Featured
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Article
| Open AccessImpact of secretin receptor homo-dimerization on natural ligand binding
GPCRs can form functionally important dimers. Here, authors study impact of dimerization of the secretin receptor on peptide ligand binding and show high receptor conformational dynamics that facilitate G protein recruitment and activation.
- Kaleeckal G. Harikumar
- , Sarah J. Piper
- & Laurence J. Miller
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Article
| Open AccessBioinformatics leading to conveniently accessible, helix enforcing, bicyclic ASX motif mimics (BAMMs)
Researchers mimic protein interface helices by stapling peptide side chains, or replacing hydrogen bonds with covalent ones, and synthetic helical mimics are heavily biased towards stapling. Here the authors describe bioinformatic discovery of hydrophobic triangles at helix N-termini, and rigid, bicyclic synthetic mimics of them.
- Tianxiong Mi
- , Duyen Nguyen
- & Kevin Burgess
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Article
| Open AccessMultimodal binding and inhibition of bacterial ribosomes by the antimicrobial peptides Api137 and Api88
Proline-rich antimicrobial peptides (PrAMPs) inhibit bacterial protein biosynthesis. Here, the authors show that the honey-bee derived PrAMPs Api137 and Api88 inhibit bacterial ribosomes through multiple mechanisms, promising for drug development.
- Simon M. Lauer
- , Maren Reepmeyer
- & Ralf Hoffmann
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Article
| Open AccessFragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF
Immunopeptidomics is crucial for the discovery of potential immunotherapy and vaccine candidates. Here, the authors generate a ground truth timsTOF dataset to fine-tune the deep learning model Prosit, improving peptide-spectrum match rescoring by up to 3-fold during immunopeptide identification.
- Charlotte Adams
- , Wassim Gabriel
- & Kurt Boonen
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Article
| Open AccessSynthetic intrinsically disordered protein fusion tags that enhance protein solubility
Insoluble protein expression continues to be a bottleneck for biotechnology. Here, Chilkoti and colleagues report a method for generating and identifying hypersoluble intrinsically disordered protein fusion tags to improve soluble protein expression and rescue protein function.
- Nicholas C. Tang
- , Jonathan C. Su
- & Ashutosh Chilkoti
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Article
| Open AccessDisordered clock protein interactions and charge blocks turn an hourglass into a persistent circadian oscillator
Many clock proteins contain intrinsically disordered regions, but how these regions mediate protein interactions is poorly understood. Here, the authors identify charge blocks within a disordered clock protein that regulate circadian timing.
- Meaghan S. Jankowski
- , Daniel Griffith
- & Jennifer M. Hurley
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Article
| Open AccessAn all-in-one tetrazine reagent for cysteine-selective labeling and bioorthogonal activable prodrug construction
Prodrugs have the potential for improving therapeutic index and expanding drug targets, but current prodrug activation strategies that are responsive to endogenous stimuli can result in unintended drug release and systemic toxicity. Here, the authors report 3-vinyl−6-oxymethyltetrazine (voTz) as an all-in-one reagent for modular preparation of tetrazine-caged prodrugs and chemoselective labeling of peptides to produce bioorthogonal activable peptide-prodrug conjugates.
- Xinyu He
- , Jie Li
- & Haoxing Wu
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Article
| Open AccessThunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS2Rescore with MS2PIP timsTOF fragmentation prediction model
Human leukocyte antigen (HLA) class I peptide ligands (HLAIps) are targets for developing vaccines and immunotherapies. Here the authors report Thunder-DDA-PASEF, an immunopeptidomics method which enhances the identification of vital HLAIps crucial for vaccine and immunotherapy development.
- David Gomez-Zepeda
- , Danielle Arnold-Schild
- & Stefan Tenzer
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Article
| Open AccessHomo-BacPROTAC-induced degradation of ClpC1 as a strategy against drug-resistant mycobacteria
Antimicrobial resistance is a global health threat and the development of alternative strategies to overcome it is of high interest. Here, the authors report proteolysis targeting chimeras active in bacteria (BacPROTACs) that bind to ClpC1, a component of the mycobacterial protein degradation machinery, and apply them for targeting a range of mycobacterial strains, including antibiotic-resistant ones.
- Lukas Junk
- , Volker M. Schmiedel
- & Guido Boehmelt
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Article
| Open AccessMirror-image ligand discovery enabled by single-shot fast-flow synthesis of D-proteins
Mirror-image phage display has the potential for high-throughput generation of biologically stable macrocyclic D-peptide binders but is hindered by the optimization required for D-protein chemical synthesis. Here, the authors report a general mirror-image phage display pipeline based on automated flow peptide synthesis and use it to prepare and characterize 12 L/D-protein pairs.
- Alex J. Callahan
- , Satish Gandhesiri
- & Bradley L. Pentelute
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Article
| Open AccessEngineering self-deliverable ribonucleoproteins for genome editing in the brain
The delivery of CRISPR RNPs has potential advantages over other genome editing approaches, including reduced off-target editing and reduced immunogenicity. Here the authors report self-deliverable Cas9 RNPs capable of robustly editing cultured cells in vitro and the mouse brain upon direct injections.
- Kai Chen
- , Elizabeth C. Stahl
- & Jennifer A. Doudna
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Article
| Open AccessA co-assembly platform engaging macrophage scavenger receptor A for lysosome-targeting protein degradation
Targeted degradation of proteins has emerged as a powerful method for modulating protein homeostasis. Here, the authors develop LYTACAs, a modular supramolecular lysosome-targeting co-assembly system, as an effective platform for lysosomal degradation of extracellular and membrane proteins.
- Qian Wang
- , Xingyue Yang
- & Suwei Dong
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Article
| Open AccessCyclic peptides discriminate BCL-2 and its clinical mutants from BCL-XL by engaging a single-residue discrepancy
Pro-survival B-cell lymphoma-2 (BCL-2) family proteins BCL-2 and BCL-XL are the targets of anti-tumour drugs, but resistance is emerging. The authors present cyclic peptides against BCL-2 and BCL-XL, with a distinct mechanism of targeting characterised.
- Fengwei Li
- , Junjie Liu
- & Dalei Wu
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Article
| Open AccessDisordered regions in proteusin peptides guide post-translational modification by a flavin-dependent RiPP brominase
Here the authors use NMR, SAXS and MD simulations to characterise the structure of proteusin peptides, which are atypically long RiPP substrates. They show a small, unstructured region in the proteusin leader is sufficient for its interaction with a halogenase that brominates the terminal tryptophan residue.
- Nguyet A. Nguyen
- , F. N. U. Vidya
- & Vinayak Agarwal
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Article
| Open AccessUncovering supramolecular chirality codes for the design of tunable biomaterials
Assembly of amyloids is important in neurodegenerative diseases, but there is limited understanding of how supramolecular chirality is controlled. Here, the authors report the design of peptide derivatives that allow chirality inversion at biologically relevant temperatures.
- Stephen J. Klawa
- , Michelle Lee
- & Ronit Freeman
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Article
| Open AccessDesign-rules for stapled peptides with in vivo activity and their application to Mdm2/X antagonists
Stapled α-helical peptides are promising for targeting challenging targets such as transcription factors, but achieving sufficient cell permeability while avoiding off-target cleavage is difficult. Here, the authors present workflows for identifying stapled peptides against Mdm2(X) with in vivo activity and no off-target effects based on comprehensive investigations of their properties.
- Arun Chandramohan
- , Hubert Josien
- & Anthony W. Partridge
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Article
| Open AccessA stapled lipopeptide platform for preventing and treating highly pathogenic viruses of pandemic potential
The ongoing emergence of highly pathogenic viruses that evade immune-based therapies or lack interventions mandates new approaches, especially for on-demand prophylaxis. Here the authors provide a stapled lipopeptide platform for the rapid development of viral fusion inhibitors to combat outbreaks.
- Gregory H. Bird
- , J. J. Patten
- & Loren D. Walensky
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Article
| Open AccessTotal wash elimination for solid phase peptide synthesis
Peptide drug manufacturing commonly uses large amounts of hazardous solvents primarily due to multiple washings after each step. Here, the authors introduce the concept of a completely wash-free methodology that enables up to 95% waste reduction.
- Jonathan M. Collins
- , Sandeep K. Singh
- & Christopher L. Houser
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Article
| Open AccessThe NERP-4–SNAT2 axis regulates pancreatic β-cell maintenance and function
Amino acids modulate insulin secretion via amino acid transporters expressed on β cells. Here, the authors show a VGF-derived peptide NERP-4 acts as a positive allosteric modulator on the amino acid transporter SNAT2/SLC38A2, thereby contributing to β-cell maintenance and function.
- Weidong Zhang
- , Ayako Miura
- & Masamitsu Nakazato
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Article
| Open AccessDesign and structural validation of peptide–drug conjugate ligands of the kappa-opioid receptor
Despite advances in GPCR structures and peptide design, creating high-affinity ligands remains a challenge. Here the authors develop a computational method, successfully identifying peptide-based molecules for KOR: their platform shows promise for streamlined GPCR ligand discovery.
- Edin Muratspahić
- , Kristine Deibler
- & Christian W. Gruber
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Article
| Open AccessAn inorganic mineral-based protocell with prebiotic radiation fitness
Protocell’s survival and fitness under prebiotic radiations are elusive. Here, the authors present a radioresistant protocell model based on the assembly of two types of coacervate droplets, formed through interactions of inorganic polyphosphate with manganese and cationic tripeptide, respectively, and show that nonenzymatic Mn antioxidants are essential for its resistance to radiation.
- Shang Dai
- , Zhenming Xie
- & Bing Tian
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Article
| Open AccessCopper assisted sequence-specific chemical protein conjugation at a single backbone amide
Direct, site-specific methods of protein functionalization are of interest, but challenging due to difficulty in chemically differentiating a single site within a large protein. Here, the authors develop a Copper Assisted Sequence-specific conjugation Tag (CAST) method to achieve rapid, site-specific protein backbone chemical modification with pinpoint accuracy, and prepare various on-demand modified recombinant proteins using CAST.
- Mengzhun Guo
- , Kai Zhao
- & Bobo Dang
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Article
| Open AccessA simple method for developing lysine targeted covalent protein reagents
The combination of a covalent electrophile with a peptide or protein-based scaffold enables the targeting of shallow protein surfaces, but the approaches to convert native peptide sequences into covalent binders are missing. Here, the authors report the design of protein-based thiomethacrylate ester electrophiles that can be installed on unprotected peptides and proteins via cysteine side chains and react efficiently and selectively with cysteine and lysine side chains on the target.
- Ronen Gabizon
- , Barr Tivon
- & Nir London
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Article
| Open AccessSequence-based prediction of the intrinsic solubility of peptides containing non-natural amino acids
Posttranslationally modified amino acids are crucial in physiology and drug development as they alter physicochemical properties such as the solubility of proteins. Here the authors describe CamSolPTM, a software that accurately predicts the solubility of proteins containing these residues.
- Marc Oeller
- , Ryan J. D. Kang
- & Michele Vendruscolo
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Article
| Open AccessCell-free biosynthesis combined with deep learning accelerates de novo-development of antimicrobial peptides
Deep learning holds a great promise for the discovery and design of bioactive peptides, but experimental approaches to validate candidates in high throughput and at low cost are needed. Here, the authors combine deep learning and cell free biosynthesis for antimicrobial peptide (AMP) development and identify 30 functional AMPs, of which six with broad-spectrum activity against drug-resistant pathogens.
- Amir Pandi
- , David Adam
- & Tobias J. Erb
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Article
| Open AccessC-terminal modification and functionalization of proteins via a self-cleavage tag triggered by a small molecule
Specific modification or functionalization of proteins at the C-terminus is of interest but remains challenging. Here, the authors report an approach for the efficient modification of C-terminus by fusion of the cysteine protease domain (CPD) on the C-terminus of the protein of interest, and subsequent functionalization with amine-containing molecules triggered by InsP6-mediated CPD self-cleavage.
- Yue Zeng
- , Wei Shi
- & Feng Tang
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Article
| Open AccessShade-induced RTFL/DVL peptides negatively regulate the shade response by directly interacting with BSKs in Arabidopsis
Shade avoidance responses help plants to compete with neighbors for light. Here, the authors show that low R:FR-induced RTFLs interact with BSK3/6 and reduce the protein levels of PIF4 to prevent exaggerated shade avoidance responses.
- Sha Huang
- , Yu Ma
- & Lin Li
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Article
| Open AccessStapling strategy for slowing helicity interconversion of α-helical peptides and isolating chiral auxiliary-free one-handed forms
In nature, α-helical peptides adopt right-handed conformations dictated by L-amino acids, but isolating one-handed α-helical peptides composed of only achiral components remains a challenge. Here, the authors achieve this by optical resolution of the corresponding racemic (quasi-)static α-helical peptide with double stapling, which effectively freezes the interconversion between the right-handed (P)- and left-handed (M)-α-helices.
- Naoki Ousaka
- , Mark J. MacLachlan
- & Shigehisa Akine
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Article
| Open AccessBiosynthesis and engineering of the nonribosomal peptides with a C-terminal putrescine
Nonribosomal peptides have diverse bioactivities and can possess unusual moieties at their C-terminus, such as polyamines. In this study, the authors identify a class of dodecapeptides glidonins that feature diverse N-terminal modifications and a uniform putrescine moiety at the C-terminus, elucidate their biosynthesis, and introduce the putrescine into the C-terminus of other nonribosomal peptides.
- Hanna Chen
- , Lin Zhong
- & Xiaoying Bian
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Article
| Open AccessDevelopment of cyclopeptide inhibitors of cGAS targeting protein-DNA interaction and phase separation
Cyclic GMP-AMP synthase (cGAS) is critical in modulating cellular inflammation. Here, the authors report a class of cyclopeptide inhibitors of cGAS targeting protein DNA interaction and phase separation.
- Xiaoquan Wang
- , Youqiao Wang
- & Junmin Quan
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Article
| Open AccessAn amide to thioamide substitution improves the permeability and bioavailability of macrocyclic peptides
Solvent shielding of the amide hydrogen bond donor through chemical modification or conformational control has been successfully utilized to impart membrane permeability to macrocyclic peptides. Here, the authors show that passive membrane permeability can also be conferred by masking the amide hydrogen bond acceptor through thioamide substitution, leading to improved pharmacological properties of peptide macrocycles.
- Pritha Ghosh
- , Nishant Raj
- & Jayanta Chatterjee
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Article
| Open AccessThe leaderless communication peptide (LCP) class of quorum-sensing peptides is broadly distributed among Firmicutes
The human pathogen Streptococcus pyogenes secretes a short peptide (LCP) that mediates intercellular communication and controls bacterial virulence. Here, the authors show that LCP homologues act as bacterial intercellular signals and regulate gene expression also in other bacteria.
- Shifu Aggarwal
- , Elaine Huang
- & Muthiah Kumaraswami
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Article
| Open AccessMolecular basis of TASL recruitment by the peptide/histidine transporter 1, PHT1
The peptide/histidine transporter 1, PHT1 (SLC15A4), is required for TLR-IRF5 activation via the adaptor protein TASL. Here, the authors determined the structure of PHT1 in the outward-open conformation and present a model of the PHT1-TASL complex where the first 16 residues of TASL bind into the central cavity of PHT1.
- Tânia F. Custódio
- , Maxime Killer
- & Christian Löw
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Article
| Open AccessGenetically encoded discovery of perfluoroaryl macrocycles that bind to albumin and exhibit extended circulation in vivo
Peptide-based therapeutics are promising therapeutic modalities, however, their prevalent drawback is poor circulation half-life in vivo. Here, the authors report the selection of albumin-binding macrocyclic peptides from genetically encoded libraries of peptides modified by perfluoroaryl-cysteine chemistry, with decafluoro-diphenylsulfone.
- Jeffrey Y. K. Wong
- , Arunika I. Ekanayake
- & Ratmir Derda
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Article
| Open AccessVisualizing the membrane disruption action of antimicrobial peptides by cryo-electron tomography
Antimicrobial peptide mechanism of membrane disruption have not been fully characterized at the cellular level. Here, authors use cryo-electron tomography and AFM to directly visualize the disruption of the outer and inner membranes of Escherichia coli by a de novo-designed peptide.
- Eric H.-L. Chen
- , Chun-Hsiung Wang
- & Rita P.-Y. Chen
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Article
| Open AccessSuppression of alpha-carbon racemization in peptide synthesis based on a thiol-labile amino protecting group
During solid-phase peptide synthesis (SPPS) inherent side reactions of the protected amino acids such as α-C racemization generate by-products that are hard to remove. Here, the authors report thiol-labile amino protecting group for SPPS, DNPBS group, which suppresses the main side reactions observed during conventional SPPS.
- Yifei Zhou
- , Hongjun Li
- & Chuanzheng Zhou
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Article
| Open AccessData-mining unveils structure–property–activity correlation of viral infectivity enhancing self-assembling peptides
Certain peptides can boost viral infectivity. However, the requirements for their activity remain unclear. Here, the authors demonstrate that peptides are efficient viral enhancers if they form hydrophobic β-sheet-rich, positively charged μm-sized aggregates.
- Kübra Kaygisiz
- , Lena Rauch-Wirth
- & Tanja Weil
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Article
| Open AccessHydrophobic interactions dominate the recognition of a KRAS G12V neoantigen
Mutation associated neoantigens are a family of highly specific therapeutic targets for the treatment of cancer. Here, the authors describe the cryo-EM structure of an antibody bound to a neoantigen complex providing insights into the specificity of the antibody.
- Katharine M. Wright
- , Sarah R. DiNapoli
- & Sandra B. Gabelli
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Article
| Open AccessExtensive breaking of genetic code degeneracy with non-canonical amino acids
Genetic code expansion is limited by the degeneracy of the 61 sense codons which encode for only 20 amino acids. Here, the authors show that by combining hyperaccurate ribosomes and in vitro transcribed tRNAs, dramatic and extensive breaking of sense codon degeneracy can be achieved.
- Clinton A. L. McFeely
- , Bipasana Shakya
- & Matthew C. T. Hartman
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Article
| Open AccessHigh-throughput characterization of HLA-E-presented CD94/NKG2x ligands reveals peptides which modulate NK cell activation
HLA-E is a highly conserved MHC-l recognized by NK and T cells. The authors characterize HLA-E-presented peptides recognized by CD94/NKG2x, identifying human and CMV-derived peptide ligands which can modulate NK cell activity when presented by HLA-E, including for selective NK cell activation.
- Brooke D. Huisman
- , Ning Guan
- & Michael E. Birnbaum
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Article
| Open AccessNitroalkanes as thioacyl equivalents to access thioamides and thiopeptides
Replacement of oxoamide units with thioamides in peptide therapeutics is a valuable tactic to improve biological activity and resistance to enzymatic hydrolysis. Here, the authors develop a direct coupling of readily available nitroalkane and amines with elemental sulfur and base and provide an efficient way to form thioamides and thiopeptides.
- Xiaonan Wang
- , Silong Xu
- & Jing Li
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Article
| Open AccessPolymorphic amyloid nanostructures of hormone peptides involved in glucose homeostasis display reversible amyloid formation
In this work, the authors highlight that conserved receptor binding segments of class B GPCR ligands have a dual nature: they serve as amyloid-prone regions involved in pH-dependent conversion from secretory amyloid fibrils to the functional folded form.
- Dániel Horváth
- , Zsolt Dürvanger
- & András Perczel
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Article
| Open AccessCryo-EM structure and polymorphic maturation of a viral transduction enhancing amyloid fibril
In this work, the authors report the Cryo-EM structure of PNF-18, a biotechnologically engineered peptide fibril that enhances retroviral infectivity. The peptide fibrils mature into polymorphic amyloid structures in a time-dependent manner. The structure provides insights into the molecular basis of peptide nanofibrils as retroviral transduction enhancers.
- Thomas Heerde
- , Desiree Schütz
- & Marcus Fändrich
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Article
| Open AccessHypoRiPPAtlas as an Atlas of hypothetical natural products for mass spectrometry database search
A gap exists between large-scale genome mining and mass spectral datasets for natural product discovery. Here the authors bridge the gap by developing HypoRiPPAtlas, an Atlas of hypothetical natural product structures, which is ready-to-use for in silico database search of tandem mass spectra.
- Yi-Yuan Lee
- , Mustafa Guler
- & Hosein Mohimani
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Article
| Open AccessLateral membrane organization as target of an antimicrobial peptidomimetic compound
The mechanism of action of the antibacterial tripeptide AMC-109 is unclear. Here, Melcrová et al. show that AMC-109 self-assembles into stable aggregates with a cationic surface, and then individual peptides insert into the bacterial membrane and disrupt membrane nanodomains, thus affecting membrane function without forming pores.
- Adéla Melcrová
- , Sourav Maity
- & Wouter H. Roos
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Article
| Open AccessModular synthesis of clickable peptides via late-stage maleimidation on C(7)-H tryptophan
Cyclic peptides are of interest due to their application in pharmaceutical industry, but currently there are limited methodologies for their synthesis. Here, the authors report an efficient and direct peptide cyclization via rhodium(III)-catalysed C(7)-H maleimidation.
- Peng Wang
- , Jiang Liu
- & Yuguo Zheng
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Article
| Open AccessActivating hidden signals by mimicking cryptic sites in a synthetic extracellular matrix
In this work, the authors synthetized hydrogels that mimic cryptic sites in the native extracellular matrix (ECM) using switch peptides. They report how in response to enzymes on the surface of endothelial cells the inert matrix is transformed into a bioadhesive synthetic ECM.
- Yumeng Zhu
- , Yulia Shmidov
- & John B. Matson
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Article
| Open AccessCoordinated adaptations define the ontogenetic shift from worm- to fish-hunting in a venomous cone snail
Challenges rearing juvenile cone snails have limited our understanding of their developmental biology. This study cultured Conus magus cone snails and revealed how complex morphological, behavioural and molecular changes facilitate the ontogenetic shift from juvenile worm-hunters to fish-hunting adults.
- Aymeric Rogalski
- , S. W. A. Himaya
- & Richard J. Lewis
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Matters Arising
| Open AccessThe G protein preference of orexin receptors is currently an unresolved issue
- Jyrki P. Kukkonen