Protein engineering articles within Nature Communications

Featured

  • Article
    | Open Access

    Bispecific antibody architecture is often important for function but rarely optimized. Here, authors present a modular approach to assemble bispecifics in varied formats using a SpyTag/SpyCatcher approach called SpyMask, and build anti-HER2 bispecifics whose activities depend on binder orientation and bispecific geometry.

    • Claudia L. Driscoll
    • , Anthony H. Keeble
    •  & Mark R. Howarth

  • Article
    | Open Access

    Conventional blue denim dyeing has both environmental and health-related consequences. Here, Bidart et al. use enzyme engineering to develop a viable method for the bulk production of indican and demonstrate dying processes which could significantly reduce the negative consequences of this billion-dollar industry.

    • Gonzalo Nahuel Bidart
    • , David Teze
    •  & Ditte Hededam Welner

  • Article
    | Open Access

    In contrast to their clinical success as inhibitors and targeting agents, antibodies have generally been ineffective as receptor agonists. Here, Romei et al. leverage a natural homotypic interface to tune antibody geometry, enabling optimization of agonist activity for multiple therapeutic targets.

    • Matthew G. Romei
    • , Brandon Leonard
    •  & Greg A. Lazar

  • Article
    | Open Access

    Genetic code expansion (GCE) is a protein engineering tool that enables programmed and site-specific installation of noncanonical amino acids into proteins. Here, authors show that cellular stress remodelling boosts GCE in mammalian cells including GCE realized by orthogonally translating organelles.

    • Mikhail E. Sushkin
    • , Christine Koehler
    •  & Edward A. Lemke

  • Article
    | Open Access

    The degradation of PET using PETase enzymes has great potential but can face problems with incomplete degradation. Here, the authors identified two BHETases from the environment and engineered them to improve their hydrolysis efficiency for applications in dual-enzyme PET recycling and tandem chemical-enzymatic PET upcycling systems.

    • Anni Li
    • , Yijie Sheng
    •  & He Huang

  • Article
    | Open Access

    β-TrCP plays an important role in diverse cellular processes such as the cell cycle and inflammation. Here the authors develop a biosensor for β-TrCP activity and use it to investigate β-TrCP dynamics during the cell cycle, and to screen a small-molecule library for β-TrCP activators and inhibitors.

    • Debasish Paul
    • , Stephen C. Kales
    •  & Steven D. Cappell

  • Article
    | Open Access

    Rational design of enzymes with new or improved properties is rarely straightforward, and artificial selection pressure approaches that link an improvement in the target to cell growth are an alternative. Here, the authors show that diverse enzymes sharing the ubiquitous cofactor NAD(P)+ can substitute for defective NAD+ regeneration, representing a very broadly-applicable artificial selection.

    • Lara Sellés Vidal
    • , James W. Murray
    •  & John T. Heap

  • Article
    | Open Access

    The ability to design functional sequences is central to protein engineering and biotherapeutics. Here the authors introduce a deep generative alignment-free model for sequence design applied to highly variable regions and design and test a diverse nanobody library with improved properties for selection experiments.

    • Jung-Eun Shin
    • , Adam J. Riesselman
    •  & Debora S. Marks

  • Article
    | Open Access

    Protein tyrosine O-sulfation is crucial for biomolecular interactions. Here the authors report in vitro engineering and in vivo validation of a tyrosyl-tRNA synthetase mutant for the genetic encoding of sulfotyrosine in mammalian cells.

    • Xinyuan He
    • , Yan Chen
    •  & Wei Niu

  • Article
    | Open Access

    RNA-encoded regulatory circuits are desirable because they do not integrate in the host and are less immunogenic, but the availability of regulatory devices is limited. Here the authors develop viral protease RNA-binding proteins and protease–protease genetic circuits that ultimately regulate mRNA translation.

    • Federica Cella
    • , Liliana Wroblewska
    •  & Velia Siciliano

  • Article
    | Open Access

    Synthetic biology principles are often used to design circuits that tune gene expression in response to changes in intracellular environments. Here the authors design a modular platform for intracellular protein sensing devices with transcriptional output.

    • Velia Siciliano
    • , Breanna DiAndreth
    •  & Ron Weiss

  • Article
    | Open Access

    The BioID approaches takes advantage of the promiscuous biotinylation enzyme (BirA*) to identify proteins that closely interact. Here the authors improve the resolution of BioID using a protein fragment complementation approach that allows the assignment of protein-protein interactions to specific complexes within a common interactome.

    • Isabel Myriam Schopp
    • , Cinthia Claudia Amaya Ramirez
    •  & Julien Béthune

  • Article
    | Open Access

    Protein nanotechnology for the fabrication of protein-based nanoscale devices is gaining momentum but assembling well-defined three-dimensional shapes is still challenging. Here, the authors use an existing prefoldin assembled system to design a template for the construction of geometrically constrained structures.

    • Dominic J. Glover
    • , Lars Giger
    •  & Douglas S. Clark

  • Article
    | Open Access

    The use of specific small molecule inhibitors can contribute to the study of kinesins' cellular functions. Here the authors develop a chemical-genetic approach to engineer kinesin motors that can be efficiently inhibited upon addition of cell-permeable molecules.

    • Martin F. Engelke
    • , Michael Winding
    •  & Kristen J. Verhey

  • Article
    | Open Access

    Heart contraction, which is decreased in disease, is determined by Ca2+binding to troponin C. Here, the authors combine a protein engineering approach with gene therapy to modulate heart contractility in mice with the use of rationally designed Troponin C variants, suggesting a new therapy for diseased hearts.

    • Vikram Shettigar
    • , Bo Zhang
    •  & Jonathan P. Davis

  • Article
    | Open Access

    Magnetic manipulation of biological systems requires the development of improved molecular handles. Here the authors isolate ferritin mutants with enhanced biomineralization from a yeast genetic screen and show their application to cell separation, multiscale imaging, and construction of sensors.

    • Yuri Matsumoto
    • , Ritchie Chen
    •  & Alan Jasanoff

  • Article
    | Open Access

    In metalloproteins, a metal cofactor participates in the formation of the correct fold. Here the authors demonstrate—using single molecule force spectroscopy and the native copper centre as an embedded internal reporter—that the blue-copper proteins azurin and plastocyanin unfold via two independent competing pathways under force.

    • Amy E. M. Beedle
    • , Ainhoa Lezamiz
    •  & Sergi Garcia-Manyes

  • Article
    | Open Access

    Mutated tRNA synthetases can incorporate non-canonical amino acids into proteins. Erdmann et al. exploit this property to metabolically label newly synthesized proteins in selected cell types in Drosophila, and demonstrate their detection using proteomics (BONCAT) and fluorescence imaging (FUNCAT).

    • Ines Erdmann
    • , Kathrin Marter
    •  & Daniela C. Dieterich

  • Article
    | Open Access

    Tryptic digestion of SUMOylated proteins generates large peptides, rendering proteomic characterisation of this post-translational modification particularly challenging unless mutant SUMO is used. Hendriks et al.present a method that allows the quantitative identification of wild-type SUMO sites.

    • Ivo A. Hendriks
    • , Rochelle C. D’Souza
    •  & Alfred C. O. Vertegaal

  • Article |

    Whether the specificity of a TCR can be changed in vitroto recognize an entirely different peptide has not been shown. Here, the authors use directed evolution to change the specificity of a human TCR from recognition of a viral peptide to that of a melanoma antigen.

    • Sheena N. Smith
    • , Yuhang Wang
    •  & David M. Kranz

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