Search Results

You searched for all publications:

with publication states 'Published (Approved)'
published in journal 'Nature Chemical Biology'

Search Again...

These results only include publications that have been reviewed and processed by Diamond Light Source. To also view papers that have not yet been processed click here.

You can use the folder icon under Actions to collate papers as required. You can then click on View Folder in the left-hand navigation to review and/or download your folder.

Exact matches
Related results

56 items found (0 items not approved), displaying 1 to 10.[First/Prev] 1, 2, 3, 4, 5, 6 [Next/Last]

Instruments / Technical Area	Publication Details	Published
Krios V-Titan Krios V at Diamond	Signal peptide mimicry primes Sec61 for client-selective inhibition Shahid Rehan , Dale Tranter , Phillip P. Sharp , Gregory B. Craven , Eric Lowe , Janet L. Anderl , Tony Muchamuel , Vahid Abrishami , Suvi Kuivanen , Nicole A. Wenzell , Andy Jennings , Chakrapani Kalyanaraman , Tomas Strandin , Matti Javanainen , Olli Vapalahti , Matthew P. Jacobson , Dustin Mcminn , Christopher J. Kirk , Juha T. Huiskonen , Jack Taunton , Ville O. Paavilainen Nature Chemical Biology 1808 DOI: 10.1038/s41589-023-01326-1 Open Access Show Abstract ▼ Abstract: Preventing the biogenesis of disease-relevant proteins is an attractive therapeutic strategy, but attempts to target essential protein biogenesis factors have been hampered by excessive toxicity. Here we describe KZR-8445, a cyclic depsipeptide that targets the Sec61 translocon and selectively disrupts secretory and membrane protein biogenesis in a signal peptide-dependent manner. KZR-8445 potently inhibits the secretion of pro-inflammatory cytokines in primary immune cells and is highly efficacious in a mouse model of rheumatoid arthritis. A cryogenic electron microscopy structure reveals that KZR-8445 occupies the fully opened Se61 lateral gate and blocks access to the lumenal plug domain. KZR-8445 binding stabilizes the lateral gate helices in a manner that traps select signal peptides in the Sec61 channel and prevents their movement into the lipid bilayer. Our results establish a framework for the structure-guided discovery of novel therapeutics that selectively modulate Sec61-mediated protein biogenesis.	May 2023
I24-Microfocus Macromolecular Crystallography	Functional E3 ligase hotspots and resistance mechanisms to small-molecule degraders Alexander Hanzl , Ryan Casement , Hana Imrichova , Scott J. Hughes , Eleonora Barone , Andrea Testa , Sophie Bauer , Jane Wright , Matthias Brand , Alessio Ciulli , Georg E. Winter Nature Chemical Biology 580 DOI: 10.1038/s41589-022-01177-2 Diamond Proposal Number(s): [14980] Show Abstract ▼ Abstract: Targeted protein degradation is a novel pharmacology established by drugs that recruit target proteins to E3 ubiquitin ligases. Based on the structure of the degrader and the target, different E3 interfaces are critically involved, thus forming defined ‘functional hotspots’. Understanding disruptive mutations in functional hotspots informs on the architecture of the assembly, and highlights residues susceptible to acquire resistance phenotypes. Here we employ haploid genetics to show that hotspot mutations cluster in substrate receptors of hijacked ligases, where mutation type and frequency correlate with gene essentiality. Intersection with deep mutational scanning revealed hotspots that are conserved or specific for chemically distinct degraders and targets. Biophysical and structural validation suggests that hotspot mutations frequently converge on altered ternary complex assembly. Moreover, we validated hotspots mutated in patients that relapse from degrader treatment. In sum, we present a fast and widely accessible methodology to characterize small-molecule degraders and associated resistance mechanisms.	Nov 2022
I03-Macromolecular Crystallography I04-Macromolecular Crystallography I23-Long wavelength MX	Functional metagenomic screening identifies an unexpected β-glucuronidase Stefanie Neun , Paul Brear , Eleanor Campbell , Theodora Tryfona , Kamel El Omari , Armin Wagner , Paul Dupree , Marko Hyvonen , Florian Hollfelder Nature Chemical Biology 48 DOI: 10.1038/s41589-022-01071-x Diamond Proposal Number(s): [18548, 25402] Show Abstract ▼ Abstract: The abundance of recorded protein sequence data stands in contrast to the small number of experimentally verified functional annotation. Here we screened a million-membered metagenomic library at ultrahigh throughput in microfluidic droplets for β-glucuronidase activity. We identified SN243, a genuine β-glucuronidase with little homology to previously studied enzymes of this type, as a glycoside hydrolase 3 family member. This glycoside hydrolase family contains only one recently added β-glucuronidase, showing that a functional metagenomic approach can shed light on assignments that are currently ‘unpredictable’ by bioinformatics. Kinetic analyses of SN243 characterized it as a promiscuous catalyst and structural analysis suggests regions of divergence from homologous glycoside hydrolase 3 members creating a wide-open active site. With a screening throughput of >107 library members per day, picolitre-volume microfluidic droplets enable functional assignments that complement current enzyme database dictionaries and provide bridgeheads for the annotation of unexplored sequence space.	Jul 2022
I03-Macromolecular Crystallography I04-1-Macromolecular Crystallography (fixed wavelength) I04-Macromolecular Crystallography I24-Microfocus Macromolecular Crystallography	Sulfated glycan recognition by carbohydrate sulfatases of the human gut microbiota Ana S. Luis , Arnaud Basle , Dominic P. Byrne , Gareth S. A. Wright , James A. London , Chunsheng Jin , Niclas G. Karlsson , Gunnar C. Hansson , Patrick A. Eyers , Mirjam Czjzek , Tristan Barbeyron , Edwin A. Yates , Eric C. Martens , Alan Cartmell Nature Chemical Biology 19 DOI: 10.1038/s41589-022-01039-x Diamond Proposal Number(s): [21970, 18598] Show Abstract ▼ Abstract: Sulfated glycans are ubiquitous nutrient sources for microbial communities that have coevolved with eukaryotic hosts. Bacteria metabolize sulfated glycans by deploying carbohydrate sulfatases that remove sulfate esters. Despite the biological importance of sulfatases, the mechanisms underlying their ability to recognize their glycan substrate remain poorly understood. Here, we use structural biology to determine how sulfatases from the human gut microbiota recognize sulfated glycans. We reveal seven new carbohydrate sulfatase structures spanning four S1 sulfatase subfamilies. Structures of S1_16 and S1_46 represent novel structures of these subfamilies. Structures of S1_11 and S1_15 demonstrate how non-conserved regions of the protein drive specificity toward related but distinct glycan targets. Collectively, these data reveal that carbohydrate sulfatases are highly selective for the glycan component of their substrate. These data provide new approaches for probing sulfated glycan metabolism while revealing the roles carbohydrate sulfatases play in host glycan catabolism.	Jun 2022
I03-Macromolecular Crystallography	A single sensor controls large variations in zinc quotas in a marine cyanobacterium Alevtina Mikhaylina , Amira Z. Ksibe , Rachael C. Wilkinson , Darbi Smith , Eleanor Marks , James P. C. Coverdale , Vilmos Fulop , David J. Scanlan , Claudia A. Blindauer Nature Chemical Biology 5 DOI: 10.1038/s41589-022-01051-1 Diamond Proposal Number(s): [14692] Open Access Show Abstract ▼ Abstract: Marine cyanobacteria are critical players in global nutrient cycles that crucially depend on trace metals in metalloenzymes, including zinc for CO2 fixation and phosphorus acquisition. How strains proliferating in the vast oligotrophic ocean gyres thrive at ultra-low zinc concentrations is currently unknown. Using Synechococcus sp. WH8102 as a model we show that its zinc-sensor protein Zur differs from all other known bacterial Zur proteins in overall structure and the location of its sensory zinc site. Uniquely, Synechococcus Zur activates metallothionein gene expression, which supports cellular zinc quotas spanning two orders of magnitude. Thus, a single zinc sensor facilitates growth across pico- to micromolar zinc concentrations with the bonus of banking this precious resource. The resultant ability to grow well at both ultra-low and excess zinc, together with overall lower zinc requirements, likely contribute to the broad ecological distribution of Synechococcus across the global oceans.	Jun 2022
I04-1-Macromolecular Crystallography (fixed wavelength)	Structure of UBE2K–Ub/E3/polyUb reveals mechanisms of K48-linked Ub chain extension Mark A. Nakasone , Karolina A. Majorek , Mads Gabrielsen , Gary J. Sibbet , Brian O. Smith , Danny T. Huang Nature Chemical Biology 67 DOI: 10.1038/s41589-021-00952-x Diamond Proposal Number(s): [21657] Open Access Show Abstract ▼ Abstract: Ubiquitin (Ub) chain types govern distinct biological processes. K48-linked polyUb chains target substrates for proteasomal degradation, but the mechanism of Ub chain synthesis remains elusive due to the transient nature of Ub handover. Here, we present the structure of a chemically trapped complex of the E2 UBE2K covalently linked to donor Ub and acceptor K48-linked di-Ub, primed for K48-linked Ub chain synthesis by a RING E3. The structure reveals the basis for acceptor Ub recognition by UBE2K active site residues and the C-terminal Ub-associated (UBA) domain, to impart K48-linked Ub specificity and catalysis. Furthermore, the structure unveils multiple Ub-binding surfaces on the UBA domain that allow distinct binding modes for K48- and K63-linked Ub chains. This multivalent Ub-binding feature serves to recruit UBE2K to ubiquitinated substrates to overcome weak acceptor Ub affinity and thereby promote chain elongation. These findings elucidate the mechanism of processive K48-linked polyUb chain formation by UBE2K.	Jan 2022
I04-Macromolecular Crystallography	Auxiliary interfaces support the evolution of specific toxin–antitoxin pairing Grzegorz J. Grabe , Rachel T. Giorgio , Alexander M. J. Hall , Rhodri M. L. Morgan , Laurent Dubois , Tyler A. Sisley , Julian A. Rycroft , Stephen A. Hare , Sophie Helaine Nature Chemical Biology 163 DOI: 10.1038/s41589-021-00862-y Diamond Proposal Number(s): [17221] Show Abstract ▼ Abstract: Toxin–antitoxin (TA) systems are a large family of genes implicated in the regulation of bacterial growth and its arrest in response to attacks. These systems encode nonsecreted toxins and antitoxins that specifically pair, even when present in several paralogous copies per genome. Salmonella enterica serovar Typhimurium contains three paralogous TacAT systems that block bacterial translation. We determined the crystal structures of the three TacAT complexes to understand the structural basis of specific TA neutralization and the evolution of such specific pairing. In the present study, we show that alteration of a discrete structural add-on element on the toxin drives specific recognition by their cognate antitoxin underpinning insulation of the three pairs. Similar to other TA families, the region supporting TA-specific pairing is key to neutralization. Our work reveals that additional TA interfaces beside the main neutralization interface increase the safe space for evolution of pairing specificity.	Sep 2021
I02-Macromolecular Crystallography I04-Macromolecular Crystallography I24-Microfocus Macromolecular Crystallography	A topological switch in CFTR modulates channel activity and sensitivity to unfolding Daniel Scholl , Maud Sigoillot , Marie Overtus , Rafael Colomer Martinez , Chloé Martens , Yiting Wang , Els Pardon , Toon Laeremans , Abel Garcia-Pino , Jan Steyaert , David N. Sheppard , Jelle Hendrix , Cedric Govaerts Nature Chemical Biology 245 DOI: 10.1038/s41589-021-00844-0 Diamond Proposal Number(s): [12718, 9426] Show Abstract ▼ Abstract: The cystic fibrosis transmembrane conductance regulator (CFTR) anion channel is essential to maintain fluid homeostasis in key organs. Functional impairment of CFTR due to mutations in the cftr gene leads to cystic fibrosis. Here, we show that the first nucleotide-binding domain (NBD1) of CFTR can spontaneously adopt an alternate conformation that departs from the canonical NBD fold previously observed. Crystallography reveals that this conformation involves a topological reorganization of NBD1. Single-molecule fluorescence resonance energy transfer microscopy shows that the equilibrium between the conformations is regulated by adenosine triphosphate binding. However, under destabilizing conditions, such as the disease-causing mutation F508del, this conformational flexibility enables unfolding of the β-subdomain. Our data indicate that, in wild-type CFTR, this conformational transition of NBD1 regulates channel function, but, in the presence of the F508del mutation, it allows domain misfolding and subsequent protein degradation. Our work provides a framework to design conformation-specific therapeutics to prevent noxious transitions.	Aug 2021
B21-High Throughput SAXS	Architecture and functional dynamics of the pentafunctional AROM complex Harshul Arora Verasztó , Maria Logotheti , Reinhard Albrecht , Alexander Leitner , Hongbo Zhu , Marcus D. Hartmann Nature Chemical Biology 64 DOI: 10.1038/s41589-020-0587-9 Diamond Proposal Number(s): [14307] Show Abstract ▼ Abstract: The AROM complex is a multifunctional metabolic machine with ten enzymatic domains catalyzing the five central steps of the shikimate pathway in fungi and protists. We determined its crystal structure and catalytic behavior, and elucidated its conformational space using a combination of experimental and computational approaches. We derived this space in an elementary approach, exploiting an abundance of conformational information from its monofunctional homologs in the Protein Data Bank. It demonstrates how AROM is optimized for spatial compactness while allowing for unrestricted conformational transitions and a decoupled functioning of its individual enzymatic entities. With this architecture, AROM poses a tractable test case for the effects of active site proximity on the efficiency of both natural metabolic systems and biotechnological pathway optimization approaches. We show that a mere colocalization of enzymes is not sufficient to yield a detectable improvement of metabolic throughput.	Jul 2020
I04-1-Macromolecular Crystallography (fixed wavelength)	Enzymatic C–H activation of aromatic compounds through CO2 fixation Godwin A. Aleku , Annica Saaret , Ruth T. Bradshaw-Allen , Sasha R. Derrington , Gabriel R. Titchiner , Irina Gostimskaya , Deepanker Gahloth , David A. Parker , Sam Hay , David Leys Nature Chemical Biology 531 DOI: 10.1038/s41589-020-0603-0 Diamond Proposal Number(s): [12788, 17773] Show Abstract ▼ Abstract: The direct C–H carboxylation of aromatic compounds is an attractive route to the corresponding carboxylic acids, but remains challenging under mild conditions. It has been proposed that the first step in anaerobic microbial degradation of recalcitrant aromatic compounds is a UbiD-mediated carboxylation. In this study, we use the UbiD enzyme ferulic acid decarboxylase (Fdc) in combination with a carboxylic acid reductase to create aromatic degradation-inspired cascade reactions, leading to efficient functionalization of styrene through CO2 fixation. We reveal that rational structure-guided laboratory evolution can expand the substrate scope of Fdc, resulting in activity on a range of mono- and bicyclic aromatic compounds through a single mutation. Selected variants demonstrated 150-fold improvement in the conversion of coumarillic acid to benzofuran + CO2 and unlocked reactivity towards naphthoic acid. Our data demonstrate that UbiD-mediated C–H activation is a versatile tool for the transformation of aryl/alkene compounds and CO2 into commodity chemicals.	Jul 2020

Publications Database

Search Results

You searched for all publications:

Search Again...

Subject Areas (check all that apply) select all

Instruments used to collect data (check all that apply) select all

Collaborations involved (check all that apply) select all

Diamond Offline Facilities used

Relevant Technical Areas (check all that apply) select all

Menu for Anonymous User