Proteomics articles within Nature Communications

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  • Article |

    Aberrant activation of β-catenin in the nucleus has been implicated in several cancers, but the mechanisms regulating nuclear β-catenin are not well understood. Here the authors identify Trim33 as new E3 ligase targeting nuclear β-catenin independently of Wnt signal.

    • Jianfei Xue
    • , Yaohui Chen
    •  & Suyun Huang

  • Article |

    During somatic cell reprogramming, the cell transits through intermediate states. Here, the authors perform an in-depth quantitative proteomic analysis of the reprogramming of mouse embryonic fibroblasts to induced pluripotent stem cells and observe two waves of proteome reorganisation.

    • Marco Benevento
    • , Peter D. Tonge
    •  & Albert J. R. Heck

  • Article |

    The development of software tools to analyse large mass spectrometry data sets lags behind the increase in diversity of the data. Here the authors develop MS-GF+, a database search tool that outperforms other popular tools in identifying peptides from a variety of data sets.

    • Sangtae Kim
    •  & Pavel A. Pevzner

  • Article
    | Open Access

    Protein N-myristoylation is a ubiquitous modification implicated in the regulation of multiple cellular processes. Here, Thinon et al. report the development of a general method to identify N-myristoylated proteins in human cells and identify over 100 endogenous post- and co-translational substrates of N-myristoyltransferase.

    • Emmanuelle Thinon
    • , Remigiusz A. Serwa
    •  & Edward W. Tate

  • Article |

    Protein–protein interactions are fundamental to nearly all molecular and cellular processes. Here Taslimi et al.describe a versatile new optogenetic module that can be used to visualize protein–protein interactions, as well as reversibly control them with light with spatiotemporal resolution.

    • Amir Taslimi
    • , Justin D. Vrana
    •  & Chandra L. Tucker

  • Article |

    Cysteine S-sulphenylation provides redox regulation of protein functions, but the extent of this post-translational modification in cells is unknown. Here, Yang et al. develop a method to detect hundreds of S-sulphenylation sites in cells, and show that many of them respond to a physiologically relevant redox stimulus.

    • Jing Yang
    • , Vinayak Gupta
    •  & Daniel C. Liebler

  • Article |

    Analyses of genome and transcriptome data are unable to accurately predict protein levels and function in tumour samples. Here, the authors carry out a comprehensive protein analysis in 3,467 samples from the cancer genome atlas, providing a resource to study the prognostic and therapeutic potential of tumour proteins.

    • Rehan Akbani
    • , Patrick Kwok Shing Ng
    •  & Gordon B. Mills

  • Article
    | Open Access

    Autism spectrum disorder (ASD) is a complex genetic trait that encompasses a range of neurodevelopmental disorders. Here, the authors clone brain-expressed alternatively-spliced isoforms of ASD risk factors and construct a network of protein interactions that provides further insight into the disease aetiology.

    • Roser Corominas
    • , Xinping Yang
    •  & Lilia M. Iakoucheva

  • 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
    | Open Access

    Many patients with breast cancer develop resistance to the drug tamoxifen and relapse. Here Johansson et al. identify the nuclear receptor retinoic acid receptor alpha (RARA) as a marker of tamoxifen resistance and show that RARA expression correlates negatively with relapse-free survival of patients.

    • Henrik J. Johansson
    • , Betzabe C. Sanchez
    •  & Janne Lehtiö

  • Article |

    The complexity and dynamic range of mammalian proteomes has stymied comprehensive protein quantification for the past twenty years. Zhou et al. develop DEEP SEQ mass spectrometry and use it to quantify a murine stem cell proteome to a depth equivalent to RNA-seq-based ribosome profiling.

    • Feng Zhou
    • , Yu Lu
    •  & Jarrod A. Marto

  • Article |

    The identification of hosts of blood-sucking insects is important for studying ecological factors that affect pathogen distribution. Önder et al. report a proteomics-based methodology for the analysis of blood remnants in ticks that identifies the host species from which the tick has fed up to 6 months earlier.

    • Özlem Önder
    • , Wenguang Shao
    •  & Dustin Brisson

  • Article
    | Open Access

    Selected reaction monitoring mass spectrometry (SRM-MS) can quantify dynamic changes in protein expression with high sensitivity. Karlsson et al. define optimal detection parameters for 10,412 distinct group A Streptococcus pyogenespeptides, which facilitates proteome-wide SRM-MS studies in this bacterium.

    • Christofer Karlsson
    • , Lars Malmström
    •  & Johan Malmström

  • Article |

    Cholesterol indirectly regulates intracellular signalling by modulating the physical properties of lipid membranes. Sheng et al.now show that many PDZ domains contain a functional cholesterol-binding motif, revealing that cholesterol can also control the localization and function of signalling proteins directly.

    • Ren Sheng
    • , Yong Chen
    •  & Wonhwa Cho

  • Article
    | Open Access

    New approaches are required to combatPlasmodium falciparuminfection. In this proteome-wide study, 1305 phosphorylation sites are identified and 36 kinases are shown to have crucial roles in parasite survival, providing new insights into parasite biology and potential new drug targets for anti-malarial chemotherapy.

    • Lev Solyakov
    • , Jean Halbert
    •  & Christian Doerig

  • Article |

    Protein microarrays are useful both in basic research and also in disease monitoring and diagnosis, but their dynamic range is limited. By using plasmonic gold substrates with near-infrared fluorescent enhancement, Tabakman et al. demonstrate a multiplexed protein array with improved detection limits and dynamic range.

    • Scott M. Tabakman
    • , Lana Lau
    •  & Hongjie Dai

  • Article
    | Open Access

    Identifying the transcripts and proteins that fluctuate in response to stimuli provides important information for understanding cell physiology. In this study, 52% of theBacillus subtilispredicted proteome is identified following glucose starvation, revealing further insight into protein dynamics at a global scale.

    • Andreas Otto
    • , Jörg Bernhardt
    •  & Dörte Becher

  • Article |

    Protein interactions in biological environments are expected to differ from the situationin vitro. In this study, a thermophoresis-based technique is described that allows the analysis of protein and small-molecule interactions in biological liquids; the work may allow more efficient drug development.

    • Christoph J. Wienken
    • , Philipp Baaske
    •  & Stefan Duhr

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