Molecular engineering articles within Nature Communications

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  • Article
    | Open Access

    Coiled-coil protein origami is a strategy for the de novo design of polypeptide nanostructures based on coiled-coil dimer forming peptides, where a single chain protein folds into a polyhedral cage. Here, the authors design a single-chain triangular bipyramid and also demonstrate that the bipyramid can be self-assembled as a heterodimeric complex, comprising pre-defined subunits.

    • Fabio Lapenta
    • , Jana Aupič
    •  & Roman Jerala

  • Article
    | Open Access

    Azoles are five-membered heterocycles found in peptidic natural products and synthetic peptiodomimetics. Here the authors demonstrate a posttranslational chemical modification method for in vitro ribosomal synthesis of peptides with exotic azole groups at specific positions.

    • Haruka Tsutsumi
    • , Tomohiro Kuroda
    •  & Hiroaki Suga

  • Article
    | Open Access

    Synthetic biologists often co-opt heterologous parts to affect new functions in living cells, yet such an approach has rarely been extended to structural components of the ribosome. Here, the authors describe generalizable methods to express ribosomes from divergent microbes in E. coli and maximize their function.

    • Natalie S. Kolber
    • , Ranan Fattal
    •  & Ahmed H. Badran

  • Review Article
    | Open Access

    One of the key limitations of CRISPR-Cas-based genome editing techniques is the PAM dependency. Here, the authors review ongoing efforts towards realizing PAM-free nucleases, address potential consequences of eliminating PAM recognition, and propose an alternative nuclease repertoire covering all possible PAM sequences.

    • Daphne Collias
    •  & Chase L. Beisel

  • Article
    | Open Access

    Family 1 glycosidases (GH1) are present in the three domains of life and share classical TIM-barrel fold. Structural and biochemical analyses of a resurrected ancestral GH1 enzyme reveal heme binding, not known in its modern descendants. Heme rigidifies the TIM-barrel and allosterically enhances catalysis.

    • Gloria Gamiz-Arco
    • , Luis I. Gutierrez-Rus
    •  & Jose M. Sanchez-Ruiz

  • Article
    | Open Access

    The PAM specificity of SpCas9 can be altered with positive selection during directed evolution. Here the authors use simultaneous positive and negative selection to improve activity on NAG PAMs while reducing activity on NGG PAMs.

    • Gregory W. Goldberg
    • , Jeffrey M. Spencer
    •  & Marcus B. Noyes

  • Article
    | Open Access

    Nonribosomal lipopeptides contain an acyl chain important for bioactivity, but its incorporation into the peptidyl backbone, mediated by the starter condensation (Cs) domain of nonribosomal peptide synthases, is not fully understood. Here, the authors show that acyl chains of different lengths can be obtained by engineering Cs domains and identify residues that determine the selectivity for acyl chains.

    • Lin Zhong
    • , Xiaotong Diao
    •  & Xiaoying Bian

  • Article
    | Open Access

    Existing optogenetic methods to induce calcium mobilisation lack selectivity and specificity. Here, the authors design and engineer a single-component light-operated calcium channel to provide optical control over calcium signals and calcium-dependent physiological responses: LOCa.

    • Lian He
    • , Liuqing Wang
    •  & Yubin Zhou

  • Article
    | Open Access

    Citrullination of arginine is crucial for several physiological processes. Here the authors report the site-specific incorporation of citrulline into proteins in mammalian cells using an engineered tRNA synthetase/tRNA pair and a photocaged-citrulline.

    • Santanu Mondal
    • , Shu Wang
    •  & Paul R. Thompson

  • Perspective
    | Open Access

    A key security challenge with biosecurity threats is determining the responsible actor. In this Perspective, the authors review recent developments in using genetic sequence to assign a lab-of-origin and the potential protection it provides against misuse of synthetic biology.

    • Gregory Lewis
    • , Jacob L. Jordan
    •  & Thomas V. Inglesby

  • Review Article
    | Open Access

    Large-scale meat production can have negative impacts on public health, the environment and animal welfare. In this Review, the authors consider plant-based and cell-based approaches to meat production and the challenges they face.

    • Natalie R. Rubio
    • , Ning Xiang
    •  & David L. Kaplan

  • Article
    | Open Access

    The potential for accidental or deliberate misuse of biotechnology is of concern for international biosecurity. Here the authors apply machine learning to DNA sequences and associated phenotypic data to facilitate genetic engineering attribution and identify country-of-origin and ancestral lab of engineered DNA sequences.

    • Ethan C. Alley
    • , Miles Turpin
    •  & Kevin M. Esvelt

  • Perspective
    | Open Access

    Advances in our ability to manipulate genetics leads to deeper understanding of biological systems. In this Perspective, the authors argue that synthetic genomics facilitates complex modifications that open up new areas of research.

    • Alessandro L. V. Coradini
    • , Cara B. Hull
    •  & Ian M. Ehrenreich

  • Article
    | Open Access

    The success of protein evolution is dependent on the sequence context mutations are introduced into. Here the authors present UMIC-seq that allows consensus generation for closely related genes by using unique molecular identifiers linked to gene variants.

    • Paul Jannis Zurek
    • , Philipp Knyphausen
    •  & Florian Hollfelder

  • Article
    | Open Access

    Large volumes of true random numbers are needed for increasing requirements of secure data encryption. Here the authors use the stochastic nature of DNA synthesis to obtain millions of gigabytes of unbiased randomness.

    • Linda C. Meiser
    • , Julian Koch
    •  & Robert N. Grass

  • Article
    | Open Access

    Automated design tools and tailored subunits are beneficial in fine-tuning all components of a complex genetic circuit. Here the authors create E. coli and B. subtilis promoter libraries using FACS and HTS, from which an online promoter design tool has been developed using CNN.

    • Maarten Van Brempt
    • , Jim Clauwaert
    •  & Marjan De Mey

  • Article
    | Open Access

    Cholesterol-dependent cytolysins (CDCs) are bacterial pore-forming virulence factors. Cryo-EM structure of an early conformation of the CDC ILY from Streptococcus intermedius, bound to the human immune receptor CD59, provides insight into ILY oligomerization and role of cholesterol in membrane lysis.

    • Nita R. Shah
    • , Tomas B. Voisin
    •  & Doryen Bubeck

  • Article
    | Open Access

    The extreme oxygen sensitive character of hydrogenases is a longstanding issue for hydrogen production in bacteria. Here, the authors build carboxysome shells in E. coli and incorporate catalytically active hydrogenases and functional partners within the empty shell for the production of hydrogen.

    • Tianpei Li
    • , Qiuyao Jiang
    •  & Lu-Ning Liu

  • Article
    | Open Access

    ADP-ribose binding macro domains facilitate the enrichment and detection of cellular ADP-ribosylation. Here, the authors generate an engineered macro domain with increased ADP-ribose affinity, improving the identification of ADP-ribosylated proteins by proteomics, western blot and immunofluorescence.

    • Kathrin Nowak
    • , Florian Rosenthal
    •  & Michael O. Hottiger

  • Comment
    | Open Access

    Synthetic biology is among the most hyped research topics this century, and in 2010 it entered its teenage years. But rather than these being a problematic time, we’ve seen synthetic biology blossom and deliver many new technologies and landmark achievements.

    • Fankang Meng
    •  & Tom Ellis

  • Article
    | Open Access

    Sialic acid-binding immunoglobulin-type lectins (Siglecs) are a family of immunomodulatory receptors expressed on cells of the hematopoietic lineage. Here the authors demonstrate an approach for the identification of the glycan ligands of Siglecs, which is also applicable to other families of glycan-binding proteins.

    • Emily Rodrigues
    • , Jaesoo Jung
    •  & Matthew S. Macauley

  • Article
    | Open Access

    RNA can be used as a programmable tool for detection of biological analytes. Here the authors use deep neural networks to predict toehold switch functionality in synthetic biology applications.

    • Nicolaas M. Angenent-Mari
    • , Alexander S. Garruss
    •  & James J. Collins

  • Article
    | Open Access

    The chemical stability of DNA makes complete erasure of DNA-encoded data difficult. Here the authors mix true and false messages, differentiated by whether a truth marker oligo is bound to it, and show that brief exposure to elevated temperatures randomizes the binding of truth markers preventing data recovery.

    • Jangwon Kim
    • , Jin H. Bae
    •  & David Yu Zhang

  • Article
    | Open Access

    In contrast to genetic circuits, here the authors develop protein biocircuits based on proteases. They show these activity-based circuits can execute Boolean logic for programmable drug delivery and perform fuzzy logic to solve a mathematical oracle problem, Learning Parity with Noise.

    • Brandon Alexander Holt
    •  & Gabriel A. Kwong

  • Article
    | Open Access

    Current gene drive strategies are restricted to sexually reproducing species. Here the authors develop a gene drive in herpesviruses that allows the spread of an engineered trait through a viral population.

    • Marius Walter
    •  & Eric Verdin

  • Article
    | Open Access

    Synthetic Biology often lacks the predictive power needed for efficient bioengineering. Here the authors present ART, a machine learning and probabilistic predictive tool to guide synthetic biology design in a systematic fashion.

    • Tijana Radivojević
    • , Zak Costello
    •  & Hector Garcia Martin

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