Molecular biophysics articles within Nature Communications

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  • Article |

    Opsin has recently been shown to equilibrate phospholipids across the photoreceptor disc membranes. Goren et al.demonstrate that the large conformational changes driven by exposure to light are not required for this activity, and provide insight into the potential mechanisms of lipid translocation.

    • Michael A. Goren
    • , Takefumi Morizumi
    •  & Anant K. Menon

  • Article
    | Open Access

    Single molecule fluorescence microscopy is a powerful technique to study protein dynamics in cells, but it has not been applied to adult animals. The authors use complementation-activated light microscopy in C. elegansto discover that dystrophin regulates the diffusion properties of voltage-dependent calcium ion channels at the surface of body-wall muscle cells.

    • Hong Zhan
    • , Ramunas Stanciauskas
    •  & Fabien Pinaud

  • Article |

    Complexin binds to synaptic vesicles and inhibits spontaneous exocytosis. Here Snead et al. show that the high curvature of the vesicle membrane is important for membrane binding, and induces a conformational change that is important for complexin’s inhibitory function.

    • David Snead
    • , Rachel T. Wragg
    •  & David Eliezer

  • Article |

    Molecular details of the synergy between integrins and syndecans are poorly understood. Here, Fiore et al. show that syndecan-4 and α5β1integrin form a trimolecular complex with Thy-1 that exhibits ‘dynamic catch’ behaviour, in which force strengthens the synergistic binding and modulates signalling at the focal adhesion level.

    • Vincent F. Fiore
    • , Lining Ju
    •  & Thomas H. Barker

  • Article |

    Insertion of proteins into a membrane bilayer driven by the Sec translocon is aided by the attributes of the inserted peptides. Here, Ulmschneider et al.measure the free energies of various insertion events and suggest that the membrane interface plays an important role in translocon-guided TM helix insertion.

    • Martin B. Ulmschneider
    • , Jakob P. Ulmschneider
    •  & Stephen H. White

  • Article |

    Heterochromatin is a ‘repressed’ chromatin state involved in the generation of centromeres, the protection of telomeres and the maintenance of genome integrity. Here Swygert et al.show that Sir3 - a key factor in the formation of heterochromatin - promotes a chromatin structure distinct from the canonical 30 nm fibre.

    • Sarah G. Swygert
    • , Benjamin J. Manning
    •  & Craig L. Peterson

  • Article
    | Open Access

    The structural cross-talk between components of the eukaryotic cytoskeleton remains poorly understood. Here the authors engineer an actin-binding microtubule tip-tracking protein that guides microtubule growth along actin bundles, and allows microtubule growing ends to pull and bundle actin filaments.

    • Magdalena Preciado López
    • , Florian Huber
    •  & Marileen Dogterom

  • Article |

    Electrical synaptic transmission is known to be modulated by intracellular magnesium. Here, Palacios-Prado et al.show that electrical synapses formed by connexin36 in the thalamic reticular nucleus are bidirectionally modulated by changes in magnesium concentration via pore-lining sensitive domains.

    • Nicolás Palacios-Prado
    • , Sandrine Chapuis
    •  & Feliksas F. Bukauskas

  • Article |

    At cell–cell adhesions, α-catenin contains a cryptic vinculin-binding site. Here, Yao et al. demonstrate, using magnetic tweezers, that physiologically relevant forces unfurl α-catenin to reveal the vinculin-binding site, and allow the reversible binding of vinculin to mechanically reinforce the adhesion.

    • Mingxi Yao
    • , Wu Qiu
    •  & Jie Yan

  • Article |

    Some viruses possess ‘decoration’ proteins, such as gpD in lambda phage, that stabilize the viral particles in poorly understood ways. Here the authors show that gpD incorporation into lambda particles provides mechanical reinforcement and increased resistance to punctual deformations and collisions.

    • M. Hernando-Pérez
    • , S. Lambert
    •  & P. J. de Pablo

  • Article |

    Antibody–antigen recognition is one of the important aspects of immunity, but the nanomechanical process of this recognition is not fully understood. Here, using high-speed atomic force microscopy, the authors observe that on membranes containing a high density of immobile antigens antibodies move in a ‘random walking’ motion.

    • Johannes Preiner
    • , Noriyuki Kodera
    •  & Peter Hinterdorfer

  • Article
    | Open Access

    Some viruses are spherical particles in which protein components are organized with well-defined icosahedral and local symmetries. Here, Gipson et al. describe a unique arrangement of proteins, breaking all expected local symmetries, in particles of a marine bacterial virus.

    • Preeti Gipson
    • , Matthew L. Baker
    •  & Wah Chiu

  • Article |

    Ribosome-associated protein biogenesis factors act during protein synthesis to facilitate modification, targeting and folding of the nascent polypeptide. Here, Bornemann et al.establish the dynamic interplay between these factors, thus providing new insight into the early steps of protein biogenesis.

    • Thomas Bornemann
    • , Wolf Holtkamp
    •  & Wolfgang Wintermeyer

  • Article |

    Telomerase reverse transcriptase extends the ends of linear chromosomes with the aid of an integral RNA subunit. Here, Parks and Stone characterize the translocation kinetics of telomerase identifying distinct steps important for the processivity of the enzyme.

    • Joseph W. Parks
    •  & Michael D. Stone

  • Article |

    Functional changes in protein structures are involved in a large number of biochemical processes. Here, the authors perform a simulation study of known protein structures to show how β-sheets possess the ability to facilitate concerted backbone motions.

    • R. Bryn Fenwick
    • , Laura Orellana
    •  & Xavier Salvatella

  • Article |

    Thyroid hormone synthesis requires import of iodide ions through the Na+/I− symporter, however its affinity for iodide is surprisingly low. Using a statistical thermodynamics approach, Nicola et al. show that sodium ion binding enhances iodide affinity, revealing a mechanism for iodide transport.

    • Juan P. Nicola
    • , Nancy Carrasco
    •  & L. Mario Amzel

  • Article |

    Cadherins are calcium-dependent adhesion molecules that can form catch bonds, characterized by longer lifetimes at higher force. Here, Manibog et al. determine the mechanism of catch bond formation, whereby tension induces hydrogen bond formation between opposing extracellular domains in a calcium-dependent manner.

    • Kristine Manibog
    • , Hui Li
    •  & Sanjeevi Sivasankar

  • Article |

    In bacteria, chromosomal architecture exhibits spatial and temporal fluctuations, which affect cellular functions. Here, Javer et al. use high-resolution tracking of chromosomal loci in E. colito uncover rare events of unusually large and fast movements, providing new insight into bacterial chromosome dynamics.

    • Avelino Javer
    • , Nathan J. Kuwada
    •  & Marco Cosentino Lagomarsino

  • Article |

    α-synuclein is a protein whose aberrant aggregation is associated with Parkinson’s disease. Here, Fusco et al.characterize α-synuclein bound to lipid membranes using a combination of solution and solid-state NMR spectroscopy and provide insights into the molecular processes associated with the aggregation of this protein.

    • Giuliana Fusco
    • , Alfonso De Simone
    •  & Gianluigi Veglia

  • Article
    | Open Access

    Cell–cell fusion in Caenorhabditis elegans is mediated by EFF-1 and AFF-1 proteins. Here, the authors present an electron cryomicroscopy 3D reconstruction of EFF-1 in the membrane, and combine snapshots of membrane fusion in vitrowith a recently reported crystal structure to propose a mechanism for the fusion process.

    • Tzviya Zeev-Ben-Mordehai
    • , Daven Vasishtan
    •  & Kay Grünewald

  • Article |

    The mechanism by which KCNEβ subunits slow the kinetics of KCNQ1 channels is controversial. Here, Barro-Soria et al.show that mutually independent voltage sensor movements underlie the initial activation delay, and a subsequent slower conformational change opens the channel.

    • Rene Barro-Soria
    • , Santiago Rebolledo
    •  & H. Peter Larsson

  • Article |

    The binding affinity of a protein for its ligand is governed by the rates of ligand association and dissociation. Here the authors show that intrinsic conformational dynamics of maltose binding protein dictate the ligand dissociation rate, and hence the affinity of the protein for maltose.

    • Moon-Hyeong Seo
    • , Jeongbin Park
    •  & Hak-Sung Kim

  • Article
    | Open Access

    Misfolded protein accumulation is a hallmark of many neurodegenerative diseases. Here Budrikis et al. model protein aggregation in the endoplasmic reticulum and show that it is the result of a non-equilibrium phase transition caused by tipping the balance from the rates of protein production to degradation.

    • Zoe Budrikis
    • , Giulio Costantini
    •  & Stefano Zapperi

  • Article |

    The non-processive motor protein myosin 1b is required for Golgi membrane tubulation. Using a minimal reconstituted system and theoretical analysis, Yamada et al.demonstrate that the mechanism of tubule extraction depends on the catch bond properties of myosin 1b.

    • Ayako Yamada
    • , Alexandre Mamane
    •  & Patricia Bassereau

  • Article |

    CorA is the major magnesium influx pathway in bacteria, but the mechanism for the uptake of magnesium by this system is not clear. Here, Dalmas et al.show that CorA is regulated by cytoplasmic magnesium levels, and determine the conformational changes required for the regulation by a negative feedback loop.

    • Olivier Dalmas
    • , Pornthep Sompornpisut
    •  & Eduardo Perozo

  • Article
    | Open Access

    The stomatin domain protein STOML3 is required for the sensation of touch. Here, Poole et al.show that STOML3 enhances the activity of mechanosensitive Piezo1 and Piezo2 ion channels by reducing their activation thresholds, and that it achieves this through its stomatin domain.

    • Kate Poole
    • , Regina Herget
    •  & Gary R. Lewin

  • Article
    | Open Access

    Regulatory T cells (Tregs) are important for the maintenance of self-tolerance and this requires their trafficking to the lymph nodes and target tissues. Here, the authors show that the recognition of self-antigens expressed by endothelial cells in target tissue is instrumental for efficient Treg recruitment in vivo.

    • Hongmei Fu
    • , Madhav Kishore
    •  & Federica M. Marelli-Berg

  • 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

    Actin-dependent motility is driven by the rapid changes in the recruitment of many different structural and regulatory proteins at the cell’s cortex. Sobczyk et al. characterize these changes in the cytoskeletal proteome on a second to minute timescale during chemotactic response in Dictyosteliumusing SILAC-based proteomics.

    • Grzegorz J. Sobczyk
    • , Jun Wang
    •  & Cornelis J. Weijer

  • Article |

    Crystallographic studies have shown that non-NMDA glutamate receptors exhibit fourfold symmetry in the transmembrane domain in the closed state; however, structural data regarding channel opening is lacking. Using chimeric receptors, Wilding et al.provide evidence that this fourfold symmetry is maintained in the open state.

    • Timothy J. Wilding
    • , Melany N. Lopez
    •  & James E. Huettner

  • Article
    | Open Access

    The structural heterogeneity of a biomolecular crystal structure is typically captured using atomic B-factors, determined during structure refinement. Here, the authors use molecular dynamics to show that this strategy is flawed, and that crystallographic B-factors underestimate structural heterogeneity.

    • Antonija Kuzmanic
    • , Navraj S. Pannu
    •  & Bojan Zagrovic

  • 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 |

    Protein allosteric interactions involve a transfer of structural changes to a remote site. Here, the authors study the relationship between allosteric binding and energy flow, showing how the energy transport mechanism conveys binding energy to remote sites.

    • Guifeng Li
    • , Donny Magana
    •  & R. Brian Dyer

  • Article |

    Many biological processes rely on fluctuations in protein structure, but the characterization of extended structural motions is challenging. Here the authors use orientation-sensitive terahertz near-field microscopy to report the optical observation of long-range protein vibrational modes.

    • Gheorghe Acbas
    • , Katherine A. Niessen
    •  & A.G. Markelz

  • Article |

    The speed of codon translation at the ribosome has a large bearing on the structure of the final protein, with faster rates thought to promote misfolding. Here the authors present a theoretical analysis suggesting that in some cases fast-translating codons may instead improve cotranslational folding.

    • Edward P. O’Brien
    • , Michele Vendruscolo
    •  & Christopher M. Dobson

  • Article |

    Binding of the Tudor domain of the PHD finger protein PHF1 to H3K36me3 inhibits Polycomb PRC2 complex methyltransferase activity. Here, Musselman et al.characterize this interaction in the context of the full nucleosome and show dual binding of the PHF1 Tudor domain to H3K36me3 and double-stranded DNA.

    • Catherine A. Musselman
    • , Matthew D. Gibson
    •  & Tatiana G. Kutateladze

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