scholarly journals Cryo-EM Structure of Mechanosensitive Channel YnaI Using SMA2000: Challenges and Opportunities

Membranes ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 849
Author(s):  
Claudio Catalano ◽  
Danya Ben-Hail ◽  
Weihua Qiu ◽  
Paul Blount ◽  
Amedee des Georges ◽  
...  
Keyword(s):  
Cell Membrane ◽  
Structural Biology ◽  
Transmembrane Domain ◽  
Membrane Lipids ◽  
Structural Information ◽  
Mechanosensitive Channels ◽  
Native Cell ◽  
Challenges And Opportunities ◽  
Nonspecific Interactions ◽  
Lipid Environment

Mechanosensitive channels respond to mechanical forces exerted on the cell membrane and play vital roles in regulating the chemical equilibrium within cells and their environment. High-resolution structural information is required to understand the gating mechanisms of mechanosensitive channels. Protein-lipid interactions are essential for the structural and functional integrity of mechanosensitive channels, but detergents cannot maintain the crucial native lipid environment for purified mechanosensitive channels. Recently, detergent-free systems have emerged as alternatives for membrane protein structural biology. This report shows that while membrane-active polymer, SMA2000, could retain some native cell membrane lipids on the transmembrane domain of the mechanosensitive-like YnaI channel, the complete structure of the transmembrane domain of YnaI was not resolved. This reveals a significant limitation of SMA2000 or similar membrane-active copolymers. This limitation may come from the heterogeneity of the polymers and nonspecific interactions between the polymers and the relatively large hydrophobic pockets within the transmembrane domain of YnaI. However, this limitation offers development opportunities for detergent-free technology for challenging membrane proteins.

scholarly journals Detergent-free systems for structural studies of membrane proteins

2021 ◽  
Author(s):  
Youzhong Guo
Keyword(s):  
High Resolution ◽  
Membrane Proteins ◽  
Cell Membrane ◽  
Membrane Protein ◽  
Structural Biology ◽  
Membrane Lipids ◽  
Native Cell ◽  
Lipid Particles ◽  
High Resolution Structure ◽  
Resolution Structure

Membrane proteins play vital roles in living organisms, serving as targets for most currently prescribed drugs. Membrane protein structural biology aims to provide accurate structural information to understand their mechanisms of action. The advance of membrane protein structural biology has primarily relied on detergent-based methods over the past several decades. However, detergent-based approaches have significant drawbacks because detergents often damage the native protein–lipid interactions, which are often crucial for maintaining the natural structure and function of membrane proteins. Detergent-free methods recently have emerged as alternatives with a great promise, e.g. for high-resolution structure determinations of membrane proteins in their native cell membrane lipid environments. This minireview critically examines the current status of detergent-free methods by a comparative analysis of five groups of membrane protein structures determined using detergent-free and detergent-based methods. This analysis reveals that current detergent-free systems, such as the styrene-maleic acid lipid particles (SMALP), the diisobutyl maleic acid lipid particles (DIBMALP), and the cycloalkane-modified amphiphile polymer (CyclAPol) technologies are not better than detergent-based approaches in terms of maintenance of native cell membrane lipids on the transmembrane domain and high-resolution structure determination. However, another detergent-free technology, the native cell membrane nanoparticles (NCMN) system, demonstrated improved maintenance of native cell membrane lipids with the studied membrane proteins, and produced particles that were suitable for high-resolution structural analysis. The ongoing development of new membrane-active polymers and their optimization will facilitate the maturation of these new detergent-free systems.

scholarly journals Active Participation of Membrane Lipids in Inhibition of Multidrug Transporter P-Glycoprotein

2020 ◽  
Author(s):  
Karan Kapoor ◽  
Shashank Pant ◽  
Emad Tajkhorshid
Keyword(s):  
Conformational Changes ◽  
Bound States ◽  
Transmembrane Domain ◽  
Membrane Lipids ◽  
Conformational Dynamics ◽  
Drug Binding ◽  
Multi Drug Resistance ◽  
Third Generation ◽  
P Glycoprotein ◽  
Lipid Environment

AbstractP-glycoprotein (Pgp) is a major efflux pump in humans, overexpressed in a variety of cancers and associated with the development of multi-drug resistance. Allosteric modulation induced by binding of various ligands (e.g., transport substrates, inhibitors, and ATP) has been bio-chemically shown to directly influence the function of Pgp. However, the molecular details of such effects are not well established. In particular, the role and involvement of the surrounding lipid environment on ligand-induced modulation of the conformational dynamics of the transporter have not been investigated at any level. Here, we employ all-atom molecular dynamics (MD) simulations to study the conformational landscape of Pgp in the presence of a high-affinity, third-generation inhibitor, tariquidar, in comparison to the nucleotide-free (APO) and the ATP-bound states, in order to shed light on and to characterize how the inhibitor blocks the function of the transporter. Simulations in a multi-component lipid bilayer show a dynamic equilibrium between open and closed inward-facing (IF) conformations in the APO-state, with binding of ATP shifting the equilibrium towards conformations feasible for ATP hydrolysis and subsequent completion of the transport cycle. In the presence of the inhibitor bound to the drug-binding pocket in the transmembrane domain (TMD), the transporter samples more open IF conformations, and the nucleotide binding domains (NBDs) are observed to become highly dynamic. Interestingly, and reproduced in multiple independent simulations, the inhibitor is observed to recruit lipid molecules into the Pgp lumen through the two proposed drug-entry portals, where the lipid head groups from the lower leaflet translocate inside the TMD, while the lipids tails remain extended into the bulk lipid environment. These “wedge-lipid” molecules likely enhance the inhibitor-induced conformational changes in the TMD leading to the differential modulation of coupling pathways observed with the NBDs downstream. We suggest a novel inhibitory mechanism for tariquidar, and for related third-generation Pgp inhibitors, where lipids are seen to enhance the inhibitory role in the catalytic cycle of membrane transporters.

Interaction of Different Extracts ofPrimula heterochromaStapf. with Red Blood Cell Membrane Lipids and Proteins: Antioxidant and Antihemolytic Effects

2012 ◽  
Vol 9 (4) ◽  
pp. 285-292 ◽  
Author(s):  
Seyed Mohammad Nabavi ◽  
Seyed Fazel Nabavi ◽  
William N. Setzer ◽  
Heshmatollah Alinezhad ◽  
Mahboobeh Zare ◽  
...  
Keyword(s):  
Cell Membrane ◽  
Blood Cell ◽  
Red Blood Cell ◽  
Membrane Lipids ◽  
Red Blood Cell Membrane

scholarly journals Applications of molecular replacement to G protein-coupled receptors

2013 ◽  
Vol 69 (11) ◽  
pp. 2287-2292 ◽  
Author(s):  
Andrew C. Kruse ◽  
Aashish Manglik ◽  
Brian K. Kobilka ◽  
William I. Weis
Keyword(s):  
G Protein ◽  
Structural Biology ◽  
Structural Information ◽  
G Protein Coupled Receptors ◽  
Integral Membrane Proteins ◽  
Molecular Replacement ◽  
Gpcr Activation ◽  
Health And Disease ◽  
Almost All ◽  
G Protein Coupled

G protein-coupled receptors (GPCRs) are a large class of integral membrane proteins involved in regulating virtually every aspect of human physiology. Despite their profound importance in human health and disease, structural information regarding GPCRs has been extremely limited until recently. With the advent of a variety of new biochemical and crystallographic techniques, the structural biology of GPCRs has advanced rapidly, offering key molecular insights into GPCR activation and signal transduction. To date, almost all GPCR structures have been solved using molecular-replacement techniques. Here, the unique aspects of molecular replacement as applied to individual GPCRs and to signaling complexes of these important proteins are discussed.

scholarly journals Insights into the Mode of Action of Chitosan as an Antibacterial Compound

2008 ◽  
Vol 74 (12) ◽  
pp. 3764-3773 ◽  
Author(s):  
Dina Raafat ◽  
Kristine von Bargen ◽  
Albert Haas ◽  
Hans-Georg Sahl
Keyword(s):  
Antimicrobial Activity ◽  
Cell Wall ◽  
Cell Membrane ◽  
Mode Of Action ◽  
Membrane Lipids ◽  
Expression Profiles ◽  
Transcriptional Response ◽  
Response Analysis ◽  
Sequence Of Events ◽  
Wide Range

ABSTRACT Chitosan is a polysaccharide biopolymer that combines a unique set of versatile physicochemical and biological characteristics which allow for a wide range of applications. Although its antimicrobial activity is well documented, its mode of action has hitherto remained only vaguely defined. In this work we investigated the antimicrobial mode of action of chitosan using a combination of approaches, including in vitro assays, killing kinetics, cellular leakage measurements, membrane potential estimations, and electron microscopy, in addition to transcriptional response analysis. Chitosan, whose antimicrobial activity was influenced by several factors, exhibited a dose-dependent growth-inhibitory effect. A simultaneous permeabilization of the cell membrane to small cellular components, coupled to a significant membrane depolarization, was detected. A concomitant interference with cell wall biosynthesis was not observed. Chitosan treatment of Staphylococcus simulans 22 cells did not give rise to cell wall lysis; the cell membrane also remained intact. Analysis of transcriptional response data revealed that chitosan treatment leads to multiple changes in the expression profiles of Staphylococcus aureus SG511 genes involved in the regulation of stress and autolysis, as well as genes associated with energy metabolism. Finally, a possible mechanism for chitosan's activity is postulated. Although we contend that there might not be a single classical target that would explain chitosan's antimicrobial action, we speculate that binding of chitosan to teichoic acids, coupled with a potential extraction of membrane lipids (predominantly lipoteichoic acid) results in a sequence of events, ultimately leading to bacterial death.

scholarly journals Structural basis of control of inward rectifier Kir2 channel gating by bulk anionic phospholipids

2016 ◽  
Vol 148 (3) ◽  
pp. 227-237 ◽  
Author(s):  
Sun-Joo Lee ◽  
Feifei Ren ◽  
Eva-Maria Zangerl-Plessl ◽  
Sarah Heyman ◽  
Anna Stary-Weinzinger ◽  
...  
Keyword(s):  
Transmembrane Domain ◽  
Membrane Lipids ◽  
Inward Rectifier ◽  
Primary Site ◽  
Structural Basis ◽  
Channel Activity ◽  
Anionic Phospholipid ◽  
X Ray ◽  
Anionic Phospholipids ◽  
Kir Channel

Inward rectifier potassium (Kir) channel activity is controlled by plasma membrane lipids. Phosphatidylinositol-4,5-bisphosphate (PIP2) binding to a primary site is required for opening of classic inward rectifier Kir2.1 and Kir2.2 channels, but interaction of bulk anionic phospholipid (PL−) with a distinct second site is required for high PIP2 sensitivity. Here we show that introduction of a lipid-partitioning tryptophan at the second site (K62W) generates high PIP2 sensitivity, even in the absence of PL−. Furthermore, high-resolution x-ray crystal structures of Kir2.2[K62W], with or without added PIP2 (2.8- and 2.0-Å resolution, respectively), reveal tight tethering of the C-terminal domain (CTD) to the transmembrane domain (TMD) in each condition. Our results suggest a refined model for phospholipid gating in which PL− binding at the second site pulls the CTD toward the membrane, inducing the formation of the high-affinity primary PIP2 site and explaining the positive allostery between PL− binding and PIP2 sensitivity.

Effect of herbicides on plant cell membrane lipids

1979 ◽  
pp. 45-76 ◽  
Author(s):  
C. M. Rivera ◽  
Donald Penner
Keyword(s):  
Cell Membrane ◽  
Plant Cell ◽  
Membrane Lipids

scholarly journals The transmembrane domain of the SNARE protein VAMP2 is highly sensitive to its lipid environment

2019 ◽  
Vol 1861 (3) ◽  
pp. 670-676 ◽  
Author(s):  
Zahia Fezoua-Boubegtiten ◽  
Benoit Hastoy ◽  
Pier Scotti ◽  
Alexandra Milochau ◽  
Katell Bathany ◽  
...  
Keyword(s):  
Transmembrane Domain ◽  
Snare Protein ◽  
Highly Sensitive ◽  
Lipid Environment

Different Protein-Lipid Interaction in Human Red Blood Cell Membrane of Rh Positive and Rh Negative Blood Compared with Rhnull

1981 ◽  
Vol 36 (11-12) ◽  
pp. 988-996 ◽  
Author(s):  
Dietmar Dorn-Zachertz ◽  
Guido Zimmer
Keyword(s):  
Cell Membrane ◽  
Blood Cell ◽  
Red Blood Cell ◽  
Disulfide Bonds ◽  
Membrane Lipids ◽  
Infrared Spectrometry ◽  
Red Blood Cell Membrane ◽  
Fluorescence Measurements ◽  
Upper Level ◽  
Lipid Interaction

Abstract 1-anilino-naphthalene-8 -sulfonate (ANS) fluorescence measurements have revealed that red blood cell membrane of the Rhnull type undergoes a transition at about 16 °C. In contrast, viscosity measurements of the extracted membrane lipids showed the usually observed transition at about 18 °C. Lower values of titratable sulfhydryl (SH) groups were observed in Rhnull membrane using 5,5′-dithiobis-(2-nitro-benzoic-acid) (Nbs2). In contrast, disulfide bonds in Rhnull membrane were estimated to be about 3 times the value of the controls. Spin labeling experiments using 2-(3-carboxypropyl)-4, 4 dimethyl-2-tridecyl 3-oxazolidinyl-oxyl were carried out with phospholipase A2 modified membranes. The mobile part of the spectra was significantly increased on the Rhnull membrane. In the presence of ᴅ-glucose, infrared spectrometry showed a larger reduction of the intensity of the POO-band in Rhnull membrane. In contrast to controls, binding of the reagent diethylpyrocarbonate resulted in no significant changes of the Rhnull membrane as determined by electron spin resonance (ESR) measurements. ᴅ-glucose transport activity was found to be at the upper level of a group of Rh positive and Rh negative persons. It is suggested that the intensity of the polar protein-lipid interaction is reduced in Rhnull membrane.

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