Molecular conformation articles within Nature Communications

Featured

  • Article |

    Activation of c-src kinase is associated with uncontrolled growth and metastasis of tumour cells. Shukla et al.model conformational changes in c-src during activation, and identify an allosteric site in an intermediate state that may provide a target for small molecule therapeutics.

    • Diwakar Shukla
    • , Yilin Meng
    •  & Vijay S. Pande

  • Article
    | Open Access

    The molecular determinants underlying ligand gating of cyclic nucleotide-modulated ion channels remain unclear. Kowal et al.determine the conformational changes underlying cAMP binding to the bacterial channel MloK1, and propose a mechanism for coupling of ligand gating and voltage sensing in eukaryotic HCN channels.

    • Julia Kowal
    • , Mohamed Chami
    •  & Henning Stahlberg

  • Article |

    ϕ analysis provides a means to tease apart the dynamics of fast conformational changes in proteins by analysing the thermodynamic impact of point mutations. Purohit et al.apply this approach on a grand scale to map energy changes associated with the opening and closing of an acetylcholine receptor.

    • Prasad Purohit
    • , Shaweta Gupta
    •  & Anthony Auerbach

  • Article |

    Bacterial chemoreceptors regulate the kinase CheA via ligand-induced conformational changes. Using long molecular dynamics simulations, Ortega et al.show that these changes are associated with flipping of the stacked aromatic rings of highly conserved phenylalanine residues within the kinase-activating domain.

    • Davi R. Ortega
    • , Chen Yang
    •  & Igor B. Zhulin

  • Article
    | Open Access

    The fidelity of DNA polymerases depends on conformational changes that promote the rejection of incorrect nucleotides. Here, by using an intramolecular single-molecule FRET assay, the authors establish and characterize the partially closed conformation as a crucial fidelity checkpoint.

    • Johannes Hohlbein
    • , Louise Aigrain
    •  & Achillefs N. Kapanidis

  • Article
    | Open Access

    In outwardly rectifying potassium channels, depolarization initiates conformational changes in voltage-sensing domains. Goldschen-Ohmet al. find that movement of three specific domains correlates with conductance levels, and rearrangements of a fourth domain results in preinactivation subconductance states.

    • Marcel P. Goldschen-Ohm
    • , Deborah L. Capes
    •  & Baron Chanda

  • Article
    | Open Access

    Sodium-gated ion channels open and close in response to the flow of ions. Here, McCusker et al.report the open structure of a sodium-gated ion channel pore from a bacterial homologue, and show, by comparison with the closed structure, that the movement of a C-terminal helix is sufficient to open the channel.

    • Emily C. McCusker
    • , Claire Bagnéris
    •  & B.A. Wallace

  • Article
    | Open Access

    Many drugs exist that target the β-adrenergic receptor, but they have different efficacies. Kofukuet al. use NMR to show that methionine 82 in the transmembrane domain undergoes conformational changes depending on whether agonists or inverse agonists are bound, explaining the differential drug efficacy.

    • Yutaka Kofuku
    • , Takumi Ueda
    •  & Ichio Shimada

  • Article |

    Glycoprotein hormone receptors show negative cooperativity following a single molecule of agonist binding to each receptor dimer. Here, constitutively active receptors are shown to display less cooperative allosteric regulation, suggesting a direct relationship between conformational changes in the transmembrane domain and allosteric behaviour of the receptor dimers.

    • Maxime Zoenen
    • , Eneko Urizar
    •  & Sabine Costagliola

  • Article |

    The TREX complex and Nxf1 are involved in the export of mRNA from the nucleus but the precise molecular function of TREX is unclear. Here, the TREX components Aly and Thoc5 are shown to bind to Nxf1 resulting in a change in Nxf1 conformation that permits binding to mRNA and nuclear export.

    • Nicolas Viphakone
    • , Guillaume M. Hautbergue
    •  & Stuart A. Wilson

  • Article
    | Open Access

    Following retinalcis/trans isomerisation, the active form of the G-protein-coupled receptor rhodopsin decays to opsin and all-trans-retinal. In this study, arrestin, a regulator of G-protein-coupled receptor activity, is shown to facilitate the concurrent sequestering of toxic all-trans-retinal and regeneration of 11-cis-retinal within the opsin population.

    • Martha E. Sommer
    • , Klaus Peter Hofmann
    •  & Martin Heck

  • Article
    | Open Access

    The Na+/K+-ATPase pump exports three Na+ ions for the exchange of two K+ ions, and three transient current components have been associated with Na+ binding and release. Now, these three components are found to be tightly correlated confirming that the binding and release of Na+ions is sequential.

    • David C. Gadsby
    • , Francisco Bezanilla
    •  & Miguel Holmgren

  • Article |

    Inward rectifier potassium channels are regulated by a range of ligands that act on a common gate, but the structural details of gating are unclear. Here, the molecular motions associated with gating of KirBac1.1 channels are assessed using small molecule fluorescent probes attached to introduced cysteines.

    • Shizhen Wang
    • , Sun-Joo Lee
    •  & Colin G. Nichols

  • Article |

    In non-NMDA glutamate receptors, intersubunit contacts within agonist binding domains affect functional desensitization. Now, NMDA receptor activation, but not desensitization, is shown to involve rearrangements at the heterodimer interface, suggesting that the intersubunit contacts of NMDA and non-NMDA receptors may have distinct functional roles.

    • William F. Borschel
    • , Swetha E. Murthy
    •  & Gabriela K. Popescu

  • Article |

    The inhibitor of apoptosis protein DIAP1 exists in an auto-inhibited conformation, but the details of its molecular interactions are poorly understood. Here, crystal structures reveal the auto-inhibition mechanism of DIAP1 and show how the active form of the protein binds to the effector caspase drICE.

    • Xiaochun Li
    • , Jiawei Wang
    •  & Yigong Shi

  • Article
    | Open Access

    Group-1 influenza A neuramidase proteins have a 150-cavity that can be targeted by drugs, but the 2009 H1N1 virus neuramidase is not thought to have a 150-cavity. Here, biophysical simulations show that the 2009 H1N1 neuramidase exists in solution with an open 150-cavity, which is stabilized by a salt bridge.

    • Rommie E. Amaro
    • , Robert V. Swift
    •  & Robin M. Bush

  • Article
    | Open Access

    von Willebrand factor (VWF) multimers mediate primary adhesion and aggregation of platelets. Jakobiet al. reveal a calcium-binding site in the VWF-A2 domain, and show that calcium binding encourages folding of the protein and has a role in mechanosensing.

    • Arjen J. Jakobi
    • , Alireza Mashaghi
    •  & Eric G. Huizinga

  • Article |

    The detailed interactions of membrane proteins with their lipid environment are poorly understood. Sonntaget al. use low-resolution X-ray crystallographic data and molecular dynamics simulations to study the manner in which the sarcoendoplasmic reticulum Ca2+–ATPase adapts to different membrane environments.

    • Yonathan Sonntag
    • , Maria Musgaard
    •  & Lea Thøgersen

  • Article |

    N-methyl-D-aspartate receptors mediate excitatory synaptic transmission, and those containing GluN2D subunits have an unusually long deactivation time. Vance et al. show that the conformational variability of the ligand-binding domain and the structure of the activating ligand influence deactivation time.

    • Katie M. Vance
    • , Noriko Simorowski
    •  & Hiro Furukawa

  • Article |

    The formation of hydrophilic protein–protein interactions cannot be explained by charge–charge interactions. Here, molecular simulations reveal that water forms an adhesive hydrogen-bonded network between proteins, stabilizing intermediate states before the bound complex forms.

    • Mazen Ahmad
    • , Wei Gu
    •  & Volkhard Helms

  • Article
    | Open Access

    Lipid phosphodiesters affect the conformation of certain potassium channels, but the details of the lipid-channel interactions are unclear. Here, the KvAP channel is found to switch from an active to a resting state when the channels are transferred from a phospholipid membrane to a bilayer lacking phosphodiesters.

    • Hui Zheng
    • , Weiran Liu
    •  & Qiu-Xing Jiang

  • Article
    | Open Access

    The gastric proton pump, H+,K+-ATPase, contributes to stomach acidification and is a target of acid suppressants. Here, the three-dimensional structure of the pump is determined using electron crystallography, providing the first structural information about the binding of a new class of acid suppressants.

    • Kazuhiro Abe
    • , Kazutoshi Tani
    •  & Yoshinori Fujiyoshi

  • Article
    | Open Access

    γ-Secretase modulators have promise in the treatment of Alzheimer's disease, but their molecular target is uncertain. Here, fluorescence resonance energy transfer is used to determine that the γ-secretase allosteric site is within the γ-secretase complex and that substrate docking is required for modulators to access the site.

    • Kengo Uemura
    • , Katherine C. Farner
    •  & Oksana Berezovska

Browse broader subjects

Browse Molecular conformation across other nature.com journals