Biological sciences articles within Nature Chemistry

Featured

  • Research Briefing |

    An infrared laser-induced temperature jump provides a rapid and broadly applicable perturbation to protein dynamics. Temperature-jump crystallography was paired with time-resolved X-ray crystallography to study the dynamic enzyme lysozyme. Measurements with and without a functional inhibitor revealed different patterns in the propagation of motion throughout the enzyme.

  • Article
    | Open Access

    Shifts in temperature alter the structure and dynamics of macromolecules. Now, infra-red laser-induced temperature jump is combined with X-ray crystallography to observe protein structural dynamics in real time. Using this method, motions related to the catalytic cycle of lysozyme, a model enzyme, are visualized at atomic resolution and across broad timescales.

    • Alexander M. Wolff
    • , Eriko Nango
    •  & Michael C. Thompson

  • Article
    | Open Access

    Biological membranes are asymmetric bilayers, but little is known about how this asymmetry modulates membrane protein folding or stability. Now, folding and stability assays with bacterial outer membrane proteins reveal an exquisite sensitivity to asymmetric membrane charge distribution and a required matching of protein charge for efficient folding.

    • Jonathan M. Machin
    • , Antreas C. Kalli
    •  & Sheena E. Radford

  • Article
    | Open Access

    Phase separation is being revealed as important in many biological processes. Most attempts to mimic and deconstruct this use engineered natural proteins. Now it is shown that de novo proteins can be designed from first principles to undergo liquid–liquid phase separation in cells, with the potential to organize multi-enzyme pathways.

    • Alexander T. Hilditch
    • , Andrey Romanyuk
    •  & Derek N. Woolfson

  • News & Views |

    Medicinal chemistry efforts typically focus on drug–protein interactions and overlook RNA binding as a source of off-target pharmacology. Now, a new method has been developed to map the interactions of small-molecule drugs with RNA in cells and characterize how these interactions can exert functional effects.

    • Christopher R. Fullenkamp
    •  & John S. Schneekloth Jr

  • Article
    | Open Access

    Ribozyme-mediated post-transcriptional RNA modification is a powerful method for site-specific RNA labelling and analysis of RNA functions. Now, an alkyltransferase ribozyme—termed SAMURI—has been shown to catalyse the transfer of a propargyl group from a stabilized synthetic S-adenosylmethionine analogue to a specific adenosine on the target RNA within cells.

    • Takumi Okuda
    • , Ann-Kathrin Lenz
    •  & Claudia Höbartner

  • Article
    | Open Access

    Molecular systems with coincident cyclic and superhelical symmetry axes have considerable advantages for materials design as they can be lengthened or shortened by changing the length of the monomers. Now a systematic approach to generate modular repeat protein oligomers with combined symmetry that can be extended by repeat propagation has been developed.

    • Neville P. Bethel
    • , Andrew J. Borst
    •  & David Baker

  • Article |

    Now a reactivity-based RNA profiling strategy can measure the global off-target transcriptome interactions of small-molecule drugs at single-nucleotide resolution. Using this approach, three FDA-approved drugs were evaluated, uncovering pervasive drug–RNA interactions and interactions that perturb RNA functions in cells.

    • Linglan Fang
    • , Willem A. Velema
    •  & Eric T. Kool

  • Article
    | Open Access

    Pump–probe measurements conventionally achieve femtosecond time resolution for X-ray crystallography of reactive processes, but the measured structural dynamics are complex. Using coherent control techniques, we show that the ultrafast crystallographic differences of a fluorescent protein are dominated by ground-state vibrational processes that are unconnected to the photoisomerization reaction of the chromophore.

    • Christopher D. M. Hutchison
    • , James M. Baxter
    •  & Jasper J. van Thor

  • Article |

    The coupling of autocatalysis to compartment growth and division is a key step in the origin of life. Now it has been shown that compartmentalizing the formose reaction in emulsion droplets leads to several crucial properties of living and evolving systems (growth, division, variation, competition, rudimentary heredity and selection).

    • Heng Lu
    • , Alex Blokhuis
    •  & Andrew D. Griffiths

  • News & Views |

    Tandem cycloaddition reactions have significant applications in organic synthetic chemistry. Now, two enzymes are shown to catalyse tandem hetero-Diels–Alder reactions with a synergistic interplay between a calcium cofactor and N-glycan post-translational modifications during the biosynthesis of bistropolone-sesquiterpene secondary metabolites.

    • Richiro Ushimaru
    •  & Ikuro Abe

  • Article
    | Open Access

    Three-protein conjugates, which have so far been produced using protein-engineering strategies, can now be generated using a chemical approach that enables the addition of small-molecule functionality. Checkpoint inhibitory T cell engagers (CiTEs) were assembled and shown to have enhanced in vitro potency compared to a traditional T cell engager.

    • Peter A. Szijj
    • , Melissa A. Gray
    •  & Vijay Chudasama

  • Article |

    Most chemoproteomic screening approaches are indirect. Now, a chemoproteomic platform based on chiral sulfonyl fluoride probes has been developed for the direct identification of probe-modified tyrosines and lysines in live cells. Stereoselective modification by structurally diverse probes was observed for 634 tyrosines and lysines across functionally diverse protein sites.

    • Ying Chen
    • , Gregory B. Craven
    •  & Jack Taunton

  • Article |

    The kinetics of liquid–liquid phase separation (LLPS) in cell-like confinements remains poorly understood. Now it has been shown that it involves complex interplay between the incipient phases and the membrane boundary, which arrests phase coarsening, deforms the membrane and couples LLPS with lipid phase separation.

    • Wan-Chih Su
    • , James C. S. Ho
    •  & Atul N. Parikh

  • Article
    | Open Access

    Allostery produces concerted functions of protein complexes by orchestrating the cooperative work between the constituent subunits. By restoring functions of pseudo-active sites that have been lost through evolution, allosteric sites have now been designed into a rotary molecular motor, V1-ATPase, resulting in its rotation being boosted allosterically.

    • Takahiro Kosugi
    • , Tatsuya Iida
    •  & Nobuyasu Koga

  • 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 |

    The design and construction of a stereo-defined DNA-encoded chemical library, featuring the four different 4-amino-proline stereoisomers as a central scaffold, has now enabled the discovery of potent ligands to proteins of pharmaceutical interest. Parallel screening with closely related isoforms (anti-targets) facilitated the isolation of hits with high selectivity ratios.

    • Sebastian Oehler
    • , Laura Lucaroni
    •  & Gabriele Bassi

  • News & Views |

    Genetic code expansion beyond α-amino acids is a major challenge, in which stitching together non-natural building blocks within the ribosome is a critical barrier. Now, the molecular determinants for the efficient incorporation of non-natural amino acids into the ribosome have been unlocked, accelerating ribosomal synthesis.

    • Souvik Sinha
    • , Mohd Ahsan
    •  & Giulia Palermo

  • Article |

    Microtubules carry patterns of post-translational modifications that are important for the regulation of key cellular processes. Now a semi-synthetic method facilitates the production of tubulins with defined post-translational modifications. Using these designer tubulins, polyglutamylation of α-tubulin is found to promote its detyrosination by enhancing the activity of the carboxypeptidase vasohibin/small vasohibin-binding protein.

    • Eduard Ebberink
    • , Simon Fernandes
    •  & Charlotte Aumeier

  • Article |

    Two glycosylated enzymes, EupfF and PycR1, have now been characterized and shown to independently catalyse the tandem intermolecular [4 + 2] cycloaddition in the biosynthesis of bistropolone-sesquiterpenes. Through analysis of enzyme–substrate co-crystal structures, together with computational and mutational studies, the origins of their catalytic activity and stereoselectivity were elucidated.

    • Jiawang Liu
    • , Jiayan Lu
    •  & Youcai Hu

  • Article |

    Celastrol is a potent anti-obesity agent found in the root of Tripterygium wilfordii, but its medicinal application is compromised by limited availability. Now, by combining plant biochemistry with metabolic engineering and chemistry, the biosynthetic pathway of celastrol has been elucidated and has afforded its scalable production in yeast.

    • Yong Zhao
    • , Nikolaj L. Hansen
    •  & Sotirios C. Kampranis

  • Article |

    Stabilization of RNAs for storage, transport and biological application remains a profound challenge. Now, it has been shown that reversible 2′-OH acylation with easily accessible acylimidazoles unlocks efficient protection of RNA. RNA can be deprotected by non-basic nucleophiles or spontaneously in cells to restore RNA functions.

    • Linglan Fang
    • , Lu Xiao
    •  & Eric T. Kool

  • Research Briefing |

    Challenges in the synthesis of heparan sulfate (HS) glycosaminoglycans have limited access to defined HS oligosaccharides bearing a diverse array of sulfation sequences. A concise, divergent synthetic approach now provides a library of 64 HS tetrasaccharides displaying a comprehensive set of sulfation sequences, offering insight into the elusive sulfation code of glycosaminoglycans.

  • Article |

    Contrary to agonist binding being the sole driver for β2-adrenergic receptor (β2AR) activation, molecular metadynamics simulations now reveal a distinct activation mechanism. Coupling β2AR with its cognate Gs protein induces considerable structural changes, activating both proteins. Gs opens its GDP binding pocket while β2AR undergoes expansion.

    • Amirhossein Mafi
    • , Soo-Kyung Kim
    •  & William A. Goddard III

  • Research Briefing |

    Protein translation is the ultimate paradigm for sequence-defined polymer synthesis. To introduce non-canonical monomers into the genetic code of living organisms, pairs of biomolecules known as aminoacyl-tRNA synthetases (aaRSs) and transfer RNAs (tRNAs) are required. The discovery and engineering of five such pairs, that do not interfere with each other or the aaRS–tRNA pairs of a bacterial host, sets the stage for highly modified genetically encoded biopolymers.

  • Article |

    The mechanism of α-synuclein amyloid aggregation via liquid–liquid phase separation has so far remained elusive. Now, the existence of nanoscale clusters of α-synuclein in sub-saturated concentrations is observed using mass photometry. These nanoscale clusters can act as precursors to both macroscopic condensate droplets as well as amyloid fibrils.

    • Soumik Ray
    • , Thomas O. Mason
    •  & Alexander K. Buell

  • Article |

    Mutually orthogonal aminoacyl transfer RNA synthetase/transfer RNA pairs are required for genetically encoding non-canonical amino acids into proteins, as well as for the encoded cellular synthesis of polymers and macrocycles; however, the scalable discovery of such pairs is challenging. A quintuply orthogonal set of pyrrolysyl-tRNA synthetase/pyrrolysyl-tRNA pairs has now been generated through tRNA screening, engineering and directed evolution.

    • Adam T. Beattie
    • , Daniel L. Dunkelmann
    •  & Jason W. Chin

  • Article
    | Open Access

    Fluorescent sensors that are responsive only in a specific subcellular location have remained elusive. Now, a chemogenetic sensing platform has been developed to sense glutathione in a user-defined organelle of interest. These tools enable quantitative studies of subcellular glutathione homeostasis using visible or near-infrared wavelengths.

    • Sarah Emmert
    • , Gianluca Quargnali
    •  & Pablo Rivera-Fuentes

  • Article
    | Open Access

    The metal-dependent, bifunctional isoprenyl diphosphate synthase PcIDS1 from the leaf beetle Phaedon cochleariae integrates substrate, product and metal-ion concentrations to tune its dynamic reactivity. Now structural and functional analyses reveal that this enzyme uses both catalytic centres to form geranyl pyrophosphate, while one domain is inactivated during farnesyl pyrophosphate production.

    • Felix Ecker
    • , Abith Vattekkatte
    •  & Michael Groll

  • Article
    | Open Access

    Genetic code expansion to incorporate non-α-amino acid monomers is limited by predictability of monomer reactivities in the context of the ribosome. Now the use of metadynamics simulations of pre-attack monomers in the ribosomal peptidyl transferase centre provides insight on whether an A-site monomer is likely to be reactive.

    • Zoe L. Watson
    • , Isaac J. Knudson
    •  & Ara M. Abramyan

  • Article |

    Incorporating polar residues into hydrophobic protein channel pores facilitates selective proton transport. Now, classical and multiscale reactive molecular dynamics simulations of designed channels reveal dynamic water wires within the channel lumen that are proton conductive according to structural and functional validation. These results provide some guiding principles for biological and engineered proton conduction.

    • Huong T. Kratochvil
    • , Laura C. Watkins
    •  & William F. DeGrado

  • Article |

    Generating aptamers for use as affinity reagents in analytical applications is important, but SELEX, the standard method for aptamer generation, is unable to select for pre-defined binding affinities. Now, by combining efficient particle display, high-performance microfluidic sorting and high-content bioinformatics, the method ‘Pro-SELEX’ can afford the quantitative generation of aptamers with programmable binding affinities.

    • Dingran Chang
    • , Zongjie Wang
    •  & Shana O. Kelley

  • Article
    | Open Access

    The ortho-substituted phenyl ring is a basic structural element in chemistry. Now, 2-oxabicyclo[2.1.1]hexanes have been developed as saturated bioisosteres of the ortho-substituted phenyl ring with improved physicochemical properties. Replacement of the phenyl ring with 2-oxabicyclo[2.1.1]hexanes in marketed agrochemicals fluxapyroxad and boscalid improved water solubility, reduced lipophilicity and retained bioactivity.

    • Aleksandr Denisenko
    • , Pavel Garbuz
    •  & Pavel K. Mykhailiuk

  • Perspective |

    Bioresponsive hyperpolarized probes contain magnetic resonance signals that can be many orders of magnitude larger than those of common, thermally polarized probes. This Perspective discusses how bioresponsive hyperpolarized probes can be directly linked to biological events to give functional information, enabling the mapping of physiological processes and diseases in real time using magnetic resonance.

    • Goran Angelovski
    • , Ben J. Tickner
    •  & Gaoji Wang

  • Article
    | Open Access

    Ribosomal incorporation of non-α-amino acid monomers into proteins is largely restricted to in vitro translation. Now, pyrrolysyl-transfer RNA synthetase variants have been shown to acylate tRNAs with α-thio acids, malonic acids, and N-formyl amino acids. This work represents a key step towards the programmed ribosomal synthesis of sequence-defined non-protein polymers in cellulo.

    • Riley Fricke
    • , Cameron V. Swenson
    •  & Alanna Schepartz

  • News & Views |

    Complexity is a hallmark of biological systems, but scientific experiments are typically conducted in simplified conditions. Now, diverse polymers that mimic the local environments of complex biological mixtures have been shown to improve protein folding, stability and function.

    • Alana P. Gudinas
    •  & Danielle J. Mai

  • News & Views |

    From humans designing machines, to machines designing biology, deep learning is turning the tables for assisted exploration of biologically active and diverse protein designs. Now, a deep-learning-based strategy has been used to design artificial enzymes that catalyse a light-emitting reaction.

    • Christian Dallago
    •  & Kevin K. Yang

  • News & Views |

    Constructing aptamers with desired target-binding affinities may lead to new applications but is challenging. Now, a new method using a high-dimensional microfluidic approach enables quantitative isolation of aptamers with programable binding affinities.

    • Ping Song
    •  & Chunhai Fan

  • Article |

    The biosynthesis of the methylated sesquiterpene sodorifen, which features a cryptic methylation pattern, has now been studied through extensive labelling experiments and computational chemistry. The methyl group formation is now understood to come from methylene carbons of the substrate farnesyl diphosphate and the absolute configuration of the biosynthetic intermediate presodorifen diphosphate has been revised.

    • Houchao Xu
    • , Lukas Lauterbach
    •  & Jeroen S. Dickschat

  • Article
    | Open Access

    Protein solutions can undergo liquid–liquid phase separation, by condensing into a dense phase that often resembles liquid droplets, which coexist with a dilute phase. Now it is shown that hydrophobic interactions, specifically at interfaces, can trigger a liquid–solid phase separation of a protein solution.

    • Daria Maltseva
    • , Sayantan Chatterjee
    •  & Mischa Bonn

  • Article
    | Open Access

    In vitro screening of a ribosomally synthesized macrocyclic peptide library containing cyclic γ2,4-amino acids (cγAA) afforded the discovery of potent inhibitors of the SARS-CoV-2 main protease (Mpro). A co-crystal structure revealed the contribution of this cγAA to Mpro binding and the proteolytic stability of these macrocycles.

    • Takashi Miura
    • , Tika R. Malla
    •  & Hiroaki Suga

  • Article
    | Open Access

    The metallophilic interaction between cyclometalated palladium complexes can facilitate supramolecular nanostructure formation in living mice, providing a phototoxic prodrug with a long circulation time and high tumour-targeting efficiency. Upon green light irradiation, this palladium-based drug destroys solid tumours, leaving non-irradiated organs intact.

    • Xue-Quan Zhou
    • , Peiyuan Wang
    •  & Sylvestre Bonnet

  • In Your Element |

    Organisms that glow are perhaps eerie. Vadim Viviani ponders on the luciferin–luciferase systems responsible for their intriguing bioluminescence.

    • Vadim R. Viviani

  • 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

  • In Your Element |

    Jane Liao and Allie C. Obermeyer explore the discovery, modification and applications of green fluorescent protein, best known for its use as a tool to cast light on cellular processes.

    • Jane Liao
    •  & Allie C. Obermeyer

  • Article |

    Water-soluble, cell-permeable, inert fluorescent tags called OregonFluors have been developed to withstand environmental changes while resistant towards non-specific binding with subcellular structures. These tags enable quantitative imaging of drug target availability in cells and tissues, providing a route for the future assessment of personalized therapies.

    • Lei G. Wang
    • , Antonio R. Montaño
    •  & Summer L. Gibbs

  • News & Views |

    Therapies that destroy senescent cells could be used to alleviate age-related disease, yet conventional drugs often suffer from low selectivity and unwanted side effects. Now, a photosensitive agent has been developed that is activated in situ in senescent cells, enabling their selective elimination.

    • Yunjie Xu
    • , Jong Seung Kim
    •  & Mingle Li

  • Article |

    The molybdenum nitrogenase catalytic cofactor is composed of seven high-spin Fe sites making it difficult to study spectroscopically. Now it has been shown that 57Fe can be incorporated into a single site and that such site-selectively labelled samples provide insights into the cofactor’s electronic structure and the mechanism of biological nitrogen fixation.

    • Edward D. Badding
    • , Suppachai Srisantitham
    •  & Daniel L. M. Suess

Browse narrower subjects

Browse Biological sciences across other nature.com journals