scholarly journals Predicting voltage sensing

2018 ◽  
Vol 150 (10) ◽  
pp. 1349-1349
Author(s):  
Caitlin Sedwick
Keyword(s):  
Membrane Proteins ◽  
Molecular Basis ◽  
New Method ◽  
Voltage Sensitivity ◽  
Voltage Sensing

New method predicts the molecular basis of membrane proteins’ voltage sensitivity.

scholarly journals Molecular basis for voltage sensitivity in membrane proteins

2018 ◽  
Author(s):  
Marina A. Kasimova ◽  
Erik Lindahl ◽  
Lucie Delemotte
Keyword(s):  
Membrane Potential ◽  
Ion Channels ◽  
Membrane Proteins ◽  
Voltage Sensitivity ◽  
Voltage Sensing ◽  
Suggested Approach ◽  
Voltage Gated ◽  
Living Organisms ◽  
Voltage Gated Ion Channels ◽  
Gated Ion Channels

ABSTRACTVoltage-sensitive membrane proteins are united by the ability to transform changes in the membrane potential into mechanical work. They are responsible for a spectrum of key physiological processes in living organisms, including electric signaling and progression along the cell cycle. While the voltage-sensing mechanism has been well characterized for some membrane proteins such as voltage-gated ion channels, for others even the location of the voltage-sensing elements remains unknown. The detection of these elements using experimental techniques is complicated due to the large diversity of membrane proteins. Here, we suggest a computational approach to predict voltage-sensing elements in any membrane protein independent of structure or function. It relies on the estimation of the capacity of a protein to respond to changes in the membrane potential. We first show how this property correlates well with voltage sensitivity by applying our approach to a set of membrane proteins including voltage-sensitive and voltage-insensitive ones. We further show that it correctly identifies true voltage-sensitive residues in the voltage sensor domain of voltage-gated ion channels. Finally, we investigate six membrane proteins for which the voltage-sensing elements have not yet been characterized and identify residues and ions potentially involved in the response to voltage. The suggested approach is fast and simple and allows for characterization of voltage sensitivity that goes beyond mere identification of charges. We anticipate that its application prior to mutagenesis experiments will allow for significant reduction of the number of potential voltage-sensitive elements to be tested.

scholarly journals Determining the molecular basis of voltage sensitivity in membrane proteins

2018 ◽  
Vol 150 (10) ◽  
pp. 1444-1458 ◽  
Author(s):  
Marina A. Kasimova ◽  
Erik Lindahl ◽  
Lucie Delemotte
Keyword(s):  
Membrane Potential ◽  
Ion Channels ◽  
Membrane Proteins ◽  
Cell Cycle Progression ◽  
Voltage Sensitivity ◽  
Voltage Sensing ◽  
Suggested Approach ◽  
Voltage Gated ◽  
Voltage Gated Ion Channels ◽  
Gated Ion Channels

Voltage-sensitive membrane proteins are united by their ability to transform changes in membrane potential into mechanical work. They are responsible for a spectrum of physiological processes in living organisms, including electrical signaling and cell-cycle progression. Although the mechanism of voltage-sensing has been well characterized for some membrane proteins, including voltage-gated ion channels, even the location of the voltage-sensing elements remains unknown for others. Moreover, the detection of these elements by using experimental techniques is challenging because of the diversity of membrane proteins. Here, we provide a computational approach to predict voltage-sensing elements in any membrane protein, independent of its structure or function. It relies on an estimation of the propensity of a protein to respond to changes in membrane potential. We first show that this property correlates well with voltage sensitivity by applying our approach to a set of voltage-sensitive and voltage-insensitive membrane proteins. We further show that it correctly identifies authentic voltage-sensitive residues in the voltage-sensor domain of voltage-gated ion channels. Finally, we investigate six membrane proteins for which the voltage-sensing elements have not yet been characterized and identify residues and ions that might be involved in the response to voltage. The suggested approach is fast and simple and enables a characterization of voltage sensitivity that goes beyond mere identification of charges. We anticipate that its application before mutagenesis experiments will significantly reduce the number of potential voltage-sensitive elements to be tested.

scholarly journals Two distinct voltage-sensing domains control voltage sensitivity and kinetics of current activation in CaV1.1 calcium channels

2016 ◽  
Vol 147 (6) ◽  
pp. 437-449 ◽  
Author(s):  
Petronel Tuluc ◽  
Bruno Benedetti ◽  
Pierre Coste de Bagneaux ◽  
Manfred Grabner ◽  
Bernhard E. Flucher
Keyword(s):  
Calcium Channels ◽  
Molecular Mechanisms ◽  
Voltage Dependence ◽  
Specific Interaction ◽  
Site Directed Mutagenesis ◽  
Control Voltage ◽  
Voltage Sensitivity ◽  
Voltage Sensing ◽  
Activation Kinetics ◽  
Transmembrane Segments

Alternative splicing of the skeletal muscle CaV1.1 voltage-gated calcium channel gives rise to two channel variants with very different gating properties. The currents of both channels activate slowly; however, insertion of exon 29 in the adult splice variant CaV1.1a causes an ∼30-mV right shift in the voltage dependence of activation. Existing evidence suggests that the S3–S4 linker in repeat IV (containing exon 29) regulates voltage sensitivity in this voltage-sensing domain (VSD) by modulating interactions between the adjacent transmembrane segments IVS3 and IVS4. However, activation kinetics are thought to be determined by corresponding structures in repeat I. Here, we use patch-clamp analysis of dysgenic (CaV1.1 null) myotubes reconstituted with CaV1.1 mutants and chimeras to identify the specific roles of these regions in regulating channel gating properties. Using site-directed mutagenesis, we demonstrate that the structure and/or hydrophobicity of the IVS3–S4 linker is critical for regulating voltage sensitivity in the IV VSD, but by itself cannot modulate voltage sensitivity in the I VSD. Swapping sequence domains between the I and the IV VSDs reveals that IVS4 plus the IVS3–S4 linker is sufficient to confer CaV1.1a-like voltage dependence to the I VSD and that the IS3–S4 linker plus IS4 is sufficient to transfer CaV1.1e-like voltage dependence to the IV VSD. Any mismatch of transmembrane helices S3 and S4 from the I and IV VSDs causes a right shift of voltage sensitivity, indicating that regulation of voltage sensitivity by the IVS3–S4 linker requires specific interaction of IVS4 with its corresponding IVS3 segment. In contrast, slow current kinetics are perturbed by any heterologous sequences inserted into the I VSD and cannot be transferred by moving VSD I sequences to VSD IV. Thus, CaV1.1 calcium channels are organized in a modular manner, and control of voltage sensitivity and activation kinetics is accomplished by specific molecular mechanisms within the IV and I VSDs, respectively.

scholarly journals SMA-PAGE: A new method to examine complexes of membrane proteins using SMALP nano-encapsulation and native gel electrophoresis

2019 ◽  
Vol 1861 (8) ◽  
pp. 1437-1445 ◽  
Author(s):  
Naomi L. Pollock ◽  
Megha Rai ◽  
Kailene S. Simon ◽  
Sophie J. Hesketh ◽  
Alvin C.K. Teo ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Gel Electrophoresis ◽  
New Method ◽  
Native Gel

The molecular basis of interaction domains of full-length PrP with lipid membranes

Nanoscale ◽  
2019 ◽  
Vol 11 (25) ◽  
pp. 12087-12091 ◽  
Author(s):  
Yangang Pan ◽  
Bin Wang ◽  
R. Alexander Reese ◽  
Bingqian Xu
Keyword(s):  
Molecular Modeling ◽  
Lipid Membranes ◽  
Molecular Basis ◽  
Full Length ◽  
New Method ◽  
Interaction Domains

A new method combining AFM measurements and molecular modeling was used to unravel the molecular basis of the interaction domains of full-length PrP with lipid membranes.

scholarly journals A novel microseeding method for the crystallization of membrane proteins in lipidic cubic phase

2016 ◽  
Vol 72 (4) ◽  
pp. 307-312 ◽  
Author(s):  
Stefan Andrew Kolek ◽  
Bastian Bräuning ◽  
Patrick Douglas Shaw Stewart
Keyword(s):  
Membrane Proteins ◽  
Soluble Protein ◽  
Protein Crystallization ◽  
Protein Structures ◽  
Integral Membrane Protein ◽  
Seed Stock ◽  
New Method ◽  
Cubic Phase ◽  
Seed Crystals ◽  
Order Of Magnitude

Random microseed matrix screening (rMMS), in which seed crystals are added to random crystallization screens, is an important breakthrough in soluble protein crystallization that increases the number of crystallization hits that are available for optimization. This greatly increases the number of soluble protein structures generated every year by typical structural biology laboratories. Inspired by this success, rMMS has been adapted to the crystallization of membrane proteins, making LCP seed stock by scaling up LCP crystallization conditions without changing the physical and chemical parameters that are critical for crystallization. Seed crystals are grown directly in LCP and, as with conventional rMMS, a seeding experiment is combined with an additive experiment. The new method was used with the bacterial integral membrane protein OmpF, and it was found that it increased the number of crystallization hits by almost an order of magnitude: without microseeding one new hit was found, whereas with LCP-rMMS eight new hits were found. It is anticipated that this new method will lead to better diffracting crystals of membrane proteins. A method of generating seed gradients, which allows the LCP seed stock to be diluted and the number of crystals in each LCP bolus to be reduced, if required for optimization, is also demonstrated.

A new method for rapid isolation of the intrinsic membrane proteins from lens

1981 ◽  
Vol 32 (4) ◽  
pp. 511-516 ◽  
Author(s):  
Paul Russell ◽  
W. Gerald Robison ◽  
Jin H. Kinoshita
Keyword(s):  
Membrane Proteins ◽  
New Method ◽  
Rapid Isolation

scholarly journals Interplay between MPIase, YidC, and PMF during Sec-independent insertion of membrane proteins

2021 ◽  
Vol 5 (1) ◽  
pp. e202101162
Author(s):  
Yuta Endo ◽  
Yuko Shimizu ◽  
Hanako Nishikawa ◽  
Katsuhiro Sawasato ◽  
Ken-ichi Nishiyama
Keyword(s):  
Membrane Proteins ◽  
Molecular Basis ◽  
Terminal Region ◽  
Integral Membrane Proteins ◽  
The Other ◽  
Other Hand ◽  
Model Protein

Integral membrane proteins with the N-out topology are inserted into membranes usually in YidC- and PMF-dependent manners. The molecular basis of the various dependencies on insertion factors is not fully understood. A model protein, Pf3-Lep, is inserted independently of both YidC and PMF, whereas the V15D mutant requires both YidC and PMF in vivo. We analyzed the mechanisms that determine the insertion factor dependency in vitro. Glycolipid MPIase was required for insertion of both proteins because MPIase depletion caused a significant defect in insertion. On the other hand, YidC depletion and PMF dissipation had no effects on Pf3-Lep insertion, whereas V15D insertion was reduced. We reconstituted (proteo)liposomes containing MPIase, YidC, and/or F0F1-ATPase. MPIase was essential for insertion of both proteins. YidC and PMF stimulated Pf3-Lep insertion as the synthesis level increased. V15D insertion was stimulated by both YidC and PMF irrespective of the synthesis level. These results indicate that charges in the N-terminal region and the synthesis level are the determinants of YidC and PMF dependencies with the interplay between MPIase, YidC, and PMF.

scholarly journals Structure of human sodium leak channel NALCN in complex with FAM155A

2020 ◽  
Author(s):  
Jiongfang Xie ◽  
Meng Ke ◽  
Lizhen Xu ◽  
Shiyi Lin ◽  
Jin Huang ◽  
...  
Keyword(s):  
Binding Site ◽  
Molecular Basis ◽  
Neuronal Excitability ◽  
Selectivity Filter ◽  
Ion Binding ◽  
Voltage Sensitivity ◽  
Auxiliary Subunits ◽  
Leak Channel ◽  
Extracellular Loops ◽  
Central Nervous Systems

Abstract NALCN, a sodium leak channel mainly expressed in the central nervous systems, is responsible for the resting Na+ permeability that controls neuronal excitability. Dysfunctions of the NALCN channelosome, NALCN with several auxiliary subunits, are associated with a variety of human diseases. Here, we reported the cryo-EM structure of human NALCN in complex with FAM155A, at an overall resolution of 3.1 angstrom. FAM155A forms extensive interactions with the extracellular loops of NALCN that help stabilize NALCN in the membrane. A Na+ ion-binding site, reminiscent of a Ca2+ binding site in Cav channels, is identified in the unique EEKE selectivity filter. Despite its ‘leaky’ nature, the intracellular gate is sealed by S6I, II-III linker and III-IV linker. Our study establishes the molecular basis of Na+ permeation and voltage sensitivity, and provides important clues to the mechanistic understanding of NALCN regulation and NALCN channelosome-related diseases.

scholarly journals Voltage Sensing in Bacterial Protein Translocation

Biomolecules ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 78 ◽  
Author(s):  
Denis G. Knyazev ◽  
Roland Kuttner ◽  
Ana-Nicoleta Bondar ◽  
Mirjam Zimmerman ◽  
Christine Siligan ◽  
...  
Keyword(s):  
Protein Translocation ◽  
Voltage Sensor ◽  
Voltage Sensitivity ◽  
Bacterial Protein ◽  
Voltage Sensing ◽  
Voltage Dependent ◽  
Membrane Spanning ◽  
Dipolar Orientation ◽  
Polypeptide Chains ◽  
Gating Charges

The bacterial channel SecYEG efficiently translocates both hydrophobic and hydrophilic proteins across the plasma membrane. Translocating polypeptide chains may dislodge the plug, a half helix that blocks the permeation of small molecules, from its position in the middle of the aqueous translocation channel. Instead of the plug, six isoleucines in the middle of the membrane supposedly seal the channel, by forming a gasket around the translocating polypeptide. However, this hypothesis does not explain how the tightness of the gasket may depend on membrane potential. Here, we demonstrate voltage-dependent closings of the purified and reconstituted channel in the presence of ligands, suggesting that voltage sensitivity may be conferred by motor protein SecA, ribosomes, signal peptides, and/or translocating peptides. Yet, the presence of a voltage sensor intrinsic to SecYEG was indicated by voltage driven closure of pores that were forced-open either by crosslinking the plug to SecE or by plug deletion. We tested the involvement of SecY’s half-helix 2b (TM2b) in voltage sensing, since clearly identifiable gating charges are missing. The mutation L80D accelerated voltage driven closings by reversing TM2b’s dipolar orientation. In contrast, the L80K mutation decelerated voltage induced closings by increasing TM2b’s dipole moment. The observations suggest that TM2b is part of a larger voltage sensor. By partly aligning the combined dipole of this sensor with the orientation of the membrane-spanning electric field, voltage may drive channel closure.

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