Protein design articles within Nature Communications

Featured

  • Article
    | Open Access

    To restore sight after retinal degeneration, one approach is to express light-sensitive proteins in remaining cells. Here the authors combine a light-sensitive engineered G protein-coupled receptor and ion channels to restore ON and OFF responses as well as superior visual pattern discrimination.

    • Michael H. Berry
    • , Amy Holt
    •  & Ehud Y. Isacoff

  • Article
    | Open Access

    Lanthipeptides are a class of cyclic post-translationally modified peptides with potential drug-like properties. Here the authors develop a phage display system by expressing lanthipeptide precursors as C-terminal fusions to the phage M13 coat protein pIII in E. coli along with the heterologous modifying enzymes.

    • Johannes H. Urban
    • , Markus A. Moosmeier
    •  & Josef Prassler

  • Article
    | Open Access

    A major drawback in the clinical use of the oral anticoagulants that directly inhibit factor Xa in order to prevent blood clot formation is the potential for life threatening bleeding events. Here the authors describe factor Xa variants that are refractory to inhibition by these anticoagulants and could serve as rescue agents in treated patients.

    • Daniël Verhoef
    • , Koen M. Visscher
    •  & Mettine H. A. Bos

  • Article
    | Open Access

    Designer organelles could allow the isolation of synthetic biological pathways from endogenous components of the host cell. Here the authors engineer a peroxisomal protein import pathway orthogonal to the naturally occurring system.

    • Laura L. Cross
    • , Rupesh Paudyal
    •  & Stuart L. Warriner

  • Article
    | Open Access

    Split fluorescent proteins (FPs) have been widely used to visualise proteins in cells. Here the authors develop a screen for engineering new split FPs, and report a yellow-green split-mNeonGreen2 with reduced background, a red split-sfCherry2 for multicolour labeling, and its photoactivatable variant for super-resolution use.

    • Siyu Feng
    • , Sayaka Sekine
    •  & Bo Huang

  • Article
    | Open Access

    Catalytic mechanisms of enzymes are well understood, but achieving diverse reaction chemistries in re-engineered proteins can be difficult. Here the authors show a highly efficient and thermostable artificial enzyme that catalyzes a diverse array of substrate oxidations coupled to the reduction of H2O2.

    • Daniel W. Watkins
    • , Jonathan M. X. Jenkins
    •  & J. L. Ross Anderson

  • 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

    Humans are less sensitive to the therapeutic effects of botulinum neurotoxin B (BoNT/B) than the animal models it is tested on due to differences between the human and the mouse receptors. Here, the authors engineer BoNT/B to improve its affinity to human receptors and enhance its therapeutic efficacy.

    • Liang Tao
    • , Lisheng Peng
    •  & Min Dong

  • Article
    | Open Access

    The properties of many transmembrane or aggregation-prone proteins make them difficult to recombinantly express. Here the authors use a modified N-terminal domain of a spider silk protein to express and purify several difficult to express proteins at levels considerably higher than with conventional tags.

    • Nina Kronqvist
    • , Médoune Sarr
    •  & Jan Johansson

  • Article
    | Open Access

    Retinal vascular disease treatments involve frequent pharmacological intraocular administrations. Here the authors present a method to increase the half-life of injected drugs by fusing these to a hyaluronan-binding peptide, which might lead to less frequent retinal disease treatments.

    • Joy G. Ghosh
    • , Andrew A. Nguyen
    •  & Michael Roguska

  • Article
    | Open Access

    Self-assembling proteins that form capsid-like structures act as molecular containers for diverse cargoes. Here, the authors solve the cryo-EM structures of lumazine synthase shells, and show that supercharged mutants form expanded assemblies, indicating that electrostatics can be exploited to engineer cage architecture.

    • Eita Sasaki
    • , Daniel Böhringer
    •  & Donald Hilvert

  • Article
    | Open Access

    The production of short chain fatty acids by microorganisms has numerous industrial and biofuel applications. Here the authors reprogrammeS. cerevisiaefatty acid synthase with five mutations to produce C6- and C8-fatty acids and identify thioesterases responsible for hydrolysis of short chain acyl-CoA hydrolysis.

    • Jan Gajewski
    • , Renata Pavlovic
    •  & Martin Grininger

  • Article
    | Open Access

    The TIM barrel fold is an evolutionarily conserved motif found in proteins with a variety of enzymatic functions. Here the authors explore the fitness landscape of the TIM barrel protein IGPS and uncover evolutionary constraints on both sequence and structure, accompanied by long range allosteric interactions.

    • Yvonne H. Chan
    • , Sergey V. Venev
    •  & C. Robert Matthews

  • Article
    | Open Access

    In the construction of single fluorescent protein biosensors, selection of the insertion point of a fluorescent protein into a ligand-binding domain is a rate-limiting step. Here, the authors develop an unbiased, high-throughput approach, called domain insertion profiling with DNA sequencing (DIP-seq), to generate a novel trehalose biosensor.

    • Dana C. Nadler
    • , Stacy-Anne Morgan
    •  & David F. Savage

  • Article
    | Open Access

    Integrins are transmembrane proteins that have important roles in cell adhesion and signalling. Here the authors design a therapeutic protein that binds integrin αvβ3, has anti-angiogenic activity, and reduces tumour growth in xenograft models, while being seemingly well tolerated.

    • Ravi Chakra Turaga
    • , Lu Yin
    •  & Zhi-Ren Liu

  • Article
    | Open Access

    Protein aggregates are associated with a wide variety of diseases. Here, in order to address how protein aggregation affects cellular homoeostasis, the authors describe a method to rapidly create protein aggregates in living cells and organisms with precise spatial and temporal control.

    • Yusuke Miyazaki
    • , Kota Mizumoto
    •  & Thomas J. Wandless

  • Article
    | Open Access

    Flexible or disordered domains often hinder the purification of proteins involved in functional interactions. Here the authors describe an approach that enables the production of stable and functional complexes of otherwise unstable proteins in quantities sufficient for structural and functional studies.

    • Nicolas Levy
    • , Sylvia Eiler
    •  & Marc Ruff

  • Article
    | Open Access

    Linking protein components in a controlled manner is crucial for assembling protein nanostructures with pre-determined architecture. Here, the authors use a chemical cross-linker to fuse the terminal helices of two proteins into a single one, forcing the protein domains in a specific orientation.

    • Woo Hyeon Jeong
    • , Haerim Lee
    •  & Jie-Oh Lee

  • Article
    | Open Access

    Designing proteins whose activities can be switched on and off by effector molecules is a central challenge in protein engineering. Here, the authors use tethered chemical ligands with two mutually exclusive binding sites as a general method to modulate protein activity in response to specific effectors.

    • Alberto Schena
    • , Rudolf Griss
    •  & Kai Johnsson

  • Article |

    Generating diverse structures with a minimum amount of synthetic effort is an important goal for drug discovery. Here, the authors report a two-phase synthesis for the generation of skeletally diverse small molecules—forming molecular scaffolds and subsequently diversifying each into multiple structures.

    • Miguel Garcia-Castro
    • , Lea Kremer
    •  & Kamal Kumar

  • Article |

    Water-soluble peptides with stable α-helical conformations are desirable for a range of applications, but incorporating charged residues to improve solubility usually leads to reduced helical stability. Here, polypeptides produced from amino acids with elongated charged side chains are found to be water soluble and exhibit very high helical stability.

    • Hua Lu
    • , Jing Wang
    •  & Jianjun Cheng

Browse broader subjects

Browse Protein design across other nature.com journals