The Cell Membrane
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Bacterial Cell Membrane
BACTERIAL CELL MEMBRANE Dr. Rakesh Sharda Department of Veterinary Microbiology NDVSU College of Veterinary Sc. & A.H., MHOW CYTOPLASMIC MEMBRANE ➢The cytoplasmic membrane, also called a cell membrane or plasma membrane, is about 7 nanometers (nm; 1/1,000,000,000 m) thick. ➢It lies internal to the cell wall and encloses the cytoplasm of the bacterium. ➢It is the most dynamic structure of a prokaryotic cell. Structure of cell membrane ➢The structure of bacterial plasma membrane is that of unit membrane, i.e., a fluid phospholipid bilayer, composed of phospholipids (40%) and peripheral and integral proteins (60%) molecules. ➢The phospholipids of bacterial cell membranes do not contain sterols as in eukaryotes, but instead consist of saturated or monounsaturated fatty acids (rarely, polyunsaturated fatty acids). ➢Many bacteria contain sterol-like molecules called hopanoids. ➢The hopanoids most likely stabilize the bacterial cytoplasmic membrane. ➢The phospholipids are amphoteric molecules with a polar hydrophilic glycerol "head" attached via an ester bond to two non-polar hydrophobic fatty acid tails. ➢The phospholipid bilayer is arranged such that the polar ends of the molecules form the outermost and innermost surface of the membrane while the non-polar ends form the center of the membrane Fluid mosaic model ➢The plasma membrane contains proteins, sugars, and other lipids in addition to the phospholipids. ➢The model that describes the arrangement of these substances in lipid bilayer is called the fluid mosaic model ➢Dispersed within the bilayer are various structural and enzymatic proteins, which carry out most membrane functions. ➢Some membrane proteins are located and function on one side or another of the membrane (peripheral proteins). -
A Computational Model of Large Conductance Voltage and Calcium
Journal of Computational Neuroscience (2019) 46:233–256 https://doi.org/10.1007/s10827-019-00713-9 A computational model of large conductance voltage and calcium activated potassium channels: implications for calcium dynamics and electrophysiology in detrusor smooth muscle cells Suranjana Gupta1 · Rohit Manchanda1 Received: 11 September 2018 / Revised: 14 February 2019 / Accepted: 19 February 2019 / Published online: 25 April 2019 © Springer Science+Business Media, LLC, part of Springer Nature 2019 Abstract The large conductance voltage and calcium activated potassium (BK) channels play a crucial role in regulating the excitability of detrusor smooth muscle, which lines the wall of the urinary bladder. These channels have been widely characterized in terms of their molecular structure, pharmacology and electrophysiology. They control the repolarising and hyperpolarising phases of the action potential, thereby regulating the firing frequency and contraction profiles of the smooth muscle. Several groups have reported varied profiles of BK currents and I-V curves under similar experimental conditions. However, no single computational model has been able to reconcile these apparent discrepancies. In view of the channels’ physiological importance, it is imperative to understand their mechanistic underpinnings so that a realistic model can be created. This paper presents a computational model of the BK channel, based on the Hodgkin-Huxley formalism, constructed by utilising three activation processes — membrane potential, calcium inflow from voltage-gated calcium channels on the membrane and calcium released from the ryanodine receptors present on the sarcoplasmic reticulum. In our model, we attribute the discrepant profiles to the underlying cytosolic calcium received by the channel during its activation. The model enables us to make heuristic predictions regarding the nature of the sub-membrane calcium dynamics underlying the BK channel’s activation. -
Membrane Protein Stabilization Strategies for Structural and Functional Studies
membranes Review Membrane Protein Stabilization Strategies for Structural and Functional Studies Ekaitz Errasti-Murugarren 1,2,*, Paola Bartoccioni 1,2 and Manuel Palacín 1,2,3,* 1 Laboratory of Amino acid Transporters and Disease, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain; [email protected] 2 CIBERER (Centro Español en Red de Biomedicina de Enfermedades Raras), 28029 Barcelona, Spain 3 Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, 08028 Barcelona, Spain * Correspondence: [email protected] (E.E.-M.); [email protected] (M.P.) Abstract: Accounting for nearly two-thirds of known druggable targets, membrane proteins are highly relevant for cell physiology and pharmacology. In this regard, the structural determination of pharmacologically relevant targets would facilitate the intelligent design of new drugs. The structural biology of membrane proteins is a field experiencing significant growth as a result of the development of new strategies for structure determination. However, membrane protein preparation for structural studies continues to be a limiting step in many cases due to the inherent instability of these molecules in non-native membrane environments. This review describes the approaches that have been developed to improve membrane protein stability. Membrane protein mutagenesis, detergent selection, lipid membrane mimics, antibodies, and ligands are described in this review as approaches to facilitate the production of purified and stable membrane proteins of interest for structural and functional studies. Keywords: membrane proteins; stability; mutagenesis; detergent; lipid; antibody; nanobody; ligand Citation: Errasti-Murugarren, E.; Bartoccioni, P.; Palacín, M. Membrane Protein Stabilization Strategies for Structural and Functional Studies. -
Spring 2013 Lecture 23
CHM333 LECTURES 23: 3/25/13 SPRING 2013 Professor Christine Hrycyna LIPIDS III EFFECT OF CHOLESTEROL ON MEMBRANES: - Bulky rigid molecule - Moderates fluidity of membranes – both increases and decreases o Cholesterol in membranes DECREASES fluidity because it is rigid o Prevents crystallization (making solid) of fatty acyl side chains by fitting between them. Disrupts close packing of fatty acyl chains. Therefore, INCREASED fluidity BIOLOGICAL MEMBRANES CONTAIN PROTEINS AS WELL AS LIPIDS: - Proteins are 20-80% of cell membrane - Rest is lipid or carbohydrate; supramolecular assembly of lipid, protein and carbohydrate - Proteins are also distributed asymmetrically - TWO classes of Membrane Proteins: o Integral Membrane Proteins o Peripheral Membrane Proteins 178 CHM333 LECTURES 23: 3/25/13 SPRING 2013 Professor Christine Hrycyna - INTEGRAL MEMBRANE PROTEINS o Located WITHIN the lipid bilayer o Usually span the bilayer one or more times – called transmembrane (TM) proteins o Hydrophobic amino acids interact with fatty acid chains in the hydrophobic core of the membrane o Can be removed from the membrane with detergents like SDS – need to disrupt the hydrophobic interactions § Membrane Disruption Animation: o http://www.youtube.com/watch?v=AHT37pvcjc0 o Function: § Transporters – moving molecules into or out of cells or cell membranes § Receptors – transmitting signals from outside of the cell to the inside - β Barrel Integral Membrane Proteins § Barrel-shaped membrane protein that is made up of antiparallel β-strands with hydrophilic (interior) and hydrophobic (facing lipid tails). § So far found only in outer membranes of Gram-negative bacteria, cell wall of Gram-positive bacteria, and outer membranes of mitochondria and chloroplasts. 179 CHM333 LECTURES 23: 3/25/13 SPRING 2013 Professor Christine Hrycyna - α-Helical Membrane Proteins - Can cross the membrane once or many times and have multiple transmembrane segments. -
Snapshot: ER-Associated Protein Degradation Pathways Shinichi Kawaguchi and Davis T.W
SnapShot: ER-Associated Protein Degradation Pathways Shinichi Kawaguchi and Davis T.W. Ng Temasek Life Sciences Laboratory and Department of Biological Sciences, National University of Singapore, Singapore 117604 1230 Cell 129, June 15, 2007 ©2007 Elsevier Inc. DOI 10.1016/j.cell.2007.06.005 See online version for legend and references. SnapShot: ER-Associated Protein Degradation Pathways Shinichi Kawaguchi and Davis T.W. Ng Temasek Life Sciences Laboratory and Department of Biological Sciences, National University of Singapore, Singapore 117604 Arrows specify the routes of individual pathways. All pathways culminate in substrate degradation by the 26S proteasome. (Left) ERAD Pathways in Budding Yeast (A) Newly synthesized secretory and membrane proteins enter the ER through the Sec61 protein-conducting channel complex unfolded. Hsp70-related molecular chaperones (Kar2p) bind to nascent polypeptides in the ER lumen and to the cytosolic domains of membrane proteins (Hsp70, B). These factors assist in substrate folding and also assist in their disposal if they fail to fold. Mannose residues on misfolded glycoproteins are trimmed by the ER mannosidase Mns1p (E). Mannose trimming facilitates the recognition of misfolded glycoproteins by luminally oriented lectin factors Htm1p and Yos9p. (C, D, and F) At least two ER membrane-localized E3 ubiquitin ligases organize protein complexes that receive and process misfolded proteins. These complexes define three pathways that recognize lesions in the cytosolic (ERAD-C), transmembrane (ERAD-M), and luminal (ERAD-L) domains of substrates. Both ERAD-M and ERAD-L use the Hrd1 ubiquitin ligase but the luminal factor Yos9p is dispensable for ERAD-M. A Hrd1 complex lacking Yos9p has been observed suggesting dedicated complexes for all three pathways. -
Membrane Structure Overview Pathology > Cellular Biology & Genetics > Cellular Biology & Genetics
Membrane Structure Overview Pathology > Cellular Biology & Genetics > Cellular Biology & Genetics PLASMA MEMBRANE • Phospholipid bilayer: bilayer that comprises mostly phospholipids • Fluid mosaic: mosaic of proteins embedded within a fluid phospholipid bilayer • Selectively permeable: some substances move through passively, others use proteins for transport MEMBRANE COMPONENTS • Phospholipids • Proteins • Cholesterol • Carbohydrates PHOSPHOLIPIDS • Amphipathic: hydrophilic head and hydrophobic fatty acid tails • Form liposomes in aqueous environment • Weak hydrophobic interactions = membrane fluidity • Saturated phospholipids: maximize hydrogens in fatty acid tails, no kinks • Unsaturated phospholipids: double bond produces kink, increases fluidity CHOLESTEROL • Temperature buffer • Moderate temperature: decreases fluidity, lessens lateral movement • Low temperature: increases fluidity, prevents solidification PROTEINS • Includes transmembrane proteins that span the bilayer (other types exist) • Proteins provide about half the mass of the membrane CARBOHYDRATES • Glycoproteins: branched carbohydrates covalently bound to proteins • Glycolipids: carbohydrates covalently bound to lipids (extracellular only) 1 / 5 CLINICAL CORRELATION: Blood types • Carbohydrates on surface of red blood cells must be compatible between donor & recipient in blood transfusion FUNCTIONS OF THE CELL MEMBRANE • Cell communication • Import and export of molecules • Cell growth • Cell motility Eukaryotes have internal membranes within the cell, prokaryotes do not. -
Nuclear Ubiquitin-Proteasome Pathways in Proteostasis Maintenance
biomolecules Review Nuclear Ubiquitin-Proteasome Pathways in Proteostasis Maintenance Dina Frani´c †, Klara Zubˇci´c † and Mirta Boban * Croatian Institute for Brain Research, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; [email protected] (D.F.); [email protected] (K.Z.) * Correspondence: [email protected] † Equal contribution. Abstract: Protein homeostasis, or proteostasis, is crucial for the functioning of a cell, as proteins that are mislocalized, present in excessive amounts, or aberrant due to misfolding or other type of damage can be harmful. Proteostasis includes attaining the correct protein structure, localization, and the for- mation of higher order complexes, and well as the appropriate protein concentrations. Consequences of proteostasis imbalance are evident in a range of neurodegenerative diseases characterized by protein misfolding and aggregation, such as Alzheimer’s, Parkinson’s, and amyotrophic lateral sclerosis. To protect the cell from the accumulation of aberrant proteins, a network of protein quality control (PQC) pathways identifies the substrates and direct them towards refolding or elimination via regulated protein degradation. The main pathway for degradation of misfolded proteins is the ubiquitin-proteasome system. PQC pathways have been first described in the cytoplasm and the endoplasmic reticulum, however, accumulating evidence indicates that the nucleus is an important PQC compartment for ubiquitination and proteasomal degradation of not only nuclear, but also cyto- plasmic proteins. In this review, we summarize the nuclear ubiquitin-proteasome pathways involved in proteostasis maintenance in yeast, focusing on inner nuclear membrane-associated degradation (INMAD) and San1-mediated protein quality control. Keywords: proteasome; ubiquitin; nucleus; inner nuclear membrane; yeast; proteostasis; protein quality control; protein misfolding Citation: Frani´c,D.; Zubˇci´c,K.; Boban, M. -
Construction and Loss of Bacterial Flagellar Filaments
biomolecules Review Construction and Loss of Bacterial Flagellar Filaments Xiang-Yu Zhuang and Chien-Jung Lo * Department of Physics and Graduate Institute of Biophysics, National Central University, Taoyuan City 32001, Taiwan; [email protected] * Correspondence: [email protected] Received: 31 July 2020; Accepted: 4 November 2020; Published: 9 November 2020 Abstract: The bacterial flagellar filament is an extracellular tubular protein structure that acts as a propeller for bacterial swimming motility. It is connected to the membrane-anchored rotary bacterial flagellar motor through a short hook. The bacterial flagellar filament consists of approximately 20,000 flagellins and can be several micrometers long. In this article, we reviewed the experimental works and models of flagellar filament construction and the recent findings of flagellar filament ejection during the cell cycle. The length-dependent decay of flagellar filament growth data supports the injection-diffusion model. The decay of flagellar growth rate is due to reduced transportation of long-distance diffusion and jamming. However, the filament is not a permeant structure. Several bacterial species actively abandon their flagella under starvation. Flagellum is disassembled when the rod is broken, resulting in an ejection of the filament with a partial rod and hook. The inner membrane component is then diffused on the membrane before further breakdown. These new findings open a new field of bacterial macro-molecule assembly, disassembly, and signal transduction. Keywords: self-assembly; injection-diffusion model; flagellar ejection 1. Introduction Since Antonie van Leeuwenhoek observed animalcules by using his single-lens microscope in the 18th century, we have entered a new era of microbiology. -
Predicting Protein-Membrane Interfaces of Peripheral Membrane
bioRxiv preprint doi: https://doi.org/10.1101/2021.06.28.450157; this version posted June 29, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Predicting protein-membrane interfaces of pe- ripheral membrane proteins using ensemble machine learning Alexios Chatzigoulas1,2,* and Zoe Cournia1,* 1Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece, 2Depart- ment of Informatics and Telecommunications, National and Kapodistrian University of Athens, 15784 Athens, Greece *To whom correspondence should be addressed. Abstract Motivation: Abnormal protein-membrane attachment is involved in deregulated cellular pathways and in disease. Therefore, the possibility to modulate protein-membrane interactions represents a new promising therapeutic strategy for peripheral membrane proteins that have been considered so far undruggable. A major obstacle in this drug design strategy is that the membrane binding domains of peripheral membrane proteins are usually not known. The development of fast and efficient algorithms predicting the protein-membrane interface would shed light into the accessibility of membrane-protein interfaces by drug-like molecules. Results: Herein, we describe an ensemble machine learning methodology and algorithm for predicting membrane-penetrating residues. We utilize available experimental data in the literature for training 21 machine learning classifiers and a voting classifier. Evaluation of the ensemble classifier accuracy pro- duced a macro-averaged F1 score = 0.92 and an MCC = 0.84 for predicting correctly membrane-pen- etrating residues on unknown proteins of an independent test set. -
Entropy-Based Regulation of Cluster Ion Channel Density
www.nature.com/scientificreports OPEN Molecular and cellular correlates in Kv channel clustering: entropy‑based regulation of cluster ion channel density Limor Lewin1, Esraa Nsasra1, Ella Golbary1, Uzi Hadad2, Irit Orr1 & Ofer Yifrach1* Scafold protein-mediated ion channel clustering at unique membrane sites is important for electrical signaling. Yet, the mechanism(s) by which scafold protein-ion channel interactions lead to channel clustering or how cluster ion channel density is regulated is mostly not known. The voltage‑activated potassium channel (Kv) represents an excellent model to address these questions as the mechanism underlying its interaction with the post-synaptic density 95 (PSD-95) scafold protein is known to be controlled by the length of the extended ‘ball and chain’ sequence comprising the C-terminal channel region. Here, using sub-difraction high-resolution imaging microscopy, we show that Kv channel ‘chain’ length regulates Kv channel density with a ‘bell’-shaped dependence, refecting a balance between thermodynamic considerations controlling ‘chain’ recruitment by PSD-95 and steric hindrance due to the spatial proximity of multiple channel molecules. Our results thus reveal an entropy‑based mode of channel cluster density regulation that mirrors the entropy‑based regulation of the Kv channel-PSD-95 interaction. The implications of these fndings for electrical signaling are discussed. Action potential generation, propagation and the evoked synaptic potential all rely on precisely timed events associated with activation and inactivation gating transitions of voltage-dependent Na + and K + channels, clus- tered in multiple copies at unique membrane sites, such as the initial segment of an axon, nodes of Ranvier, pre-synaptic terminals or at the post-synaptic density (PSD)1–3. -
An Overview of Lipid Membrane Models for Biophysical Studies
biomimetics Review Mimicking the Mammalian Plasma Membrane: An Overview of Lipid Membrane Models for Biophysical Studies Alessandra Luchini 1 and Giuseppe Vitiello 2,3,* 1 Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark; [email protected] 2 Department of Chemical, Materials and Production Engineering, University of Naples Federico II, Piazzale Tecchio 80, 80125 Naples, Italy 3 CSGI-Center for Colloid and Surface Science, via della Lastruccia 3, 50019 Sesto Fiorentino (Florence), Italy * Correspondence: [email protected] Abstract: Cell membranes are very complex biological systems including a large variety of lipids and proteins. Therefore, they are difficult to extract and directly investigate with biophysical methods. For many decades, the characterization of simpler biomimetic lipid membranes, which contain only a few lipid species, provided important physico-chemical information on the most abundant lipid species in cell membranes. These studies described physical and chemical properties that are most likely similar to those of real cell membranes. Indeed, biomimetic lipid membranes can be easily prepared in the lab and are compatible with multiple biophysical techniques. Lipid phase transitions, the bilayer structure, the impact of cholesterol on the structure and dynamics of lipid bilayers, and the selective recognition of target lipids by proteins, peptides, and drugs are all examples of the detailed information about cell membranes obtained by the investigation of biomimetic lipid membranes. This review focuses specifically on the advances that were achieved during the last decade in the field of biomimetic lipid membranes mimicking the mammalian plasma membrane. In particular, we provide a description of the most common types of lipid membrane models used for biophysical characterization, i.e., lipid membranes in solution and on surfaces, as well as recent examples of their Citation: Luchini, A.; Vitiello, G. -
Membrane Fluidity and the Perception of Environmental Signals In
Progress in Lipid Research 42 (2003) 527–543 www.elsevier.com/locate/plipres Review Membrane fluidity and the perception of environmental signals in cyanobacteria and plants Koji Mikami, Norio Murata* Department of Regulation Biology, National Institute for Basic Biology, Okazaki 444-8585, Japan Accepted 22 April 2003 Abstract Photosynthetic organisms, namely, plants and cyanobacteria, are directly exposed to changes in their environment and their survival depends on their ability to acclimate to such changes. Several lines of evi- dence suggest that temperature stress, such as unusually low or high temperatures, and osmotic stress might be perceived by plants and cyanobacteria via changes in the fluidity of their cell membranes. The availability of techniques for gene-targeted mutagenesis and gene transfer, as well as for the analysis of genomes and transcripts, has allowed us to examine and evaluate this hypothesis and its implications. In this review, we summarize recent studies of the regulation of gene expression by changes in the extent of unsaturation of fatty acids and membrane fluidity, and we present a discussion of the induction of gene expression by environmental stress and of sensors of environmental conditions and relationships between their activity and the fluidity of membranes in cyanobacteria and plants. # 2003 Elsevier Ltd. All rights reserved. Contents 1. Introduction ..........................................................................................................................................................