scholarly journals Theoretical and computational modeling of the dynamics of multicellular and lipid membrane systems

2016 ◽  
Author(s):  
◽  
Matthew McCune
Keyword(s):  
Computational Modeling ◽  
Neutron Scattering ◽  
Lipid Bilayers ◽  
Lipid Membranes ◽  
Drug Testing ◽  
Lipid Membrane ◽  
Dynamic Properties ◽  
Practical Implication ◽  
Free Standing ◽  
Silica Substrate

This dissertation presents two research projects that apply theoretical and computational modeling to (1) describe and predict the formation and shape evolution of three-dimensional (3D) bioprinted tissue constructs, and (2) investigate the effect of a silica substrate on the structural and dynamic properties of a single fully hydrated lipid bilayer. (1) Bioprinting, a novel tissue engineering technique, has the ultimate goal of using 3D printers with bioink made from a person’s own cells to create tissues in the laboratory for transplantation or drug testing. The outcome of the post-bioprinting process, where the bioink particles fuse to form the desired 3D tissue construct, is difficult to predict and experimental techniques have generally been optimized through trial and error. To address this shortcoming, by employing theoretical modeling and computer simulations, we have developed and implemented an effective procedure that is capable of describing and predicting the shape dynamics during post-printing structure formation in 3D bioprinting. In particular, we have explained and demonstrated that the post-printing fusion process is considerably faster when using cylindrical instead of spheroidal bioink particles, a result that has considerable practical implication for extrusion bioprinting. (2) The study of lipid bilayers using neutron scattering experiments requires samples that contain a large stack of membranes. The analysis and computer simulation of such systems is challenging mainly due to the unknown amount of water separating the membranes. To overcome this difficulty, more recent experiments place single lipid membranes onto a support and stack about a hundred of them together. In this project we use molecular dynamics simulations of both free-standing and hydrated single-supported lipid bilayers to investigate the effect of the silica substrate on the structural and dynamical properties of the lipids and hydration waters. Our results may provide useful information in interpreting some recent neutron scattering experiments.

scholarly journals Theoretical and computational modeling of peptide-lipid bilayer interaction studied by dynamic force spectroscopy

2019 ◽  
Author(s):  
◽  
Milica Utjesanovic
Keyword(s):  
Computational Modeling ◽  
Lipid Bilayer ◽  
Lipid Bilayers ◽  
Lipid Membranes ◽  
Lipid Membrane ◽  
Conformational Dynamics ◽  
Quantitative Description ◽  
Md Simulations ◽  
Dynamic Force ◽  
Detachment Rate

This thesis consists of three interrelated theoretical and computational modeling projects that investigate different aspects of peptide-lipid membrane interactions. (1) A general theoretical approach is formulated for the quantitative description of the detachment force distribution, P(F), and the corresponding force dependent detachment rate, k(F), of a peptide from a lipid bilayer, by assuming that peptide detachment from lipid membranes occurs stochastically along a few dominant diffusive pathways. Besides providing a consistent interpretation of the experimental data, the new method also predicts that k(F) exhibits catch-bond behavior (when, counter intuitively, the detachment rate decreases with increasing force). (2) The proposed multiple detachment pathways method is tested and validated for a particular peptide (SecA2-11) interacting with both zwitterionic POPC lipid and polar E. Coli membranes. Furthermore, molecular dynamics (MD) simulations are used to explored the conformational dynamics of SecA2-11 during its interaction with both POPC and anionic POPG lipid bilayers. (3) Finally, MD simulations are used to explore the conformational dynamics and energetics of the peptide melittin (MWT) and its diastereomer (MD4) interacting with POPC and POPG lipid bilayers. The obtained results provide further insight into the role of secondary structure in peptide-lipid bilayer interactions.

scholarly journals The Structural Integrity of the Model Lipid Membrane during Induced Lipid Peroxidation: The Role of Flavonols in the Inhibition of Lipid Peroxidation

Antioxidants ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 430 ◽  
Author(s):  
Anja Sadžak ◽  
Janez Mravljak ◽  
Nadica Maltar-Strmečki ◽  
Zoran Arsov ◽  
Goran Baranović ◽  
...  
Keyword(s):  
Lipid Peroxidation ◽  
Lipid Bilayers ◽  
Lipid Membranes ◽  
Structural Changes ◽  
Structural Integrity ◽  
Lipid Membrane ◽  
Membrane Properties ◽  
Structural Reorganization ◽  
Unsaturated Lipids ◽  
Oxidative Attack

The structural integrity, elasticity, and fluidity of lipid membranes are critical for cellular activities such as communication between cells, exocytosis, and endocytosis. Unsaturated lipids, the main components of biological membranes, are particularly susceptible to the oxidative attack of reactive oxygen species. The peroxidation of unsaturated lipids, in our case 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), induces the structural reorganization of the membrane. We have employed a multi-technique approach to analyze typical properties of lipid bilayers, i.e., roughness, thickness, elasticity, and fluidity. We compared the alteration of the membrane properties upon initiated lipid peroxidation and examined the ability of flavonols, namely quercetin (QUE), myricetin (MCE), and myricitrin (MCI) at different molar fractions, to inhibit this change. Using Mass Spectrometry (MS) and Fourier Transform Infrared Spectroscopy (FTIR), we identified various carbonyl products and examined the extent of the reaction. From Atomic Force Microscopy (AFM), Force Spectroscopy (FS), Small Angle X-Ray Scattering (SAXS), and Electron Paramagnetic Resonance (EPR) experiments, we concluded that the membranes with inserted flavonols exhibit resistance against the structural changes induced by the oxidative attack, which is a finding with multiple biological implications. Our approach reveals the interplay between the flavonol molecular structure and the crucial membrane properties under oxidative attack and provides insight into the pathophysiology of cellular oxidative injury.

Small-Angle Neutron Scattering of Bilayer Vesicles Made with Synthetic Phospholipids

1998 ◽  
Vol 550 ◽  
Author(s):  
S. F. Trevino ◽  
Robert lvkov ◽  
Gary R. Matyas ◽  
Frank J. Lebeda
Keyword(s):  
Neutron Scattering ◽  
Lipid Bilayers ◽  
Small Angle ◽  
Lipid Membranes ◽  
Small Angle Neutron Scattering ◽  
Bilayer Lipid Membranes ◽  
Lipid Concentration ◽  
The Core ◽  
Delivery Vehicles ◽  
Therapeutic Compounds

AbstractWe have used Small-Angle Neutron Scattering to investigate the structure of bilayer lipid membranes in aqueous solution. The lipids consist of equimolar concentrations of two molecules DMPG and DMPC (see text). The structures consist of solvent filled cores surrounded by shells composed of the lipid bilayers. In particular the radii of the core and shell thickness are measured as a function of lipid concentration and temperature. Other features which reveal themselves are vesicle forming ability of the lipids, additional larger structures and inter-vesicle interactions at large vesicle concentrations. The study is motivated by the possible use of these systems as delivery vehicles for various beneficial therapeutic compounds.

scholarly journals Dynamic properties of a reconstituted myelin sheath

2010 ◽  
Vol 24 (6) ◽  
pp. 585-592 ◽  
Author(s):  
W. Knoll ◽  
F. Natali ◽  
J. Peters ◽  
R. Nanekar ◽  
C. Wang ◽  
...  
Keyword(s):  
Nervous System ◽  
Neutron Scattering ◽  
Peripheral Nervous System ◽  
Myelin Sheath ◽  
Lipid Membrane ◽  
Dynamic Properties ◽  
Signal Transmission ◽  
Demyelinating Diseases ◽  
Specific Proteins ◽  
Molecular Components

Myelin is a multilamellar membrane which, wrapping the nerve axons, increases the efficiency of nervous signal transmission. Indeed, the molecular components of the myelin sheath interact tightly with each other and molecules on the axonal surface to drive myelination, to keep both myelin and the axon intact, and to transduce signals from myelin to the axon and vice versa. Myelin is strongly affected in human demyelinating diseases in both the central and peripheral nervous system (CNS and PNS, respectively). Despite the presence of a well-defined set of myelin-specific proteins, little is known about the structure and the dynamics of these proteins, their interactions with the membrane and their influence on myelin stability. We present here the first neutron scattering results on the dynamics of the myelin sheath in PNS and of the interaction between its constituents. Specifically, the human P2 protein is shown to stabilize the lipid membrane upon binding to it.

scholarly journals Modulation of physiological and pathological activities of lysozyme by biological membranes

2012 ◽  
Vol 17 (3) ◽  
Author(s):  
Valeriya Trusova
Keyword(s):  
Lipid Bilayers ◽  
Lipid Membranes ◽  
Dynamic Properties ◽  
Biological Activities ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Lipid Vesicles ◽  
Bacterial Cells ◽  
Oligomeric Protein ◽  
Wide Range

AbstractThe molecular details of interactions between lipid membranes and lysozyme (Lz), a small polycationic protein with a wide range of biological activities, have long been the focus of numerous studies. The biological consequences of this process are considered to embrace at least two aspects: i) correlation between antimicrobial and membranotropic properties of this protein, and ii) lipid-mediated Lz amyloidogenesis. The mechanisms underlying the lipid-assisted protein fibrillogenesis and membrane disruption exerted by Lz in bacterial cells are believed to be similar. The present investigation was undertaken to gain further insight into Lz-lipid interactions and explore the routes by which Lz exerts its antimicrobial and amyloidogenic actions. Binding and Förster resonance energy transfer studies revealed that upon increasing the content of anionic lipids in lipid vesicles, Lz forms aggregates in a membrane environment. Total internal reflection fluorescence microscopy and pyrene excimerization reaction were employed to study the effect of Lz on the structural and dynamic properties of lipid bilayers. It was found that Lz induces lipid demixing and reduction of bilayer free volume, the magnitude of this effect being much more pronounced for oligomeric protein.

scholarly journals Mimicking the Mammalian Plasma Membrane: An Overview of Lipid Membrane Models for Biophysical Studies

Biomimetics ◽  
2020 ◽  
Vol 6 (1) ◽  
pp. 3
Author(s):  
Alessandra Luchini ◽  
Giuseppe Vitiello
Keyword(s):  
Plasma Membrane ◽  
Lipid Bilayers ◽  
Lipid Membranes ◽  
Cell Membranes ◽  
Lipid Membrane ◽  
Lipid Phase ◽  
Chemical Information ◽  
Lipid Species ◽  
Membrane Models ◽  
The Impact

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 applications for the investigation of protein-lipid and drug-lipid interactions. Altogether, promising directions for future developments of biomimetic lipid membranes are the further implementation of natural lipid mixtures for the development of more biologically relevant lipid membranes, as well as the development of sample preparation protocols that enable the incorporation of membrane proteins in the biomimetic lipid membranes.

Measurement of membrane tension of free standing lipid bilayers via laser-induced surface deformation spectroscopy

Soft Matter ◽  
2015 ◽  
Vol 11 (44) ◽  
pp. 8641-8647 ◽  
Author(s):  
Tomohiko Takei ◽  
Tatsuya Yaguchi ◽  
Takuya Fujii ◽  
Tomonori Nomoto ◽  
Taro Toyota ◽  
...  
Keyword(s):  
Lipid Bilayers ◽  
Lipid Membranes ◽  
Surface Deformation ◽  
Membrane Tension ◽  
Free Standing ◽  
Black Lipid Membranes ◽  
Non Invasive ◽  
Invasive Measurement

Non-invasive measurement of the membrane tension of free-standing black lipid membranes (BLMs), with sensitivity on the order of μN m−1, was achieved using laser-induced surface deformation (LISD) spectroscopy.

scholarly journals Accumulation of styrene oligomers alters lipid membrane phase order and miscibility

2021 ◽  
Vol 118 (4) ◽  
pp. e2016037118
Author(s):  
Mattia I. Morandi ◽  
Monika Kluzek ◽  
Jean Wolff ◽  
André Schroder ◽  
Fabrice Thalmann ◽  
...  
Keyword(s):  
Phase Behavior ◽  
Lipid Bilayers ◽  
Lipid Membranes ◽  
Lipid Membrane ◽  
Spatial Modulation ◽  
Plastic Materials ◽  
Polymeric Species ◽  
Cell Components ◽  
Membrane Models ◽  
Membrane Mechanical Properties

Growth of plastic waste in the natural environment, and in particular in the oceans, has raised the accumulation of polystyrene and other polymeric species in eukyarotic cells to the level of a credible and systemic threat. Oligomers, the smallest products of polymer degradation or incomplete polymerization reactions, are the first species to leach out of macroscopic or nanoscopic plastic materials. However, the fundamental mechanisms of interaction between oligomers and polymers with the different cell components are yet to be elucidated. Simulations performed on lipid bilayers showed changes in membrane mechanical properties induced by polystyrene, but experimental results performed on cell membranes or on cell membrane models are still missing. We focus here on understanding how embedded styrene oligomers affect the phase behavior of model membranes using a combination of scattering, fluorescence, and calorimetric techniques. Our results show that styrene oligomers disrupt the phase behavior of lipid membranes, modifying the thermodynamics of the transition through a spatial modulation of lipid composition.

The dynamic face of lipid membranes

Soft Matter ◽  
2021 ◽  
Author(s):  
Sudipta Gupta ◽  
Rana Ashkar
Keyword(s):  
Neutron Scattering ◽  
Lipid Membranes ◽  
Dynamic Properties ◽  
Spatiotemporal Dynamics ◽  
Live Cells ◽  
Biological Functions

Lipid membranes envelope live cells and mediate vital biological functions through regulated spatiotemporal dynamics. This review highlights the role of neutron scattering, among other approaches, in uncovering the dynamic properties of lipid membranes.

scholarly journals Structure, Formation, and Biological Interactions of Supported Lipid Bilayers (SLB) Incorporating Lipopolysaccharide

Coatings ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 981
Author(s):  
Palak Sondhi ◽  
Dhanbir Lingden ◽  
Keith J. Stine
Keyword(s):  
Lipid Bilayers ◽  
Lipid Membranes ◽  
Lipid Membrane ◽  
Biologically Active ◽  
Supported Lipid Bilayers ◽  
Biological Interactions ◽  
Relevant Model ◽  
Biologically Relevant ◽  
Model Lipid Membranes ◽  
Biomimetic Membrane

Biomimetic membrane systems play a crucial role in the field of biosensor engineering. Over the years, significant progress has been achieved creating artificial membranes by various strategies from vesicle fusion to Langmuir transfer approaches to meet an ever-growing demand for supported lipid bilayers on various substrates such as glass, mica, gold, polymer cushions, and many more. This paper reviews the diversity seen in the preparation of biologically relevant model lipid membranes which includes monolayers and bilayers of phospholipid and other crucial components such as proteins, characterization techniques, changes in the physical properties of the membranes during molecular interactions and the dynamics of the lipid membrane with biologically active molecules with special emphasis on lipopolysaccharides (LPS).

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