Linhua Tai - Academia.edu (original) (raw)

Papers by Linhua Tai

Research paper thumbnail of Novel cleavage sites identified in SARS-CoV-2 spike protein reveal mechanism for cathepsin L-facilitated viral infection and treatment strategies

Cell Discovery

The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an impor... more The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an important target for vaccine and drug development. However, the rapid emergence of variant strains with mutated S proteins has rendered many treatments ineffective. Cleavage of the S protein by host proteases is essential for viral infection. Here, we discovered that the S protein contains two previously unidentified Cathepsin L (CTSL) cleavage sites (CS-1 and CS-2). Both sites are highly conserved among all known SARS-CoV-2 variants. Our structural studies revealed that CTSL cleavage promoted S to adopt receptor-binding domain (RBD) “up” activated conformations, facilitating receptor-binding and membrane fusion. We confirmed that CTSL cleavage is essential during infection of all emerged SARS-CoV-2 variants (including the recently emerged Omicron variant) by pseudovirus (PsV) infection experiment. Furthermore, we found CTSL-specific inhibitors not only blocked infection of PsV/live virus in ...

Research paper thumbnail of 8 Å structure of the outer rings of the Xenopus laevis nuclear pore complex obtained by cryo-EM and AI

Protein & Cell, 2022

The nuclear pore complex (NPC), one of the largest protein complexes in eukaryotes, serves as a p... more The nuclear pore complex (NPC), one of the largest protein complexes in eukaryotes, serves as a physical gate to regulate nucleocytoplasmic transport. Here, we determined the 8 Å resolution cryo-electron microscopic (cryo-EM) structure of the outer rings containing nuclear ring (NR) and cytoplasmic ring (CR) from the Xenopus laevis NPC, with local resolutions reaching 4.9 Å. With the aid of AlphaFold2, we managed to build a pseudoatomic model of the outer rings, including the Y complexes and flanking components. In this most comprehensive and accurate model of outer rings to date, the almost complete Y complex structure exhibits much tighter interaction in the hub region. In addition to two copies of Y complexes, each asymmetric subunit in CR contains five copies of Nup358, two copies of the Nup214 complex, two copies of Nup205 and one copy of newly identified Nup93, while that in NR contains one copy of Nup205, one copy of ELYS and one copy of Nup93. These in-depth structural featu...

Research paper thumbnail of The Unusual Homodimer of a Heme‐Copper Terminal Oxidase Allows Itself to Utilize Two Electron Donors

Angewandte Chemie International Edition, 2021

The heme-copper oxidase superfamily comprises cytochrome cand ubiquinol oxidases.These enzymes ca... more The heme-copper oxidase superfamily comprises cytochrome cand ubiquinol oxidases.These enzymes catalyze the transfer of electrons from different electron donors onto molecular oxygen. AB-family cytochrome coxidase from the hyperthermophilic bacterium Aquifex aeolicus was discovered previously to be able to use both cytochrome ca nd naphthoquinol as electron donors.Its molecular mechanism as well as the evolutionary significance are yet unknown. Here we solved its 3.4 resolution electron cryo-microscopic structure and discovered an ovel dimeric structure mediated by subunit I (CoxA2) that would be essential for naphthoquinol binding and oxidation. The unique structural features in both proton and oxygen pathways suggest an evolutionary adaptation of this oxidase to its hyperthermophilic environment. Our results add anew conceptual understanding of structural variation of cytochrome co xidases in different species.

Research paper thumbnail of Nanometer-resolution in situ structure of the SARS-CoV-2 postfusion spike protein

Proceedings of the National Academy of Sciences, 2021

Significance Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a severe threat to p... more Significance Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a severe threat to public health and the global economy. Its spike protein is responsible for the membrane fusion and is thus a major target for vaccine and drug development. Our study presents the in situ structure of the spike protein in the postfusion state with higher resolution, giving further insights into the design of a viral entry inhibitor. Our observation of the oligomerization states of spikes on the viral membrane implies a possible mechanism of membrane fusion for viral infection.

Research paper thumbnail of Determining the architecture of nuclear ring of Xenopus laevis nuclear pore complex using integrated approaches

ABSTRACTThe nuclear pore complexes (NPCs) are large protein assemblies as a physical gate to regu... more ABSTRACTThe nuclear pore complexes (NPCs) are large protein assemblies as a physical gate to regulate nucleocytoplasmic transport. Here, using integrated approaches including cryo-electron microscopy, hybrid homology modeling and cell experiment, we determined the architecture of the nuclear ring (NR) from Xenopus laevis oocytes NPC at subnanometer resolution. In addition to the improvement of the Y complex model, eight copies of Nup205 and ELYS were assigned in NR. Nup205 connects the inner and outer Y complexes and contributes to the assembly and stability of the NR. By interacting with both the inner Nup160 and the nuclear envelope (NE), the N-terminal β-propeller and α-solenoid domains of ELYS were found to be essential for accurate assembly of the NPC on the NE.

Research paper thumbnail of 8 Å structure of the cytoplasmic ring of the Xenopus laevis nuclear pore complex solved by cryo-EM and AI

ABSTRACTAs one of the largest protein complexes in eukaryotes, the nuclear pore complex (NPC) for... more ABSTRACTAs one of the largest protein complexes in eukaryotes, the nuclear pore complex (NPC) forms a conduit regulating nucleocytoplasmic transport. Here, we determined 8 Å resolution cryo-electron microscopic (cryo-EM) structure of the cytoplasmic ring (CR) from the Xenopus laevis NPC. With the aid of AlphaFold2, we managed to build a most comprehensive and accurate pseudoatomic model of the CR to date, including the Y complexes and flanking components of Nup358, Nup214 complexes, Nup205 and Nup93. Comparing with previously reported CR model, the Y complex structure in our model exhibits much tighter interactions in the hub region mediated by α-solenoid domain in Nup160 C-terminus. Five copies of Nup358 are identified in each CR subunit to provide rich interactions with other Nups in stem regions of Y complexes. Two copies of Nup214 complexes lay in a parallel pattern and attach to the short arm region of Y complexes towards the central channel of NPC. Besides, the structural deta...

Research paper thumbnail of 8 Å structure of the nuclear ring of the Xenopus laevis nuclear pore complex solved by cryo-EM and AI

ABSTRACTThe nuclear pore complex (NPC), one of the largest protein complexes in eukaryotes, serve... more ABSTRACTThe nuclear pore complex (NPC), one of the largest protein complexes in eukaryotes, serves as a physical gate to regulate nucleocytoplasmic transport. Here, we determined the 8 Å resolution cryo-electron microscopic (cryo-EM) structure of the nuclear ring (NR) from the Xenopus laevis NPC, with local resolutions reaching 4.9 Å. With the aid of AlphaFold2, we managed to build a pseudoatomic model of the NR, including the Y complexes and flanking components. In this most comprehensive and accurate model to date, the almost complete Y complex structure exhibits much tighter interaction in the hub region. Each NR asymmetric subunit contains two copies of Y complexes, one copy of Nup205 that connects the Y complexes to the neighbouring complex, one copy of ELYS that stabilizes the long arm region of the inner Y complex, and one copy of newly identified Nup93 that forms a bridge across the stems of Y complexes. These in-depth structural features represent a great advance in underst...

Research paper thumbnail of Structure-based evidence for the enhanced transmissibility of the dominant SARS-CoV-2 B.1.1.7 variant (Alpha)

Research paper thumbnail of Novel sites for Cathepsin L cleavage in SARS-CoV-2 spike guide treatment strategies

The spike (S) protein of SARS coronavirus 2 (SARS-CoV-2) is an ideal target for the development o... more The spike (S) protein of SARS coronavirus 2 (SARS-CoV-2) is an ideal target for the development of specific vaccines or drugs. However, treatments targeting viruses with mutant S proteins that have recently emerged in many countries are limited. Cleavage of the S protein by host proteases is essential for viral infection. Here, we discovered two novel sites (CS-1 and CS-2) in the S protein for cleavage by the protease Cathepsin L (CTSL). Both sites are highly conserved among all SARS-CoV-2 variants of concern. Cryo-electron microscopy structural studies revealed that CTSL cleavage increases the dynamics of the receptor binding domain of S and induces novel conformations. In our pseudovirus (PsV) infection experiment, alteration of the cleavage site significantly reduced the infection efficiency, and CTSL inhibitors markedly inhibited infection with PsVs of both the wild-type and emerged SARS-CoV-2 variants. Furthermore, six highly efficient CTSL inhibitors were found to effectively ...

Research paper thumbnail of Structural basis of G s and G i recognition by the human glucagon receptor

Science, 2020

Choosing a partner that fits G protein–coupled receptors (GPCRs) are responsible for transducing ... more Choosing a partner that fits G protein–coupled receptors (GPCRs) are responsible for transducing diverse signals from outside to inside cells. This process requires specificity both in ligand binding to GPCRs and in coupling between GPCRs and their intracellular partners, G proteins. Qiao et al. determined the structure of the human glucagon receptor (GCGR), a type B GPCR, bound to glucagon and one of two heterotrimeric G proteins, G s or G i1 . GCGR signals mainly through G s , and the structures provide a basis for this specificity. Conformational changes in GCGR, relative to the inactive state, create a binding cavity for the G proteins. The pocket is opened sufficiently to accommodate a bulky binding motif in G s . G i1 can still bind but the pocket does not close around it, so there is a smaller interaction interface. Science , this issue p. 1346

Research paper thumbnail of Structures of human mGlu2 and mGlu7 homo- and heterodimers

Nature, 2021

The metabotropic glutamate receptors (mGlus) are involved in the modulation of synaptic transmiss... more The metabotropic glutamate receptors (mGlus) are involved in the modulation of synaptic transmission and neuronal excitability in the central nervous system1. These receptors probably exist as both homo- and heterodimers that have unique pharmacological and functional properties2-4. Here we report four cryo-electron microscopy structures of the human mGlu subtypes mGlu2 and mGlu7, including inactive mGlu2 and mGlu7 homodimers; mGlu2 homodimer bound to an agonist and a positive allosteric modulator; and inactive mGlu2-mGlu7 heterodimer. We observed a subtype-dependent dimerization mode for these mGlus, as a unique dimer interface that is mediated by helix IV (and that is important for limiting receptor activity) exists only in the inactive mGlu2 structure. The structures provide molecular details of the inter- and intra-subunit conformational changes that are required for receptor activation, which distinguish class C G-protein-coupled receptors from those in classes A and B. Furthermore, our structure and functional studies of the mGlu2-mGlu7 heterodimer suggest that the mGlu7 subunit has a dominant role in controlling dimeric association and G-protein activation in the heterodimer. These insights into mGlu homo- and heterodimers highlight the complex landscape of mGlu dimerization and activation.

Research paper thumbnail of Novel cleavage sites identified in SARS-CoV-2 spike protein reveal mechanism for cathepsin L-facilitated viral infection and treatment strategies

Cell Discovery

The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an impor... more The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an important target for vaccine and drug development. However, the rapid emergence of variant strains with mutated S proteins has rendered many treatments ineffective. Cleavage of the S protein by host proteases is essential for viral infection. Here, we discovered that the S protein contains two previously unidentified Cathepsin L (CTSL) cleavage sites (CS-1 and CS-2). Both sites are highly conserved among all known SARS-CoV-2 variants. Our structural studies revealed that CTSL cleavage promoted S to adopt receptor-binding domain (RBD) “up” activated conformations, facilitating receptor-binding and membrane fusion. We confirmed that CTSL cleavage is essential during infection of all emerged SARS-CoV-2 variants (including the recently emerged Omicron variant) by pseudovirus (PsV) infection experiment. Furthermore, we found CTSL-specific inhibitors not only blocked infection of PsV/live virus in ...

Research paper thumbnail of 8 Å structure of the outer rings of the Xenopus laevis nuclear pore complex obtained by cryo-EM and AI

Protein & Cell, 2022

The nuclear pore complex (NPC), one of the largest protein complexes in eukaryotes, serves as a p... more The nuclear pore complex (NPC), one of the largest protein complexes in eukaryotes, serves as a physical gate to regulate nucleocytoplasmic transport. Here, we determined the 8 Å resolution cryo-electron microscopic (cryo-EM) structure of the outer rings containing nuclear ring (NR) and cytoplasmic ring (CR) from the Xenopus laevis NPC, with local resolutions reaching 4.9 Å. With the aid of AlphaFold2, we managed to build a pseudoatomic model of the outer rings, including the Y complexes and flanking components. In this most comprehensive and accurate model of outer rings to date, the almost complete Y complex structure exhibits much tighter interaction in the hub region. In addition to two copies of Y complexes, each asymmetric subunit in CR contains five copies of Nup358, two copies of the Nup214 complex, two copies of Nup205 and one copy of newly identified Nup93, while that in NR contains one copy of Nup205, one copy of ELYS and one copy of Nup93. These in-depth structural featu...

Research paper thumbnail of The Unusual Homodimer of a Heme‐Copper Terminal Oxidase Allows Itself to Utilize Two Electron Donors

Angewandte Chemie International Edition, 2021

The heme-copper oxidase superfamily comprises cytochrome cand ubiquinol oxidases.These enzymes ca... more The heme-copper oxidase superfamily comprises cytochrome cand ubiquinol oxidases.These enzymes catalyze the transfer of electrons from different electron donors onto molecular oxygen. AB-family cytochrome coxidase from the hyperthermophilic bacterium Aquifex aeolicus was discovered previously to be able to use both cytochrome ca nd naphthoquinol as electron donors.Its molecular mechanism as well as the evolutionary significance are yet unknown. Here we solved its 3.4 resolution electron cryo-microscopic structure and discovered an ovel dimeric structure mediated by subunit I (CoxA2) that would be essential for naphthoquinol binding and oxidation. The unique structural features in both proton and oxygen pathways suggest an evolutionary adaptation of this oxidase to its hyperthermophilic environment. Our results add anew conceptual understanding of structural variation of cytochrome co xidases in different species.

Research paper thumbnail of Nanometer-resolution in situ structure of the SARS-CoV-2 postfusion spike protein

Proceedings of the National Academy of Sciences, 2021

Significance Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a severe threat to p... more Significance Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a severe threat to public health and the global economy. Its spike protein is responsible for the membrane fusion and is thus a major target for vaccine and drug development. Our study presents the in situ structure of the spike protein in the postfusion state with higher resolution, giving further insights into the design of a viral entry inhibitor. Our observation of the oligomerization states of spikes on the viral membrane implies a possible mechanism of membrane fusion for viral infection.

Research paper thumbnail of Determining the architecture of nuclear ring of Xenopus laevis nuclear pore complex using integrated approaches

ABSTRACTThe nuclear pore complexes (NPCs) are large protein assemblies as a physical gate to regu... more ABSTRACTThe nuclear pore complexes (NPCs) are large protein assemblies as a physical gate to regulate nucleocytoplasmic transport. Here, using integrated approaches including cryo-electron microscopy, hybrid homology modeling and cell experiment, we determined the architecture of the nuclear ring (NR) from Xenopus laevis oocytes NPC at subnanometer resolution. In addition to the improvement of the Y complex model, eight copies of Nup205 and ELYS were assigned in NR. Nup205 connects the inner and outer Y complexes and contributes to the assembly and stability of the NR. By interacting with both the inner Nup160 and the nuclear envelope (NE), the N-terminal β-propeller and α-solenoid domains of ELYS were found to be essential for accurate assembly of the NPC on the NE.

Research paper thumbnail of 8 Å structure of the cytoplasmic ring of the Xenopus laevis nuclear pore complex solved by cryo-EM and AI

ABSTRACTAs one of the largest protein complexes in eukaryotes, the nuclear pore complex (NPC) for... more ABSTRACTAs one of the largest protein complexes in eukaryotes, the nuclear pore complex (NPC) forms a conduit regulating nucleocytoplasmic transport. Here, we determined 8 Å resolution cryo-electron microscopic (cryo-EM) structure of the cytoplasmic ring (CR) from the Xenopus laevis NPC. With the aid of AlphaFold2, we managed to build a most comprehensive and accurate pseudoatomic model of the CR to date, including the Y complexes and flanking components of Nup358, Nup214 complexes, Nup205 and Nup93. Comparing with previously reported CR model, the Y complex structure in our model exhibits much tighter interactions in the hub region mediated by α-solenoid domain in Nup160 C-terminus. Five copies of Nup358 are identified in each CR subunit to provide rich interactions with other Nups in stem regions of Y complexes. Two copies of Nup214 complexes lay in a parallel pattern and attach to the short arm region of Y complexes towards the central channel of NPC. Besides, the structural deta...

Research paper thumbnail of 8 Å structure of the nuclear ring of the Xenopus laevis nuclear pore complex solved by cryo-EM and AI

ABSTRACTThe nuclear pore complex (NPC), one of the largest protein complexes in eukaryotes, serve... more ABSTRACTThe nuclear pore complex (NPC), one of the largest protein complexes in eukaryotes, serves as a physical gate to regulate nucleocytoplasmic transport. Here, we determined the 8 Å resolution cryo-electron microscopic (cryo-EM) structure of the nuclear ring (NR) from the Xenopus laevis NPC, with local resolutions reaching 4.9 Å. With the aid of AlphaFold2, we managed to build a pseudoatomic model of the NR, including the Y complexes and flanking components. In this most comprehensive and accurate model to date, the almost complete Y complex structure exhibits much tighter interaction in the hub region. Each NR asymmetric subunit contains two copies of Y complexes, one copy of Nup205 that connects the Y complexes to the neighbouring complex, one copy of ELYS that stabilizes the long arm region of the inner Y complex, and one copy of newly identified Nup93 that forms a bridge across the stems of Y complexes. These in-depth structural features represent a great advance in underst...

Research paper thumbnail of Structure-based evidence for the enhanced transmissibility of the dominant SARS-CoV-2 B.1.1.7 variant (Alpha)

Research paper thumbnail of Novel sites for Cathepsin L cleavage in SARS-CoV-2 spike guide treatment strategies

The spike (S) protein of SARS coronavirus 2 (SARS-CoV-2) is an ideal target for the development o... more The spike (S) protein of SARS coronavirus 2 (SARS-CoV-2) is an ideal target for the development of specific vaccines or drugs. However, treatments targeting viruses with mutant S proteins that have recently emerged in many countries are limited. Cleavage of the S protein by host proteases is essential for viral infection. Here, we discovered two novel sites (CS-1 and CS-2) in the S protein for cleavage by the protease Cathepsin L (CTSL). Both sites are highly conserved among all SARS-CoV-2 variants of concern. Cryo-electron microscopy structural studies revealed that CTSL cleavage increases the dynamics of the receptor binding domain of S and induces novel conformations. In our pseudovirus (PsV) infection experiment, alteration of the cleavage site significantly reduced the infection efficiency, and CTSL inhibitors markedly inhibited infection with PsVs of both the wild-type and emerged SARS-CoV-2 variants. Furthermore, six highly efficient CTSL inhibitors were found to effectively ...

Research paper thumbnail of Structural basis of G s and G i recognition by the human glucagon receptor

Science, 2020

Choosing a partner that fits G protein–coupled receptors (GPCRs) are responsible for transducing ... more Choosing a partner that fits G protein–coupled receptors (GPCRs) are responsible for transducing diverse signals from outside to inside cells. This process requires specificity both in ligand binding to GPCRs and in coupling between GPCRs and their intracellular partners, G proteins. Qiao et al. determined the structure of the human glucagon receptor (GCGR), a type B GPCR, bound to glucagon and one of two heterotrimeric G proteins, G s or G i1 . GCGR signals mainly through G s , and the structures provide a basis for this specificity. Conformational changes in GCGR, relative to the inactive state, create a binding cavity for the G proteins. The pocket is opened sufficiently to accommodate a bulky binding motif in G s . G i1 can still bind but the pocket does not close around it, so there is a smaller interaction interface. Science , this issue p. 1346

Research paper thumbnail of Structures of human mGlu2 and mGlu7 homo- and heterodimers

Nature, 2021

The metabotropic glutamate receptors (mGlus) are involved in the modulation of synaptic transmiss... more The metabotropic glutamate receptors (mGlus) are involved in the modulation of synaptic transmission and neuronal excitability in the central nervous system1. These receptors probably exist as both homo- and heterodimers that have unique pharmacological and functional properties2-4. Here we report four cryo-electron microscopy structures of the human mGlu subtypes mGlu2 and mGlu7, including inactive mGlu2 and mGlu7 homodimers; mGlu2 homodimer bound to an agonist and a positive allosteric modulator; and inactive mGlu2-mGlu7 heterodimer. We observed a subtype-dependent dimerization mode for these mGlus, as a unique dimer interface that is mediated by helix IV (and that is important for limiting receptor activity) exists only in the inactive mGlu2 structure. The structures provide molecular details of the inter- and intra-subunit conformational changes that are required for receptor activation, which distinguish class C G-protein-coupled receptors from those in classes A and B. Furthermore, our structure and functional studies of the mGlu2-mGlu7 heterodimer suggest that the mGlu7 subunit has a dominant role in controlling dimeric association and G-protein activation in the heterodimer. These insights into mGlu homo- and heterodimers highlight the complex landscape of mGlu dimerization and activation.