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Article ; Online: Structures and coordination chemistry of transporters involved in manganese and iron homeostasis.

Ray, Shamayeeta / Gaudet, Rachelle

2023 Volume 51, Issue 3, Page(s) 897–923

Abstract: A repertoire of transporters plays a crucial role in maintaining homeostasis of biologically essential transition metals, manganese, and iron, thus ensuring cell viability. Elucidating the structure and function of many of these transporters has provided ...

Abstract	A repertoire of transporters plays a crucial role in maintaining homeostasis of biologically essential transition metals, manganese, and iron, thus ensuring cell viability. Elucidating the structure and function of many of these transporters has provided substantial understanding into how these proteins help maintain the optimal cellular concentrations of these metals. In particular, recent high-resolution structures of several transporters bound to different metals enable an examination of how the coordination chemistry of metal ion-protein complexes can help us understand metal selectivity and specificity. In this review, we first provide a comprehensive list of both specific and broad-based transporters that contribute to cellular homeostasis of manganese (Mn2+) and iron (Fe2+ and Fe3+) in bacteria, plants, fungi, and animals. Furthermore, we explore the metal-binding sites of the available high-resolution metal-bound transporter structures (Nramps, ABC transporters, P-type ATPase) and provide a detailed analysis of their coordination spheres (ligands, bond lengths, bond angles, and overall geometry and coordination number). Combining this information with the measured binding affinity of the transporters towards different metals sheds light into the molecular basis of substrate selectivity and transport. Moreover, comparison of the transporters with some metal scavenging and storage proteins, which bind metal with high affinity, reveal how the coordination geometry and affinity trends reflect the biological role of individual proteins involved in the homeostasis of these essential transition metals.
MeSH term(s)	Animals ; Manganese/metabolism ; Metals/metabolism ; Iron/chemistry ; Biological Transport ; Homeostasis
Chemical Substances	Manganese (42Z2K6ZL8P) ; Metals ; Iron (E1UOL152H7)
Language	English
Publishing date	2023-06-07
Publishing country	England
Document type	Review ; Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	184237-7
ISSN	1470-8752 ; 0300-5127
ISSN (online)	1470-8752
ISSN	0300-5127
DOI	10.1042/BST20210699
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Article: They all rock: A systematic comparison of conformational movements in LeuT-fold transporters.

Licht, Jacob A / Berry, Samuel P / Gutierrez, Michael A / Gaudet, Rachelle

bioRxiv : the preprint server for biology

2024

Abstract: Many membrane transporters share the LeuT fold-two five-helix repeats inverted across the membrane plane. Despite hundreds of structures, whether distinct conformational mechanisms are supported by the LeuT fold has not been systematically determined. ... ...

Abstract	Many membrane transporters share the LeuT fold-two five-helix repeats inverted across the membrane plane. Despite hundreds of structures, whether distinct conformational mechanisms are supported by the LeuT fold has not been systematically determined. After annotating published LeuT-fold structures, we analyzed distance difference matrices (DDMs) for nine proteins with multiple available conformations. We identified rigid bodies and relative movements of transmembrane helices (TMs) during distinct steps of the transport cycle. In all transporters the bundle (first two TMs of each repeat) rotates relative to the hash (third and fourth TMs). Motions of the arms (fifth TM) to close or open the intracellular and outer vestibules are common, as is a TM1a swing, with notable variations in the opening-closing motions of the outer vestibule. Our analyses suggest that LeuT-fold transporters layer distinct motions on a common bundle-hash rock and demonstrate that systematic analyses can provide new insights into large structural datasets.
Language	English
Publishing date	2024-01-29
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.01.24.577062
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Article ; Online: Extending the reach of homology by using successive computational filters to find yeast pheromone genes.

Srikant, Sriram / Gaudet, Rachelle / Murray, Andrew W

Current biology : CB

2023 Volume 33, Issue 19, Page(s) 4098–4110.e3

Abstract: The mating of fungi depends on pheromones that mediate communication between two mating types. Most species use short peptides as pheromones, which are either unmodified (e.g., α-factor in Saccharomyces cerevisiae) or C-terminally farnesylated (e.g., a- ... ...

Abstract	The mating of fungi depends on pheromones that mediate communication between two mating types. Most species use short peptides as pheromones, which are either unmodified (e.g., α-factor in Saccharomyces cerevisiae) or C-terminally farnesylated (e.g., a-factor in S. cerevisiae). Peptide pheromones have been found by genetics or biochemistry in a small number of fungi, but their short sequences and modest conservation make it impossible to detect homologous sequences in most species. To overcome this problem, we used a four-step computational pipeline to identify candidate a-factor genes in sequenced genomes of the Saccharomycotina, the fungal clade that contains most of the yeasts: we require that candidate genes have a C-terminal prenylation motif, are shorter than 100 amino acids long, and contain a proteolytic-processing motif upstream of the potential mature pheromone sequence and that closely related species contain highly conserved homologs of the potential mature pheromone sequence. Additional manual curation exploits the observation that many species carry more than one a-factor gene, encoding identical or nearly identical pheromones. From 332 Saccharomycotina genomes, we identified strong candidate pheromone genes in 241 genomes, covering 13 clades that are each separated from each other by at least 100 million years, the time required for evolution to remove detectable sequence homology among small pheromone genes. For one small clade, the Yarrowia, we demonstrated that our algorithm found the a-factor genes: deleting all four related genes in the a-mating type of Yarrowia lipolytica prevents mating.
MeSH term(s)	Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Pheromones/metabolism ; Peptides/metabolism ; Ascomycota/metabolism ; Genes, Fungal ; Mating Factor/genetics ; Mating Factor/metabolism
Chemical Substances	Pheromones ; Peptides ; Mating Factor (61194-02-3)
Language	English
Publishing date	2023-09-11
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1071731-6
ISSN	1879-0445 ; 0960-9822
ISSN (online)	1879-0445
ISSN	0960-9822
DOI	10.1016/j.cub.2023.08.039
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Zs.A 3208: Show issues

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Article ; Online: Molecular Mechanism of Nramp-Family Transition Metal Transport.

Bozzi, Aaron T / Gaudet, Rachelle

Journal of molecular biology

2021 Volume 433, Issue 16, Page(s) 166991

Abstract: The Natural resistance-associated macrophage protein (Nramp) family of transition metal transporters enables uptake and trafficking of essential micronutrients that all organisms must acquire to survive. Two decades after Nramps were identified as proton- ...

Abstract	The Natural resistance-associated macrophage protein (Nramp) family of transition metal transporters enables uptake and trafficking of essential micronutrients that all organisms must acquire to survive. Two decades after Nramps were identified as proton-driven, voltage-dependent secondary transporters, multiple Nramp crystal structures have begun to illustrate the fine details of the transport process and provide a new framework for understanding a wealth of preexisting biochemical data. Here we review the relevant literature pertaining to Nramps' biological roles and especially their conserved molecular mechanism, including our updated understanding of conformational change, metal binding and transport, substrate selectivity, proton transport, proton-metal coupling, and voltage dependence. We ultimately describe how the Nramp family has adapted the LeuT fold common to many secondary transporters to provide selective transition-metal transport with a mechanism that deviates from the canonical model of symport.
MeSH term(s)	Biological Transport ; Cation Transport Proteins/chemistry ; Cation Transport Proteins/genetics ; Cation Transport Proteins/metabolism ; Ions/metabolism ; Metals/metabolism ; Multigene Family ; Protein Binding ; Structure-Activity Relationship
Chemical Substances	Cation Transport Proteins ; Ions ; Metals ; natural resistance-associated macrophage protein 1
Language	English
Publishing date	2021-04-16
Publishing country	Netherlands
Document type	Journal Article ; Meta-Analysis ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2021.166991
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Zs.A 867: Show issues

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Article ; Online: Structure and function of prodrug-activating peptidases.

Velilla, José A / Kenney, Grace E / Gaudet, Rachelle

Biochimie

2022 Volume 205, Page(s) 124–135

Abstract: Bacteria protect themselves from the toxicity of antimicrobial metabolites they produce through several strategies. In one resistance mechanism, bacteria assemble a non-toxic precursor on an N-acyl-d-asparagine prodrug motif in the cytoplasm, then export ...

Abstract	Bacteria protect themselves from the toxicity of antimicrobial metabolites they produce through several strategies. In one resistance mechanism, bacteria assemble a non-toxic precursor on an N-acyl-d-asparagine prodrug motif in the cytoplasm, then export it to the periplasm where a dedicated d-amino peptidase hydrolyzes the prodrug motif. These prodrug-activating peptidases contain an N-terminal periplasmic S12 hydrolase domain and C-terminal transmembrane domains (TMDs) of varying lengths: type I peptidases contain three transmembrane helices, and type II peptidases have an additional C-terminal ABC half-transporter. We review studies which have addressed the role of the TMD in function, the substrate specificity, and the biological assembly of ClbP, the type I peptidase that activates colibactin. We use modeling and sequence analyses to extend those insights to other prodrug-activating peptidases and ClbP-like proteins which are not part of prodrug resistance gene clusters. These ClbP-like proteins may play roles in the biosynthesis or degradation of other natural products, including antibiotics, may adopt different TMD folds, and have different substrate specificity compared to prodrug-activating homologs. Finally, we review the data supporting the long-standing hypothesis that ClbP interacts with transporters in the cell and that this association is important for the export of other natural products. Future investigations of this hypothesis as well as of the structure and function of type II peptidases will provide a complete account of the role of prodrug-activating peptidases in the activation and secretion of bacterial toxins.
MeSH term(s)	Peptide Hydrolases/chemistry ; Prodrugs/pharmacology ; Prodrugs/metabolism ; Escherichia coli/genetics ; Escherichia coli Proteins/metabolism
Chemical Substances	Peptide Hydrolases (EC 3.4.-) ; Prodrugs ; Escherichia coli Proteins
Language	English
Publishing date	2022-11-08
Publishing country	France
Document type	Journal Article ; Review
ZDB-ID	120345-9
ISSN	1638-6183 ; 0300-9084
ISSN (online)	1638-6183
ISSN	0300-9084
DOI	10.1016/j.biochi.2022.07.019
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Article ; Online: Structural basis of ligand specificity and channel activation in an insect gustatory receptor.

Frank, Heather M / Walujkar, Sanket / Walsh, Richard M / Laursen, Willem J / Theobald, Douglas L / Garrity, Paul A / Gaudet, Rachelle

Cell reports

2024 Volume 43, Issue 4, Page(s) 114035

Abstract: Gustatory receptors (GRs) are critical for insect chemosensation and are potential targets for controlling pests and disease vectors, making their structural investigation a vital step toward such applications. We present structures of Bombyx mori Gr9 ( ... ...

Abstract	Gustatory receptors (GRs) are critical for insect chemosensation and are potential targets for controlling pests and disease vectors, making their structural investigation a vital step toward such applications. We present structures of Bombyx mori Gr9 (BmGr9), a fructose-gated cation channel, in agonist-free and fructose-bound states. BmGr9 forms a tetramer similar to distantly related insect odorant receptors (ORs). Upon fructose binding, BmGr9's channel gate opens through helix S7b movements. In contrast to ORs, BmGr9's ligand-binding pocket, shaped by a kinked helix S4 and a shorter extracellular S3-S4 loop, is larger and solvent accessible in both agonist-free and fructose-bound states. Also, unlike ORs, fructose binding by BmGr9 involves helix S5 and a pocket lined with aromatic and polar residues. Structure-based sequence alignments reveal distinct patterns of ligand-binding pocket residue conservation in GR subfamilies associated with different ligand classes. These data provide insight into the molecular basis of GR ligand specificity and function.
MeSH term(s)	Animals ; Ligands ; Bombyx/metabolism ; Insect Proteins/metabolism ; Insect Proteins/chemistry ; Insect Proteins/genetics ; Binding Sites ; Amino Acid Sequence ; Models, Molecular ; Protein Binding ; Receptors, Cell Surface/metabolism ; Receptors, Cell Surface/chemistry ; Receptors, Odorant/metabolism ; Receptors, Odorant/chemistry
Chemical Substances	Ligands ; Insect Proteins ; Receptors, Cell Surface ; Receptors, Odorant
Language	English
Publishing date	2024-04-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2024.114035
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Article ; Online: Inroads into Membrane Physiology through Transport Nanomachines.

Stockbridge, Randy B / Gaudet, Rachelle / Grabe, Michael / Minor, Daniel L

Journal of molecular biology

2021 Volume 433, Issue 16, Page(s) 167101

MeSH term(s)	Biological Transport ; Cell Membrane/chemistry ; Cell Membrane/physiology ; Cell Membrane/ultrastructure ; Humans
Language	English
Publishing date	2021-06-11
Publishing country	Netherlands
Document type	Editorial
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2021.167101
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Zs.A 867: Show issues

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Article ; Online: Molecular Mechanism of Nramp-Family Transition Metal Transport

Bozzi, Aaron T. / Gaudet, Rachelle

Journal of Molecular Biology. 2021 Aug., v. 433, no. 16 p.166991-

2021

Abstract	The Natural resistance-associated macrophage protein (Nramp) family of transition metal transporters enables uptake and trafficking of essential micronutrients that all organisms must acquire to survive. Two decades after Nramps were identified as proton-driven, voltage-dependent secondary transporters, multiple Nramp crystal structures have begun to illustrate the fine details of the transport process and provide a new framework for understanding a wealth of preexisting biochemical data. Here we review the relevant literature pertaining to Nramps’ biological roles and especially their conserved molecular mechanism, including our updated understanding of conformational change, metal binding and transport, substrate selectivity, proton transport, proton-metal coupling, and voltage dependence. We ultimately describe how the Nramp family has adapted the LeuT fold common to many secondary transporters to provide selective transition-metal transport with a mechanism that deviates from the canonical model of symport.
Keywords	electric potential difference ; macrophages ; models ; molecular biology ; iron homeostasis ; manganese ; APC superfamily ; proton-coupled transport ; secondary transporter
Language	English
Dates of publication	2021-08
Publishing place	Elsevier Ltd
Document type	Article ; Online
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2021.166991
Database	NAL-Catalogue (AGRICOLA)

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Article: Structure of an insect gustatory receptor.

Frank, Heather M / Walujkar, Sanket / Walsh, Richard M / Laursen, Willem J / Theobald, Douglas L / Garrity, Paul A / Gaudet, Rachelle

bioRxiv : the preprint server for biology

2023

Abstract: Gustatory Receptors (GRs) are critical for insect chemosensation and are potential targets for controlling pests and disease vectors. However, GR structures have not been experimentally determined. We present structures ... ...

Abstract	Gustatory Receptors (GRs) are critical for insect chemosensation and are potential targets for controlling pests and disease vectors. However, GR structures have not been experimentally determined. We present structures of
Language	English
Publishing date	2023-12-19
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.12.19.572336
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Article ; Online: Mechanics and pharmacology of substrate selection and transport by eukaryotic ABC exporters.

Srikant, Sriram / Gaudet, Rachelle

Nature structural & molecular biology

2019 Volume 26, Issue 9, Page(s) 792–801

Abstract: Much structural information has been amassed on ATP-binding cassette (ABC) transporters, including hundreds of structures of isolated domains and an increasing array of full-length transporters. The structures capture different steps in the transport ... ...

Abstract	Much structural information has been amassed on ATP-binding cassette (ABC) transporters, including hundreds of structures of isolated domains and an increasing array of full-length transporters. The structures capture different steps in the transport cycle and have aided in the design and interpretation of computational simulations and biophysics experiments. These data provide a maturing, although still incomplete, elucidation of the protein dynamics and mechanisms of substrate selection and transit through the transporters. We present an updated view of the classical alternating-access mechanism as it applies to eukaryotic ABC transporters, focusing on type I exporters. Our model helps frame the progress in, and remaining questions about, transporter energetics, how substrates are selected and how ATP is consumed to perform work at the molecular scale. Many human ABC transporters are associated with disease; we highlight progress in understanding their pharmacology through the lens of structural biology and describe how this knowledge suggests approaches to pharmacologically targeting these transporters.
MeSH term(s)	ATP-Binding Cassette Transporters/chemistry ; ATP-Binding Cassette Transporters/metabolism ; Eukaryotic Cells/enzymology ; Models, Molecular ; Protein Conformation ; Substrate Specificity
Chemical Substances	ATP-Binding Cassette Transporters
Language	English
Publishing date	2019-08-26
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	2126708-X
ISSN	1545-9985 ; 1545-9993
ISSN (online)	1545-9985
ISSN	1545-9993
DOI	10.1038/s41594-019-0280-4
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