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59


Structures of the T cell potassium channel Kv1.3 with immunoglobulin modulators

Selvakumar, Purushotham; Fernández-Mariño, Ana I; Khanra, Nandish; He, Changhao; Paquette, Alice J; Wang, Bing; Huang, Ruiqi; Smider, Vaughn V; Rice, William J; Swartz, Kenton J; Meyerson, Joel R
The Kv1.3 potassium channel is expressed abundantly on activated T cells and mediates the cellular immune response. This role has made the channel a target for therapeutic immunomodulation to block its activity and suppress T cell activation. Here, we report structures of human Kv1.3 alone, with a nanobody inhibitor, and with an antibody-toxin fusion blocker. Rather than block the channel directly, four copies of the nanobody bind the tetramer's voltage sensing domains and the pore domain to induce an inactive pore conformation. In contrast, the antibody-toxin fusion docks its toxin domain at the extracellular mouth of the channel to insert a critical lysine into the pore. The lysine stabilizes an active conformation of the pore yet blocks ion permeation. This study visualizes Kv1.3 pore dynamics, defines two distinct mechanisms to suppress Kv1.3 channel activity with exogenous inhibitors, and provides a framework to aid development of emerging T cell immunotherapies.
PMCID:9253088
PMID: 35788586
ISSN: 2041-1723
CID: 5278332

The ups and downs of elevator-type di-/tricarboxylate membrane transporters

Sauer, David B; Wang, Bing; Sudar, Joseph C; Song, Jinmei; Marden, Jennifer; Rice, William J; Wang, Da-Neng
The divalent anion sodium symporter (DASS) family contains both sodium-driven anion cotransporters and anion/anion exchangers. The family belongs to a broader ion transporter superfamily (ITS), which comprises 24 families of transporters, including those of AbgT antibiotic efflux transporters. The human proteins in the DASS family play major physiological roles and are drug targets. We recently determined multiple structures of the human sodium-dependent citrate transporter (NaCT) and the succinate/dicarboxylate transporter from Lactobacillus acidophilus (LaINDY). Structures of both proteins show high degrees of structural similarity to the previously determined VcINDY fold. Conservation between these DASS protein structures and those from the AbgT family indicates that the VcINDY fold represents the overall protein structure for the entire ITS. The new structures of NaCT and LaINDY are captured in the inward- or outward-facing conformations, respectively. The domain arrangements in these structures agree with a rigid body elevator-type transport mechanism for substrate translocation across the membrane. Two separate NaCT structures in complex with a substrate or an inhibitor allowed us to explain the inhibition mechanism and propose a detailed classification scheme for grouping disease-causing mutations in the human protein. Structural understanding of multiple kinetic states of DASS proteins is a first step toward the detailed characterization of their entire transport cycle.
PMID: 34403567
ISSN: 1742-4658
CID: 5066842

One-pot synthesis of linear triblock terpolymers and their aqueous self-Assembly

Ahmed, Eman; Womble, C. Tyler; Cho, Jinwon; Dancel-Manning, Kristen; Rice, William J.; Jang, Seung Soon; Weck, Marcus
Compartmentalized micelles are prepared through the self-Assembly of linear triblock terpolymers containing hydrophilic (H), lipophilic (L), and fluorophilic (F) domains. The triblock copolymers were synthesized via living ring-opening metathesis polymerization (ROMP) of norbornene-based monomers. Our terpolymer design offers a facile approach for the synthesis of the target materials with fast polymerization kinetics, complete block incorporation and control over block sequence. Various triblock terpolymers are prepared with variations in block sequence and block ratio and self-Assembled in aqueous media. Interaction parameter (χ) values between each block are determined using a Flory-Huggins based computational model. "Core-shell-corona", "disk-like", "raspberry-like"and "worm-like"morphologies are observed through cryogenic transmission electron microscopy and dissipative particle dynamics simulations. This journal is
SCOPUS:85103833988
ISSN: 1759-9954
CID: 4860932

Structure and inhibition mechanism of the human citrate transporter NaCT

Sauer, David B; Song, Jinmei; Wang, Bing; Hilton, Jacob K; Karpowich, Nathan K; Mindell, Joseph A; Rice, William J; Wang, Da-Neng
Citrate is best known as an intermediate in the tricarboxylic acid cycle of the cell. In addition to this essential role in energy metabolism, the tricarboxylate anion also acts as both a precursor and a regulator of fatty acid synthesis1-3. Thus, the rate of fatty acid synthesis correlates directly with the cytosolic concentration of citrate4,5. Liver cells import citrate through the sodium-dependent citrate transporter NaCT (encoded by SLC13A5) and, as a consequence, this protein is a potential target for anti-obesity drugs. Here, to understand the structural basis of its inhibition mechanism, we determined cryo-electron microscopy structures of human NaCT in complexes with citrate or a small-molecule inhibitor. These structures reveal how the inhibitor-which binds to the same site as citrate-arrests the transport cycle of NaCT. The NaCT-inhibitor structure also explains why the compound selectively inhibits NaCT over two homologous human dicarboxylate transporters, and suggests ways to further improve the affinity and selectivity. Finally, the NaCT structures provide a framework for understanding how various mutations abolish the transport activity of NaCT in the brain and thereby cause epilepsy associated with mutations in SLC13A5 in newborns (which is known as SLC13A5-epilepsy)6-8.
PMID: 33597751
ISSN: 1476-4687
CID: 4788372

Leginon: New Features and Applications

Cheng, Anchi; Negro, Carl; Bruhn, Jessica F; Rice, William J; Dallakyan, Sargis; Eng, Edward T; Waterman, David G; Potter, Clinton S; Carragher, Bridget
Leginon is a system for automated data acquisition from a transmission electron microscope. Here we provide an updated summary of the overall Leginon architecture and an update of the current state of the package. We also highlight a few recent developments to provide some concrete examples and use cases. This article is protected by copyright. All rights reserved.
PMID: 33030237
ISSN: 1469-896x
CID: 4640782

Zinc induced structural changes in the intrinsically disordered BDNF Met prodomain confer synaptic elimination

Wang, Jing; Anastasia, Agustin; Bains, Henrietta; Giza, Joanna I; Clossey, David G; Deng, Jingjing; Neubert, Thomas A; Rice, William J; Lee, Francis S; Hempstead, Barbara L; Bracken, Clay
Human brain derived neurotrophic factor (BDNF) encodes a protein product consisting of a C-terminal mature domain (mature BDNF) and an N-terminal prodomain, which is an intrinsically disordered protein. A common single nucleotide polymorphism in humans results in a methionine substitution for valine at position 66 of the prodomain, and is associated with memory deficits, depression and anxiety disorders. The BDNF Met66 prodomain, but not the Val66 prodomain, promotes rapid structural remodeling of hippocampal neurons' growth cones and dendritic spines by interacting directly with the SorCS2 receptor. While it has been reported that the Met66 and Val66 prodomains exhibit only modest differences in structural propensities in the apo state, here we show that Val66 and Met66 prodomains differentially bind zinc (Zn). Zn2+ binds with higher affinity and more broadly impacts residues on the Met66 prodomain compared to the Val66 prodomain as shown by NMR and ITC. Zn2+ binding to the Met66 and Val66 prodomains results in distinct conformational and macroscopic differences observed by NMR, light scattering and cryoEM. To determine if Zn2+ mediated conformational change in the Met66 prodomain is required for biological effect, we mutated His40, a Zn2+ binding site, and observed a loss of Met66 prodomain bioactivity. As the His40 site is distant from the known region of the prodomain involved in receptor binding, we suggest that Met66 prodomain bioactivity involves His40 mediated stabilization of the multimeric structure. Our results point to the necessity of a Zn2+-mediated higher order molecular assembly of the Met66 prodomain to mediate neuronal remodeling.
PMID: 32744273
ISSN: 1756-591x
CID: 4704002

Structure of human GABAB receptor in an inactive state

Park, Jinseo; Fu, Ziao; Frangaj, Aurel; Liu, Jonathan; Mosyak, Lidia; Shen, Tong; Slavkovich, Vesna N; Ray, Kimberly M; Taura, Jaume; Cao, Baohua; Geng, Yong; Zuo, Hao; Kou, Yongjun; Grassucci, Robert; Chen, Shaoxia; Liu, Zheng; Lin, Xin; Williams, Justin P; Rice, William J; Eng, Edward T; Huang, Rick K; Soni, Rajesh K; Kloss, Brian; Yu, Zhiheng; Javitch, Jonathan A; Hendrickson, Wayne A; Slesinger, Paul A; Quick, Matthias; Graziano, Joseph; Yu, Hongtao; Fiehn, Oliver; Clarke, Oliver B; Frank, Joachim; Fan, Qing R
The human GABAB receptor-a member of the class C family of G-protein-coupled receptors (GPCRs)-mediates inhibitory neurotransmission and has been implicated in epilepsy, pain and addiction1. A unique GPCR that is known to require heterodimerization for function2-6, the GABAB receptor has two subunits, GABAB1 and GABAB2, that are structurally homologous but perform distinct and complementary functions. GABAB1 recognizes orthosteric ligands7,8, while GABAB2 couples with G proteins9-14. Each subunit is characterized by an extracellular Venus flytrap (VFT) module, a descending peptide linker, a seven-helix transmembrane domain and a cytoplasmic tail15. Although the VFT heterodimer structure has been resolved16, the structure of the full-length receptor and its transmembrane signalling mechanism remain unknown. Here we present a near full-length structure of the GABAB receptor at atomic resolution, captured in an inactive state by cryo-electron microscopy. Our structure reveals several ligands that preassociate with the receptor, including two large endogenous phospholipids that are embedded within the transmembrane domains to maintain receptor integrity and modulate receptor function. We also identify a previously unknown heterodimer interface between transmembrane helices 3 and 5 of both subunits, which serves as a signature of the inactive conformation. A unique 'intersubunit latch' within this transmembrane interface maintains the inactive state, and its disruption leads to constitutive receptor activity.
PMID: 32581365
ISSN: 1476-4687
CID: 4517862

Author Correction: Structure of human GABAB receptor in an inactive state

Park, Jinseo; Fu, Ziao; Frangaj, Aurel; Liu, Jonathan; Mosyak, Lidia; Shen, Tong; Slavkovich, Vesna N; Ray, Kimberly M; Taura, Jaume; Cao, Baohua; Geng, Yong; Zuo, Hao; Kou, Yongjun; Grassucci, Robert; Chen, Shaoxia; Liu, Zheng; Lin, Xin; Williams, Justin P; Rice, William J; Eng, Edward T; Huang, Rick K; Soni, Rajesh K; Kloss, Brian; Yu, Zhiheng; Javitch, Jonathan A; Hendrickson, Wayne A; Slesinger, Paul A; Quick, Matthias; Graziano, Joseph; Yu, Hongtao; Fiehn, Oliver; Clarke, Oliver B; Frank, Joachim; Fan, Qing R
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
PMID: 32665714
ISSN: 1476-4687
CID: 4529112

Ribosome-associated vesicles: A dynamic subcompartment of the endoplasmic reticulum in secretory cells

Carter, Stephen D; Hampton, Cheri M; Langlois, Robert; Melero, Roberto; Farino, Zachary J; Calderon, Michael J; Li, Wen; Wallace, Callen T; Tran, Ngoc Han; Grassucci, Robert A; Siegmund, Stephanie E; Pemberton, Joshua; Morgenstern, Travis J; Eisenman, Leanna; Aguilar, Jenny I; Greenberg, Nili L; Levy, Elana S; Yi, Edward; Mitchell, William G; Rice, William J; Wigge, Christoph; Pilli, Jyotsna; George, Emily W; Aslanoglou, Despoina; Courel, Maïté; Freyberg, Robin J; Javitch, Jonathan A; Wills, Zachary P; Area-Gomez, Estela; Shiva, Sruti; Bartolini, Francesca; Volchuk, Allen; Murray, Sandra A; Aridor, Meir; Fish, Kenneth N; Walter, Peter; Balla, Tamas; Fass, Deborah; Wolf, Sharon G; Watkins, Simon C; Carazo, José María; Jensen, Grant J; Frank, Joachim; Freyberg, Zachary
The endoplasmic reticulum (ER) is a highly dynamic network of membranes. Here, we combine live-cell microscopy with in situ cryo-electron tomography to directly visualize ER dynamics in several secretory cell types including pancreatic β-cells and neurons under near-native conditions. Using these imaging approaches, we identify a novel, mobile form of ER, ribosome-associated vesicles (RAVs), found primarily in the cell periphery, which is conserved across different cell types and species. We show that RAVs exist as distinct, highly dynamic structures separate from the intact ER reticular architecture that interact with mitochondria via direct intermembrane contacts. These findings describe a new ER subcompartment within cells.
PMCID:7112762
PMID: 32270040
ISSN: 2375-2548
CID: 4494502

Structure of human GABAB receptor in an inactive state

Park, J; Fu, Z; Frangaj, A; Liu, J; Mosyak, L; Shen, T; Slavkovich, V N; Ray, K M; Taura, J; Cao, B; Geng, Y; Zuo, H; Kou, Y; Grassucci, R; Chen, S; Liu, Z; Lin, X; Williams, J P; Rice, W J; Eng, E T; Huang, R K; Soni, R K; Kloss, B; Yu, Z; Javitch, J A; Hendrickson, W A; Slesinger, P A; Quick, M; Graziano, J; Yu, H; Fiehn, O; Clarke, O B; Frank, J; Fan, Q R
The human GABAB receptor-a member of the class C family of G-protein-coupled receptors (GPCRs)-mediates inhibitory neurotransmission and has been implicated in epilepsy, pain and addiction1. A unique GPCR that is known to require heterodimerization for function2-6, the GABAB receptor has two subunits, GABAB1 and GABAB2, that are structurally homologous but perform distinct and complementary functions. GABAB1 recognizes orthosteric ligands7,8, while GABAB2 couples with G proteins9-14. Each subunit is characterized by an extracellular Venus flytrap (VFT) module, a descending peptide linker, a seven-helix transmembrane domain and a cytoplasmic tail15. Although the VFT heterodimer structure has been resolved16, the structure of the full-length receptor and its transmembrane signalling mechanism remain unknown. Here we present a near full-length structure of the GABAB receptor at atomic resolution, captured in an inactive state by cryo-electron microscopy. Our structure reveals several ligands that preassociate with the receptor, including two large endogenous phospholipids that are embedded within the transmembrane domains to maintain receptor integrity and modulate receptor function. We also identify a previously unknown heterodimer interface between transmembrane helices 3 and 5 of both subunits, which serves as a signature of the inactive conformation. A unique 'intersubunit latch' within this transmembrane interface maintains the inactive state, and its disruption leads to constitutive receptor activity.
Copyright
EMBASE:2005291782
ISSN: 0028-0836
CID: 4511912