Computational biophysics articles within Nature Communications

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  • Article
    | Open Access

    Sensor histidine kinases (SHK) consist of sensor, linker and kinase modules and different models for SHK signal transduction have been proposed. Here the authors present nano- to millisecond time-resolved X-ray scattering measurements, which reveal a structural mechanism for kinase domain activation in SHK.

    • Oskar Berntsson
    • , Ralph P. Diensthuber
    •  & Sebastian Westenhoff

  • Article
    | Open Access

    The mechanisms that cause different cells to segregate into distinct tissues are unclear. Here the authors show in Xenopus that formation of a boundary between two tissues is driven by local tension along the interface rather than by global differences in adhesion or cortical contractility.

    • Laura Canty
    • , Eleyine Zarour
    •  & François Fagotto

  • Article
    | Open Access

    X-ray crystallography is the main method for protein structure determination. Here the authors combine solid-state NMR measurements and molecular dynamics simulations and show that crystal packing alters the thermodynamics and kinetics of local conformational exchange as well as overall rocking motion of protein molecules in the crystal lattice.

    • Vilius Kurauskas
    • , Sergei A. Izmailov
    •  & Paul Schanda

  • Article
    | Open Access

    Cells in the connective tissue are surrounded by a heterogeneous network of biopolymers. Here, the authors investigate how such heterogeneity affects cellular mechanosensing by simulating the deformation response of experimental and modelled biopolymer networks to locally applied forces.

    • Farzan Beroz
    • , Louise M. Jawerth
    •  & Ned S. Wingreen

  • Article
    | Open Access

    The emergence of novel catalytic functions in ancient proteins likely played a role in the evolution of modern enzymes. Here, the authors use protein sequences from Precambrian beta-lactamases and demonstrate that a single hydrophobic-to-ionizable amino acid mutation can lead to substantial Kemp eliminase activity.

    • Valeria A. Risso
    • , Sergio Martinez-Rodriguez
    •  & Jose M. Sanchez-Ruiz

  • Article
    | Open Access

    Circular dorsal ruffles (CDRs) are important for the vesicular uptake of extracellular matter, but the basis of their wave dynamics is not understood. Here, the authors propose and experimentally test a bistable reaction-diffusion system, which they show accounts for the typical CDR expansion and shrinkage and for aberrant formation of pinned waves and spirals.

    • Erik Bernitt
    • , Hans-Günther Döbereiner
    •  & Arik Yochelis

  • Article
    | Open Access

    Identifying pathways and transition states is critical to understanding chemical and biological reactions. Here, the authors introduce a capable computational approach using conformational space annealing to find multiple reaction pathways via global optimization of the Onsager-Machlup action.

    • Juyong Lee
    • , In-Ho Lee
    •  & Bernard R. Brooks

  • Article
    | Open Access

    Cell migration is sensitive to environmental stiffness, but how cells sense optimal stiffness is not known. Here the authors develop a model that predicts that the optimum can be shifted by altering the number of active molecular motors and clutches, and verify their model in two cell types.

    • Benjamin L. Bangasser
    • , Ghaidan A. Shamsan
    •  & David J. Odde

  • Article
    | Open Access

    Plastoquinone (PLQ) shuttles electrons between photosystem II (PSII) and cytochrome b6f. Here the authors perform molecular dynamics simulations and propose that PLQ enters the exchange cavity of PSII by a promiscuous diffusion mechanism whereby three different channels each act as entry and exit points.

    • Floris J. Van Eerden
    • , Manuel N. Melo
    •  & Siewert J. Marrink

  • Article
    | Open Access

    Studying the reactivity of ribozymes under extreme pressure could provide insights to optimize biocatalytic RNA design. Here, the authors show that at high pressure the transesterification step of the hairpin ribozyme self-cleavage reaction accelerates, while the overall process is slower.

    • Caroline Schuabb
    • , Narendra Kumar
    •  & Roland Winter

  • Article
    | Open Access

    Natural supplies of bryostatin, a compound in clinical trials for Alzheimer’s disease, cancer, and HIV, are scarce. Here, the authors perform molecular dynamics simulations to understand how bryostatin interacts with membrane-bound protein kinase C, offering insights for the design of bryostatin analogs.

    • Steven M. Ryckbosch
    • , Paul A. Wender
    •  & Vijay S. Pande

  • Article
    | Open Access

    The activity of G-protein-coupled receptors is regulated by their interaction with arrestins. Here the authors show that loops located on C-edge of arrestin-1 serve as a membrane anchor during the multi-step binding process that leads to a stable receptor–arrestin complex.

    • Ciara C M. Lally
    • , Brian Bauer
    •  & Martha E Sommer

  • Article
    | Open Access

    Tip-link filaments convey force to activate hair cells, important sensory receptors. Here the authors solve a partial structure of human protocadherin-15, a tip-link component with an unusual Ca2+–free linker that bends and is predicted to confer flexibility to this filament during inner-ear mechanotransduction.

    • Raul Araya-Secchi
    • , Brandon L. Neel
    •  & Marcos Sotomayor

  • Article
    | Open Access

    The translation of mRNA by the ribosome is governed by a series of large-scale conformational transitions. Here the authors use MD simulations to demonstrate how the rate of dissociation of elongation factor Tu affects the dynamics of tRNA accommodation and proofreading.

    • Jeffrey K. Noel
    •  & Paul C. Whitford

  • Article
    | Open Access

    The pH dependence of the activity of Escherichia colimain sodium-proton antiporter NhaA is still not fully understood. Here, the authors use continuous constant pH molecular dynamics simulations to identify NhaA proton carrier residues and elucidate its gating and ion transport processes.

    • Yandong Huang
    • , Wei Chen
    •  & Jana Shen

  • Article
    | Open Access

    Measuring the size distribution of nanomaterials in biological fluids is crucial to understand their properties in vivo. Here, the authors apply fluorescence recovery after photobleaching to measure protein aggregation in serum and to study permeability of biological membranes in mouse models.

    • Ranhua Xiong
    • , Roosmarijn E. Vandenbroucke
    •  & Kevin Braeckmans

  • Article
    | Open Access

    Over 5,000 km of open ocean separate central and eastern Pacific coral reefs. Here, the authors combine a biophysical dispersal model with genetic data to show that eastern Pacific coral populations have been isolated from western sources of larval recruitment since the 1997-98 El Niño-induced bleaching event.

    • S. Wood
    • , I. B. Baums
    •  & E. J. Hendy

  • Article
    | Open Access

    Conventional methods to quantify the migratory behaviour of cells assume that underlying parameters are constant. Mark et al.apply a superstatistical approach to extract time-dependent parameters of motile cells, and demonstrate an enhanced ability to distinguish between different migration strategies.

    • Claus Metzner
    • , Christoph Mark
    •  & Ben Fabry

  • Article
    | Open Access

    Epithelial sheet migration proceeds via a series of actomyosin contractions, called pulses, that are stabilized, or ratcheted. Here, Xie and Martin develop a computational framework to determine how pulses are coordinated, and show that ratcheting of pulses allows collective migration by preventing competition with neighbouring pulses.

    • Shicong Xie
    •  & Adam C. Martin

  • Article |

    Cold denaturation is the process by which globular proteins lose their structural integrity at sufficiently low temperatures. Here, the authors present an all-atom MD simulation of cold denaturation of the 16-mer hairpin peptide MrH1 using an explicit water model.

    • Changwon Yang
    • , Soonmin Jang
    •  & Youngshang Pak

  • Article
    | Open Access

    How microtubules are organized correctly in plant cells is not well understood. Ambroseet al. use 4D imaging and computer modelling to show that sharp cell edges induce microtubule depolymerization and that the microtubule-associated protein CLASP mitigates this process to modulate array organization.

    • Chris Ambrose
    • , Jun F. Allard
    •  & Geoffrey O. Wasteneys

  • Article |

    Seahorses evolved from pipefish, which have a remarkably different body shape. Here, by examining seahorse feeding behaviour and using a mathematical model, Van Wassenberghet al. demonstrate that the head, neck and trunk posture of the seahorse allows for the effective capture of their prey.

    • Sam Van Wassenbergh
    • , Gert Roos
    •  & Lara Ferry

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