Fluid Lipid Membranes – a Primer
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Curvature Increases Permeability of the Plasma Membrane For
bioRxiv preprint doi: https://doi.org/10.1101/602177; this version posted April 8, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Curvature increases permeability of the plasma membrane for ions, water and the anti-cancer drugs cisplatin and gemcitabine Semen Yesylevskyy 1,2*, Timothée Rivel 1, Christophe Ramseyer 1 1 Laboratoire Chrono Environnement UMR CNRS 6249, Université de Bourgogne Franche- Comté, 16 route de Gray, 25030 Besançon Cedex, France. 2 Department of Physics of Biological Systems, Institute of Physics of the National Academy of Sciences of Ukraine, Prospect Nauky 46, 03028 Kyiv, Ukraine. Corresponding Author * [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/602177; this version posted April 8, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. ABSTARCT In this work the permeability of a model asymmetric plasma membrane, for ions, water and the anti-cancer drugs cisplatin and gemcitabine is studied by means of all-atom molecular dynamics simulations. It is shown that permeability of the membranes increases from one to three orders of magnitude upon membrane bending depending on the compound and the sign of curvature. Our results show that the membrane curvature is an important factor which should be considered during evaluation of drug translocation. TOC GRAPHICS KEYWORDS Membrane curvature, membrane permeability, molecular dynamics, plasma membrane, cisplatin, gemcitabine. 2 bioRxiv preprint doi: https://doi.org/10.1101/602177; this version posted April 8, 2019. -
Modelling of Red Blood Cell Morphological and Deformability Changes During In-Vitro Storage
applied sciences Article Modelling of Red Blood Cell Morphological and Deformability Changes during In-Vitro Storage Nadeeshani Geekiyanage 1 , Emilie Sauret 1,*, Suvash Saha 2 , Robert Flower 3 and YuanTong Gu 1 1 School of Mechanical, Medical and Process Engineering, Science and Engineering Faculty, Queensland University of Technology (QUT), Brisbane City, QLD 4000, Australia; [email protected] (N.G.); [email protected] (Y.G.) 2 School of Mechanical and Mechatronic Engineering, University of Technology Sydney (UTS), Ultimo, NSW 2007, Australia; [email protected] 3 Research and Development, Australian Red Cross Lifeblood, Kelvin Grove, QLD 4059, Australia; [email protected] * Correspondence: [email protected] Received: 28 February 2020; Accepted: 27 April 2020; Published: 4 May 2020 Featured Application: Red blood cell (RBC) storage lesion is a critical issue facing transfusion treatments, and significant changes in RBC morphology and deformability are observed due to the storage lesion. RBCs require high deformability to sustain in-vivo circulation, and impaired deformability leads to several post-transfusion adverse outcomes. Therefore, improved understanding of the interrelation between the morphological and deformability changes and the quality and viability of the stored RBCs is essential to prevent or reduce the transfusion related adverse outcomes. To support this requisite, the influence on RBC deformability due to several aspects of the storage lesion, namely, the changes in cell morphology, surface area and volume, RBC membrane biomechanics, and cytoskeletal structural integrity are explored numerically in this study. Abstract: Storage lesion is a critical issue facing transfusion treatments, and it adversely affects the quality and viability of stored red blood cells (RBCs). -
J-Integral Analysis of the Mixed-Mode Fracture Behaviour of Composite Bonded Joints
J-Integral analysis of the mixed-mode fracture behaviour of composite bonded joints FERNANDO JOSÉ CARMONA FREIRE DE BASTOS LOUREIRO novembro de 2019 J-INTEGRAL ANALYSIS OF THE MIXED-MODE FRACTURE BEHAVIOUR OF COMPOSITE BONDED JOINTS Fernando José Carmona Freire de Bastos Loureiro 1111603 Equation Chapter 1 Section 1 2019 ISEP – School of Engineering Mechanical Engineering Department J-INTEGRAL ANALYSIS OF THE MIXED-MODE FRACTURE BEHAVIOUR OF COMPOSITE BONDED JOINTS Fernando José Carmona Freire de Bastos Loureiro 1111603 Dissertation presented to ISEP – School of Engineering to fulfil the requirements necessary to obtain a Master's degree in Mechanical Engineering, carried out under the guidance of Doctor Raul Duarte Salgueiral Gomes Campilho. 2019 ISEP – School of Engineering Mechanical Engineering Department JURY President Doctor Elza Maria Morais Fonseca Assistant Professor, ISEP – School of Engineering Supervisor Doctor Raul Duarte Salgueiral Gomes Campilho Assistant Professor, ISEP – School of Engineering Examiner Doctor Filipe José Palhares Chaves Assistant Professor, IPCA J-Integral analysis of the mixed-mode fracture behaviour of composite Fernando José Carmona Freire de Bastos bonded joints Loureiro ACKNOWLEDGEMENTS To Doctor Raul Duarte Salgueiral Gomes Campilho, supervisor of the current thesis for his outstanding availability, support, guidance and incentive during the development of the thesis. To my family for the support, comprehension and encouragement given. J-Integral analysis of the mixed-mode fracture behaviour of composite -
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. -
Contact Mechanics in Gears a Computer-Aided Approach for Analyzing Contacts in Spur and Helical Gears Master’S Thesis in Product Development
Two Contact Mechanics in Gears A Computer-Aided Approach for Analyzing Contacts in Spur and Helical Gears Master’s Thesis in Product Development MARCUS SLOGÉN Department of Product and Production Development Division of Product Development CHALMERS UNIVERSITY OF TECHNOLOGY Gothenburg, Sweden, 2013 MASTER’S THESIS IN PRODUCT DEVELOPMENT Contact Mechanics in Gears A Computer-Aided Approach for Analyzing Contacts in Spur and Helical Gears Marcus Slogén Department of Product and Production Development Division of Product Development CHALMERS UNIVERSITY OF TECHNOLOGY Göteborg, Sweden 2013 Contact Mechanics in Gear A Computer-Aided Approach for Analyzing Contacts in Spur and Helical Gears MARCUS SLOGÉN © MARCUS SLOGÉN 2013 Department of Product and Production Development Division of Product Development Chalmers University of Technology SE-412 96 Göteborg Sweden Telephone: + 46 (0)31-772 1000 Cover: The picture on the cover page shows the contact stress distribution over a crowned spur gear tooth. Department of Product and Production Development Göteborg, Sweden 2013 Contact Mechanics in Gears A Computer-Aided Approach for Analyzing Contacts in Spur and Helical Gears Master’s Thesis in Product Development MARCUS SLOGÉN Department of Product and Production Development Division of Product Development Chalmers University of Technology ABSTRACT Computer Aided Engineering, CAE, is becoming more and more vital in today's product development. By using reliable and efficient computer based tools it is possible to replace initial physical testing. This will result in cost savings, but it will also reduce the development time and material waste, since the demand of physical prototypes decreases. This thesis shows how a computer program for analyzing contact mechanics in spur and helical gears has been developed at the request of Vicura AB. -
Cookbook for Rheological Models ‒ Asphalt Binders
CAIT-UTC-062 Cookbook for Rheological Models – Asphalt Binders FINAL REPORT May 2016 Submitted by: Offei A. Adarkwa Nii Attoh-Okine PhD in Civil Engineering Professor Pamela Cook Unidel Professor University of Delaware Newark, DE 19716 External Project Manager Karl Zipf In cooperation with Rutgers, The State University of New Jersey And State of Delaware Department of Transportation And U.S. Department of Transportation Federal Highway Administration Disclaimer Statement The contents of this report reflect the views of the authors, who are responsible for the facts and the accuracy of the information presented herein. This document is disseminated under the sponsorship of the Department of Transportation, University Transportation Centers Program, in the interest of information exchange. The U.S. Government assumes no liability for the contents or use thereof. The Center for Advanced Infrastructure and Transportation (CAIT) is a National UTC Consortium led by Rutgers, The State University. Members of the consortium are the University of Delaware, Utah State University, Columbia University, New Jersey Institute of Technology, Princeton University, University of Texas at El Paso, Virginia Polytechnic Institute, and University of South Florida. The Center is funded by the U.S. Department of Transportation. TECHNICAL REPORT STANDARD TITLE PAGE 1. Report No. 2. Government Accession No. 3. Recipient’s Catalog No. CAIT-UTC-062 4. Title and Subtitle 5. Report Date Cookbook for Rheological Models – Asphalt Binders May 2016 6. Performing Organization Code CAIT/University of Delaware 7. Author(s) 8. Performing Organization Report No. Offei A. Adarkwa Nii Attoh-Okine CAIT-UTC-062 Pamela Cook 9. Performing Organization Name and Address 10. -
Idealized 3D Auxetic Mechanical Metamaterial: an Analytical, Numerical, and Experimental Study
materials Article Idealized 3D Auxetic Mechanical Metamaterial: An Analytical, Numerical, and Experimental Study Naeim Ghavidelnia 1 , Mahdi Bodaghi 2 and Reza Hedayati 3,* 1 Department of Mechanical Engineering, Amirkabir University of Technology (Tehran Polytechnic), Hafez Ave, Tehran 1591634311, Iran; [email protected] 2 Department of Engineering, School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, UK; [email protected] 3 Novel Aerospace Materials, Faculty of Aerospace Engineering, Delft University of Technology (TU Delft), Kluyverweg 1, 2629 HS Delft, The Netherlands * Correspondence: [email protected] or [email protected] Abstract: Mechanical metamaterials are man-made rationally-designed structures that present un- precedented mechanical properties not found in nature. One of the most well-known mechanical metamaterials is auxetics, which demonstrates negative Poisson’s ratio (NPR) behavior that is very beneficial in several industrial applications. In this study, a specific type of auxetic metamaterial structure namely idealized 3D re-entrant structure is studied analytically, numerically, and experi- mentally. The noted structure is constructed of three types of struts—one loaded purely axially and two loaded simultaneously flexurally and axially, which are inclined and are spatially defined by angles q and j. Analytical relationships for elastic modulus, yield stress, and Poisson’s ratio of the 3D re-entrant unit cell are derived based on two well-known beam theories namely Euler–Bernoulli and Timoshenko. Moreover, two finite element approaches one based on beam elements and one based on volumetric elements are implemented. Furthermore, several specimens are additively Citation: Ghavidelnia, N.; Bodaghi, manufactured (3D printed) and tested under compression. -
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 Proteins Are Associated with the Membrane of a Cell Or Particular Organelle and Are Generally More Problematic to Purify Than Water-Soluble Proteins
Strategies for the Purification of Membrane Proteins Sinéad Marian Smith Department of Clinical Medicine, School of Medicine, Trinity College Dublin, Ireland. Email: [email protected] Abstract Although membrane proteins account for approximately 30 % of the coding regions of all sequenced genomes and play crucial roles in many fundamental cell processes, there are relatively few membranes with known 3D structure. This is likely due to technical challenges associated with membrane protein extraction, solubilization and purification. Membrane proteins are classified based on the level of interaction with membrane lipid bilayers, with peripheral membrane proteins associating non- covalently with the membrane, and integral membrane proteins associating more strongly by means of hydrophobic interactions. Generally speaking, peripheral membrane proteins can be purified by milder techniques than integral membrane proteins, whose extraction require phospholipid bilayer disruption by detergents. Here, important criteria for strategies of membrane protein purification are addressed, with a focus on the initial stages of membrane protein solublilization, where problems are most frequently are encountered. Protocols are outlined for the successful extraction of peripheral membrane proteins, solubilization of integral membrane proteins, and detergent removal which is important not only for retaining native protein stability and biological functions, but also for the efficiency of downstream purification techniques. Key Words: peripheral membrane protein, integral membrane protein, detergent, protein purification, protein solubilization. 1. Introduction Membrane proteins are associated with the membrane of a cell or particular organelle and are generally more problematic to purify than water-soluble proteins. Membrane proteins represent approximately 30 % of the open-reading frames of an organism’s genome (1-4), and play crucial roles in basic cell functions including signal transduction, energy production, nutrient uptake and cell-cell communication. -
The Structure of Biological Membranes
The Structure of Biological Membranes Func7ons of Cellular Membranes 1. Plasma membrane acts as a selecvely permeable barrier to the environment • Uptake of nutrients • Waste disposal • Maintains intracellular ionic milieau 2. Plasma membrane facilitates communicaon • With the environment • With other cells • Protein secreon 3. Intracellular membranes allow compartmentalizaon and separaon of different chemical reac7on pathways • Increased efficiency through proximity • Prevent fu8le cycling through separaon Composi7on of Animal Cell Membranes • Hydrated, proteinaceous lipid bilayers • By weight: 20% water, 80% solids • Solids: Lipid Protein ~90% Carbohydrate (~10%) • Phospholipids responsible for basic membrane bilayer structure and physical proper8es • Membranes are 2-dimensional fluids into which proteins are dissolved or embedded The Most Common Class of PhospholipiD is FormeD from a Gycerol-3-P Backbone SaturateD FaJy AciD •Palmitate and stearate most common •14-26 carbons •Even # of carbons UnsaturateD FaJy AciD Structure of PhosphoglyceriDes All Membrane LipiDs are Amphipathic Figure 10-2 Molecular Biology of the Cell (© Garland Science 2008) PhosphoglyceriDes are Classified by their Head Groups Phosphadylethanolamine Phosphadylcholine Phosphadylserine Phosphadylinositol Ether Bond at C1 PS and PI bear a net negave charge at neutral pH Sphingolipids are the SeconD Major Class of PhospholipiD in Animal Cells Sphingosine Ceramides contain sugar moies in ether linkage to sphingosine GlycolipiDs are AbunDant in Brain Cells Figure 10-18 Molecular -
Membrane Curvature, Trans-Membrane Area Asymmetry, Budding, Fission and Organelle Geometry
International Journal of Molecular Sciences Review Membrane Curvature, Trans-Membrane Area Asymmetry, Budding, Fission and Organelle Geometry Alexander A. Mironov 1,* , Anna Mironov 2, Jure Derganc 3 and Galina V. Beznoussenko 1,* 1 Department of Cell Biology, The FIRC Institute of Molecular Oncology, 20139 Milan, Italy 2 Imaging Facility, Universita Vita-Salute San Raffaele, 20132 Milan, Italy; [email protected] 3 Institute of Biophysics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; [email protected] * Correspondence: [email protected] (A.A.M.); [email protected] (G.V.B.) Received: 21 September 2020; Accepted: 9 October 2020; Published: 14 October 2020 Abstract: In biology, the modern scientific fashion is to mostly study proteins. Much less attention is paid to lipids. However, lipids themselves are extremely important for the formation and functioning of cellular membrane organelles. Here, the role of the geometry of the lipid bilayer in regulation of organelle shape is analyzed. It is proposed that during rapid shape transition, the number of lipid heads and their size (i.e., due to the change in lipid head charge) inside lipid leaflets modulates the geometrical properties of organelles, in particular their membrane curvature. Insertion of proteins into a lipid bilayer and the shape of protein trans-membrane domains also affect the trans-membrane asymmetry between surface areas of luminal and cytosol leaflets of the membrane. In the cases where lipid molecules with a specific shape are not predominant, the shape of lipids (cylindrical, conical, or wedge-like) is less important for the regulation of membrane curvature, due to the flexibility of their acyl chains and their high ability to diffuse. -
RHEOLOGY and DYNAMIC MECHANICAL ANALYSIS – What They Are and Why They’Re Important
RHEOLOGY AND DYNAMIC MECHANICAL ANALYSIS – What They Are and Why They’re Important Presented for University of Wisconsin - Madison by Gregory W Kamykowski PhD TA Instruments May 21, 2019 TAINSTRUMENTS.COM Rheology: An Introduction Rheology: The study of the flow and deformation of matter. Rheological behavior affects every aspect of our lives. Dynamic Mechanical Analysis is a subset of Rheology TAINSTRUMENTS.COM Rheology: The study of the flow and deformation of matter Flow: Fluid Behavior; Viscous Nature F F = F(v); F ≠ F(x) Deformation: Solid Behavior F Elastic Nature F = F(x); F ≠ F(v) 0 1 2 3 x Viscoelastic Materials: Force F depends on both Deformation and Rate of Deformation and F vice versa. TAINSTRUMENTS.COM 1. ROTATIONAL RHEOLOGY 2. DYNAMIC MECHANICAL ANALYSIS (LINEAR TESTING) TAINSTRUMENTS.COM Rheological Testing – Rotational - Unidirectional 2 Basic Rheological Methods 10 1 10 0 1. Apply Force (Torque)and 10 -1 measure Deformation and/or 10 -2 (rad/s) Deformation Rate (Angular 10 -3 Displacement, Angular Velocity) - 10 -4 Shear Rate Shear Controlled Force, Controlled 10 3 10 4 10 5 Angular Velocity, Velocity, Angular Stress Torque, (µN.m)Shear Stress 2. Control Deformation and/or 10 5 Displacement, Angular Deformation Rate and measure 10 4 10 3 Force needed (Controlled Strain (Pa) ) Displacement or Rotation, 10 2 ( Controlled Strain or Shear Rate) 10 1 Torque, Stress Torque, 10 -1 10 0 10 1 10 2 10 3 s (s) TAINSTRUMENTS.COM Steady Simple Shear Flow Top Plate Velocity = V0; Area = A; Force = F H y Bottom Plate Velocity = 0 x vx = (y/H)*V0 .