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Article ; Online: The COVID-19 Pandemic: A Special Challenge for the Journal's Editors.

Kronbichler, Andreas / Gregg, L Parker / Bargman, Joanne M

Journal of the American Society of Nephrology : JASN

2023 Volume 34, Issue 12, Page(s) 1945–1947

MeSH term(s)	Humans ; Pandemics ; COVID-19
Language	English
Publishing date	2023-11-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1085942-1
ISSN	1533-3450 ; 1046-6673
ISSN (online)	1533-3450
ISSN	1046-6673
DOI	10.1681/ASN.0000000000000251
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Article ; Online: Molecular basis for pH sensing in the KDEL trafficking receptor.

Wu, Zhiyi / Smith, Kathryn / Gerondopoulos, Andreas / Sobajima, Tomoaki / Parker, Joanne L / Barr, Francis A / Newstead, Simon / Biggin, Philip C

Structure (London, England : 1993)

2024

Abstract: Trafficking receptors control protein localization through the recognition of specific signal sequences that specify unique cellular locations. Differences in luminal pH are important for the vectorial trafficking of cargo receptors. The KDEL receptor is ...

Abstract	Trafficking receptors control protein localization through the recognition of specific signal sequences that specify unique cellular locations. Differences in luminal pH are important for the vectorial trafficking of cargo receptors. The KDEL receptor is responsible for maintaining the integrity of the ER by retrieving luminally localized folding chaperones in a pH-dependent mechanism. Structural studies have revealed the end states of KDEL receptor activation and the mechanism of selective cargo binding. However, precisely how the KDEL receptor responds to changes in luminal pH remains unclear. To explain the mechanism of pH sensing, we combine analysis of X-ray crystal structures of the KDEL receptor at neutral and acidic pH with advanced computational methods and cell-based assays. We show a critical role for ordered water molecules that allows us to infer a direct connection between protonation in different cellular compartments and the consequent changes in the affinity of the receptor for cargo.
Language	English
Publishing date	2024-04-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	1213087-4
ISSN	1878-4186 ; 0969-2126
ISSN (online)	1878-4186
ISSN	0969-2126
DOI	10.1016/j.str.2024.03.013
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Article ; Online: Molecular basis for selective uptake and elimination of organic anions in the kidney by OAT1.

Parker, Joanne L / Kato, Takafumi / Kuteyi, Gabriel / Sitsel, Oleg / Newstead, Simon

Nature structural & molecular biology

2023 Volume 30, Issue 11, Page(s) 1786–1793

Abstract: In mammals, the kidney plays an essential role in maintaining blood homeostasis through the selective uptake, retention or elimination of toxins, drugs and metabolites. Organic anion transporters (OATs) are responsible for the recognition of metabolites ... ...

Abstract	In mammals, the kidney plays an essential role in maintaining blood homeostasis through the selective uptake, retention or elimination of toxins, drugs and metabolites. Organic anion transporters (OATs) are responsible for the recognition of metabolites and toxins in the nephron and their eventual urinary excretion. Inhibition of OATs is used therapeutically to improve drug efficacy and reduce nephrotoxicity. The founding member of the renal organic anion transporter family, OAT1 (also known as SLC22A6), uses the export of α-ketoglutarate (α-KG), a key intermediate in the Krebs cycle, to drive selective transport and is allosterically regulated by intracellular chloride. However, the mechanisms linking metabolite cycling, drug transport and intracellular chloride remain obscure. Here, we present cryogenic-electron microscopy structures of OAT1 bound to α-KG, the antiviral tenofovir and clinical inhibitor probenecid, used in the treatment of Gout. Complementary in vivo cellular assays explain the molecular basis for α-KG driven drug elimination and the allosteric regulation of organic anion transport in the kidney by chloride.
MeSH term(s)	Animals ; Organic Anion Transport Protein 1/metabolism ; Chlorides/metabolism ; Kidney/metabolism ; Biological Transport ; Anions/metabolism ; Ketoglutaric Acids/metabolism ; Mammals/metabolism
Chemical Substances	Organic Anion Transport Protein 1 ; Chlorides ; Anions ; Ketoglutaric Acids
Language	English
Publishing date	2023-07-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	2126708-X
ISSN	1545-9985 ; 1545-9993
ISSN (online)	1545-9985
ISSN	1545-9993
DOI	10.1038/s41594-023-01039-y
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Zs.A 4101: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Bioorthogonal Radiolabeling of Azide-Modified Bacteria Using [

Alanizi, Aryn A / Sorlin, Alexandre M / Parker, Matthew F L / López-Álvarez, Marina / Qin, Hecong / Lee, Sang Hee / Blecha, Joseph / Rosenberg, Oren S / Engel, Joanne / Ohliger, Michael A / Flavell, Robert R / Wilson, David M

Bioconjugate chemistry

2024 Volume 35, Issue 4, Page(s) 517–527

Abstract: Purpose: ...

Abstract	Purpose:
MeSH term(s)	Humans ; Animals ; Mice ; Azides/chemistry ; Tissue Distribution ; Peptidoglycan ; Positron-Emission Tomography ; Bacteria ; Amino Acids ; Alanine ; Fluorine Radioisotopes/chemistry
Chemical Substances	Azides ; Peptidoglycan ; Amino Acids ; Alanine (OF5P57N2ZX) ; Fluorine Radioisotopes
Language	English
Publishing date	2024-03-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	1024041-x
ISSN	1520-4812 ; 1043-1802
ISSN (online)	1520-4812
ISSN	1043-1802
DOI	10.1021/acs.bioconjchem.4c00024
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Zs.A 3400: Show issues

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Article ; Online: Gateway to the Golgi: molecular mechanisms of nucleotide sugar transporters.

Parker, Joanne L / Newstead, Simon

Current opinion in structural biology

2019 Volume 57, Page(s) 127–134

Abstract: The Golgi apparatus plays a central role in the secretory pathway as a hub for posttranslational modification, protein sorting and quality control. To date, there is little structural or biochemical information concerning the function of transporters ... ...

Abstract	The Golgi apparatus plays a central role in the secretory pathway as a hub for posttranslational modification, protein sorting and quality control. To date, there is little structural or biochemical information concerning the function of transporters that reside within this organelle. The SLC35 family of nucleotide sugar transporters link the synthesis of activated sugar molecules and sulfate in the cytoplasm, with the luminal transferases that catalyse their attachment to proteins and lipids during glycosylation and sulfation. A recent crystal structure of the GDP-mannose transporter has revealed key sequence motifs that direct ligand recognition and transport. Further biochemical studies unexpectedly found a requirement for short chain lipids in activating the transporter, suggesting a possible route for transport regulation within the Golgi.
MeSH term(s)	Animals ; Golgi Apparatus/metabolism ; Humans ; Membrane Transport Proteins/chemistry ; Membrane Transport Proteins/metabolism ; Nucleotides/metabolism ; Sugars/metabolism
Chemical Substances	Membrane Transport Proteins ; Nucleotides ; Sugars
Language	English
Publishing date	2019-04-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1068353-7
ISSN	1879-033X ; 0959-440X
ISSN (online)	1879-033X
ISSN	0959-440X
DOI	10.1016/j.sbi.2019.03.019
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Zs.A 3206: Show issues

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Article ; Online: Peptidoglycan-Targeted [

Sorlin, Alexandre M / López-Álvarez, Marina / Biboy, Jacob / Gray, Joe / Rabbitt, Sarah J / Rahim, Junaid Ur / Lee, Sang Hee / Bobba, Kondapa Naidu / Blecha, Joseph / Parker, Mathew F L / Flavell, Robert R / Engel, Joanne / Ohliger, Michael / Vollmer, Waldemar / Wilson, David M

JACS Au

2024 Volume 4, Issue 3, Page(s) 1039–1047

Abstract: Imaging is increasingly used to detect and monitor bacterial infection. Both anatomic (X-rays, computed tomography, ultrasound, and MRI) and nuclear medicine ([ ...

Abstract	Imaging is increasingly used to detect and monitor bacterial infection. Both anatomic (X-rays, computed tomography, ultrasound, and MRI) and nuclear medicine ([
Language	English
Publishing date	2024-02-26
Publishing country	United States
Document type	Journal Article
ISSN	2691-3704
ISSN (online)	2691-3704
DOI	10.1021/jacsau.3c00776
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Article ; Online: Structural basis of nucleotide sugar transport across the Golgi membrane.

Parker, Joanne L / Newstead, Simon

Nature

2017 Volume 551, Issue 7681, Page(s) 521–524

Abstract: Glycosylation is a fundamental cellular process that, in eukaryotes, occurs in the lumen of both the Golgi apparatus and the endoplasmic reticulum. Nucleotide sugar transporters (NSTs) are an essential component of the glycosylation pathway, providing ... ...

Abstract	Glycosylation is a fundamental cellular process that, in eukaryotes, occurs in the lumen of both the Golgi apparatus and the endoplasmic reticulum. Nucleotide sugar transporters (NSTs) are an essential component of the glycosylation pathway, providing the diverse range of substrates required for the glycosyltransferases. NSTs are linked to several developmental and immune disorders in humans, and in pathogenic microbes they have an important role in virulence. How NSTs recognize and transport activated monosaccharides, however, is currently unclear. Here we present the crystal structure of an NST, the GDP-mannose transporter Vrg4, in both the substrate-free and the bound states. A hitherto unobserved requirement of short-chain lipids in activating the transporter supports a model for regulation within the highly dynamic membranes of the Golgi apparatus. Our results provide a structural basis for understanding nucleotide sugar recognition, and provide insights into the transport and regulatory mechanism of this family of intracellular transporters.
Language	English
Publishing date	2017-11-23
Publishing country	England
Document type	Journal Article
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/nature24464
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Article ; Online: Cryo-EM structure and resistance landscape of M. tuberculosis MmpL3: An emergent therapeutic target.

Adams, Oliver / Deme, Justin C / Parker, Joanne L / Fowler, Philip W / Lea, Susan M / Newstead, Simon

Structure (London, England : 1993)

2021 Volume 29, Issue 10, Page(s) 1182–1191.e4

Abstract: Tuberculosis (TB) is the leading cause of death from a single infectious agent and in 2019 an estimated 10 million people worldwide contracted the disease. Although treatments for TB exist, continual emergence of drug-resistant variants necessitates ... ...

Abstract	Tuberculosis (TB) is the leading cause of death from a single infectious agent and in 2019 an estimated 10 million people worldwide contracted the disease. Although treatments for TB exist, continual emergence of drug-resistant variants necessitates urgent development of novel antituberculars. An important new target is the lipid transporter MmpL3, which is required for construction of the unique cell envelope that shields Mycobacterium tuberculosis (Mtb) from the immune system. However, a structural understanding of the mutations in Mtb MmpL3 that confer resistance to the many preclinical leads is lacking, hampering efforts to circumvent resistance mechanisms. Here, we present the cryoelectron microscopy structure of Mtb MmpL3 and use it to comprehensively analyze the mutational landscape of drug resistance. Our data provide a rational explanation for resistance variants local to the central drug binding site, and also highlight a potential alternative route to resistance operating within the periplasmic domain.
MeSH term(s)	Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Cryoelectron Microscopy ; Drug Resistance, Bacterial ; Membrane Transport Proteins/chemistry ; Membrane Transport Proteins/genetics ; Membrane Transport Proteins/metabolism ; Mutation
Chemical Substances	Bacterial Proteins ; Membrane Transport Proteins ; MmpL3 protein, Mycobacterium tuberculosis
Language	English
Publishing date	2021-07-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1213087-4
ISSN	1878-4186 ; 0969-2126
ISSN (online)	1878-4186
ISSN	0969-2126
DOI	10.1016/j.str.2021.06.013
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Article: Membrane Protein Crystallisation: Current Trends and Future Perspectives.

Parker, Joanne L / Newstead, Simon

Advances in experimental medicine and biology

2016 Volume 922, Page(s) 61–72

Abstract: Alpha helical membrane proteins are the targets for many pharmaceutical drugs and play important roles in physiology and disease processes. In recent years, substantial progress has been made in determining their atomic structure using X-ray ... ...

Abstract	Alpha helical membrane proteins are the targets for many pharmaceutical drugs and play important roles in physiology and disease processes. In recent years, substantial progress has been made in determining their atomic structure using X-ray crystallography. However, a major bottleneck still remains; the identification of conditions that give crystals that are suitable for structure determination. Over the past 10 years we have been analysing the crystallisation conditions reported for alpha helical membrane proteins with the aim to facilitate a rational approach to the design and implementation of successful crystallisation screens. The result has been the development of MemGold, MemGold2 and the additive screen MemAdvantage. The associated analysis, summarised and updated in this chapter, has revealed a number of surprisingly successfully strategies for crystallisation and detergent selection.
MeSH term(s)	Animals ; Bacterial Proteins/chemistry ; Bacterial Proteins/isolation & purification ; Buffers ; Chemical Precipitation ; Crystallization ; Crystallography, X-Ray ; Detergents/pharmacology ; Humans ; Hydrogen-Ion Concentration ; Membrane Proteins/chemistry ; Membrane Proteins/isolation & purification ; Protein Structure, Secondary ; Salts/chemistry
Chemical Substances	Bacterial Proteins ; Buffers ; Detergents ; Membrane Proteins ; Salts
Language	English
Publishing date	2016-08-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2214-8019 ; 0065-2598
ISSN (online)	2214-8019
ISSN	0065-2598
DOI	10.1007/978-3-319-35072-1_5
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Article ; Online: Structural basis for proton coupled cystine transport by cystinosin.

Löbel, Mark / Salphati, Sacha P / El Omari, Kamel / Wagner, Armin / Tucker, Stephen J / Parker, Joanne L / Newstead, Simon

Nature communications

2022 Volume 13, Issue 1, Page(s) 4845

Abstract: Amino acid transporters play a key role controlling the flow of nutrients across the lysosomal membrane and regulating metabolism in the cell. Mutations in the gene encoding the transporter cystinosin result in cystinosis, an autosomal recessive ... ...

Abstract	Amino acid transporters play a key role controlling the flow of nutrients across the lysosomal membrane and regulating metabolism in the cell. Mutations in the gene encoding the transporter cystinosin result in cystinosis, an autosomal recessive metabolic disorder characterised by the accumulation of cystine crystals in the lysosome. Cystinosin is a member of the PQ-loop family of solute carrier (SLC) transporters and uses the proton gradient to drive cystine export into the cytoplasm. However, the molecular basis for cystinosin function remains elusive, hampering efforts to develop novel treatments for cystinosis and understand the mechanisms of ion driven transport in the PQ-loop family. To address these questions, we present the crystal structures of cystinosin from Arabidopsis thaliana in both apo and cystine bound states. Using a combination of in vitro and in vivo based assays, we establish a mechanism for cystine recognition and proton coupled transport. Mutational mapping and functional characterisation of human cystinosin further provide a framework for understanding the molecular impact of disease-causing mutations.
MeSH term(s)	Amino Acid Transport Systems, Neutral/genetics ; Amino Acid Transport Systems, Neutral/metabolism ; Biological Transport ; Cystine/metabolism ; Cystinosis/genetics ; Humans ; Lysosomes/metabolism ; Protons
Chemical Substances	Amino Acid Transport Systems, Neutral ; Protons ; Cystine (48TCX9A1VT)
Language	English
Publishing date	2022-08-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-32589-2
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