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1.
Cell ; 153(5): 1064-79, 2013 May 23.
Article in English | MEDLINE | ID: mdl-23706743

ABSTRACT

Metabolic adaptation is essential for cell survival during nutrient deprivation. We report that eukaryotic elongation factor 2 kinase (eEF2K), which is activated by AMP-kinase (AMPK), confers cell survival under acute nutrient depletion by blocking translation elongation. Tumor cells exploit this pathway to adapt to nutrient deprivation by reactivating the AMPK-eEF2K axis. Adaptation of transformed cells to nutrient withdrawal is severely compromised in cells lacking eEF2K. Moreover, eEF2K knockdown restored sensitivity to acute nutrient deprivation in highly resistant human tumor cell lines. In vivo, overexpression of eEF2K rendered murine tumors remarkably resistant to caloric restriction. Expression of eEF2K strongly correlated with overall survival in human medulloblastoma and glioblastoma multiforme. Finally, C. elegans strains deficient in efk-1, the eEF2K ortholog, were severely compromised in their response to nutrient depletion. Our data highlight a conserved role for eEF2K in protecting cells from nutrient deprivation and in conferring tumor cell adaptation to metabolic stress. PAPERCLIP:


Subject(s)
Caenorhabditis elegans/metabolism , Elongation Factor 2 Kinase/metabolism , Neoplasms/physiopathology , Peptide Chain Elongation, Translational , Signal Transduction , AMP-Activated Protein Kinases/metabolism , Animals , Brain Neoplasms/physiopathology , Caenorhabditis elegans/genetics , Cell Survival , Cell Transformation, Neoplastic , Elongation Factor 2 Kinase/genetics , Food Deprivation , Glioblastoma/physiopathology , HeLa Cells , Humans , Mice , Mice, Nude , NIH 3T3 Cells , Neoplasm Transplantation , Peptide Elongation Factor 2/metabolism , Transplantation, Heterologous
2.
J Am Chem Soc ; 145(4): 2414-2420, 2023 02 01.
Article in English | MEDLINE | ID: mdl-36669466

ABSTRACT

Genetic code expansion has pushed protein chemistry past the canonical 22 amino acids. The key enzymes that make this possible are engineered aminoacyl tRNA synthetases. However, as the number of genetically encoded amino acids has increased over the years, obvious limits in the type and size of novel side chains that can be accommodated by the synthetase enzyme become apparent. Here, we show that chemically acylating tRNAs allow for robust, site-specific incorporation of unnatural amino acids into proteins in zebrafish embryos, an important model organism for human health and development. We apply this approach to incorporate a unique photocaged histidine analogue for which synthetase engineering efforts have failed. Additionally, we demonstrate optical control over different enzymes in live embryos by installing photocaged histidine into their active sites.


Subject(s)
Amino Acyl-tRNA Synthetases , RNA, Transfer , Zebrafish , Animals , Amino Acids/chemistry , Amino Acyl-tRNA Synthetases/genetics , Amino Acyl-tRNA Synthetases/metabolism , Genetic Code , Histidine/genetics , RNA, Transfer/genetics , RNA, Transfer/metabolism , Zebrafish/genetics , Zebrafish/metabolism
3.
Proc Natl Acad Sci U S A ; 113(48): 13905-13910, 2016 11 29.
Article in English | MEDLINE | ID: mdl-27849612

ABSTRACT

Docosahexaenoic acid (DHA), a polyunsaturated ω-3 fatty acid enriched in oily fish, contributes to better health by affecting multiple targets. Large-conductance Ca2+- and voltage-gated Slo1 BK channels are directly activated by nanomolar levels of DHA. We investigated DHA-channel interaction by manipulating both the fatty acid structure and the channel composition through the site-directed incorporation of unnatural amino acids. Electrophysiological measurements show that the para-group of a Tyr residue near the ion conduction pathway has a critical role. To robustly activate the channel, ionization must occur readily by a fatty acid for a good efficacy, and a long nonpolar acyl tail with a Z double bond present at the halfway position for a high affinity. The results suggest that DHA and the channel form an ion-dipole bond to promote opening and demonstrate the channel druggability. DHA, a marine-derived nutraceutical, represents a promising lead compound for rational drug design and discovery.


Subject(s)
Docosahexaenoic Acids/chemistry , Fatty Acids, Omega-3/chemistry , Fatty Acids, Unsaturated/chemistry , Large-Conductance Calcium-Activated Potassium Channel alpha Subunits/metabolism , Docosahexaenoic Acids/metabolism , Docosahexaenoic Acids/therapeutic use , Fatty Acids, Omega-3/metabolism , Fatty Acids, Unsaturated/metabolism , Fatty Acids, Unsaturated/therapeutic use , Fish Oils/chemistry , Fish Oils/metabolism , Humans , Ion Channel Gating/genetics , Large-Conductance Calcium-Activated Potassium Channel alpha Subunits/chemistry , Large-Conductance Calcium-Activated Potassium Channels/chemistry , Large-Conductance Calcium-Activated Potassium Channels/metabolism
4.
Proc Natl Acad Sci U S A ; 111(8): 3032-7, 2014 Feb 25.
Article in English | MEDLINE | ID: mdl-24516159

ABSTRACT

Oxidative stress plays a key role in late onset diseases including cancer and neurodegenerative diseases such as Huntington disease. Therefore, uncovering regulators of the antioxidant stress responses is important for understanding the course of these diseases. Indeed, the nuclear factor erythroid 2-related factor 2 (NRF2), a master regulator of the cellular antioxidative stress response, is deregulated in both cancer and neurodegeneration. Similar to NRF2, the tumor suppressor Homologous to the E6-AP Carboxyl Terminus (HECT) domain and Ankyrin repeat containing E3 ubiquitin-protein ligase 1 (HACE1) plays a protective role against stress-induced tumorigenesis in mice, but its roles in the antioxidative stress response or its involvement in neurodegeneration have not been investigated. To this end we examined Hace1 WT and KO mice and found that Hace1 KO animals exhibited increased oxidative stress in brain and that the antioxidative stress response was impaired. Moreover, HACE1 was found to be essential for optimal NRF2 activation in cells challenged with oxidative stress, as HACE1 depletion resulted in reduced NRF2 activity, stability, and protein synthesis, leading to lower tolerance against oxidative stress triggers. Strikingly, we found a reduction of HACE1 levels in the striatum of Huntington disease patients, implicating HACE1 in the pathology of Huntington disease. Moreover, ectopic expression of HACE1 in striatal neuronal progenitor cells provided protection against mutant Huntingtin-induced redox imbalance and hypersensitivity to oxidative stress, by augmenting NRF2 functions. These findings reveal that the tumor suppressor HACE1 plays a role in the NRF2 antioxidative stress response pathway and in neurodegeneration.


Subject(s)
Huntington Disease/metabolism , NF-E2-Related Factor 2/metabolism , Oxidative Stress/physiology , Ubiquitin-Protein Ligases/metabolism , Animals , Blotting, Western , Cell Fractionation , Corpus Striatum/metabolism , DNA Primers/genetics , Fluorescent Antibody Technique , HEK293 Cells , Humans , Huntingtin Protein , Mice , Nerve Tissue Proteins/metabolism , Reactive Oxygen Species/metabolism , Real-Time Polymerase Chain Reaction
5.
Plant Cell Rep ; 33(12): 2023-32, 2014 Dec.
Article in English | MEDLINE | ID: mdl-25187293

ABSTRACT

KEY MESSAGE: Human glucocerebrosidase with vacuolar anchoring domains was targeted to protein storage vacuoles (PSVs) of Arabidopsis seeds, but unexpectedly via the Golgi complex. PSV-targeting to effectively avoid problematic N-glycans is protein dependent. Plant-specific N-glycosylation patterns elaborated within the Golgi complex are a major limitation of using plants to produce biopharmaceuticals as the presence of ß1,2 xylose and/or α1,3 fucose residues on the recombinant glycoprotein can render the product immunogenic if administrated parenterally. A reporter protein fused to a vacuolar membrane targeting motif comprised of the BP-80 transmembrane domain (TMD), and the cytoplasmic tail (CT) of α-tonoplast intrinsic protein (α-TIP) is delivered to protein storage vacuoles (PSVs) of tobacco seeds by ER-derived transport vesicles that bypass the Golgi complex. This prompted us to investigate whether a pharmaceutical glycoprotein is targeted to PSVs using the same targeting sequences, thus avoiding the unwanted plant-Golgi-specific complex N-glycan modifications. The human lysosomal acid ß-glucosidase (glucocerebrosidase; GCase) (EC 3.2.1.45) fused to the BP-80 TMD and α-TIP CT was produced in Arabidopsis thaliana wild-type (Col-0) seeds. The chimeric GCase became localized in PSVs but transited through the Golgi complex, as indicated by biochemical analyses of the recombinant protein's N-glycans. Our findings suggest that use of this PSV-targeting strategy to avoid problematic N-glycan maturation on recombinant therapeutic proteins is not consistently effective, as it is likely protein- and/or species-specific.


Subject(s)
Arabidopsis/metabolism , Cell Membrane/metabolism , Glucosylceramidase/chemistry , Glucosylceramidase/metabolism , Polysaccharides/metabolism , Recombinant Proteins/metabolism , Vacuoles/metabolism , Arabidopsis/genetics , Enteropeptidase/metabolism , Golgi Apparatus/metabolism , Humans , Plants, Genetically Modified , Protein Structure, Tertiary , Seeds/metabolism , Seeds/ultrastructure , Vacuoles/ultrastructure
6.
Nat Chem Biol ; 7(9): 617-23, 2011 Jul 24.
Article in English | MEDLINE | ID: mdl-21785425

ABSTRACT

Voltage-sensor domains couple membrane potential to conformational changes in voltage-gated ion channels and phosphatases. Highly coevolved acidic and aromatic side chains assist the transfer of cationic side chains across the transmembrane electric field during voltage sensing. We investigated the functional contribution of negative electrostatic potentials from these residues to channel gating and voltage sensing with unnatural amino acid mutagenesis, electrophysiology, voltage-clamp fluorometry and ab initio calculations. The data show that neutralization of two conserved acidic side chains in transmembrane segments S2 and S3, namely Glu293 and Asp316 in Shaker potassium channels, has little functional effect on conductance-voltage relationships, although Glu293 appears to catalyze S4 movement. Our results suggest that neither Glu293 nor Asp316 engages in electrostatic state-dependent charge-charge interactions with S4, likely because they occupy, and possibly help create, a water-filled vestibule.


Subject(s)
Membrane Potentials , Potassium Channels, Voltage-Gated/chemistry , Amino Acid Sequence , Animals , Aspartic Acid/chemistry , Aspartic Acid/genetics , Glutamic Acid/chemistry , Glutamic Acid/genetics , Ion Channel Gating/physiology , Molecular Sequence Data , Potassium Channels, Voltage-Gated/genetics , Static Electricity , Xenopus
7.
J Gen Physiol ; 155(4)2023 04 03.
Article in English | MEDLINE | ID: mdl-36695813

ABSTRACT

Phosphoregulation is ubiquitous in biology. Defining the functional roles of individual phosphorylation sites within a multivalent system remains particularly challenging. We have therefore applied a chemical biology approach to light-control the state of single candidate phosphoserines in the canonical anion channel CFTR while simultaneously measuring channel activity. The data show striking non-equivalency among protein kinase A consensus sites, which vary from <10% to >1,000% changes in channel activity upon phosphorylation. Of note, slow phosphorylation of S813 suggests that this site is rate-limiting to the full activation of CFTR. Further, this approach reveals an unexpected coupling between the phosphorylation of S813 and a nearby site, S795. Overall, these data establish an experimental route to understanding roles of specific phosphoserines within complex phosphoregulatory domains. This strategy may be employed in the study of phosphoregulation of other eukaryotic proteins.


Subject(s)
Cystic Fibrosis Transmembrane Conductance Regulator , Cystic Fibrosis Transmembrane Conductance Regulator/metabolism , Phosphorylation , Anions/metabolism
8.
Nat Commun ; 14(1): 59, 2023 01 04.
Article in English | MEDLINE | ID: mdl-36599844

ABSTRACT

The aromatic side-chains of phenylalanine, tyrosine, and tryptophan interact with their environments via both hydrophobic and electrostatic interactions. Determining the extent to which these contribute to protein function and stability is not possible with conventional mutagenesis. Serial fluorination of a given aromatic is a validated method in vitro and in silico to specifically alter electrostatic characteristics, but this approach is restricted to a select few experimental systems. Here, we report a group of pyrrolysine-based aminoacyl-tRNA synthetase/tRNA pairs (tRNA/RS pairs) that enable the site-specific encoding of a varied spectrum of fluorinated phenylalanine amino acids in E. coli and mammalian (HEK 293T) cells. By allowing the cross-kingdom expression of proteins bearing these unnatural amino acids at biochemical scale, these tools may potentially enable the study of biological mechanisms which utilize aromatic interactions in structural and cellular contexts.


Subject(s)
Amino Acyl-tRNA Synthetases , Phenylalanine , Amino Acids/metabolism , Amino Acyl-tRNA Synthetases/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism , Halogenation , Phenylalanine/metabolism , RNA, Transfer/metabolism , Humans , HEK293 Cells
9.
J Neuroendocrinol ; 35(11): e13255, 2023 11.
Article in English | MEDLINE | ID: mdl-36970756

ABSTRACT

Adrenomedullary chromaffin cells respond to splanchnic (sympathetic) nerve stimulation by releasing stress hormones into the circulation. The signal for hormone secretion is encoded in the neurotransmitters - especially acetylcholine (ACh) and pituitary adenylate cyclase activating polypeptide (PACAP) - that are released into the splanchnic-chromaffin cell synapse. However, functional differences in the effects of ACh and PACAP on the chromaffin cell secretory response are not well defined. Here, selective agonists of PACAP receptors or nicotinic and muscarinic acetylcholine receptors were applied to chromaffin cells. The major differences in the effects of these agents were not on exocytosis, per se, but rather on the steps upstream of exocytosis. In almost every respect, the properties of individual fusion events triggered by PACAP and cholinergic agonists were similar. On the other hand, the properties of the Ca2+ transients evoked by PACAP differed in several ways from those evoked by muscarinic and nicotinic receptor stimulation. A defining feature of the PACAP-stimulated secretory pathway was its dependence on signaling through exchange protein directly activated by cAMP (Epac) and PLCε. However, the absence of PLCε did not disrupt Ca2+ transients evoked by cholinergic agonists. Accordingly, inhibition of Epac activity did not disrupt secretion triggered by acetylcholine or specific agonists of muscarinic and nicotinic receptors. Thus, PACAP and acetylcholine stimulate chromaffin cell secretion via separate and independent pathways. This feature of stimulus-secretion coupling may be important for sustaining hormone release from the adrenal medulla under conditions associated with the sympathetic stress response.


Subject(s)
Chromaffin Cells , Pituitary Adenylate Cyclase-Activating Polypeptide , Acetylcholine/metabolism , Catecholamines/metabolism , Catecholamines/pharmacology , Cholinergic Agonists/metabolism , Cholinergic Agonists/pharmacology , Chromaffin Cells/metabolism , Guanine Nucleotide Exchange Factors/metabolism , Hormones , Pituitary Adenylate Cyclase-Activating Polypeptide/metabolism , Animals , Mice , Receptors, Cholinergic/metabolism
10.
J Biol Chem ; 286(40): 35129-36, 2011 Oct 07.
Article in English | MEDLINE | ID: mdl-21835920

ABSTRACT

Glycine receptors (GlyRs) are chloride channels that mediate fast inhibitory neurotransmission and are members of the pentameric ligand-gated ion channel (pLGIC) family. The interface between the ligand binding domain and the transmembrane domain of pLGICs has been proposed to be crucial for channel gating and is lined by a number of charged and aromatic side chains that are highly conserved among different pLGICs. However, little is known about specific interactions between these residues that are likely to be important for gating in α1 GlyRs. Here we use the introduction of cysteine pairs and the in vivo nonsense suppression method to incorporate unnatural amino acids to probe the electrostatic and hydrophobic contributions of five highly conserved side chains near the interface, Glu-53, Phe-145, Asp-148, Phe-187, and Arg-218. Our results suggest a salt bridge between Asp-148 in loop 7 and Arg-218 in the pre-M1 domain that is crucial for channel gating. We further propose that Phe-145 and Phe-187 play important roles in stabilizing this interaction by providing a hydrophobic environment. In contrast to the equivalent residues in loop 2 of other pLGICs, the negative charge at Glu-53 α1 GlyRs is not crucial for normal channel function. These findings help decipher the GlyR gating pathway and show that distinct residue interaction patterns exist in different pLGICs. Furthermore, a salt bridge between Asp-148 and Arg-218 would provide a possible mechanistic explanation for the pathophysiologically relevant hyperekplexia, or startle disease, mutant Arg-218 → Gln.


Subject(s)
Receptors, Glycine/chemistry , Allosteric Site , Amino Acid Sequence , Biophysics/methods , Conserved Sequence , DNA, Complementary/metabolism , Electrophysiology/methods , Glycine/chemistry , Humans , Ligands , Molecular Sequence Data , Mutagenesis, Site-Directed , Protein Binding , Reflex, Abnormal/genetics , Reflex, Startle/genetics , Salts/chemistry , Sequence Homology, Amino Acid , Static Electricity
11.
Glycobiology ; 22(4): 492-503, 2012 Apr.
Article in English | MEDLINE | ID: mdl-22061999

ABSTRACT

There is a clear need for efficient methods to produce protein therapeutics requiring mannose-termination for therapeutic efficacy. Here we report on a unique system for production of active human lysosomal acid ß-glucosidase (glucocerebrosidase, GCase, EC 3.2.1.45) using seeds of the Arabidopsis thaliana complex-glycan-deficient (cgl) mutant, which are deficient in the activity of N-acetylglucosaminyl transferase I (EC 2.4.1.101). Gaucher disease is a prevalent lysosomal storage disease in which affected individuals inherit mutations in the gene (GBA1) encoding GCase. A gene cassette optimized for seed expression was used to generate the human enzyme in seeds of the cgl (C5) mutant, and the recombinant GCase was mainly accumulated in the apoplast. Importantly, the enzymatic properties including kinetic parameters, half-maximal inhibitory concentration of isofagomine and thermal stability of the cgl-derived GCase were comparable with those of imiglucerase, a commercially available recombinant human GCase used for enzyme replacement therapy in Gaucher patients. N-glycan structural analyses of recombinant cgl-GCase showed that the majority of the N-glycans (97%) were mannose terminated. Additional purification was required to remove ∼15% of the plant-derived recombinant GCase that possessed potentially immunogenic (xylose- and/or fucose-containing) N-glycans. Uptake of cgl-derived GCase by mouse macrophages was similar to that of imiglucerase. The cgl seed system requires no addition of foreign (non-native) amino acids to the mature recombinant GCase protein, and the dry transgenic seeds represent a stable repository of the therapeutic protein. Other strategies that may completely prevent plant-like complex N-glycans are discussed, including the use of a null cgl mutant.


Subject(s)
Arabidopsis/genetics , Glucosylceramidase/biosynthesis , Plants, Genetically Modified , Seeds/genetics , Animals , Arabidopsis/cytology , Carbohydrate Conformation , Carbohydrate Sequence , Cells, Cultured , Enzyme Stability , Glucosylceramidase/isolation & purification , Glucosylceramidase/metabolism , Glycosylation , Humans , Kinetics , Macrophages/metabolism , Mannose , Mice , Molecular Sequence Data , Recombinant Proteins/biosynthesis , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , Seeds/cytology
12.
J Gen Physiol ; 154(7)2022 07 04.
Article in English | MEDLINE | ID: mdl-35657726

ABSTRACT

The essential transmembrane Na+ and K+ gradients in animal cells are established by the Na+/K+ pump, a P-type ATPase that exports three Na+ and imports two K+ per ATP hydrolyzed. The mechanism by which the Na+/K+ pump distinguishes between Na+ and K+ at the two membrane sides is poorly understood. Crystal structures identify two sites (sites I and II) that bind Na+ or K+ and a third (site III) specific for Na+. The side chain of a conserved tyrosine at site III of the catalytic α-subunit (Xenopus-α1 Y780) has been proposed to contribute to Na+ binding by cation-π interaction. We substituted Y780 with natural and unnatural amino acids, expressed the mutants in Xenopus oocytes and COS-1 cells, and used electrophysiology and biochemistry to evaluate their function. Substitutions disrupting H-bonds impaired Na+ interaction, while Y780Q strengthened it, likely by H-bond formation. Utilizing the non-sense suppression method previously used to incorporate unnatural derivatives in ion channels, we were able to analyze Na+/K+ pumps with fluorinated tyrosine or phenylalanine derivatives inserted at position 780 to diminish cation-π interaction strength. In line with the results of the analysis of mutants with natural amino acid substitutions, the results with the fluorinated derivatives indicate that Na+-π interaction with the phenol ring at position 780 contributes minimally, if at all, to the binding of Na+. All Y780 substitutions decreased K+ apparent affinity, highlighting that a state-dependent H-bond network is essential for the selectivity switch at sites I and II when the pump changes conformational state.


Subject(s)
Sodium-Potassium-Exchanging ATPase , Tyrosine , Animals , Binding Sites , Cations/metabolism , Potassium/metabolism , Sodium/metabolism , Sodium-Potassium-Exchanging ATPase/metabolism
13.
Nat Commun ; 13(1): 7508, 2022 12 06.
Article in English | MEDLINE | ID: mdl-36473856

ABSTRACT

Chloride homeostasis is regulated in all cellular compartments. CLC-type channels selectively transport Cl- across biological membranes. It is proposed that side-chains of pore-lining residues determine Cl- selectivity in CLC-type channels, but their spatial orientation and contributions to selectivity are not conserved. This suggests a possible role for mainchain amides in selectivity. We use nonsense suppression to insert α-hydroxy acids at pore-lining positions in two CLC-type channels, CLC-0 and bCLC-k, thus exchanging peptide-bond amides with ester-bond oxygens which are incapable of hydrogen-bonding. Backbone substitutions functionally degrade inter-anion discrimination in a site-specific manner. The presence of a pore-occupying glutamate side chain modulates these effects. Molecular dynamics simulations show backbone amides determine ion energetics within the bCLC-k pore and how insertion of an α-hydroxy acid alters selectivity. We propose that backbone-ion interactions are determinants of Cl- specificity in CLC channels in a mechanism reminiscent of that described for K+ channels.


Subject(s)
Amides , Ion Channels
14.
J Gen Physiol ; 153(9)2021 09 06.
Article in English | MEDLINE | ID: mdl-34228044

ABSTRACT

The human voltage-gated proton channel Hv1 is a drug target for cancer, ischemic stroke, and neuroinflammation. It resides on the plasma membrane and endocytic compartments of a variety of cell types, where it mediates outward proton movement and regulates the activity of NOX enzymes. Its voltage-sensing domain (VSD) contains a gated and proton-selective conduction pathway, which can be blocked by aromatic guanidine derivatives such as 2-guanidinobenzimidazole (2GBI). Mutation of Hv1 residue F150 to alanine (F150A) was previously found to increase 2GBI apparent binding affinity more than two orders of magnitude. Here, we explore the contribution of aromatic interactions between the inhibitor and the channel in the presence and absence of the F150A mutation, using a combination of electrophysiological recordings, classic mutagenesis, and site-specific incorporation of fluorinated phenylalanines via nonsense suppression methodology. Our data suggest that the increase in apparent binding affinity is due to a rearrangement of the binding site allowed by the smaller residue at position 150. We used this information to design new arginine mimics with improved affinity for the nonrearranged binding site of the wild-type channel. The new compounds, named "Hv1 Inhibitor Flexibles" (HIFs), consist of two "prongs," an aminoimidazole ring, and an aromatic group connected by extended flexible linkers. Some HIF compounds display inhibitory properties that are superior to those of 2GBI, thus providing a promising scaffold for further development of high-affinity Hv1 inhibitors.


Subject(s)
Arginine , Ion Channels , Binding Sites , Humans , Ion Channels/metabolism , Ligands , Protons
15.
Elife ; 92020 04 28.
Article in English | MEDLINE | ID: mdl-32343228

ABSTRACT

The CLC family comprises H+-coupled exchangers and Cl- channels, and mutations causing their dysfunction lead to genetic disorders. The CLC exchangers, unlike canonical 'ping-pong' antiporters, simultaneously bind and translocate substrates through partially congruent pathways. How ions of opposite charge bypass each other while moving through a shared pathway remains unknown. Here, we use MD simulations, biochemical and electrophysiological measurements to identify two conserved phenylalanine residues that form an aromatic pathway whose dynamic rearrangements enable H+ movement outside the Cl- pore. These residues are important for H+ transport and voltage-dependent gating in the CLC exchangers. The aromatic pathway residues are evolutionarily conserved in CLC channels where their electrostatic properties and conformational flexibility determine gating. We propose that Cl- and H+ move through physically distinct and evolutionarily conserved routes through the CLC channels and transporters and suggest a unifying mechanism that describes the gating mechanism of both CLC subtypes.


Subject(s)
Antiporters/physiology , Chloride Channels/physiology , Chlorides/metabolism , Ion Channel Gating/physiology , Ion Transport/physiology , Antiporters/chemistry , Chloride Channels/chemistry , Escherichia coli Proteins/physiology , Molecular Dynamics Simulation , Protons
16.
Nat Commun ; 9(1): 5055, 2018 11 29.
Article in English | MEDLINE | ID: mdl-30498243

ABSTRACT

Membrane proteins are universal signal decoders. The helical transmembrane segments of these proteins play central roles in sensory transduction, yet the mechanistic contributions of secondary structure remain unresolved. To investigate the role of main-chain hydrogen bonding on transmembrane function, we encoded amide-to-ester substitutions at sites throughout the S4 voltage-sensing segment of Shaker potassium channels, a region that undergoes rapid, voltage-driven movement during channel gating. Functional measurements of ester-harboring channels highlight a transitional region between α-helical and 310 segments where hydrogen bond removal is particularly disruptive to voltage-gating. Simulations of an active voltage sensor reveal that this region features a dynamic hydrogen bonding pattern and that its helical structure is reliant upon amide support. Overall, the data highlight the specialized role of main-chain chemistry in the mechanism of voltage-sensing; other catalytic transmembrane segments may enlist similar strategies in signal transduction mechanisms.


Subject(s)
Molecular Dynamics Simulation , Potassium Channels/chemistry , Potassium Channels/metabolism , Hydrogen Bonding , Mutagenesis/genetics , Mutagenesis/physiology , Potassium Channels/genetics , Potassium Channels, Voltage-Gated/chemistry , Potassium Channels, Voltage-Gated/genetics , Potassium Channels, Voltage-Gated/metabolism , Protein Structure, Secondary , Shaker Superfamily of Potassium Channels/chemistry , Shaker Superfamily of Potassium Channels/genetics , Shaker Superfamily of Potassium Channels/metabolism
17.
J Gen Physiol ; 150(7): 1017-1024, 2018 07 02.
Article in English | MEDLINE | ID: mdl-29866793

ABSTRACT

Voltage-dependent activation of voltage-gated cation channels results from the outward movement of arginine-bearing helices within proteinaceous voltage sensors. The voltage-sensing residues in potassium channels have been extensively characterized, but current functional approaches do not allow a distinction between the electrostatic and steric contributions of the arginine side chain. Here we use chemical misacylation and in vivo nonsense suppression to encode citrulline, a neutral and nearly isosteric analogue of arginine, into the voltage sensor of the Shaker potassium channel. We functionally characterize the engineered channels and compare them with those bearing conventional mutations at the same positions. We observe effects on both voltage sensitivity and gating kinetics, enabling dissection of the roles of residue structure versus positive charge in channel function. In some positions, substitution with citrulline causes mild effects on channel activation compared with natural mutations. In contrast, substitution of the fourth S4 arginine with citrulline causes substantial changes in the conductance-voltage relationship and the kinetics of the channel, which suggests that a positive charge is required at this position for efficient voltage sensor deactivation and channel closure. The encoding of citrulline is expected to enable enhanced precision for the study of arginine residues located in crowded transmembrane environments in other membrane proteins. In addition, the method may facilitate the study of citrullination in vivo.


Subject(s)
Arginine/chemistry , Citrulline/chemistry , Ion Channel Gating , Shaker Superfamily of Potassium Channels/chemistry , Amino Acid Substitution , Animals , Arginine/genetics , Citrulline/genetics , Membrane Potentials , Mice , Protein Domains , Shaker Superfamily of Potassium Channels/genetics , Shaker Superfamily of Potassium Channels/metabolism , Static Electricity , Xenopus
18.
Sci Rep ; 8(1): 5166, 2018 03 26.
Article in English | MEDLINE | ID: mdl-29581437

ABSTRACT

Chemical aminoacylation of orthogonal tRNA allows for the genetic encoding of a wide range of synthetic amino acids without the need to evolve specific aminoacyl-tRNA synthetases. This method, when paired with protein expression in the Xenopus laevis oocyte expression system, can extract atomic scale functional data from a protein structure to advance the study of membrane proteins. The utility of the method depends on the orthogonality of the tRNA species used to deliver the amino acid. Here, we report that the pyrrolysyl tRNA (pylT) from Methanosarcina barkeri fusaro is orthogonal and highly competent for genetic code expansion experiments in the Xenopus oocyte. The data show that pylT is amendable to chemical acylation in vitro; it is then used to rescue a cytoplasmic site within a voltage-gated sodium channel. Further, the high fidelity of the pylT is demonstrated via encoding of lysine within the selectivity filter of the sodium channel, where sodium ion recognition by the distal amine of this side-chain is essential. Thus, pylT is an appropriate tRNA species for delivery of amino acids via nonsense suppression in the Xenopus oocyte. It may prove useful in experimental contexts wherein reacylation of suppressor tRNAs have been observed.


Subject(s)
Lysine/analogs & derivatives , Oocytes/metabolism , RNA, Transfer/genetics , RNA, Transfer/metabolism , Xenopus laevis/metabolism , Amino Acids/metabolism , Amino Acyl-tRNA Synthetases/metabolism , Aminoacylation , Animals , Anticodon , Codon, Terminator , Genetic Code , Humans , Lysine/metabolism , Methanosarcina barkeri/chemistry , Patch-Clamp Techniques/methods , Protein Biosynthesis , Rats , Tetrahymena thermophila/chemistry , Transfer RNA Aminoacylation , Voltage-Gated Sodium Channels/metabolism
19.
Elife ; 62017 12 05.
Article in English | MEDLINE | ID: mdl-29206105

ABSTRACT

TRPV1 channels support the detection of noxious and nociceptive input. Currently available functional and structural data suggest that TRPV1 channels have two gates within their permeation pathway: one formed by a 'bundle-crossing' at the intracellular entrance and a second constriction at the selectivity filter. To describe conformational changes associated with channel gating, the fluorescent non-canonical amino acid coumarin-tyrosine was genetically encoded at Y671, a residue proximal to the selectivity filter. Total internal reflection fluorescence microscopy was performed to image the conformational dynamics of the channels in live cells. Photon counts and optical fluctuations from coumarin encoded within TRPV1 tetramers correlates with channel activation by capsaicin, providing an optical marker of conformational dynamics at the selectivity filter. In agreement with the fluorescence data, molecular dynamics simulations display alternating solvent exposure of Y671 in the closed and open states. Overall, the data point to a dynamic selectivity filter that may serve as a gate for permeation.


Cells use proteins on their surface as sensors to help them to assess and explore their environments and adapt to external conditions. The transient receptor potential (TRP) ion channels form one such family of proteins. Sodium, potassium and calcium ions can move through TRP channels to enter and exit cells, and by doing so trigger changes in the cell that help it respond to an external stimulus. The channels have physical "gates" that can open and close to control the flow of the ions. When the TRP channel detects a stimulus ­ which could take the form of specific chemicals, or a change in temperature, pressure or voltage ­ it changes shape, causing the gate to open. Researchers have a number of unanswered questions about how TRP channels work. Where in the channels are gates located? How do the channels control the flow of ions, and how do they communicate with each other? And which regions of the protein sense environmental cues? As a result, new technologies are being developed to make it easier to study the types of rearrangements that TRP channels experience when they activate. Steinberg, Kasimova et al. have used total internal reflection microscopy ­ a method that images fluorescent molecules ­ to measure the conformational change of a single TRP channel in a living cell. This channel, called TRPV1, senses external heat and plays an important role in pain perception. Its gate can also be opened by the pungent compound of chili pepper, capsaicin. The results of the experiments suggest that a selectivity filter region in TRPV1 channels changes its shape when the channel opens in response to capsaicin. Then, this selectivity filter appears to do double duty ­ it controls which types of ions pass through the channels as well as controlling their flow rate. Because of its role in pain perception, having a better understanding of how TRPV1 works will be valuable for researchers who are trying to develop new pain relief treatments. The so-called 'seeing is believing' method used by Steinberg, Kasimova et al. could also be used to study other membrane proteins, both to guide drug development and to improve our understanding of how cells interact with their environment.


Subject(s)
Coumarins/analysis , TRPV Cation Channels/chemistry , TRPV Cation Channels/metabolism , Tyrosine/analysis , Capsaicin/metabolism , HEK293 Cells , Humans , Intravital Microscopy , Microscopy, Fluorescence , Models, Molecular , Molecular Dynamics Simulation , Protein Conformation , Staining and Labeling , TRPV Cation Channels/genetics
20.
Plant Biotechnol J ; 4(2): 169-81, 2006 Mar.
Article in English | MEDLINE | ID: mdl-17177794

ABSTRACT

As an initial step to develop plants as systems to produce enzymes for the treatment of lysosomal storage disorders, Arabidopsis thaliana wild-type (Col-0) plants were transformed with a construct to express human alpha-l-iduronidase (IDUA; EC 3.2.1.76) in seeds using the promoter and other regulatory sequences of the Phaseolus vulgaris arcelin 5-I gene. IDUA protein was easily detected on Western blots of extracts from the T(2) seeds, and extracts contained IDUA activity as high as 2.9 nmol 4-methylumbelliferone (4 MU)/min/mg total soluble protein (TSP), corresponding to approximately 0.06 microg IDUA/mg TSP. The purified protein reacted with an antibody specific for xylose-containing plant complex glycans, indicating its transit through the Golgi complex. In an attempt to avoid maturation of the N-linked glycans of IDUA, the same IDUA transgene was introduced into the Arabidopsis cgl background, which is deficient in the activity of N-acetylglucosaminyl transferase I (EC 2.4.1.101), the first enzyme in the pathway of complex glycan biosynthesis. IDUA activity and protein levels were significantly higher in transgenic cgl vs. wild-type seeds (e.g. maximum levels were 820 nmol 4 MU/min/mg TSP, or 18 microg IDUA/mg TSP). Affinity-purified IDUA derived from cgl mutant seeds showed a markedly reduced reaction with the antibody specific for plant complex glycans, despite transit of the protein to the apoplast. Furthermore, gel mobility changes indicated that a greater proportion of its N-linked glycans were susceptible to digestion by Streptomyces endoglycosidase H, as compared to IDUA derived from seeds of wild-type Arabidopsis plants. The combined results indicate that IDUA produced in cgl mutant seeds contains glycans primarily in the high-mannose form. This work clearly supports the viability of using plants for the production of human therapeutics with high-mannose glycans.


Subject(s)
Arabidopsis/genetics , Iduronidase/metabolism , Plants, Genetically Modified/enzymology , Golgi Apparatus/enzymology , Humans , Iduronidase/analysis , Iduronidase/genetics , Mannose/metabolism , Mutation , N-Acetylglucosaminyltransferases/genetics , N-Acetylglucosaminyltransferases/metabolism , Polysaccharides/metabolism , Protein Transport , Recombinant Fusion Proteins/metabolism , Seeds/enzymology , Seeds/genetics , Transformation, Genetic
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