1
|
Thompson MJ, Mansoub Bekarkhanechi F, Ananchenko A, Nury H, Baenziger JE. A release of local subunit conformational heterogeneity underlies gating in a muscle nicotinic acetylcholine receptor. Nat Commun 2024; 15:1803. [PMID: 38413583 PMCID: PMC10899235 DOI: 10.1038/s41467-024-46028-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 02/12/2024] [Indexed: 02/29/2024] Open
Abstract
Synaptic receptors respond to neurotransmitters by opening an ion channel across the post-synaptic membrane to elicit a cellular response. Here we use recent Torpedo acetylcholine receptor structures and functional measurements to delineate a key feature underlying allosteric communication between the agonist-binding extracellular and channel-gating transmembrane domains. Extensive mutagenesis at this inter-domain interface re-affirms a critical energetically coupled role for the principal α subunit β1-β2 and M2-M3 loops, with agonist binding re-positioning a key β1-β2 glutamate/valine to facilitate the outward motions of a conserved M2-M3 proline to open the channel gate. Notably, the analogous structures in non-α subunits adopt a locally active-like conformation in the apo state even though each L9' hydrophobic gate residue in each pore-lining M2 α-helix is closed. Agonist binding releases local conformational heterogeneity transitioning all five subunits into a conformationally symmetric open state. A release of conformational heterogeneity provides a framework for understanding allosteric communication in pentameric ligand-gated ion channels.
Collapse
Affiliation(s)
- Mackenzie J Thompson
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | | | - Anna Ananchenko
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Hugues Nury
- Université Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France
| | - John E Baenziger
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada.
| |
Collapse
|
2
|
Miles SA, Nillama JA, Hunter L. Tinker, Tailor, Soldier, Spy: The Diverse Roles That Fluorine Can Play within Amino Acid Side Chains. Molecules 2023; 28:6192. [PMID: 37687021 PMCID: PMC10489206 DOI: 10.3390/molecules28176192] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/17/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023] Open
Abstract
Side chain-fluorinated amino acids are useful tools in medicinal chemistry and protein science. In this review, we outline some general strategies for incorporating fluorine atom(s) into amino acid side chains and for elaborating such building blocks into more complex fluorinated peptides and proteins. We then describe the diverse benefits that fluorine can offer when located within amino acid side chains, including enabling 19F NMR and 18F PET imaging applications, enhancing pharmacokinetic properties, controlling molecular conformation, and optimizing target-binding.
Collapse
Affiliation(s)
| | | | - Luke Hunter
- School of Chemistry, The University of New South Wales (UNSW), Sydney 2052, Australia
| |
Collapse
|
3
|
Gurung D, Danielson JA, Tasnim A, Zhang JT, Zou Y, Liu JY. Proline Isomerization: From the Chemistry and Biology to Therapeutic Opportunities. BIOLOGY 2023; 12:1008. [PMID: 37508437 PMCID: PMC10376262 DOI: 10.3390/biology12071008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/27/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023]
Abstract
Proline isomerization, the process of interconversion between the cis- and trans-forms of proline, is an important and unique post-translational modification that can affect protein folding and conformations, and ultimately regulate protein functions and biological pathways. Although impactful, the importance and prevalence of proline isomerization as a regulation mechanism in biological systems have not been fully understood or recognized. Aiming to fill gaps and bring new awareness, we attempt to provide a wholistic review on proline isomerization that firstly covers what proline isomerization is and the basic chemistry behind it. In this section, we vividly show that the cause of the unique ability of proline to adopt both cis- and trans-conformations in significant abundance is rooted from the steric hindrance of these two forms being similar, which is different from that in linear residues. We then discuss how proline isomerization was discovered historically followed by an introduction to all three types of proline isomerases and how proline isomerization plays a role in various cellular responses, such as cell cycle regulation, DNA damage repair, T-cell activation, and ion channel gating. We then explore various human diseases that have been linked to the dysregulation of proline isomerization. Finally, we wrap up with the current stage of various inhibitors developed to target proline isomerases as a strategy for therapeutic development.
Collapse
Affiliation(s)
- Deepti Gurung
- Department of Medicine, University of Toledo College of Medicine, Toledo, OH 43614, USA
- Department of Cell and Cancer Biology, University of Toledo College of Medicine, Toledo, OH 43614, USA
| | - Jacob A Danielson
- Department of Medicine, University of Toledo College of Medicine, Toledo, OH 43614, USA
| | - Afsara Tasnim
- Department of Bioengineering, University of Toledo College of Engineering, Toledo, OH 43606, USA
| | - Jian-Ting Zhang
- Department of Cell and Cancer Biology, University of Toledo College of Medicine, Toledo, OH 43614, USA
| | - Yue Zou
- Department of Cell and Cancer Biology, University of Toledo College of Medicine, Toledo, OH 43614, USA
| | - Jing-Yuan Liu
- Department of Medicine, University of Toledo College of Medicine, Toledo, OH 43614, USA
- Department of Cell and Cancer Biology, University of Toledo College of Medicine, Toledo, OH 43614, USA
- Department of Bioengineering, University of Toledo College of Engineering, Toledo, OH 43606, USA
| |
Collapse
|
4
|
Phylogenetic analyses of 5-hydroxytryptamine 3 (5-HT3) receptors in Metazoa. PLoS One 2023; 18:e0281507. [PMID: 36857360 PMCID: PMC9977066 DOI: 10.1371/journal.pone.0281507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 01/24/2023] [Indexed: 03/02/2023] Open
Abstract
The 5-hydroxytrptamine 3 (5-HT3) receptor is a member of the 'Cys-loop' family and the only pentameric ligand gated ion channel among the serotonin receptors. 5-HT3 receptors play an important role in controlling growth, development, and behaviour in animals. Several 5-HT3 receptor antagonists are used to treat diseases (e.g., irritable bowel syndrome, nausea and emesis). Humans express five different subunits (A-E) enabling a variety of heteromeric receptors to form but all contain 5HT3A subunits. However, the information available about the 5-HT3 receptor subunit occurrence among the metazoan lineages is minimal. In the present article we searched for 5-HT3 receptor subunit homologs from different phyla in Metazoa. We identified more than 1000 5-HT3 receptor subunits in Metazoa in different phyla and undertook simultaneous phylogenetic analysis of 526 5HT3A, 358 5HT3B, 239 5HT3C, 70 5HT3D, and 173 5HT3E sequences. 5-HT3 receptor subunits were present in species belonging to 11 phyla: Annelida, Arthropoda, Chordata, Cnidaria, Echinodermata, Mollusca, Nematoda, Orthonectida, Platyhelminthes, Rotifera and Tardigrada. All subunits were most often identified in Chordata phylum which was strongly represented in searches. Using multiple sequence alignment, we investigated variations in the ligand binding region of the 5HT3A subunit protein sequences in the metazoan lineage. Several critical amino acid residues important for ligand binding (common structural features) are commonly present in species from Nematoda and Platyhelminth gut parasites through to Chordata. Collectively, this better understanding of the 5-HT3 receptor evolutionary patterns raises possibilities of future pharmacological challenges facing Metazoa including effects on parasitic and other species in ecosystems that contain 5-HT3 receptor ligands.
Collapse
|
5
|
Izquierdo PG, Charvet CL, Neveu C, Green AC, Tattersall JEH, Holden-Dye L, O'Connor V. Modelling organophosphate intoxication in C. elegans highlights nicotinic acetylcholine receptor determinants that mitigate poisoning. PLoS One 2023; 18:e0284786. [PMID: 37083685 PMCID: PMC10121051 DOI: 10.1371/journal.pone.0284786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 04/06/2023] [Indexed: 04/22/2023] Open
Abstract
Organophosphate intoxication via acetylcholinesterase inhibition executes neurotoxicity via hyper stimulation of acetylcholine receptors. Here, we use the organophosphate paraoxon-ethyl to treat C. elegans and use its impact on pharyngeal pumping as a bio-assay to model poisoning through these neurotoxins. This assay provides a tractable measure of acetylcholine receptor mediated contraction of body wall muscle. Investigation of the time dependence of organophosphate treatment and the genetic determinants of the drug-induced inhibition of pumping highlight mitigating modulation of the effects of paraoxon-ethyl. We identified mutants that reduce acetylcholine receptor function protect against the consequence of intoxication by organophosphates. Data suggests that reorganization of cholinergic signalling is associated with organophosphate poisoning. This reinforces the under investigated potential of using therapeutic approaches which target a modulation of nicotinic acetylcholine receptor function to treat the poisoning effects of this important class of neurotoxins.
Collapse
Affiliation(s)
- Patricia G Izquierdo
- Biological Sciences, Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Claude L Charvet
- French National Institute for Agricultural Research (INRA), Infectiologie Animale et Santé Publique, Nouzilly, France
| | - Cedric Neveu
- French National Institute for Agricultural Research (INRA), Infectiologie Animale et Santé Publique, Nouzilly, France
| | - A Christopher Green
- Dstl, Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - John E H Tattersall
- Dstl, Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Lindy Holden-Dye
- Dstl, Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Vincent O'Connor
- Biological Sciences, Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| |
Collapse
|
6
|
Kubyshkin V, Davis R, Budisa N. Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement. Beilstein J Org Chem 2021; 17:439-460. [PMID: 33727970 PMCID: PMC7934785 DOI: 10.3762/bjoc.17.40] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/22/2021] [Indexed: 12/12/2022] Open
Abstract
Due to the heterocyclic structure and distinct conformational profile, proline is unique in the repertoire of the 20 amino acids coded into proteins. Here, we summarize the biochemical work on the replacement of proline with (4R)- and (4S)-fluoroproline as well as 4,4-difluoroproline in proteins done mainly in the last two decades. We first recapitulate the complex position and biochemical fate of proline in the biochemistry of a cell, discuss the physicochemical properties of fluoroprolines, and overview the attempts to use these amino acids as proline replacements in studies of protein production and folding. Fluorinated proline replacements are able to elevate the protein expression speed and yields and improve the thermodynamic and kinetic folding profiles of individual proteins. In this context, fluoroprolines can be viewed as useful tools in the biotechnological toolbox. As a prospect, we envision that proteome-wide proline-to-fluoroproline substitutions could be possible. We suggest a hypothetical scenario for the use of laboratory evolutionary methods with fluoroprolines as a suitable vehicle to introduce fluorine into living cells. This approach may enable creation of synthetic cells endowed with artificial biodiversity, containing fluorine as a bioelement.
Collapse
Affiliation(s)
- Vladimir Kubyshkin
- Department of Chemistry, University of Manitoba, 144 Dysart Rd., Winnipeg, R3T 2N2, Canada
| | - Rebecca Davis
- Department of Chemistry, University of Manitoba, 144 Dysart Rd., Winnipeg, R3T 2N2, Canada
| | - Nediljko Budisa
- Department of Chemistry, University of Manitoba, 144 Dysart Rd., Winnipeg, R3T 2N2, Canada.,Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str. 10, 10623 Berlin, Germany
| |
Collapse
|
7
|
Gibbs E, Chakrapani S. Structure, Function and Physiology of 5-Hydroxytryptamine Receptors Subtype 3. Subcell Biochem 2021; 96:373-408. [PMID: 33252737 DOI: 10.1007/978-3-030-58971-4_11] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
5-hydroxytryptamine receptor subtype 3 (5-HT3R) is a pentameric ligand-gated ion channel (pLGIC) involved in neuronal signaling. It is best known for its prominent role in gut-CNS signaling though there is growing interest in its other functions, particularly in modulating non-serotonergic synaptic activity. Recent advances in structural biology have provided mechanistic understanding of 5-HT3R function and present new opportunities for the field. This chapter gives a broad overview of 5-HT3R from a physiological and structural perspective and then discusses the specific details of ion permeation, ligand binding and allosteric coupling between these two events. Biochemical evidence is summarized and placed within a physiological context. This perspective underscores the progress that has been made as well as outstanding challenges and opportunities for future 5-HT3R research.
Collapse
Affiliation(s)
- Eric Gibbs
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106-4970, USA.
| | - Sudha Chakrapani
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106-4970, USA. .,Department of Neuroscience, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106-4970, USA.
| |
Collapse
|
8
|
Braun N, Sheikh ZP, Pless SA. The current chemical biology tool box for studying ion channels. J Physiol 2020; 598:4455-4471. [DOI: 10.1113/jp276695] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 07/06/2020] [Indexed: 12/13/2022] Open
Affiliation(s)
- N. Braun
- Department of Drug Design and Pharmacology University of Copenhagen Jagtvej 160 Copenhagen 2100 Denmark
| | - Z. P. Sheikh
- Department of Drug Design and Pharmacology University of Copenhagen Jagtvej 160 Copenhagen 2100 Denmark
| | - S. A. Pless
- Department of Drug Design and Pharmacology University of Copenhagen Jagtvej 160 Copenhagen 2100 Denmark
| |
Collapse
|
9
|
Kubyshkin V. Polarity effects in 4-fluoro- and 4-(trifluoromethyl)prolines. Beilstein J Org Chem 2020; 16:1837-1852. [PMID: 32765799 PMCID: PMC7385359 DOI: 10.3762/bjoc.16.151] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/06/2020] [Indexed: 12/14/2022] Open
Abstract
Fluorine-containing analogues of proline are valuable tools in engineering and NMR spectroscopic studies of peptides and proteins. Their use relies on the fundamental understanding of the interplay between the substituents and the main chain groups of the amino acid residue. This study aims to showcase the polarity-related effects that arise from the interaction between the functional groups in molecular models. Properties such as conformation, acid-base transition, and amide-bond isomerism were examined for diastereomeric 4-fluoroprolines, 4-(trifluoromethyl)prolines, and 1,1-difluoro-5-azaspiro[2.4]heptane-6-carboxylates. The preferred conformation on the proline ring originated from a preferential axial positioning for a single fluorine atom, and an equatorial positioning for a trifluoromethyl- or a difluoromethylene group. This orientation of the substituents explains the observed trends in the pK a values, lipophilicity, and the kinetics of the amide bond rotation. The study also provides a set of evidences that the transition state of the amide-bond rotation in peptidyl-prolyl favors C4-exo conformation of the pyrrolidine ring.
Collapse
|