scholarly journals Tuning the tetraethylammonium sensitivity of potassium channel Kcv by subunit combination

2012 ◽  
Vol 139 (4) ◽  
pp. 295-304 ◽  
Author(s):  
Qiulin Tan ◽  
Brandon Ritzo ◽  
Kai Tian ◽  
Li-Qun Gu
Keyword(s):  
Potassium Channel ◽  
Binding Site ◽  
Specific Interaction ◽  
Site Directed Mutagenesis ◽  
Molecular Probe ◽  
K Channel ◽  
Optimal Conformation ◽  
Subunit Combination ◽  
Insight Into

Tetraethylammonium (TEA) is a potassium (K+) channel inhibitor that has been extensively used as a molecular probe to explore the structure of channels’ ion pathway. In this study, we identified that Leu70 of the virus-encoded potassium channel Kcv is a key amino acid that plays an important role in regulating the channel’s TEA sensitivity. Site-directed mutagenesis of Leu70 can change the TEA sensitivity by 1,000-fold from ∼100 µM to ∼100 mM. Because no compelling trends exist to explain this amino acid’s specific interaction with TEA, the role of Leu70 at the binding site is likely to ensure an optimal conformation of the extracellular mouth that confers high TEA affinity. We further assembled the subunits of mutant and wt-Kcv into a series of heterotetramers. The differences in these heterochannels suggest that all of the four subunits in a Kcv channel additively participate in the TEA binding, and each of the four residues at the binding site independently contributes an equal binding energy. We therefore can present a series of mutant/wild-type tetramer combinations that can probe TEA over three orders of magnitude in concentration. This study may give insight into the mechanism for the interaction between the potassium channel and its inhibitor.

scholarly journals The functional role of the αM4 transmembrane helix in the muscle nicotinic acetylcholine receptor probed through mutagenesis and coevolutionary analyses

2020 ◽  
Vol 295 (32) ◽  
pp. 11056-11067 ◽  
Author(s):  
Mackenzie J. Thompson ◽  
Jaimee A. Domville ◽  
John E. Baenziger
Keyword(s):  
Acetylcholine Receptor ◽  
Nicotinic Acetylcholine Receptor ◽  
Site Directed Mutagenesis ◽  
Induced Response ◽  
Independent Manner ◽  
Nicotinic Acetylcholine ◽  
Α Subunit ◽  
Lipid Sensing ◽  
Insight Into

The activity of the muscle-type Torpedo nicotinic acetylcholine receptor (nAChR) is highly sensitive to lipids, but the underlying mechanisms remain poorly understood. The nAChR transmembrane α-helix, M4, is positioned at the perimeter of each subunit in direct contact with lipids and likely plays a central role in lipid sensing. To gain insight into the mechanisms underlying nAChR lipid sensing, we used homology modeling, coevolutionary analyses, site-directed mutagenesis, and electrophysiology to examine the role of the α-subunit M4 (αM4) in the function of the adult muscle nAChR. Ala substitutions for most αM4 residues, including those in clusters of polar residues at both the N and C termini, and deletion of up to 11 C-terminal residues had little impact on the agonist-induced response. Even Ala substitutions for coevolved pairs of residues at the interface between αM4 and the adjacent helices, αM1 and αM3, had little effect, although some impaired nAChR expression. On the other hand, Ala substitutions for Thr422 and Arg429 caused relatively large losses of function, suggesting functional roles for these specific residues. Ala substitutions for aromatic residues at the αM4-αM1/αM3 interface generally led to gains of function, as previously reported for the prokaryotic homolog, the Erwinia chrysanthemi ligand-gated ion channel (ELIC). The functional effects of individual Ala substitutions in αM4 were found to be additive, although not in a completely independent manner. Our results provide insight into the structural features of αM4 that are important. They also suggest how lipid-dependent changes in αM4 structure ultimately modify nAChR function.

Making biochemistry count: life among the amino acid dehydrogenases

2011 ◽  
Vol 39 (2) ◽  
pp. 425-429 ◽  
Author(s):  
Paul C. Engel
Keyword(s):  
Amino Acid ◽  
Site Directed Mutagenesis ◽  
Coenzyme Binding ◽  
Guiding Principle ◽  
Glutamate Binding ◽  
Metabolic Role ◽  
Structure Solution ◽  
Unexpected Outcomes ◽  
Insight Into

The guiding principle of the IAS Medal Lecture and of the research it covered was that searching mathematical analysis, depending on good measurements, must underpin sound biochemical conclusions. This was illustrated through various experiences with the amino acid dehydrogenases. Topics covered in the present article include: (i) the place of kinetic measurement in assessing the metabolic role of GDH (glutamate dehydrogenase); (ii) the discovery of complex regulatory behaviour in mammalian GDH, involving negative co-operativity in coenzyme binding; (iii) an X-ray structure solution for a bacterial GDH providing insight into catalysis; (iv) almost total positive co-operativity in glutamate binding to clostridial GDH; (v) unexpected outcomes with mutations at the catalytic aspartate site in GDH; (vi) reactive cysteine as a counting tool in the construction of hybrid oligomers to probe the basis of allosteric interaction; (vii) tryptophan-to-phenylalanine mutations in analysis of allosteric conformational change; (viii) site-directed mutagenesis to alter substrate specificity in GDH and PheDH (phenylalanine dehydrogenase); and (ix) varying strengths of binding of the ‘wrong’ enantiomer in engineered mutant enzymes and implications for resolution of racemates.

scholarly journals The role of residues glutamate-50 and phenylalanine-496 in Zymomonas mobilis pyruvate decarboxylase

1996 ◽  
Vol 315 (3) ◽  
pp. 745-751 ◽  
Author(s):  
Judith M. CANDY ◽  
Jinichiro KOGA ◽  
Peter F. NIXON ◽  
Ronald G. DUGGLEBY
Keyword(s):  
Fluorescence Quenching ◽  
Zymomonas Mobilis ◽  
Specific Interaction ◽  
Pyruvate Decarboxylase ◽  
Site Directed Mutagenesis ◽  
Kinetic Properties ◽  
Subunit Structure ◽  
Wild Type ◽  
Cloned Gene

Several enzymes require thiamine diphosphate (ThDP) as an essential cofactor, and we have used one of these, pyruvate decarboxylase (PDC; EC 4.1.1.1) from Zymomonas mobilis, as a model for this group of enzymes. It is well suited for this purpose because of its stability, ease of purification, homotetrameric subunit structure and simple kinetic properties. Crystallographic analyses of three ThDP-dependent enzymes [Müller, Lindqvist, Furey, Schulz, Jordan and Schneider (1993) Structure 1, 95–103] have suggested that an invariant glutamate participates in catalysis. In order to evaluate the role of this residue, identified in PDC from Zymomonas mobilis as Glu-50, it has been altered to glutamine and aspartate by site-directed mutagenesis of the cloned gene. The mutant proteins were expressed in Escherichia coli. Here we demonstrate that substitution with aspartate yields an enzyme with 3% of the activity of the wild-type, but with normal kinetics for pyruvate. Replacement of Glu-50 with glutamine yields an enzyme with only 0.5% of the catalytic activity of the wild-type enzyme. Each of these mutant enzymes has a decreased affinity for both ThDP and Mg2+. It has been reported that the binding of cofactors to apoPDC quenches the intrinsic tryptophan fluorescence [Diefenbach and Duggleby (1991) Biochem. J. 276, 439–445] and we have identified the residue responsible as Trp-487 [Diefenbach, Candy, Mattick and Duggleby (1992) FEBS Lett. 296, 95–98]. Although this residue is some distance from the cofactor binding site, it lies in the dimer interface, and the proposal has been put forward [Dyda, Furey, Swaminathan, Sax, Farrenkopf and Jordan (1993) Biochemistry 32, 6165–6170] that alteration of ring stacking with Phe-496 of the adjacent subunit is the mechanism of fluorescence quenching when cofactors bind. The closely related enzyme indolepyruvate decarboxylase (from Enterobacter cloacae) has a leucine residue at the position corresponding to Phe-496 but shows fluorescence quenching properties that are similar to those of PDC. This suggests that the fluorescence quenching is due to some perturbation of the local environment of Trp-487 rather than to a specific interaction with Phe-496. This latter hypothesis is supported by our data: mutation of this phenylalanine to leucine, isoleucine or histidine in PDC does not eliminate the fluorescence quenching upon addition of cofactors.

scholarly journals On the role of ball and chain interactions in recovery from the inactivation of the shaker potassium channel

2008 ◽  
Vol 13 (4) ◽  
Author(s):  
Przemysław Borys ◽  
Zbigniew Grzywna
Keyword(s):  
Potassium Channel ◽  
Binding Site ◽  
Chain Model ◽  
Shaker Potassium Channel ◽  
Recovery From Inactivation

AbstractWe describe a new factor in the recovery from inactivation in the ball and chain model. We propose a model in which the tension from the chain may help pull the ball away from its binding site, reducing the duration of the inactivation period. A corresponding model was built and analysed.

scholarly journals Identification of Functional Amino Acids in the Macrolide 2′-Phosphotransferase II

1999 ◽  
Vol 43 (8) ◽  
pp. 2063-2065 ◽  
Author(s):  
Kazuo Taniguchi ◽  
Akio Nakamura ◽  
Kazue Tsurubuchi ◽  
Aki Ishii ◽  
Koji O’Hara ◽  
...  
Keyword(s):  
Amino Acids ◽  
Binding Site ◽  
Site Directed Mutagenesis ◽  
Macrolide Antibiotics ◽  
Directed Mutagenesis ◽  
Atp Binding ◽  
Atp Binding Site ◽  
Mutant Strains

ABSTRACT Macrolide 2′-phosphotransferase [MPH(2′)] transfers the γ phosphate of ATP to the 2′-OH group of macrolide antibiotics. The role of aspartic acids in the putative ATP-binding site of MPH(2′)II was investigated through the substitution of alanine for aspartate by site-directed mutagenesis. D200A, D209A, D219A, and D231A mutant strains were unable to inactivate the substrate oleandomycin, while a D227A mutant retained 7% of the activity of the original enzyme.

scholarly journals How an intrinsic ligand tunes the activity of a potassium channel

2018 ◽  
Vol 150 (4) ◽  
pp. 517-520 ◽  
Author(s):  
Keith K. Khoo ◽  
Stephan A. Pless
Keyword(s):  
Ion Channels ◽  
Potassium Channel ◽  
New Work ◽  
Mechanistic Insight ◽  
Insight Into

Khoo and Pless examine new work that provides mechanistic insight into the role of the intrinsic ligand in KCNH ion channels.​

scholarly journals A role of the CTCF binding site at enhancer Eα in the dynamic chromatin organization of the Tcra–Tcrd locus

2020 ◽  
Vol 48 (17) ◽  
pp. 9621-9636
Author(s):  
Hao Zhao ◽  
Zhaoqiang Li ◽  
Yongchang Zhu ◽  
Shasha Bian ◽  
Yan Zhang ◽  
...  
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Gene Rearrangement ◽  
Cell Receptor ◽  
Ctcf Binding ◽  
Ctcf Binding Site ◽  
Long Distance ◽  
Distance Regulation ◽  
Insight Into

Abstract The regulation of T cell receptor Tcra gene rearrangement has been extensively studied. The enhancer Eα plays an essential role in Tcra rearrangement by establishing a recombination centre in the Jα array and a chromatin hub for interactions between Vα and Jα genes. But the mechanism of the Eα and its downstream CTCF binding site (here named EACBE) in dynamic chromatin regulation is unknown. The Hi-C data showed that the EACBE is located at the sub-TAD boundary which separates the Tcra–Tcrd locus and the downstream region including the Dad1 gene. The EACBE is required for long-distance regulation of the Eα on the proximal Vα genes, and its deletion impaired the Tcra rearrangement. We also noticed that the EACBE and Eα regulate the genes in the downstream sub-TAD via asymmetric chromatin extrusion. This study provides a new insight into the role of CTCF binding sites at TAD boundaries in gene regulation.

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