Peptides articles within Nature Communications

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  • Article
    | Open Access

    Naturally occurring peptides with high membrane permeability often have backbone ester bonds. Here, the authors investigated the effect of an amide-to-ester substitution on membrane permeability of peptides and found the substitution is useful for improving membrane permeability of cyclic peptides.

    • Yuki Hosono
    • , Satoshi Uchida
    •  & Shinsuke Sando

  • Article
    | Open Access

    The molecular mechanisms underlying the formation of biomolecular condensates have not been fully elucidated. Here the authors show that the LLPS propensity, dynamics, and encapsulation efficiency of designed peptide condensates can be tuned by subtle changes to the peptide composition.

    • Avigail Baruch Leshem
    • , Sian Sloan-Dennison
    •  & Ayala Lampel

  • Article
    | Open Access

    Phase separation provides intracellular organisation via membraneless entities called biomolecular condensates. Here, the authors show that short, cationic peptide tags can drive biomolecular condensation of engineered proteins in E. coli through associative interactions with RNA.

    • Vivian Yeong
    • , Jou-wen Wang
    •  & Allie C. Obermeyer

  • Article
    | Open Access

    The rapid protease degradation of peptides is currently limiting their therapeutic utility. Here, the authors report functionalised thiocarbazate scaffolds as precursors of aza-amino acids that can be integrated in peptide sequences, extending their bioavailability, and demonstrate this on FSSE/P5779 and bradykinin.

    • Ahmad Altiti
    • , Mingzhu He
    •  & Yousef Al-Abed

  • Article
    | Open Access

    Targeting biomedically relevant protein-protein interactions is a long-lasting challenge in medicinal chemistry. Here, the authors develop a single α-helical peptide scaffold that can be tailored to target globular proteins of biomedical interest.

    • Albert Escobedo
    • , Jonathan Piccirillo
    •  & Xavier Salvatella

  • Article
    | Open Access

    The modification of peptides and proteins for application in drug discovery and chemical biology is currently a rapidly growing field of research. Here, the authors report a photocatalytic diselenide contraction method for the dimerization and site-specific functionalisation of peptides and protein.

    • Luke J. Dowman
    • , Sameer S. Kulkarni
    •  & Richard J. Payne

  • Article
    | Open Access

    Phosphorylation is a mechanism used by cells to promote proteins-biomolecules association. Here, the authors show the effect of the interactions between proteins equipped with positively charged arginines and peptides harbouring negatively charged phosphoserines, enabling rate acceleration and chemical processes in dilute conditions.

    • Nathalie Ollivier
    • , Magalie Sénéchal
    •  & Oleg Melnyk

  • Article
    | Open Access

    4(3H)-quinazolinone is the core scaffold in more than 200 natural alkaloids and numerous drugs. Here, the authors show an alternative assembly machinery for 4(3H)-quinazolinone mainly includes a two-module NRPS catalysing tripeptide formation, unusual N-3 original sources and an α-KGD catalysing the C-N bond oxidative cleavage of a tripeptide to form a dipeptide.

    • Xi-Wei Chen
    • , Li Rao
    •  & Yi Zou

  • Article
    | Open Access

    Translation of 100 to 300 micropeptides from small ORFs within lncRNA was detected by Ribosomal Profiling in Drosophila embryos. These translated small ORFs showed natural selection conserving micropeptide sequence and function.

    • Pedro Patraquim
    • , Emile G. Magny
    •  & Juan Pablo Couso

  • Article
    | Open Access

    The occurrence of isomers of the bicyclic octapeptide α-amanitin, which presents a macrolactam with a tryptathionine cross-link forming a handle, has been reported under the term of atropoisomers. Here, the authors synthesize its analogs and analyse their isomers, proposing and describing for them the term ansamer.

    • Guiyang Yao
    • , Simone Kosol
    •  & Roderich D. Süssmuth

  • Article
    | Open Access

    Bioactive peptides regulate many physiological functions but progress in discovering them has been slow. Here, the authors use a machine learning framework to predict mammalian peptide candidates from the global and local structure of large-scale tissue-specific mass spectrometry data.

    • Christian T. Madsen
    • , Jan C. Refsgaard
    •  & Ulrik de Lichtenberg

  • Article
    | Open Access

    Ribosomally synthesized and post-translationally modified peptides are a source of antimicrobials. Here, the authors report a platform for the rapid evaluation and characterization of biosynthetic gene clusters that enables the identification of 30 structurally diverse modified peptides, including three showing antimicrobial activities.

    • Richard S. Ayikpoe
    • , Chengyou Shi
    •  & Huimin Zhao

  • Article
    | Open Access

    Genetic mutations of insulin receptor (IR) cause severe insulin resistance syndromes with no current treatment or cure. Here, the authors present that insulin-independent IR activation mechanism by peptide agonist which activate non-functional IR mutants that cause the insulin resistance syndromes.

    • Junhee Park
    • , Jie Li
    •  & Eunhee Choi

  • Article
    | Open Access

    Therapeutic modulation of the complement system has gained interest over the past two decades. Here, the authors provide molecular-level insight into the mode-of-action, target selectivity and species specificity of the compstatin family of complement inhibitors, which entered the clinic in 2021.

    • Christina Lamers
    • , Xiaoguang Xue
    •  & Daniel Ricklin

  • Article
    | Open Access

    Protein networks have been widely explored but most binding affinities remain unknown, limiting the quantitative interpretation of interactomes. Here the authors measure affinities of 65,000 interactions involving human PDZ domains and target sequence motifs relevant for viral infection and cancer.

    • Gergo Gogl
    • , Boglarka Zambo
    •  & Gilles Travé

  • Article
    | Open Access

    The catalytic chaperone tapasin assists peptide loading onto MHC-I molecules for antigen presentation and immune recognition. Here, the authors present crystal structures that provide insights into the molecular mechanism of tapasin-mediated peptide exchange.

    • Jiansheng Jiang
    • , Daniel K. Taylor
    •  & Kannan Natarajan

  • Article
    | Open Access

    Alpha-helix nanopores have a range of potential applications and the inclusion of non-natural amino acids allows for modification. Here, the authors report on the creation of alpha-helix pores using D-amino acids and show the pores formed, have different properties to the L-counterparts and were resistant to proteases.

    • Smrithi Krishnan R
    • , Kalyanashis Jana
    •  & Kozhinjampara R. Mahendran

  • Article
    | Open Access

    The chemical diversity of peptides from ribosomal origin is a growing field of research. Here, the authors report the discovery, genomic and biosynthetic investigations of kintamdin, a ribosomally synthesized and post-translationally modified peptides featuring a beta-enamino acid and a bis-thioether macrocyclic motif.

    • Shan Wang
    • , Sixing Lin
    •  & Hai Deng

  • Article
    | Open Access

    Engineering peptide assembly that controls integrin ligand presentation on the molecular level possesses by far the highest ligand density, expanding the perspective of ligand-density-dependent modulation.

    • Xunwu Hu
    • , Sona Rani Roy
    •  & Ye Zhang

  • Article
    | Open Access

    Molecular chaperones play an important part in protein folding and delivery in nature. Here, the authors report on the creation of a synthetic chaperone to control the folding of therapeutic peptides from random coil to alpha helix and demonstrate enhanced therapeutic potential in an in vivo tumour model.

    • Il-Soo Park
    • , Seongchan Kim
    •  & Dal-Hee Min

  • Article
    | Open Access

    Macrocycles have potential as therapeutics, but their libraries are currently not large enough for high-throughput screening. Here, the authors show a combinatorial approach to generate a library of almost 20’000 macrocycles by conjugating carboxylic-acid fragments to macrocyclic scaffolds, identifying nanomolar inhibitors against thrombin and binders of MDM2.

    • Sevan Habeshian
    • , Manuel Leonardo Merz
    •  & Christian Heinis

  • Article
    | Open Access

    Macromolecular aggregates may have played an important role in the origin of life. Here, the authors report hydrophobic-cationic peptides that form insoluble aggregates, which reversibly accrete RNA on their surfaces, and enhance RNA polymerization by a ribozyme.

    • Peiying Li
    • , Philipp Holliger
    •  & Shunsuke Tagami

  • Article
    | Open Access

    The expansion of GGGGCC repeats in the C9ORF72 gene results in the production of disease causing abnormal proteins with polymeric glycine-arginine (poly-GR) and polymeric proline-arginine (poly-PR). Here the authors demonstrate a structural mechanism of how poly-GR and poly-PR inhibit translation and how they might also perturb ribosome assembly.

    • Anna B. Loveland
    • , Egor Svidritskiy
    •  & Andrei A. Korostelev

  • Article
    | Open Access

    One of the early processes enabling the origins of life is thought to be the condensation of building blocks into oligomers and polymers. In this article, the authors report the synthesis of thiodepsipeptides and HS-peptides under mild temperatures and various pH, suggesting they could have formed on early prebiotic Earth.

    • Moran Frenkel-Pinter
    • , Marcos Bouza
    •  & Aikomari Guzman-Martinez

  • Article
    | Open Access

    The authors show that the N-acetyltransferase PamZ acts as a self-resistance factor disabling the antibacterial paenilamicin that is produced by the honey bee larvae pathogen Paenibacillus larvae.

    • Tam Dang
    • , Bernhard Loll
    •  & Roderich D. Süssmuth

  • Article
    | Open Access

    Darobactin is a ribosomally synthesized and post-translationally modified peptide featuring a unique scaffold and potent activity against Gram-negative bacteria. Here, the authors identify darobactin synthase DarE as responsible for the bicyclic scaffold formation and propose the name daropeptide for this growing class of enzymes.

    • Sijia Guo
    • , Shu Wang
    •  & Qi Zhang

  • Article
    | Open Access

    Peptide heterodimers are prevalent in nature, which are not only functional macromolecules but molecular tools for chemical and synthetic biology. Here the authors report de novo design and directed folding of peptide heterodimers crosslinked through multiple disulfide bonds, which can be explored as chemical tools for orthogonal labeling of proteins and preparing protein hybrids.

    • Sicong Yao
    • , Adam Moyer
    •  & Chuanliu Wu

  • Article
    | Open Access

    Pattern-triggered immunity is activated by recognition of microbe-derived structures by host pattern recognition receptors. Here the authors use a genotype-by sequencing approach to show that bacterial translation initiation factor 1 triggers PTI in Arabidopsis thaliana after recognition by the RLP32 receptor.

    • Li Fan
    • , Katja Fröhlich
    •  & Thorsten Nürnberger

  • Article
    | Open Access

    The proteasome complexes, composed of 20S core particles and one or two regulatory particles (proteasome activators), degrade most eukaryotic proteins. Here, the authors identify a sequence motif and resolve its interactions mediating the activation of the human 20S proteasome.

    • Kwadwo A. Opoku-Nsiah
    • , Andres H. de la Pena
    •  & Jason E. Gestwicki

  • Article
    | Open Access

    Gluten peptides from wheat enter the bloodstream and are excreted in urine but are yet to be chemically characterised. Here, the authors show by mass spectrometry that quantitative and qualitative differences in urinary peptides can be detected between healthy people and patients with celiac disease.

    • Brad A. Palanski
    • , Nielson Weng
    •  & Joshua E. Elias

  • Article
    | Open Access

    Strategies capable of stapling unprotected peptides in a straightforward, chemoselective, and clean manner, as well as promoting cellular uptake are of great interest. Here the authors report a peptide macrocyclization and stapling strategy which satisfies those criteria, based on a fluorine thiol displacement reaction.

    • Md Shafiqul Islam
    • , Samuel L. Junod
    •  & Rongsheng E. Wang

  • Article
    | Open Access

    Methods for peptide stapling, or covalently linking amino acid residues to create a non-linear structure, mostly rely on cysteine residues, which imposes a significant practical limitation. Here the authors disclose a method to chemoselectively macrocyclize two free-amine-containing residues in mild, peptide-relevant conditions, using a commercially available reagent.

    • Bo Li
    • , Lan Wang
    •  & Gong Chen

  • Article
    | Open Access

    Generic approach for rapid prototyping is essential for the progress of synthetic biology. Here the authors modify the cell-free translation system to control protein aggregation and folding and validate the approach by using single conditions for prototyping of various disulfide-constrained polypeptides.

    • Yue Wu
    • , Zhenling Cui
    •  & Sergey Mureev

  • Article
    | Open Access

    Chiral communication can propagate in secondary structures within the effective intermolecular force (IMF) range but it is not known whether long-range chiral communication exists between tertiary peptide structures. Here, the authors use single-molecule force spectroscopy to investigate chiral interaction between DNA duplexes/triplexes and peptide coiled-coils and demonstrate chiral communication beyond the IMF distance.

    • Shankar Pandey
    • , Shankar Mandal
    •  & Hanbin Mao

  • Article
    | Open Access

    AlphaFold2 has originally been developed to provide highly accurate predictions of protein monomer structures. Here, the authors present a simple adaptation of AlphaFold2 that enables structural modeling of peptide–protein complexes, and explore the underlying mechanisms and limitations of this approach.

    • Tomer Tsaban
    • , Julia K. Varga
    •  & Ora Schueler-Furman

  • Article
    | Open Access

    Here, we present TP-DB; a pattern-based search engine based on 1.67 million helices from the Protein Database (PDB). We demonstrate the utility of TP-DB in identifying microbe-specific antigens, as well as the design of antimicrobial peptides and Protein-protein interaction blockers.

    • Cheng-Yu Tsai
    • , Emmanuel Oluwatobi Salawu
    •  & Lee-Wei Yang

  • Article
    | Open Access

    Peptide bond formation is one of the key biochemical reactions needed for the formation of life, but is thermodynamically unfavoured in water. Here, the authors report on the possibility of complex oligomer formation in liquid sulphur dioxide which may have existed on early Earth at the emergence of life.

    • Fabian Sauer
    • , Maren Haas
    •  & Oliver Trapp

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