scholarly journals Ligand discrimination and gating in cyclic nucleotide-gated ion channels from apo and partial agonist-bound cryo-EM structures

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Jan Rheinberger ◽  
Xiaolong Gao ◽  
Philipp AM Schmidpeter ◽  
Crina M Nimigean
Keyword(s):  
Cyclic Nucleotide ◽  
Molecular Mechanisms ◽  
Single Channel ◽  
Structural Information ◽  
Partial Agonist ◽  
Visual Signal ◽  
Functional Responses ◽  
Binding Domains ◽  
Single Channel Activity ◽  
Functional States

Cyclic nucleotide-modulated channels have important roles in visual signal transduction and pacemaking. Binding of cyclic nucleotides (cAMP/cGMP) elicits diverse functional responses in different channels within the family despite their high sequence and structure homology. The molecular mechanisms responsible for ligand discrimination and gating are unknown due to lack of correspondence between structural information and functional states. Using single particle cryo-electron microscopy and single-channel recording, we assigned functional states to high-resolution structures of SthK, a prokaryotic cyclic nucleotide-gated channel. The structures for apo, cAMP-bound, and cGMP-bound SthK in lipid nanodiscs, correspond to no, moderate, and low single-channel activity, respectively, consistent with the observation that all structures are in resting, closed states. The similarity between apo and ligand-bound structures indicates that ligand-binding domains are strongly coupled to pore and SthK gates in an allosteric, concerted fashion. The different orientations of cAMP and cGMP in the ‘resting’ and ‘activated’ structures suggest a mechanism for ligand discrimination.

scholarly journals Insight into dynamics of APOBEC3G protein in complexes with DNA assessed by high speed AFM

2019 ◽  
Author(s):  
Yangang Pan ◽  
Luda S. Shlyakhtenko ◽  
Yuri L. Lyubchenko
Keyword(s):  
High Speed ◽  
Molecular Mechanisms ◽  
Catalytic Domain ◽  
Structural Information ◽  
Dynamic Structure ◽  
Time Lapse ◽  
Ssdna Binding ◽  
Binding Domains ◽  
Ssdna Binding Protein ◽  
Dumbbell Structure

AbstractAPOBEC3G (A3G) is a single-stranded DNA (ssDNA) binding protein that restricts the HIV virus by deamination of dC to dU during reverse transcription of the viral genome. A3G has two zing-binding domains: the N-terminal domain (NTD), which efficiently binds ssDNA, and the C-terminal catalytic domain (CTD), which supports deaminase activity of A3G. Until now, structural information on A3G has lacked, preventing elucidation of the molecular mechanisms underlying its interaction with ssDNA and deaminase activity. We have recently built computational model for the full-length A3G monomer and validated its structure by data obtained from time-lapse High-Speed Atomic Force Microscopy (HS AFM). Here time-lapse HS AFM was applied to directly visualize the structure and dynamics of A3G in complexes with ssDNA. Our results demonstrate a highly dynamic structure of A3G, where two domains of the protein fluctuate between compact globular and extended dumbbell structures. Quantitative analysis of our data revealed a substantial increase in the number of A3G dumbbell structures in the presence of the DNA substrate, suggesting the interaction of A3G with the ssDNA substrate stabilizes this dumbbell structure. Based on these data, we developed a model explaining the interaction of globular and dumbbell structures of A3G with ssDNA and suggested a possible role of the dumbbell structure in A3G function.

scholarly journals Stimulation of Drosophila TrpL by capacitative Ca2+ entry

1999 ◽  
Vol 341 (1) ◽  
pp. 41-49 ◽  
Author(s):  
Mark ESTACION ◽  
William G. SINKINS ◽  
William P. SCHILLING
Keyword(s):  
Transient Receptor Potential ◽  
Single Channel ◽  
Receptor Potential ◽  
Photoreceptor Cells ◽  
Channel Activity ◽  
Terminal Domain ◽  
Binding Domains ◽  
Single Channel Activity ◽  
Transient Receptor ◽  
Stimulation Of

Trp-like protein (TrpL, where Trp is transient receptor-potential protein) of Drosophila, a non-selective cation channel activated in photoreceptor cells by a phospholipase C-dependent mechanism, is thought to be a prototypical receptor-activated channel. Our previous studies showed that TrpL channels are not activated by depletion of internal Ca2+ stores when expressed in Sf9 cells. Using fura-2 to measure cation influx via TrpL, and cell-attached patch recordings to monitor TrpL single-channel activity directly, we have found a thapsigargin-induced increase in TrpL activity in the presence of extracellular bivalent cations, with Ca2+ > Sr2+ Ba2+. The increase in TrpL channel activity was blocked by concentrations of La3+ that completely inhibited endogenous capacitative Ca2+ entry (CCE), but have no effect on TrpL, suggesting that TrpL exhibits trans-stimulation by cation entry via CCE. TrpL has two putative calmodulin (CaM)-binding domains, designated CBS-1 and CBS-2. To determine which site may be required for stimulation of TrpL by the cytosolic free Ca2+ concentration ([Ca2+]i), a chimaeric construct was created in which the C-terminal domain of TrpL containing CBS-2 was attached to human TrpC1, a short homologue of Trp that is not activated by depletion of internal Ca2+ stores or by a rise in [Ca2+]i. This gain-of-function mutant, designated TrpC1-TrpL, exhibited trans-stimulation by Ca2+ entry via CCE. Examination of CaM binding in gel-overlay experiments showed that TrpL and the TrpC1-TrpL chimaera bound CaM, but TrpC1 or a truncated version of TrpL lacking CBS-2 did not. These results suggest that only CBS-2 binds CaM in native TrpL and that the C-terminal domain containing this site is important for trans-stimulation of TrpL by CCE.

scholarly journals Discovery of a Bradykinin B2 Partial Agonist Profile of Raloxifene in a Drug Repurposing Campaign

2020 ◽  
Vol 22 (1) ◽  
pp. 257
Author(s):  
Patricia Gomez-Gutierrez ◽  
Juan J. Perez
Keyword(s):  
Virtual Screening ◽  
Molecular Mechanisms ◽  
Partial Agonist ◽  
Drug Repurposing ◽  
Cytokine Storm ◽  
Bradykinin Receptors ◽  
Screening Process ◽  
Bradykinin Antagonists ◽  
Illness Progression

Covid-19 urges a deeper understanding of the underlying molecular mechanisms involved in illness progression to provide a prompt therapeutical response with an adequate use of available drugs, including drug repurposing. Recently, it was suggested that a dysregulated bradykinin signaling can trigger the cytokine storm observed in patients with severe Covid-19. In the scope of a drug repurposing campaign undertaken to identify bradykinin antagonists, raloxifene was identified as prospective compound in a virtual screening process. The pharmacodynamics profile of raloxifene towards bradykinin receptors is reported in the present work, showing a weak selective partial agonist profile at the B2 receptor. In view of this new profile, its possible use as a therapeutical agent for the treatment of severe Covid-19 is discussed.

scholarly journals Simultaneous Acquisition of Ultrasound and Gamma Signals with a Single-Channel Readout

Sensors ◽  
2021 ◽  
Vol 21 (4) ◽  
pp. 1048
Author(s):  
Muhammad Nasir Ullah ◽  
Yuseung Park ◽  
Gyeong Beom Kim ◽  
Chanho Kim ◽  
Chansun Park ◽  
...  
Keyword(s):  
Radiation Source ◽  
Analog Circuit ◽  
Single Channel ◽  
Structural Information ◽  
Gamma Probe ◽  
Water Tank ◽  
Switching Circuit ◽  
Single Output ◽  
Analog Switch ◽  
The Us

We propose an integrated front-end data acquisition circuit for a hybrid ultrasound (US)-gamma probe. The proposed circuit consists of three main parts: (1) a preamplifier for the gamma probe, (2) a preprocessing analog circuit for the US, and (3) a digitally controlled analog switch. By exploiting the long idle time of the US system, an analog switch can be used to acquire data of both systems using a single output channel simultaneously. On the nuclear medicine (NM) gamma probe side, energy resolutions of 18.4% and 17.5% were acquired with the standalone system and with the proposed switching circuit, respectively, when irradiated with a Co-57 radiation source. Similarly, signal-to-noise ratios of 14.89 and 13.12 dB were achieved when US echo signals were acquired with the standalone system and with the proposed switching circuit, respectively. Lastly, a combined US-gamma probe was used to scan a glass target and a sealed radiation source placed in a water tank. The results confirmed that, by using a hybrid US-gamma probe system, it is possible to distinguish between the two objects and acquire structural information (ultrasound) alongside molecular information (gamma radiation source).

ATP-activated chloride channel inhibited by an antibody to P glycoprotein

1994 ◽  
Vol 267 (4) ◽  
pp. C1095-C1102 ◽  
Author(s):  
J. J. Zhang ◽  
T. J. Jacob
Keyword(s):  
Single Channel ◽  
Disulfonic Acid ◽  
Fiber Cells ◽  
Cl Channel ◽  
P Glycoprotein ◽  
Voltage Curve ◽  
Current Voltage ◽  
Single Channel Activity ◽  
Current Voltage Curve

In this report, we present the characteristics of a Cl- channel found in lens fiber cells. The single channel has a conductance of 17 pS, a linear current-voltage curve, is activated by ATP or strong depolarization and is blocked by verapamil, quinidine, 4,4'-diisothiocyanostilbene-2,2'-disulfonic acid, 5-nitro-2-(3- phenylpropylamino)benzoate, dideoxyforskolin, and tamoxifen. These properties are similar to those reported for a volume-activated Cl- channel associated with the multidrug resistance (MDR) gene product, P glycoprotein (24). Confirming this connection, we demonstrate that our lens Cl- channel is inhibited by an antibody to P glycoprotein. The data we present here may, therefore, be the first characterization of the single channel activity of the Cl- channel associated with P glycoprotein.

Divalent cations block the cyclic nucleotide-gated channel of olfactory receptor neurons

1993 ◽  
Vol 69 (5) ◽  
pp. 1758-1768 ◽  
Author(s):  
F. Zufall ◽  
S. Firestein
Keyword(s):  
Cyclic Amp ◽  
Calcium Channels ◽  
Cyclic Nucleotide ◽  
Olfactory Receptor ◽  
Single Channel ◽  
Divalent Cations ◽  
Olfactory Receptor Neurons ◽  
Gated Channel ◽  
Receptor Neurons ◽  
Single Channel Currents

1. The effects of external divalent cations on odor-dependent, cyclic AMP-activated single-channel currents from olfactory receptor neurons of the tiger salamander (Ambystoma tigrinum) were studied in inside-out membrane patches taken from dendritic regions of freshly isolated sensory cells. 2. Channels were reversibly activated by 100 microM cyclic AMP. In the absence of divalent cations, the channel had a linear current-voltage relation giving a conductance of 45 pS. With increasing concentrations of either Ca2+ or Mg2+ in the external solution, the channel displayed a rapid flickering behavior. At higher concentrations of divalent cations, the transitions were too rapid to be fully resolved and appeared as a reduction in mean unitary single-channel current amplitude. 3. This effect was voltage dependent, and on analysis was shown to be due to an open channel block by divalent ions. In the case of Mg2+, the block increased steadily with hyperpolarization. In contrast, for Ca2+ the block first increased with hyperpolarization and then decreased with further hyperpolarization beyond -70 mV, providing evidence for Ca2+ permeation of this channel. 4. This block is similar to that seen in voltage-gated calcium channels. Additionally, the cyclic nucleotide-gated channel shows some pharmacological similarities with L-type calcium channels, including a novel block of the cyclic nucleotide channel by nifedipine (50 microM). 5. Our results indicate that the sensory generator current simultaneously depends on the presence of the second messenger and on the membrane potential of the olfactory neuron.

scholarly journals Structural basis of substrate recognition and translocation by human ABCD1

2021 ◽  
Author(s):  
Zhipeng Chen ◽  
Da Xu ◽  
Liang Wang ◽  
Cong-Zhao Zhou ◽  
Wen-Tao Hou ◽  
...  
Keyword(s):  
Genetic Disorder ◽  
Substrate Recognition ◽  
Acyl Chain ◽  
Chain Fatty Acid ◽  
Structural Basis ◽  
Long Chain Fatty Acid ◽  
Lateral Entry ◽  
Binding Domains ◽  
Acyl Chains ◽  
Functional States

Human ATP-binding cassette (ABC) subfamily D transporter ABCD1 can transport CoA esters of saturated/monounsaturated long/very long chain fatty acid into the peroxisome for β-oxidation. Dysfunction of human ABCD1 causes X-linked adrenoleukodystrophy, which is a severe progressive genetic disorder affecting the nervous system. Nevertheless, the mechanistic details of substrate recognition and translocation by ABCD1 remains obscure. Here, we present three cryo-EM structures of human ABCD1 in distinct functional states. In the apo-form structure of 3.53 Å resolution, ABCD1 exhibits an inward-facing conformation, allowing the lateral entry of substrate from the lipid bilayer. In the 3.59 Å structure of substrate-bound ABCD1, two molecules of C22:0-CoA, the physiological substrate of ABCD1, is symmetrically bound in two transmembrane domains (TMDs). Each C22:0-CoA adopts a L-shape, with its CoA portion and acyl chain components bound to two TMDs respectively, resembling a pair of strings that pull the TMDs closer, resultantly generating a narrower outward-facing conformation. In the 2.79 Å ATP-bound ABCD1 structure, the two nucleotide-binding domains dimerize, leading to an outward-facing conformation, which opens the translocation cavity exit towards the peroxisome matrix side and releases the substrates. Our study provides a molecular basis to understand the mechanism of ABCD1-mediated substrate recognition and translocation, and suggests a unique binding pattern for amphipathic molecules with long acyl chains.

scholarly journals Structure insights of the human peroxisomal ABC transporter ALDP

2021 ◽  
Author(s):  
Yutian Jia ◽  
Yanming Zhang ◽  
Jianlin Lei ◽  
Guanghui Yang
Keyword(s):  
Structural Information ◽  
Free State ◽  
Head Group ◽  
Working Mechanism ◽  
Peroxisomal Membrane ◽  
Binding Domains ◽  
Cryo Electron Microscopy ◽  
Ligand Free ◽  
Clinical Description

Adrenoleukodystrophy protein (ALDP) is responsible for the transport of free very-long-chain fatty acids (VLCFAs) and corresponding CoA-esters across the peroxisomal membrane. ALDP belongs to the ATP-binding cassette sub-family D, which is also named as ABCD1. Dysfunction of ALDP leads to peroxisomal metabolic disorder exemplified by X-linked adrenoleukodystrophy (ALD). Hundreds of ALD-causing mutations are identified on ALDP. However, the pathogenic mechanisms of these mutations are restricted to clinical description due to limited structural information. Furthermore, ALDP plays a role in myelin maintenance, which is tightly associated with axon regeneration. Here we report the cryo-electron microscopy (cryo-EM) structure of human ALDP with nominal resolution of 3.4 angstrom in nucleotide free state. The structure of ALDP exhibits a typical assembly of ABC transporters. The nucleotide binding domains (NBDs) displays a ligand free state. ALDP exhibits an inward-open conformation to the cytosol. A short helix is located at the peroxisomal side, which is different from other three members of ABCD transporters. The two transmembrane domains (TMDs) of ALDP form a cavity, in which two lipid-like densities can be recognized as the head group of an coenzyme-A ester of a lipid. This structure provides a framework for understanding the working mechanism of ALDP and classification of the disease-causing mutations.

scholarly journals A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit

2020 ◽  
Author(s):  
Andreas Schedlbauer ◽  
Idoia Iturrioz ◽  
Borja Ochoa-Lizarralde ◽  
Tammo Diercks ◽  
Jorge Pedro López-Alonso ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Structural Information ◽  
Ribosomal Subunit ◽  
Ribosome Assembly ◽  
Structural Description ◽  
Sequential Order ◽  
Bacterial Ribosome ◽  
Core Set ◽  
Assembly Factors ◽  
Conformational Landscape

While a structural description of the molecular mechanisms guiding ribosome assembly in eukaryotic systems is emerging, bacteria employ an unrelated core set of assembly factors for which high-resolution structural information is still missing. To address this, we used single-particle cryo-EM to visualize the effects of bacterial ribosome assembly factors RimP, RbfA, RsmA, and RsgA on the conformational landscape of the 30S ribosomal subunit and obtained eight snapshots representing late steps in the folding of the decoding center. Analysis of these structures identifies a conserved secondary structure switch in the 16S rRNA central to decoding site maturation, and suggests both a sequential order of action and molecular mechanisms for the assembly factors in coordinating and controlling this switch. Structural and mechanistic parallels between bacterial and eukaryotic systems indicate common folding features inherent to all ribosomes.

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