Proteins articles within Nature Chemistry

Featured

  • Article
    | Open Access

    Negatively charged lysine acylations—malonylation, succinylation and glutarylation—impact protein structure and function, which can affect cellular processes. Now temporarily masked thioester derivatives of succinylation and glutarylation can be used for site-specific modification of diverse bacterial and mammalian proteins, which can facilitate the study of how these lysine modifications impact enzymatic activity and control protein–protein and protein–DNA interactions.

    • Maria Weyh
    • , Marie-Lena Jokisch
    •  & Kathrin Lang

  • Article
    | Open Access

    The underlying mechanism for how heterotypic protein–RNA interactions modulate the liquid to amyloid transition of hnRNPA1A, a protein involved in amyotrophic lateral sclerosis, has so far remained elusive. Now characterization of hnRNPA1A condensate formation and aggregation in vitro reveals that the RNA/protein stoichiometry affects the molecular pathways leading to amyloid formation.

    • Chiara Morelli
    • , Lenka Faltova
    •  & Paolo Arosio

  • Article |

    The lack of effective methods for mirror-image (d-) protein sequencing hampers the development of mirror-image biology systems and related applications. Now, total chemical synthesis of mirror-image trypsin enables the sequencing of long d-peptides and d-proteins, which may facilitate applications of d-peptides and d-proteins as potential therapeutic and informational tools.

    • Guanwei Zhang
    •  & Ting F. Zhu

  • Article
    | Open Access

    Understanding of the molecular mechanisms underlying the maturation of protein condensates into amyloid fibrils associated with neurodegenerative diseases has so far remained elusive. Now it has been shown that in condensates formed by the low-complexity domain of the amyotrophic lateral sclerosis-associated protein hnRNPA1, fibril formation is promoted at the interface, which provides a potential therapeutic target for counteracting aberrant protein aggregation.

    • Miriam Linsenmeier
    • , Lenka Faltova
    •  & Paolo Arosio

  • Article
    | Open Access

    An enzymatic reaction installs endogenous β-amino acids in proteins with unique reactivity. Now it has been shows that this reaction can be used for site-specific modification with tetrazine dienophiles to introduce labels onto target proteins. Applications include generation of a radiolabel chelator-modified Her2-binding Affibody and intracellular, fluorescently labelled cell division protein FtsZ.

    • Daniel Richter
    • , Edgars Lakis
    •  & Jörn Piel

  • Article |

    Techniques to specifically modulate protein activity are needed to interrogate spatial effects in cellular processes. A genetically encoded method for site-specific protein–protein conjugation based on a photoclick chemical reaction has now been developed. This method permits rapid and irreversible reassembly of bioactive proteins from non-functional split fragment pairs with full spatiotemporal control in solution, biomaterials and living mammalian cells.

    • Emily R. Ruskowitz
    • , Brizzia G. Munoz-Robles
    •  & Cole A. DeForest

  • Article |

    Protein–carbohydrate interactions remain challenging to study due to their low binding affinity and non-covalent nature. Now, a genetically encoded bioreactive unnatural amino acid containing sulfonyl fluoride has been shown to crosslink a protein with its bound glycan, offering a solution to probe and exploit protein–carbohydrate interactions.

    • Shanshan Li
    • , Nanxi Wang
    •  & Lei Wang

  • Article |

    The β1-adrenergic receptor (β1AR) contains empty cavities in its preactive conformation, which disappear in the active one. Now, using X-ray crystallography of xenon-derivatized β1AR crystals, a cavity has been shown to be in contact with the cholesterol-binding pocket. Monitoring the binding of a cholesterol analogue in solution has explained the function of cholesterol as a negative allosteric modulator of β1AR.

    • Layara Akemi Abiko
    • , Raphael Dias Teixeira
    •  & Stephan Grzesiek

  • Review Article |

    Viruses use the cellular machinery of their host organism to reproduce. This Review discusses how [FeS] cluster-containing proteins activate, support and modulate the innate immune response to restrict viral infections as well as highlighting how some of these proteins simultaneously support the replication of viruses.

    • Kourosh Honarmand Ebrahimi
    • , Simone Ciofi-Baffoni
    •  & Fraser A. Armstrong

  • Article |

    An integrated multiprotein nanopore has been fabricated using components from all three domains of life. This molecular machine opens the door to two approaches in single-molecule protein analysis, in which selected substrate proteins are unfolded, fed to into the proteasomal chamber and then processed either as fragmented peptides or intact polypeptides.

    • Shengli Zhang
    • , Gang Huang
    •  & Giovanni Maglia

  • Thesis |

    Bruce C. Gibb reminds us that buffers are not necessarily innocent bystanders and that they can bind to biomacromolecules too.

    • Bruce C. Gibb

  • Article |

    Non-canonical amino acids can be incorporated into proteins through translation of orthogonal mRNAs. Now, automating the design of orthogonal mRNAs—which are more selectively and efficiently translated—in combination with compact orthogonal aminoacyl-tRNA synthetase/tRNA expression systems, enables the incorporation of four distinct non-canonical monomers via a 68-codon genetic code.

    • Daniel L. Dunkelmann
    • , Sebastian B. Oehm
    •  & Jason W. Chin

  • Article |

    The opening mechanism of the SARS-CoV-2 spike protein has been studied by integrating computational and experimental data. Combining weighted ensemble molecular dynamics simulations, biolayer interferometry and ManifoldEM analysis of cryo-EM data revealed that the glycan at N343 plays a gating role in the opening mechanism of the SARS-CoV-2 spike protein.

    • Terra Sztain
    • , Surl-Hee Ahn
    •  & Rommie E. Amaro

  • Article |

    Simulations of the SARS-CoV-2 proteome that include over 0.1 s of aggregate data are reported. Spike opening was observed, revealing cryptic epitopes that differ between variants, explaining differential interactions with antibodies and receptors that determine pathogenicity. The cryptic pockets described provide new targets for antivirals and a wealth of mechanistic insight.

    • Maxwell I. Zimmerman
    • , Justin R. Porter
    •  & Gregory R. Bowman

  • Article |

    RNA origami can be used for the modular design of RNA nanoscaffolds but can be challenging to design. Newly developed computer-aided design software has now been shown to improve the folding yield of kilobase-sized RNA origami. These structures fold from a single strand during transcription by an RNA polymerase, and are able to position small molecules and protein components with nanoscale precision.

    • Cody Geary
    • , Guido Grossi
    •  & Ebbe S. Andersen

  • Article |

    The post-translational modification O-GlcNAc on amyloid-forming proteins can inhibit their aggregation. Now, it has been shown that O-GlcNAc modification of small heat shock proteins HSP27, αA- and αB-crystallin can increase their anti-amyloid activity and block the amyloid formation of both α-synuclein and Aβ(1–42). A mechanism for this protective effect based on decreased physical interactions is also proposed.

    • Aaron T. Balana
    • , Paul M. Levine
    •  & Matthew R. Pratt

  • News & Views |

    Site-specific attachment of a programmable motif, such as a synthetic nucleic acid tag, on a target protein can facilitate functional studies of proteins in cells or modulation of protein activity. Now, a small genetically encoded peptide enables the templated incorporation of a peptide nucleic acid tag onto membrane proteins in live cells.

    • Jerrin Thomas George
    •  & Sarit S. Agasti

  • Article |

    A method for the covalent labelling of proteins by installing a biostable peptide nucleic acid (PNA) tag has now been developed. The PNA label serves as a generic landing platform that enables the recruitment of fluorescent dyes via nucleic acid hybridization and fluorophore removal by toehold-mediated strand displacement. Imaging of cell surface receptors, including internalized receptors, has been demonstrated using this approach.

    • Georgina C. Gavins
    • , Katharina Gröger
    •  & Oliver Seitz

  • News & Views |

    An approach to design artificial intrinsically disordered proteins using a short peptide as a repeating unit has been reported. This design enables the phase behaviour of the protein to be finely tuned inside cells and enabled the formation of phase-separated condensates that can modulate chemical reactions.

    • Soumik Ray
    •  & Samir K. Maji

  • Article |

    Many bacterial pathogens release effector enzymes belonging to the large Fic family, which modify host targets with nucleotide monophosphates. Now, recombinantly produced Fic enzymes have been equipped with synthetic thiol-reactive nucleotide derivatives to make covalent binary probes. The reaction of modified Fic enzymes with their targets permits covalent substrate capture and the structural determination of low-affinity ternary enzyme–nucleotide–substrate complexes.

    • Burak Gulen
    • , Marie Rosselin
    •  & Aymelt Itzen

  • Article |

    The mechanism of nucleation for α-synuclein (α-Syn) aggregation and amyloid formation in Parkinson’s disease is unclear. Now, α-Syn has been shown to undergo liquid–liquid phase separation and a liquid-to-solid-like transition leading to amyloid fibril formation. This raises the possibility that liquid–liquid phase separation is a key pathogenic mechanism behind α-Syn aggregation in Parkinson’s disease.

    • Soumik Ray
    • , Nitu Singh
    •  & Samir K. Maji

  • Article |

    A method to fabricate heterotrimeric three-stranded coiled-coil peptide structures has now been developed using coordination around a Pb(ii) centre. The heterotrimeric structures require only three cysteines that bind to Pb(ii) to form a trigonal pyramidal structure, and the formation of an adjacent cavity in which water can hydrogen bond to the cysteine sulfur atoms.

    • Audrey E. Tolbert
    • , Catherine S. Ervin
    •  & Vincent L. Pecoraro

  • Article |

    Screening commercial kinase inhibitors for antibacterial activity identified the anticancer drug sorafenib as a major hit. Subsequent structure–activity optimization created a new antibacterial analogue with high potency against methicillin-resistant Staphylococcus aureus, including challenging persisters and biofilms, as well as demonstrating efficacy in an in vivo mouse model. The mode of action involves stimulation of protein secretion and inhibition of menaquinone biosynthesis.

    • Philipp Le
    • , Elena Kunold
    •  & Stephan A. Sieber

  • Article |

    A method for engineering chemically modified proteins has now been developed using a chemoenzymatic cascade of sortase-mediated transpeptidation and protein trans-splicing. Using this one-pot approach enabled the generation of site-specifically modified proteins in vitro and in isolated cell nuclei.

    • Robert E. Thompson
    • , Adam J. Stevens
    •  & Tom. W. Muir

  • Article |

    Symmetrical protein oligomers perform key structural and catalytic functions in nature, but engineering such oligomers synthetically is challenging. Now, oppositely supercharged synthetic variants of normally monomeric proteins have been shown to assemble via specific, introduced electrostatic contacts into symmetrical, highly well-defined oligomers.

    • Anna J. Simon
    • , Yi Zhou
    •  & Andrew D. Ellington

  • Article |

    The preparation of conjugates between proteins and small molecules is often challenging and requires several synthetic steps to functionalize each component for conjugation. Now, a conjugation methodology that leverages an electrophilic Se–S bond of selenocysteine to create bioconjugates between polypeptides and complex small molecules has been described.

    • Daniel T. Cohen
    • , Chi Zhang
    •  & Bradley L. Pentelute

  • Article |

    Pyrrolysyl-tRNA synthetase(PylRS)/PyltRNACUA pairs that lack the N-terminal domain but are active and orthogonal are discovered, and pairs that are mutually orthogonal to existing PylRS/PyltRNACUA pairs are developed. Mutually orthogonal PylRS/PyltRNA pairs are combined to genetically encode the incorporation of distinct ncAAs into proteins synthesized in E. coli.

    • Julian C. W. Willis
    •  & Jason W. Chin

  • Article |

    Living systems rely on externally tuneable and stimuli-responsive conformational changes of proteins and protein assemblies for a wide range of essential functions. A combination of experimental and computational analyses has now enabled the fabrication of a rationally designed, synthetic, stimuli-responsive protein assembly through modulation of its free-energy landscape.

    • Robert Alberstein
    • , Yuta Suzuki
    •  & F. Akif Tezcan

  • Article |

    Molecules that mimic the charge surface of B-DNA could enable the inhibition of DNA processive enzymes. Now, helically folded aromatic oligoamide scaffolds have been synthesized that display anions at positions similar to that of B-DNA phosphates. These foldamer mimics can recognize some DNA binding proteins and inhibit enzymes such as HIV integrase and topoisomerase 1.

    • Krzysztof Ziach
    • , Céline Chollet
    •  & Ivan Huc

  • News & Views |

    Mass spectrometry is a powerful technique for analysing proteins, yet linking higher-order protein structure to amino acid sequence and post-translational modifications is far from simple. Now, a native top-down method has been developed that can provide information on higher-order protein structure and different proteoforms at the same time.

    • Kathrin Breuker

  • Article |

    A computational method to design cyclic protein homo-oligomers has been developed. Using this approach, a series of idealized repeat proteins incorporating designed interfaces that direct their assembly into complexes possessing cyclic symmetry were fabricated. 15 out of 96 oligomers that were characterized experimentally were shown to be consistent with the computational model.

    • Jorge A. Fallas
    • , George Ueda
    •  & David Baker

  • Article |

    Difficulties in experimentally achieving simultaneous structural sensitivity and time resolution have hindered the real-time mapping of the vibrational energy relaxation pathways in biomacromolecules. Now, using ultrashort light pulses to locally deposit excess energy in a protein-bound haem, the temporal evolution of the subsequent energy flow has been monitored, unravelling vibrational couplings that lead to mode-specific temperature changes.

    • C. Ferrante
    • , E. Pontecorvo
    •  & T. Scopigno

  • Article |

    A generally applicable small-molecule switch for protein function in live cells has been developed based on selective protein protection using unnatural amino acid mutagenesis and a bioorthogonal deprotection via Staudinger reduction.

    • Ji Luo
    • , Qingyang Liu
    •  & Alexander Deiters

  • Article |

    G proteins are the key mediators of G protein-coupled receptor signalling, facilitating a number of important physiological processes. Now, the total synthesis and structure–activity relationship studies have been reported for the only known selective Gq protein inhibitors, the natural cyclic depsipeptides YM-254890 and FR900359.

    • Xiao-Feng Xiong
    • , Hang Zhang
    •  & Kristian Strømgaard

  • Article |

    Selectively degrading the pathogenic, aggregated amyloid state of proteins, without affecting the functional state, is a potential therapeutic strategy for treating amyloid diseases. Now, photooxygenation catalysts that are active only when bound to the cross-β-sheet structure of the amyloid form have been developed.

    • Atsuhiko Taniguchi
    • , Yusuke Shimizu
    •  & Motomu Kanai

  • Editorial |

    Nitric oxide (NO) is an important signalling molecule in biological systems, but it is unclear exactly how it interacts with some metalloproteins. Now, a collection of articles in this issue reveal how NO binds to proteins containing type-1 copper sites.

  • News & Views |

    Nitric oxide (NO) has important functions in all forms of life and serves, for example, as a signalling molecule in mammals. Now, two complementary studies have uncovered how NO binds to blue copper proteins. This research suggests a mechanism by which NO could regulate the activity of blue copper proteins involved in denitrification.

    • Subhra Samanta
    •  & Nicolai Lehnert

  • Article |

    Cell-sized asymmetric giant lipid vesicles containing a very small amount of organic solvent have now been formed via inhomogeneous break-up of a lipid microtube that was generated by applying a jet flow to an asymmetric planar lipid bilayer. The asymmetric giant vesicles were used to investigate the dynamic responses of lipid molecules and the effect of asymmetry on biochemical reactions.

    • Koki Kamiya
    • , Ryuji Kawano
    •  & Shoji Takeuchi

  • News & Views |

    The low-complexity-protein, liquid phases of membraneless organelles have now been established to selectively partition biomolecules. The specialized microenvironment that they provide differs chemically from the surrounding medium and enables specific nucleic-acid remodelling reactions.

    • James Shorter

  • Article |

    A mirror-image polymerase—a version of African swine fever virus polymerase X made from D-amino acids—has now been chemically synthesized. This polymerase can catalyse template-directed L-DNA replication and transcription from L-DNA into L-RNA. These reactions represent two key steps in the central dogma of molecular biology—but demonstrated using the opposite chirality.

    • Zimou Wang
    • , Weiliang Xu
    •  & Ting F. Zhu

  • Review Article |

    Chemical protein synthesis can enable the preparation of proteins containing post-translational modifications or unnatural variations such as D-amino acids. Such modified proteins are not easily fabricated by other methods. This Review provides an overview of the current approaches for the chemical synthesis of proteins.

    • Somasekhar Bondalapati
    • , Muhammad Jbara
    •  & Ashraf Brik

  • Article |

    Nature's speciality is to direct and control the reactivity of species, which are otherwise fatally destructive. However, the processes and design rules required to achieve such precise control are not clear. A de novo designed metalloprotein that stabilizes an otherwise unstable organic radical has now been developed to guide our understanding.

    • Gözde Ulas
    • , Thomas Lemmin
    •  & William F. DeGrado

  • News & Views |

    The discovery of a tetrapeptide containing a reactive cysteine provides a method to site-selectively modify peptides and proteins, even if other cysteine residues are present in the polypeptide chain.

    • Yichao Huang
    •  & Lei Liu

  • Editorial |

    The modification of proteins with fluorophores, drugs and polymers is required for many applications, yet conjugation reactions often generate a heterogeneous mixture of products. A collection of articles in this issue focuses on methods to modify proteins in a site-selective manner.

  • Article |

    Incorporation of a π-clamp—a four-residue sequence (Phe-Cys-Pro-Phe)—into a protein enables the site-specific modification of the π-clamp cysteine side-chain. The π-clamp can be genetically encoded and does not require protecting-groups or catalysts to provide selective conjugation.

    • Chi Zhang
    • , Matthew Welborn
    •  & Bradley L. Pentelute

  • Perspective |

    Synthetic vaccines offer one method to avoid the drawbacks associated with vaccines derived from whole organisms. This Perspective highlights the improvements and significant recent progress that has been achieved in developing well-defined synthetic vaccines using a variety of molecular antigens.

    • Lyn H. Jones

  • Article |

    O-linked N-acetyl-glucosamine (O-GlcNAc) has been identified as an endogenous modification of α-synuclein; however, its effect on the properties of the protein is unclear. Now, recombinant protein and synthetic peptides have been combined to produce both unmodified and site-specifically O-GlcNAc-modified α-synuclein. The O-GlcNAc modification at threonine 72 was shown to inhibit the aggregation and associated toxicity of α-synuclein.

    • Nicholas P. Marotta
    • , Yu Hsuan Lin
    •  & Matthew R. Pratt

  • Article |

    Protein PEGylation is routinely used to produce molecules with improved pharmacokinetic properties. However, despite their importance, the structure of PEGylated proteins has remained elusive. Now, the first crystal structure of a model β-sheet protein modified with a single PEG chain has been reported. NMR spectroscopy data indicates that the protein and PEG behave as independent domains.

    • Giada Cattani
    • , Lutz Vogeley
    •  & Peter B. Crowley

Browse broader subjects

Browse narrower subjects

Browse Proteins across other nature.com journals