ORCID Profile
0000-0002-2070-6030
Current Organisations
Victor Chang Cardiac Research Institute
,
University of New South Wales
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Characterisation of Biological Macromolecules | Biochemistry and Cell Biology | Structural Biology (incl. Macromolecular Modelling)
Publisher: Elsevier BV
Date: 03-2017
DOI: 10.1016/J.JSB.2017.01.002
Abstract: The bacterial A/V-type ATPase/synthase rotary motor couples ATP hydrolysis/synthesis with proton translocation across biological membranes. The A/V-type ATPase/synthase from Thermus thermophilus has been extensively studied both structurally and functionally for many years. Here we provide an 8.7Å resolution cryo-electron microscopy 3D reconstruction of this complex bound to single-domain antibody fragments, small monomeric antibodies containing just the variable heavy domain. Docking of known structures into the density revealed the molecular orientation of the domain antibodies, suggesting that structure determination of co-domain antibody:protein complexes could be a useful avenue for unstable or smaller proteins. Although previous studies suggested that the presence of fluoroaluminate in this complex could change the rotary state of this enzyme, we observed no gross structural rearrangements under these conditions.
Publisher: Cold Spring Harbor Laboratory
Date: 14-01-2020
DOI: 10.1101/2020.01.13.905216
Abstract: Chaperonins are biomolecular complexes that assist protein folding. Thermophilic Factor 55 (TF55) is a group II chaperonin found in the archaeal genus Sulfolobus that has α, β and γ subunits. Using cryo-electron microscopy, we have determined the structure of the β-only complex of S. solfataricus TF55 complexes to 3.6–4.2 Å resolution and a filamentous form to 5.2 Å resolution. The structures of the TF55β complexes formed in the presence of ADP or ATP highlighted an open state in which nucleotide exchange can occur before progressing in the refolding cycle. The structure of the filamentous state indicates how helical protrusions facilitate end-on-end interactions. The isolated complex and filamentous forms of TF55β chaperonin from the thermophilic archaea Sulfolobus solfataricus are reported. Using cryo-EM, nucleotide-bound complexes of TF55β at 3.6–4.2 Å resolution reveal an open conformation, while a 5.2 Å reconstruction of the filamentous chaperonin reveals contacts at the apical domain similar to crystal-packed structures.
Publisher: Springer Science and Business Media LLC
Date: 21-02-2010
DOI: 10.1038/NSMB.1761
Publisher: Springer Science and Business Media LLC
Date: 16-02-2014
DOI: 10.1038/NCHEM.1868
Publisher: Springer Science and Business Media LLC
Date: 21-02-2012
DOI: 10.1038/NCOMMS1693
Publisher: Springer Science and Business Media LLC
Date: 19-12-2016
Publisher: eLife Sciences Publications, Ltd
Date: 16-12-0001
Publisher: Cold Spring Harbor Laboratory
Date: 28-02-2023
Abstract: The GIGYF proteins interact with 4EHP and RNA-associated proteins to elicit transcript-specific translational repression. However, the mechanism by which the GIGYF1/2–4EHP complex is recruited to its target transcripts remain unclear. Here we report the crystal structures of the GYF domains from GIGYF1 and GIGYF2 in complex with proline-rich sequences from miRISC-binding proteins TNRC6C and TNRC6A, respectively. The TNRC6 proline-rich motifs bind to a conserved array of aromatic residues on the surface of the GIGYF1/2 GYF domain, thereby bridging 4EHP to Argonaute–miRNA complexes. Our structures also reveal a phenylalanine residue conserved from yeast to human GYF domains that contributes to GIGYF2 thermostability. The molecular details we outline here are likely to be conserved between GIGYF1/2 and other RNA-binding proteins to elicit 4EHP-mediated repression in different biological contexts.
Publisher: Cold Spring Harbor Laboratory
Date: 20-10-2022
DOI: 10.1101/2022.10.19.512954
Abstract: Emerging variants of concern (VOCs) are threatening to limit the effectiveness of SARS-CoV-2 monoclonal antibodies and vaccines currently used in clinical practice broadly neutralizing antibodies and strategies for their identification are therefore urgently required. Here we demonstrate that broadly neutralizing antibodies can be isolated from peripheral blood mononuclear cells (PBMCs) of convalescent patients using SARS-CoV-2 receptor binding domains (RBDs) carrying epitope-specific mutations. This is exemplified by two human antibodies, GAR05, binding to epitope class 1, and GAR12, binding to a new epitope class 6 (located between class 3 and class 5). Both antibodies broadly neutralize VOCs, exceeding the potency of the clinical monoclonal sotrovimab (mAb S309) by orders of magnitude. They also provide potent prophylactic and therapeutic in vivo protection of hACE2 mice against viral challenge. Our results indicate that exposure to Wuhan SARS-CoV-2 induces antibodies that maintain potent and broad neutralization against emerging VOCs using two unique strategies: either by targeting the ergent class 1 epitope in a manner resistant to VOCs (ACE2 mimicry, as illustrated by GAR05 and mAbs P2C-1F11/S2K14) or alternatively, by targeting rare and highly conserved epitopes, such as the new class 6 epitope identified here (as illustrated by GAR12). Our results provide guidance for next generation monoclonal antibody development and vaccine design.
Publisher: Springer Science and Business Media LLC
Date: 11-10-2023
Publisher: American Association for the Advancement of Science (AAAS)
Date: 16-11-2018
Abstract: Insights into the architecture and stoichiometry of membrane complexes have grown with advances in cryo–electron microscopy and native mass spectroscopy. However, most of these studies are not in the context of native membrane. Chorev et al. released intact membrane complexes directly from native lipid membrane vesicles into a mass spectrometer. They analyzed components of the Escherichia coli inner and outer membranes and the bovine mitochondrial inner membrane. For several identified complexes, they found a stoichiometry that differs from published results and, in some cases, confirmed interactions that could not be characterized structurally. Science , this issue p. 829
Publisher: Springer Science and Business Media LLC
Date: 11-01-2023
DOI: 10.1038/S42003-023-04414-Z
Abstract: F 1 F o ATP synthase functions as a biological generator and makes a major contribution to cellular energy production. Proton flow generates rotation in the F o motor that is transferred to the F 1 motor to catalyze ATP production, with flexible F 1 /F o coupling required for efficient catalysis. F 1 F o ATP synthase can also operate in reverse, hydrolyzing ATP and pumping protons, and in bacteria this function can be regulated by an inhibitory ε subunit. Here we present cryo-EM data showing E. coli F 1 F o ATP synthase in different rotational and inhibited sub-states, observed following incubation with 10 mM MgATP. Our structures demonstrate how structural transitions within the inhibitory ε subunit induce torsional movement in the central stalk, thereby enabling its rotation within the F ο motor. This highlights the importance of the central rotor for flexible coupling of the F 1 and F o motors and provides further insight into the regulatory mechanism mediated by subunit ε.
Publisher: International Union of Crystallography (IUCr)
Date: 03-2021
DOI: 10.1107/S2053230X21002223
Abstract: Chaperonins are biomolecular complexes that assist in protein folding. Thermophilic factor 55 (TF55) is a group II chaperonin found in the archaeal genus Sulfolobus that has α, β and γ subunits. Using cryo-electron microscopy, structures of the β-only complex of S. solfataricus TF55 (TF55β) were determined to 3.6–4.2 Å resolution. The structures of the TF55β complexes formed in the presence of ADP or ATP highlighted an open state in which nucleotide exchange can occur before progressing in the refolding cycle.
Publisher: Wiley
Date: 05-03-2018
DOI: 10.1113/JP274888
Publisher: Cold Spring Harbor Laboratory
Date: 20-08-2021
DOI: 10.1101/2021.08.20.457040
Abstract: The GIGYF proteins associate with 4EHP and RNA-associated proteins to elicit transcript-specific translational repression. However, the mechanism by which the GIGYF1/2-4EHP complex is recruited to its target transcripts remain unclear. Here we report the crystal structures of the GYF domains from GIGYF1 and GIGYF2 in complex with proline-rich sequences from miRISC-binding proteins TNRC6C and TNRC6A, respectively. The TNRC6 proline-rich motifs bind to a conserved array of aromatic residues on the surface of the GIGYF1/2 GYF domain, bridging 4EHP to Argonaute-miRNA mRNA targets. Our structures also reveal a phenylalanine residue conserved from yeast to human GYF domains that contributes to GIGYF2 thermostability. The molecular details we outline here are likely to be conserved between GIGYF1/2 and other RNA-binding proteins to elicit 4EHP-mediated repression in different biological contexts.
Publisher: Public Library of Science (PLoS)
Date: 24-08-2017
Publisher: Springer Science and Business Media LLC
Date: 08-02-2023
DOI: 10.1038/S41467-023-36295-5
Abstract: Emerging variants of concern (VOCs) are threatening to limit the effectiveness of SARS-CoV-2 monoclonal antibodies and vaccines currently used in clinical practice broadly neutralizing antibodies and strategies for their identification are therefore urgently required. Here we demonstrate that broadly neutralizing antibodies can be isolated from peripheral blood mononuclear cells of convalescent patients using SARS-CoV-2 receptor binding domains carrying epitope-specific mutations. This is exemplified by two human antibodies, GAR05, binding to epitope class 1, and GAR12, binding to a new epitope class 6 (located between class 3 and 5). Both antibodies broadly neutralize VOCs, exceeding the potency of the clinical monoclonal sotrovimab (S309) by orders of magnitude. They also provide prophylactic and therapeutic in vivo protection of female hACE2 mice against viral challenge. Our results indicate that exposure to SARS-CoV-2 induces antibodies that maintain broad neutralization against emerging VOCs using two unique strategies: either by targeting the ergent class 1 epitope in a manner resistant to VOCs (ACE2 mimicry, as illustrated by GAR05 and mAbs P2C-1F11/S2K14) or alternatively, by targeting rare and highly conserved epitopes, such as the new class 6 epitope identified here (as illustrated by GAR12). Our results provide guidance for next generation monoclonal antibody development and vaccine design.
Publisher: Research Square Platform LLC
Date: 08-12-2021
DOI: 10.21203/RS.3.RS-1105661/V1
Abstract: The exquisite fine tuning of biological electrical signalling is mediated by variations in the rates of opening and closing of different ion channels(1). In addition to open and closed conformations, ion channels can exist in an inactivated state, which prevents conduction in the presence of a prolonged activating stimulus(2). Human ether-a-go-go related gene (HERG) K+ channels undergo uniquely rapid and voltage dependent inactivation(3-5), which confers upon them a critical role in protecting against cardiac arrhythmias and sudden death(6). Previous structural studies have captured only the open state of the HERG channel(7,8). Here, we have exploited the K+ sensitivity of HERG inactivation to determine structures of both the conductive state and the elusive inactivated state of HERG. We show that hERG inactivation is facilitated by two competing networks of hydrogen bonds behind the selectivity filter that enable rapid and voltage dependent flipping of the valine carbonyls in the centre of the selectivity filter. Our data also explains how changes in extracellular K+ affects the distribution between conductive and inactivated states(9,10) and thereby explains why hypokalaemia reduces HERG channel activity thereby increasing the risk of cardiac arrhythmias(11).
Publisher: Cold Spring Harbor Laboratory
Date: 29-04-2019
DOI: 10.1101/622084
Abstract: F 1 F o ATP synthase functions as a biological rotary generator and makes a major contribution to cellular energy production. It is comprised of two motors that are coupled together by a central “rotor” and peripheral “stator” stalk. Proton flow through the F o motor generates rotation of the central stalk that induces conformation changes that catalyze production of ATP in the F 1 motor. Here we provide 3-4 Å resolution cryo-EM structures of E. coli F 1 F o ATP synthase in 10 mM MgADP. In addition to generating a comprehensive structural model of E. coli F 1 F o ATP synthase to provide a framework to interpret mutagenesis studies, we describe a rotational sub-step of the F o motor c -ring associated with long-range conformational changes that suggests an elegant mechanism by which the F 1 and F o motors can be coupled with minimal energy loss.
Publisher: eLife Sciences Publications, Ltd
Date: 26-03-2019
DOI: 10.7554/ELIFE.43864
Abstract: ATP synthase produces the majority of cellular energy in most cells. We have previously reported cryo-EM maps of autoinhibited E. coli ATP synthase imaged without addition of nucleotide (Sobti et al. 2016), indicating that the subunit ε engages the α, β and γ subunits to lock the enzyme and prevent functional rotation. Here we present multiple cryo-EM reconstructions of the enzyme frozen after the addition of MgATP to identify the changes that occur when this ε inhibition is removed. The maps generated show that, after exposure to MgATP, E. coli ATP synthase adopts a different conformation with a catalytic subunit changing conformation substantially and the ε C-terminal domain transitioning via an intermediate ‘half-up’ state to a condensed ‘down’ state. This work provides direct evidence for unique conformational states that occur in E. coli ATP synthase when ATP binding prevents the ε C-terminal domain from entering the inhibitory ‘up’ state.
Publisher: Springer Science and Business Media LLC
Date: 17-02-2021
Publisher: Springer Science and Business Media LLC
Date: 03-08-2021
DOI: 10.1038/S41467-021-25029-0
Abstract: F 1 F o ATP synthase interchanges phosphate transfer energy and proton motive force via a rotary catalysis mechanism. Isolated F 1 -ATPase catalytic cores can hydrolyze ATP, passing through six intermediate conformational states to generate rotation of their central γ-subunit. Although previous structural studies have contributed greatly to understanding rotary catalysis in the F 1 -ATPase, the structure of an important conformational state (the binding-dwell) has remained elusive. Here, we exploit temperature and time-resolved cryo-electron microscopy to determine the structure of the binding- and catalytic-dwell states of Bacillus PS3 F 1 -ATPase. Each state shows three catalytic β-subunits in different conformations, establishing the complete set of six states taken up during the catalytic cycle and providing molecular details for both the ATP binding and hydrolysis strokes. We also identify a potential phosphate-release tunnel that indicates how ADP and phosphate binding are coordinated during synthesis. Overall these findings provide a structural basis for the entire F 1 -ATPase catalytic cycle.
Publisher: Informa UK Limited
Date: 2021
Publisher: Elsevier BV
Date: 12-2021
Publisher: Springer US
Date: 15-10-2020
DOI: 10.1007/978-1-4939-9869-2_5
Abstract: ATP synthase is an essential enzyme found in all known forms of life, generating the majority of cellular energy via a rotary catalytic mechanism. Here, we describe the in-depth methods for expression, purification, and functional assessment of E. coli ATP synthase.
Publisher: Elsevier BV
Date: 05-2016
DOI: 10.1016/J.JMB.2015.10.023
Abstract: Proteins are translated in the cytoplasm, but many need to access the nucleus to perform their functions. Understanding how these nuclear proteins are transported through the nuclear envelope and how the import processes are regulated is therefore an important aspect of understanding cell function. Structural biology has played a key role in understanding the molecular events during the transport processes and their regulation, including the recognition of nuclear targeting signals by the corresponding receptors. Here, we review the structural basis of the principal nuclear import pathways and the molecular basis of their regulation. The pathways involve transport factors that are members of the β-karyopherin family, which can bind cargo directly (e.g., importin-β, transportin-1, transportin-3, importin-13) or through adaptor proteins (e.g., importin-α, snurportin-1, symportin-1), as well as unrelated transport factors such as Hikeshi, involved in the transport of heat-shock proteins, and NTF2, involved in the transport of RanGDP. Solenoid proteins feature prominently in these pathways. Nuclear transport factors recognize nuclear targeting signals on the cargo proteins, including the classical nuclear localization signals, recognized by the adaptor importin-α, and the PY nuclear localization signals, recognized by transportin-1. Post-translational modifications, particularly phosphorylation, constitute key regulatory mechanisms operating in these pathways.
Publisher: Elsevier BV
Date: 11-2012
DOI: 10.1016/J.STR.2012.10.003
Abstract: In this issue of Structure, Oot and colleagues present the crystal structure of the eukaryotic V-ATPase peripheral stalk in complex with one of its binding partners, revealing conformational flexibility that may be important for priming the complex for rapid disassembly in response to external stimuli.
Publisher: Elsevier BV
Date: 03-2016
DOI: 10.1016/J.STR.2015.12.016
Abstract: Chaperonins are essential biological complexes assisting protein folding in all kingdoms of life. Whereas homooligomeric bacterial GroEL binds hydrophobic substrates non-specifically, the heterooligomeric eukaryotic CCT binds specifically to distinct classes of substrates. Sulfolobales, which survive in a wide range of temperatures, have evolved three different chaperonin subunits (α, β, γ) that form three distinct complexes tailored for different substrate classes at cold, normal, and elevated temperatures. The larger octadecameric β complexes cater for substrates under heat stress, whereas smaller hexadecameric αβ complexes prevail under normal conditions. The cold-shock complex contains all three subunits, consistent with greater substrate specificity. Structural analysis using crystallography and electron microscopy reveals the geometry of these complexes and shows a novel arrangement of the α and β subunits in the hexadecamer enabling incorporation of the γ subunit.
Publisher: eLife Sciences Publications, Ltd
Date: 21-12-2016
DOI: 10.7554/ELIFE.21598
Abstract: A molecular model that provides a framework for interpreting the wealth of functional information obtained on the E. coli F-ATP synthase has been generated using cryo-electron microscopy. Three different states that relate to rotation of the enzyme were observed, with the central stalk’s ε subunit in an extended autoinhibitory conformation in all three states. The Fo motor comprises of seven transmembrane helices and a decameric c-ring and invaginations on either side of the membrane indicate the entry and exit channels for protons. The proton translocating subunit contains near parallel helices inclined by ~30° to the membrane, a feature now synonymous with rotary ATPases. For the first time in this rotary ATPase subtype, the peripheral stalk is resolved over its entire length of the complex, revealing the F1 attachment points and a coiled-coil that bifurcates toward the membrane with its helices separating to embrace subunit a from two sides.
Publisher: Springer Science and Business Media LLC
Date: 26-05-2020
DOI: 10.1038/S41467-020-16387-2
Abstract: F 1 F o ATP synthase functions as a biological rotary generator that makes a major contribution to cellular energy production. It comprises two molecular motors coupled together by a central and a peripheral stalk. Proton flow through the F o motor generates rotation of the central stalk, inducing conformational changes in the F 1 motor that catalyzes ATP production. Here we present nine cryo-EM structures of E. coli ATP synthase to 3.1–3.4 Å resolution, in four discrete rotational sub-states, which provide a comprehensive structural model for this widely studied bacterial molecular machine. We observe torsional flexing of the entire complex and a rotational sub-step of F o associated with long-range conformational changes that indicates how this flexibility accommodates the mismatch between the 3- and 10-fold symmetries of the F 1 and F o motors. We also identify density likely corresponding to lipid molecules that may contribute to the rotor/stator interaction within the F o motor.
Publisher: Informa UK Limited
Date: 2013
DOI: 10.4161/BIOA.23301
Publisher: Oxford University Press (OUP)
Date: 17-12-2016
DOI: 10.1093/NAR/GKV1466
Publisher: Elsevier BV
Date: 2018
DOI: 10.1016/J.CELREP.2017.12.069
Abstract: The TCP-1 ring complex (TRiC) is a multi-subunit group II chaperonin that assists nascent or misfolded proteins to attain their native conformation in an ATP-dependent manner. Functional studies in yeast have suggested that TRiC is an essential and generalized component of the protein-folding machinery of eukaryotic cells. However, TRiC's involvement in specific cellular processes within multicellular organisms is largely unknown because little validation of TRiC function exists in animals. Our in vivo analysis reveals a surprisingly specific role of TRiC in the biogenesis of skeletal muscle α-actin during sarcomere assembly in myofibers. TRiC acts at the sarcomere's Z-disk, where it is required for efficient assembly of actin thin filaments. Binding of ATP specifically by the TRiC subunit Cct5 is required for efficient actin folding in vivo. Furthermore, mutant α-actin isoforms that result in nemaline myopathy in patients obtain their pathogenic conformation via this function of TRiC.
Publisher: Cold Spring Harbor Laboratory
Date: 30-09-2020
DOI: 10.1101/2020.09.30.320408
Abstract: F 1 F o ATP synthase functions as a biological rotary generator that makes a major contribution to cellular energy production. Proton flow through the F o motor generates rotation of the central stalk, inducing conformational changes in the F 1 motor that catalyzes ATP production via flexible coupling. Here we present a range of cryo-EM structures of E. coli ATP synthase in different rotational and inhibited states observed following a 45 second incubation with 10 mM MgATP. The structures generated describe multiple changes that occur following addition of MgATP, with the inhibitory C-terminal domain of subunit ε (εCTD) disassociating from the central stalk to adopt a condensed “down” conformation. The transition to the εCTD down state increases the torsional flexibility of the central stalk allowing its foot to rotate by ∼50°, with further flexing in the peripheral stalk enabling the c -ring to rotate by two sub-steps in the F o motor. Truncation mutants lacking the second helix of the εCTD suggest that central stalk rotational flexibility is important for F 1 F o ATP synthase function. Overall this study identifies the potential role played by torsional flexing within the rotor and how this could be influenced by the ε subunit.
Publisher: Elsevier BV
Date: 04-2014
DOI: 10.1016/J.SBI.2013.11.013
Abstract: Recent work has provided the detailed overall architecture and subunit composition of three subtypes of rotary ATPases. Composite models of F-type, V-type and A-type ATPases have been constructed by fitting high-resolution X-ray structures of in idual components into electron microscopy derived envelopes of the intact enzymes. Electron cryo-tomography has provided new insights into the supra-molecular arrangement of eukaryotic ATP synthases within mitochondria. An inherent flexibility in rotary ATPases observed by different techniques suggests greater dynamics during operation than previously envisioned. The concerted movement of subunits within the complex might provide means of regulation and information transfer between distant parts of rotary ATPases thereby fine tuning these molecular machines to their cellular environment, while optimizing their efficiency.
Location: United Kingdom of Great Britain and Northern Ireland
Start Date: 2019
End Date: End date not available
Funder: National Health and Medical Research Council
View Funded ActivityStart Date: 04-2017
End Date: 12-2017
Amount: $850,000.00
Funder: Australian Research Council
View Funded Activity