

Share Document