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The presence of
ethanol Ethanol (abbr. EtOH; also called ethyl alcohol, grain alcohol, drinking alcohol, or simply alcohol) is an organic compound. It is an Alcohol (chemistry), alcohol with the chemical formula . Its formula can be also written as or (an ethyl ...
can lead to the formations of non-lamellar phases also known as non-bilayer phases. Ethanol has been recognized as being an excellent solvent in an aqueous solution for inducing non-lamellar phases in
phospholipids Phospholipids, are a class of lipids whose molecule has a hydrophilic "head" containing a phosphate group and two hydrophobic "tails" derived from fatty acids, joined by an alcohol residue (usually a glycerol molecule). Marine phospholipids typ ...
. The formation of non-lamellar phases in phospholipids is not completely understood, but it is significant that this amphiphilic molecule is capable of doing so. The formation of non-lamellar phases is significant in biomedical studies which include drug delivery, the transport of polar and non-polar ions using
solvents A solvent (s) (from the Latin '' solvō'', "loosen, untie, solve") is a substance that dissolves a solute, resulting in a solution. A solvent is usually a liquid but can also be a solid, a gas, or a supercritical fluid. Water is a solvent for p ...
capable of penetrating the
biomembrane A biological membrane, biomembrane or cell membrane is a selectively permeable membrane that separates the interior of a cell from the external environment or creates intracellular compartments by serving as a boundary between one part of the ce ...
, increasing the elasticity of the biomembrane when it is being disrupted by unwanted substances (
virus A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Since Dmitri Ivanovsky's 1 ...
es,
bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...
, solvents, etc.) and functioning as a channel or transporter of biomaterial.


Biomembranes and phospholipid bilayers

Biological membranes A biological membrane, biomembrane or cell membrane is a selectively permeable membrane that separates the interior of a cell from the external environment or creates intracellular compartments by serving as a boundary between one part of the ce ...
are found in both
prokaryotic A prokaryote () is a Unicellular organism, single-celled organism that lacks a cell nucleus, nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek language, Greek wikt:πρό#Ancient Greek, πρό (, 'before') a ...
and
eukaryotic Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacte ...
cells.Yeagle, Philip. ''The Membrane of Cells''. 2nd ed. Academic Press, 1993. 1–7 They surround cells and
organelle In cell biology, an organelle is a specialized subunit, usually within a cell, that has a specific function. The name ''organelle'' comes from the idea that these structures are parts of cells, as organs are to the body, hence ''organelle,'' the ...
s with a semi-permeable barrier that prevents free flow of substances. The membrane consists of a
phospholipid bilayer The lipid bilayer (or phospholipid bilayer) is a thin polar membrane made of two layers of lipid molecules. These membranes are flat sheets that form a continuous barrier around all cells. The cell membranes of almost all organisms and many vir ...
structure and often embedded or otherwise associated proteins, along with
cholesterol Cholesterol is any of a class of certain organic molecules called lipids. It is a sterol (or modified steroid), a type of lipid. Cholesterol is biosynthesized by all animal cells and is an essential structural component of animal cell mem ...
and
glycolipid Glycolipids are lipids with a carbohydrate attached by a glycosidic (covalent) bond. Their role is to maintain the stability of the cell membrane and to facilitate cellular recognition, which is crucial to the immune response and in the connec ...
s.Lodish, Harvey; Berk, Arnold; Matsudaira, Paul; Berk, Arnold; Matsudaira, Paul; Kaiser, Chris A.; Krieger, Monty; Scott, Matthew P.; Zipursky, S. Lawrence; Darnell, James. ''Molecular Cell Biology''. 5th ed. W.H. Freeman and Company New York, 2004. 535–539. The
phospholipid Phospholipids, are a class of lipids whose molecule has a hydrophilic "head" containing a phosphate group and two hydrophobic "tails" derived from fatty acids, joined by an alcohol residue (usually a glycerol molecule). Marine phospholipids typ ...
bilayer is a two-layer structure mainly composed of phospholipids, which are
amphiphilic An amphiphile (from the Greek αμφις amphis, both, and φιλíα philia, love, friendship), or amphipath, is a chemical compound possessing both hydrophilic (''water-loving'', polar) and lipophilic (''fat-loving'') properties. Such a compoun ...
molecules that have
hydrophilic A hydrophile is a molecule or other molecular entity that is attracted to water molecules and tends to be dissolved by water.Liddell, H.G. & Scott, R. (1940). ''A Greek-English Lexicon'' Oxford: Clarendon Press. In contrast, hydrophobes are no ...
and
hydrophobic In chemistry, hydrophobicity is the physical property of a molecule that is seemingly repelled from a mass of water (known as a hydrophobe). In contrast, hydrophiles are attracted to water. Hydrophobic molecules tend to be nonpolar and, th ...
regions. The hydrophilic region contains the polar head group. This region is exposed to aqueous substances located mainly in the exterior portion of the biomembrane. The hydrophilic region consists of the non-polar acyl chains or fatty acids groups facing the interior of the biomembrane. Phospholipids consist of two non-polar hydrocarbon chains with ester or ether bonds to the phosphate group which is also linked by ester or ether bonds to the polar hydrophilic region. The phospholipid carries a negative charge due to the presence of the phosphate group. Its overall polarity depends on the charges of the hydroxyl groups or alcohols such as choline, ethanolamine, inositol, serine, etc. attached to the phosphate group. There are six basic functions that are associated with biomembranes: #Controlling chemical potential and gradient for chemical species and charges across opposite sides of the membrane #Organizing enzymes and protein complexes for signal transduction or signaling #Managing protein and lipid interactions #Functioning as a substrate #Transferring vital information and material across the membrane #Compartmentalization by maintaining physical separation amongst membranes but still allowing proper communication


Factors that affect biomembranes and lipid formations

There are two basic terms used to describe lipid phases: lamellar and non-lamellar phases. Lipids can undergo polymorphic or mesomorphic changes leading to the formation of lamellar or non-lamellar phases. Various factors can affect the overall function of the biomembrane and decrease its ability to function as a protective barrier and maintained the order of the inner components. The bilayer thickness, surface charge, intermolecular forces, amphiphilic molecules, changes in free energy, alternating or spontaneous curvatures, increase or decrease in temperature, solvents, and the environment are all examples of different conditions that cause changes in biomembranes.Andrey A. Gurtovenko and Jamshed Anwar. "Interaction of Ethanol with Biological Membranes: The Formation of Non-Bilayer Structures within the Membrane Interior and their Significance". ''J. Phys. Chem. B'', 2009, 113 (7), 1983–1992. Yeagle, Philip. ''The Structure of Biological Membranes''. 2nd. ed. CRC Press, (2005). 173–194. For example, the strength of the intermolecular forces within the biomembrane are fairly strong but when lipids are extracted from biomembranes for analytical purposes there is a decrease in the constraints by the intermolecular forces against the phospholipids which may cause the lipid to undergo polymorphism as well as a temporary rearrangement of other lipids or proteins in the biomembrane. The thickness of the biomembrane determines the permeability of the membrane and ethanol, which can be used as a solvent, is able to reduce the thickness of the biomembrane which is one way this amphiphilic molecule is able to permeate through the biomembrane. There can also be free energy changes that can increase or decrease during the phase transitions of the phospholipids during polymorphism or mesmorphism which can also affect the curvature of lipids. All lipids can experience some sort of positive or negative alternating or spontaneous curvature due to variations in sizes between the hydrophobic and the hydrophilic region.Digging Deeper the Surfactant
Accessed: February 2, 2009.
Temperature changes can also lead to changes in the biomembrane.


Non-lamellar phases vs.

lamellar phase Lamellar phase refers generally to packing of polar-headed long chain nonpolar-tail molecules in an environment of bulk polar liquid, as sheets of bilayers separated by bulk liquid. In biophysics, polar lipids (mostly, phospholipids, and rarely, gly ...
s

When
lipid Lipids are a broad group of naturally-occurring molecules which includes fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The functions of lipids include ...
s are extracted or isolated from biomembranes, Polymorphism and mesomorphism can occur because they are then no longer under the intermolecular constraints that are present within the biomembrane. This can lead to formation of non-
lamellar A ''lamella'' (plural ''lamellae'') is a small plate or flake, from the Latin, and may also be used to refer to collections of fine sheets of material held adjacent to one another, in a gill-shaped structure, often with fluid in between though s ...
(non-bilayer) or lamellar phases in
phospholipids Phospholipids, are a class of lipids whose molecule has a hydrophilic "head" containing a phosphate group and two hydrophobic "tails" derived from fatty acids, joined by an alcohol residue (usually a glycerol molecule). Marine phospholipids typ ...
. "Polymorphism" refers to formation of diverse structures such as three-dimensional tubes, rods, and structures with cubic symmetry. Mesomorphism refers to
phase transitions In chemistry, thermodynamics, and other related fields, a phase transition (or phase change) is the physical process of transition between one state of a medium and another. Commonly the term is used to refer to changes among the basic states of ...
when heat is applied. For example, a lipid can be in the lamellar phase at a lower temperature, but as the temperature increases, it transitions into a non-lamellar phase. It is important to consider the size of the hydrophilic region versus the hydrophobic region. For example, if the hydrophilic region and hydrophobic region are similar, a cylindrical shape
lipid bilayer The lipid bilayer (or phospholipid bilayer) is a thin polar membrane made of two layers of lipid molecules. These membranes are flat sheets that form a continuous barrier around all cells. The cell membranes of almost all organisms and many vir ...
is formed; but when the hydrophilic regions is smaller than the hydrophobic region a cone-shaped lipid bilayer is formed.Gerrit Van Meer. Cellular Lipidomics. ''The EMBO Journal'' (2005) 24, 3159–3165, . Published online 1 September 2005 Another example is the formation of
micelles A micelle () or micella () (plural micelles or micellae, respectively) is an aggregate (or supramolecular assembly) of surfactant amphipathic lipid molecules dispersed in a liquid, forming a colloid, colloidal suspension (also known as associat ...
which has a non-lamellar formation in which the hydrophilic region is significantly larger compared to the hydrophobic region. There are various liquid-crystalline phases that can exist in lipids. Liquid-crystalline phases are when the hydrophobic chain regions are not motionless but are allowed to move about freely in a fluid-like melted state. The lamellar phase (Lα) is the most common and dominant phase in lipids and are aligned as stacks of bilayers on top of bilayers oriented in one single direction.Synchrotron studies of surfactants: SRD Annual Report 1995–1996
accessed February 3, 2009.
Non-lamellar phases are known as non-bilayer liquid-crystalline phases without lamellar symmetry (Lα). They include
hexagonal In geometry, a hexagon (from Greek , , meaning "six", and , , meaning "corner, angle") is a six-sided polygon. The total of the internal angles of any simple (non-self-intersecting) hexagon is 720°. Regular hexagon A '' regular hexagon'' has ...
(I), hexagonal (II), and three-dimensional cubic phases. ''Hexagonal (I) phases'' are non-inverted or oil-in-water phases in which a net convex curvature is present and this is similar to micelles. ''Hexagonal(II) phases'' are inverted water-in-oil phases with net concave curvatures describing the lipid and water interactions. ''Cubic phases'' (Pn3m, Im3m, la3d, etc.) or bicontinuous cubic phases composed of multiple connected bilayers that resemble a three-dimensional cube.Interaction of Antimicrobial Peptides with Microbial Lipid Extracts: Evidence for Cubic Phase Formation.
E. Staudegger, H. Amenitsch, M. Kriechbaum and K. Lohner. Institute of Biophysics and X-ray Structure Research, Austrian Academy of Sciences. accessed February 2, 2009.
The presence of non-lamellar lipids in biomembranes affect the elasticity of the lipid bilayer, especially when it is disrupted, for example during phase transitions,
membrane fusion A membrane is a selective barrier; it allows some things to pass through but stops others. Such things may be molecules, ions, or other small particles. Membranes can be generally classified into synthetic membranes and biological membranes. B ...
and fission or interactions with membrane peptides and proteins.


Analytical techniques used for characterizing lipids

There are various analytical instruments and techniques used to characterized and monitor the different properties of
lipid Lipids are a broad group of naturally-occurring molecules which includes fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The functions of lipids include ...
s;
X-ray diffraction X-ray crystallography is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions. By measuring the angles ...
,
differential scanning calorimetry Differential scanning calorimetry (DSC) is a thermoanalytical technique in which the difference in the amount of heat required to increase the temperature of a sample and reference is measured as a function of temperature. Both the sample and ref ...
(DSC),
nuclear magnetic resonance Nuclear magnetic resonance (NMR) is a physical phenomenon in which nuclei in a strong constant magnetic field are perturbed by a weak oscillating magnetic field (in the near field) and respond by producing an electromagnetic signal with a ...
which include 2HNMR and 31PNMR,
thin layer chromatography Thin-layer chromatography (TLC) is a chromatography technique used to separate non-volatile mixtures. Thin-layer chromatography is performed on a sheet of an inert substrate such as glass, plastic, or aluminium foil, which is coated with a t ...
(TLC),
fluorescence recovery after photobleaching Fluorescence recovery after photobleaching (FRAP) is a method for determining the kinetics of diffusion through tissue or cells. It is capable of quantifying the two dimensional lateral diffusion of a molecularly thin film containing fluorescently ...
(FRAP), nearest-neighbor recognition (NNR), and atomic molecular dynamics simulations (AMDS).


X-ray diffraction

X-ray scattering X-ray scattering techniques are a family of non-destructive analytical techniques which reveal information about the crystal structure, chemical composition, and physical properties of materials and thin films. These techniques are based on observ ...
techniques are some of the most useful techniques for determining the structural identification and shape of
lipid Lipids are a broad group of naturally-occurring molecules which includes fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The functions of lipids include ...
s. An X-ray beam of light is applied to the lipid in which a distinct X-ray pattern is revealed. This lattice pattern is based on the electron density and localization of electrons dispersed throughout the lipid in order to determine atomic positions. The disadvantage is that it can be difficult to determine patterns in lipids that are not well oriented such as non-
lamellar A ''lamella'' (plural ''lamellae'') is a small plate or flake, from the Latin, and may also be used to refer to collections of fine sheets of material held adjacent to one another, in a gill-shaped structure, often with fluid in between though s ...
phases. Although this can be a limitation in producing electron density reconstructions in lipids, X-ray diffraction is still a reliable method for obtaining structural information and distinguishing between lamellar and non-lamellar phases.


Differential scanning calorimetry

Differential scanning calorimetry Differential scanning calorimetry (DSC) is a thermoanalytical technique in which the difference in the amount of heat required to increase the temperature of a sample and reference is measured as a function of temperature. Both the sample and ref ...
(DSC) is an analytical technique used to examine
thermodynamic Thermodynamics is a branch of physics that deals with heat, work, and temperature, and their relation to energy, entropy, and the physical properties of matter and radiation. The behavior of these quantities is governed by the four laws of ther ...
properties of
molecules A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and bioche ...
. It can study the thermal behavior of materials as they undergo physical and chemical changes during heat treatment.Skoog, Douglas A; West, Donald M; Holler, James F.; Crouch, Stanly R. ''Fundamentals of Analytical Chemistry''. 8th ed. Brooks/Cole, 2004.Sibilia, John. ''A Guide to Materials Characterization and Chemical Analysis.'' VCH Publishers, Inc. 1988 The parameters that are measured are referred to as the glass transition value (Tg) and melting temperature (Tm). These values are measured over time and are comparable between an inert reference sample and the
analyte An analyte, component (in clinical chemistry), or chemical species is a substance or chemical constituent that is of interest in an analytical procedure. The purest substances are referred to as analytes, such as 24 karat gold, NaCl, water, etc. ...
. Changes in the (Tm) and (Tg) values evaluate phase changes (solid, liquid-gel, liquid, etc.) in which an
endothermic In thermochemistry, an endothermic process () is any thermodynamic process with an increase in the enthalpy (or internal energy ) of the system.Oxtoby, D. W; Gillis, H.P., Butler, L. J. (2015).''Principle of Modern Chemistry'', Brooks Cole. p. ...
or
exothermic In thermodynamics, an exothermic process () is a thermodynamic process or reaction that releases energy from the system to its surroundings, usually in the form of heat, but also in a form of light (e.g. a spark, flame, or flash), electricity (e ...
process occurs. This technique is useful for monitoring the phase changes in
phospholipids Phospholipids, are a class of lipids whose molecule has a hydrophilic "head" containing a phosphate group and two hydrophobic "tails" derived from fatty acids, joined by an alcohol residue (usually a glycerol molecule). Marine phospholipids typ ...
by providing information such as the amount of heat released or absorbed and time for phase transitions to occur, etc. DSC monitoring can occur at slow rates which is a disadvantage in monitoring fast phase transitions within phospholipids.


Hydrogen nuclear magnetic resonance

Hydrogen
nuclear magnetic resonance Nuclear magnetic resonance (NMR) is a physical phenomenon in which nuclei in a strong constant magnetic field are perturbed by a weak oscillating magnetic field (in the near field) and respond by producing an electromagnetic signal with a ...
(2HNMR) is a technique that uses an external magnetic field and
deuterium Deuterium (or hydrogen-2, symbol or deuterium, also known as heavy hydrogen) is one of two Stable isotope ratio, stable isotopes of hydrogen (the other being Hydrogen atom, protium, or hydrogen-1). The atomic nucleus, nucleus of a deuterium ato ...
to replace the ordinary form of
hydrogen Hydrogen is the chemical element with the symbol H and atomic number 1. Hydrogen is the lightest element. At standard conditions hydrogen is a gas of diatomic molecules having the formula . It is colorless, odorless, tasteless, non-toxic, an ...
. The ordinary form of hydrogen refers to the elemental form of hydrogen with a molecular weight of approximately 1 g/mol. It contains only one proton and has no neutrons. Deuterium is the isotope form of hydrogen which has a heavier mass compared to ordinary hydrogen. It contains one proton and neutron and has a molecular weight of approximately 2 g/mol. This technique can be used to investigate motions of acyl chains in
lipid Lipids are a broad group of naturally-occurring molecules which includes fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The functions of lipids include ...
s. It measures
carbon Carbon () is a chemical element with the symbol C and atomic number 6. It is nonmetallic and tetravalent In chemistry, the valence (US spelling) or valency (British spelling) of an element is the measure of its combining capacity with o ...
and deuterium interactions and the mobility of these interactions within various regions of the lipid and also determines order parameters. The process involves using
quadrupole A quadrupole or quadrapole is one of a sequence of configurations of things like electric charge or current, or gravitational mass that can exist in ideal form, but it is usually just part of a multipole expansion of a more complex structure refl ...
signaling properties for examining
lamellar A ''lamella'' (plural ''lamellae'') is a small plate or flake, from the Latin, and may also be used to refer to collections of fine sheets of material held adjacent to one another, in a gill-shaped structure, often with fluid in between though s ...
versus non–lamellar phases as well. An external magnetic field monitors the alignment of
paramagnetic Paramagnetism is a form of magnetism whereby some materials are weakly attracted by an externally applied magnetic field, and form internal, induced magnetic fields in the direction of the applied magnetic field. In contrast with this behavior, d ...
compounds and uses changes in the positive or negative magnetic spin values to detect these changes.


Phosphorus nuclear magnetic resonance

Phosphorus
nuclear magnetic resonance Nuclear magnetic resonance (NMR) is a physical phenomenon in which nuclei in a strong constant magnetic field are perturbed by a weak oscillating magnetic field (in the near field) and respond by producing an electromagnetic signal with a ...
(31PNMR) is a type of nuclear magnetic resonance technique that utilizes 31
phosphorus Phosphorus is a chemical element with the symbol P and atomic number 15. Elemental phosphorus exists in two major forms, white phosphorus and red phosphorus, but because it is highly reactive, phosphorus is never found as a free element on Ear ...
instead of
deuterium Deuterium (or hydrogen-2, symbol or deuterium, also known as heavy hydrogen) is one of two Stable isotope ratio, stable isotopes of hydrogen (the other being Hydrogen atom, protium, or hydrogen-1). The atomic nucleus, nucleus of a deuterium ato ...
. 31P is dependent upon changes in the mobility and diffusion of a molecule. It also applies an external magnetic field to analyze the alignment of the paramagnetic compounds and uses changes in the positive or negative magnetic spin values to detect these changes. It is useful in distinguishing between lamellar and hexagonal phases that contain phosphate groups based on their distinct patterns and signals. A disadvantage to this technique is that it is limited to phospholipids.


Thin layer chromatography

Thin layer chromatography Thin-layer chromatography (TLC) is a chromatography technique used to separate non-volatile mixtures. Thin-layer chromatography is performed on a sheet of an inert substrate such as glass, plastic, or aluminium foil, which is coated with a t ...
(TLC) is a type of chromatography technique that is used characterized or separate lipids. The lipids are separated based on the polarity of the head groups or hydrophilic region, not the hydrophobic region. Certain stains like iodine can be used to label the lipids but will sometimes destroy the lipids. This process can also be used to determine whether or not lipids have denatured.Poole, Colin F. The Essence of Chromatography. Elsevier, 2003 and Skoog, Douglas A; West, Donald M; Holler, James F.; Crouch, Stanly R. Fundamentals of Analytical Chemistry. 8th ed. Brooks/Cole, 2004. For example, originally a TLC analysis shows the presence of two lipids. One week later the same sample is reanalyzed but shows the presence of more lipids, which indicates the lipid has denatured.


Fluorescence recovery after photobleaching

Fluorescence recovery after photobleaching Fluorescence recovery after photobleaching (FRAP) is a method for determining the kinetics of diffusion through tissue or cells. It is capable of quantifying the two dimensional lateral diffusion of a molecularly thin film containing fluorescently ...
(FRAP) is a
photochemical Photochemistry is the branch of chemistry concerned with the chemical effects of light. Generally, this term is used to describe a chemical reaction caused by absorption of ultraviolet (wavelength from 100 to 400  nm), visible light (400–7 ...
process applied to
fluorophores A fluorophore (or fluorochrome, similarly to a chromophore) is a fluorescent chemical compound that can re-emit light upon light excitation. Fluorophores typically contain several combined aromatic groups, or planar or cyclic molecules with sev ...
when they lose their fluorescent properties. It can be used to measure the viscosity and lateral diffusion of a lipid bilayer. It also rejuvenates the fluorescence of the fluorophore and monitors how long this process takes to occur over time.Fluorescence Recovery After Photobleaching (FRAP).


Nearest neighbor recognition

Nearest neighbor recognition (NNR) is a technique used to describe
molecular A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and bioche ...
interactions and patterns between
lipid Lipids are a broad group of naturally-occurring molecules which includes fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The functions of lipids include ...
formations. Under thermal conditions it is used to recognize the preferences of lipids to closely interact with another lipid that has similar or different properties.Jianbing Zhang, Honghua Cao, Bingwen Jing, and Steven L. Regen. Ethanol-Induced Reorganization of the Liquid-Ordered Phase: Enhancement of Cholesterol-Phospholipid Association. ''J. Am. Chem. Soc''., 2006, 128 (1), 265–269 * It provides a molecular depiction of lipid bilayer formations by detecting and quantifying the tendency of exchangeable monomers to become what is termed as "nearest-neighbors" of one another in similar environments.


Molecular dynamics simulations

Molecular dynamics Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the ...
(MD) simulations are useful for simulating the motions of atoms and molecules according to physical laws. MD simulations are often applied to lipids to study atom-scale properties that may be difficult to observe otherwise. Force field parameters vary based on atom and molecule types. MD simulations may observe interactions between targeted lipids, proteins, hydrocarbons, water, hydrophilic/hydrophobic regions, ions, solvents, and other components that are present near the exterior and interior of a biomembrane.


Current issues

There are various usages of
ethanol Ethanol (abbr. EtOH; also called ethyl alcohol, grain alcohol, drinking alcohol, or simply alcohol) is an organic compound. It is an Alcohol (chemistry), alcohol with the chemical formula . Its formula can be also written as or (an ethyl ...
which include an additive to gasoline, a primary ingredient for
food preservation Food preservation includes processes that make food more resistant to microorganism growth and slow the oxidation of fats. This slows down the decomposition and rancidification process. Food preservation may also include processes that inhibit ...
as well as alcoholic beverages and being used for transdermal drug delivery. For example, it can function as an
antiseptic An antiseptic (from Greek ἀντί ''anti'', "against" and σηπτικός ''sēptikos'', "putrefactive") is an antimicrobial substance or compound that is applied to living tissue/skin to reduce the possibility of infection, sepsis, or putre ...
in topical creams to kill bacteria by denaturing proteins. Ethanol is an amphiphilic molecule meaning that it has chemical and physical properties associated with hydrophobic and hydrophilic molecules. Although, studies show that when penetrating through the biomembrane its hydrophobic abilities appear to be limited based on its preference to bind closely to the hydrophilic region of the phospholipids. There are various issues presented in regards to ethanol's ability to penetrate through the biomembrane and cause a reorganization of the phospholipids towards non-lamellar phases. The issues are: 1) how the alteration of the phospholipids' phase occurs 2) understanding the significance of ethanol's interaction with membrane proteins and membrane phospholipids 3) understanding the permeability of the biomembrane based on the tolerance and adaptation level in the presence of ethanol although this process appears to be concentration-dependent 4) determining the significance of ethanol's amphiphilic character as it relates to its ability to partition throughout the membrane by increasing the fluidity of it. Ethanol's hydrophobic properties are limited and primarily binds close the hydrophilic region of the phospholipid. This bonds creates strong hydrogen bonds and leads to a strong interlocking amongst the acyl chains 5) why the presence of cholesterol; a sterol compound, inhibits ethanol's ability to disrupt the membrane and 6) deriving the molecular-level mechanism of the entire process.


Research areas


NNR

;Research overview: This study involves creating a combination of model membranes which contain 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1,2-distearoly-sn-glycero-3-phosphocholine (DSPC) referred to as the "host membranes", phospholipids labeled as 1,2,& 3 referred to as "exchanging molecules" or "reporting molecules" and varied cholesterol mole percentages in the presence of an aqueous solution containing 5% ethanol (v/v). The host membranes were chosen because their phase diagrams are well understood and have been extensively characterized by different analytical techniques.6 The nearest neighbor recognition technique is being applied to the formation of the modeled membranes to observe the association between cholesterol and phospholipids as well as the effects that the presence of ethanol has against this interaction. Researchers are observing whether or not ethanol enhances or disrupts the liquid-ordered phase by reorganizing this formation into a liquid-disordered phase. The liquid-ordered phase is similar to a lamellar phase and the liquid-disordered phase represents the non-lamellar phases but the exact type of each phase (hexagonal, cubic, etc.) is not described. As previously mentioned several different combinations of the host membranes, exchanging molecules, and cholesterol are created to form the model membranes. It is important to mention that the exchanging molecules selected have similar properties to the host membranes. The exchanging lipids contain disulfide bonds as well as diacylglycerol groups that are not necessarily present in the host membranes. Studies provide evidence through monolayer measurements, condensing properties, and nearly identical gel to liquid-crystalline phase transition temperatures (Tm) to the host membranes that the presence of these bonds do not play a major role or interfere in the recognition or packing formation of the modeled membranes in the presence of ethanol. The disulfide bonds, diacylglycerol bonds, and similar sterol framework are only present to mimic the physical properties of DSPC, DPPC, and cholesterol as well as aid in the monomer exchanging processes to form exchangeable dimers. The exchangeable lipids undergo a monomer interchanging process through the disulfide bridges in which they either mix ideally, homogenously, or heterogeneously. Their interactions are measured by the equilibrium constant (K) which will be described in further detail under the significance of results section. Overall, the monomer interchanging process is necessary in order to demonstrate the nearest neighbor recognition technique effective by observing changes in the phase composition of the host membranes/phospholipids. Each model membrane consists of a high concentration of one of the host membranes/phospholipids (95% mol %), low concentrations of two exchanging lipids (2.5 
mol% In chemistry, the mole fraction or molar fraction (''xi'' or ) is defined as unit of the amount of a constituent (expressed in moles), ''ni'', divided by the total amount of all constituents in a mixture (also expressed in moles), ''n''tot. This ex ...
each for a total of 5%), varied mole percentages of cholesterol (0–30 mol %) plus a constant concentration of ethanol (5% v/v). An aqueous buffer solution contains the 5% ethanol (v/v) which is desired but due to evaporation, the value is lowered to approximately 2.9% ethanol. ;Significance of research: All experiments are carried out at 60 °C. Changes in the equilibrium constant (K) are used to determine what type of lipid interactions are occurring within the modeled membrane as well as observe liquid-ordered versus liquid-disorder regions. The value of the equilibrium constant determine the following: 1) if monomers are mixed ideally (K = 4.0) 2) when the monomers are mixed homogenously also referred to as a homo-association (K < 4.0) and 3) if the monomers have interchanged heterogeneously which is referred to as an hetero-association (K > 4.0) A plot of (K) is then created versus the cholesterol mol%. Each plot has similar trends in which the value of the equilibrium constant increased as the mol% increased with and without the presence of ethanol indicating a linear regression. Initially all the model membranes were organized in a liquid order phase but as the addition of cholesterol increase a liquid-disorder phase was observed. The following was determined regarding the liquid-order and liquid-disordered transitions during the addition of cholesterol in the presence of ethanol in each model membrane: 1) 0–15 mol% cholesterol a liquid-disordered phase was present 2) from 15 to 30 mol% there was a co-existence of both phases and 3) above 27 mole% of cholesterol the model membrane completed converted back to the original liquid-order phase within a two-hour time frame. The linear regression maxed out at 30 mol% of cholesterol. It is important to mention that ESR studies were also performed that show a coexistence of the liquid-order/liquid-disorder phase from 0 to 8 mole% and as well as 8–27 mol%. The model membrane containing DPPC, cholesterol, and exchanging lipids 1 and 2 show a drastic increase in the linear relationship between (K) versus the mol% of cholesterol. At approximately 8 mol% of cholesterol the start of the liquid-disordered phase begins. This same relationship is observed in the DSPC, cholesterol, and exchanging lipids 2 and 3 but the start of the liquid-disorder phase occurs at approximately 5.2 mole% with and without the presence of ethanol. Also, there is a higher equilibrium constant value in which the studies relate it to the stronger acyl chain interactions due to this region having longer carbon chains which results in a higher melting point as well. This study not only proves that in the presence of ethanol a reorganization or induced phase change takes place between the cholesterol-phospholipid interaction but that by using higher concentrations of sterol compounds like cholesterol it can hinder the effects of ethanol. The research also suggests that ethanol enhances the association between cholesterol-phospholipids within the liquid-ordered bilayers. The mechanism on how ethanol induces the liquid-disorder phase as well as enhances the cholesterol-phospholipid association is still not understood. The researchers have mentioned that part of the liquid-disorder formation occurs possibly be interrupting the hydrophobic region of the phospholipids, by binding closely towards the hydrophilic region of the phospholipid, and acting as "filler" since ethanol cannot closely align with the neighboring phospholipids. All of these possible mechanisms can be contributed to ethanol's amphiphilic nature.


AMDS

;Research overview: In this study there are several atomic-scale molecular dynamics simulations created to illustrate how ethanol affects biomembranes containing phospholipids. The phospholipid membrane systems are comparable to the model membranes above but it only consists of one phospholipid which is palmitoyl-oleoyl-phosphatidylcholine (POPC) or palmitoyl-oleoyl-phosphatidylethanolamine (POPE). The primary difference between the phosphatidlycholine (PC) and phosphatidylethanolamine (PE) is that the three methyl groups attached to the Nitrogen atom for the PC structure is replaced by three hydrogen groups. The overall purpose of this study is similar to the study described above determining the effects of ethanol on biomembranes and how it is able to increase disorder in the membrane interior region forming non-lamellar phases in phospholipids. The experimental method and analytical technique is quite different. In the previous study, it emphasized the NNR technique using a set of host phospholipids, exchanging lipids, ethanol, and cholesterol to create model membranes. An aqueous solution containing 5% ethanol (v/v) was maintained but the concentration of cholesterol was varied to prove how this sterol compound can inhibit the effects of ethanol (inducing a liquid-disorder phase or non-lamellar phases) which is depicted in the different plots of the equilibrium constant (K) versus the mol% of cholesterol for each model membrane. In this study, phospholipid membrane is comparable to the model membrane which consists of POPC, ethanol, water and in some cases the addition of monovalent ions (Na+, K+, and Cl) that are transported throughout the membrane in the presence of ethanol. The concentration of ethanol varies ranging from 2.5 to 30 mol% in an aqueous solution but there is no addition of any sterol compound. The atomic-scale molecular dynamics simulations are used to monitor the changes in the phospholipid membrane. All the simulations are carried out using GROMACS simulation suite software along with other methods that are essential to perform the simulations. The temperature and pressure are controlled at 310K and 1bar. The simulations are measured at various time frames which include ficoseconds (fs), picoseconds (ps), and nanoseconds (ns). A typical simulation is composed of approximately 128 POPC lipids and 8000 solvent molecules which include water and ethanol. In each simulation ethanol molecules, water molecules, head group regions, acyl chains, and the monovalent ions are all color-coded which aids in interpreting the results of the simulations. The concentrations of ethanol are 2.5, 5.0, 15.0 and 30 mol%. The amount of ethanol molecules depend on the concentration of ethanol present in the phospholipid membrane. Force field parameters are measured for the POPC lipids and monovalent ions (Na+, K+, and Cl), which are very important. A summary of the atomic-scale molecular dynamics simulations is then provided which contains important information as follows: 1) a system number that corresponds to a particular phospholipid simulation 2) the concentration of ethanol mol% used in a particular simulation 3) the concentration of ethanol (v/v%) used for the simulation 3) the ethanol/lipid ratio that is derived from the simulation 4) the area (nm2) of the phospholipid membrane which details the expansion of the membranes as the concentration of ethanol is increased 5) the thickness of the membrane which is based on the distance between the average positions of the phosphorus atoms on opposite sides of the phospholipid membrane and 6) the tilt of the head group of the POPC lipid based on changes in the angle towards the interior region of the phospholipid membrane which was surprisingly not very significant. ;Significance of research: The summary of the POPC simulations described above shows that the POPC system's initial area per lipid value was initially .65 ± .01 but it increases by more than 70% to 1.09 ± .03 at 10 mol% of ethanol which indicates the membrane begins to swell and expand as ethanol permeates through its exterior region. Due to the expansion of the membrane, the membrane thickness decreases from 3.83 ± .06 to 2.92 ± .05 which relates to the distance between the phosphorus atoms on opposite sides of the membrane. The study also supports the fact that ethanol prefers to bond just below the hydrophilic region of the phospholipids near the phosphate groups. The location of the ethanol creates a strong hydrogen bond between the water molecules. The results are depicted in the simulations and supported by mass density profiles as well. The mass density profiles show the location of the POPC lipids, water, and ethanol relevant to the hydrophobic core of the membrane and the concentration of ethanol. The mass density of ethanol increases as the concentration increases which indicates ethanol is moving towards the hydrophobic core of the membrane. The membrane becomes partially destroyed. The simulations also support that the interior of the membrane starts to become more hydrophilic due to the presence of water molecules in the interior region once the membrane is partially destroyed. The presence of ethanol also induced the formation of non-lamellar phases (non-bilayer) within the interior region (hydrophobic cored) of the phospholipid membrane. The results are supported by the simulations which show that at approximately 12 mol% of ethanol the membrane was no longer able to tolerate and adapt to the presence of the ethanol resulting in non-lamellar phases. The formations of the non-lamellar phases are described as being irreversible inverted-micelles. This irreversibility of the inverted-micelles are supported by mass density profiles which display an overlapping of leaflets from opposite membranes that interact forming a strong interlocking between the acyl chains or hydrophobic region with and without the presence of ethanol. Snapshots of the simulations are produced at 100 ns which compared the phospholipid membrane system in the presence of ethanol and in the absence of ethanol which continues to support ethanol's preference to bind near the hydrophilic region of the phospholipid. The researchers also added monovalent ions as salt ions (NaCl) to the phospholipid membrane system which formed non-lamellar phases (micelles) as well. This phenomenon is important because they predict that in the presence of ethanol the micelles can serve as transporters for hydrophilic structures across the membrane. Overall, in this study it shows that ethanol is able to penetrate throughout the membrane. I very important point that was revealed in this study is the fact that ethanol can destroy epithelial tissues (lips, throat, stomach, mouth) in humans. Therefore, one must consider some of the damaging effects of some alcoholic beverages that can contain up to 40% of ethanol (v/v).


Conclusion and possible further research studies

The following was concluded based on ethanol's ability to induce non-lamellar phases: #Ethanol does induce non-lamellar phases (non-bilayer) but this process is concentration-dependent. On average the bilayers is preserved at approximately less than 10 mol%. #Ethanol prefers to bond in the hydrophilic region near phosphate groups which could be contributed to its amphiphilic character. #The effects of ethanol can be reversed or hindered in the presence of cholesterol (sterol compounds) #It may be necessary to perform a future study to compare the maximum amount of cholesterol (30 mol%) obtained in the NNR study to varied concentrations of ethanol as depicted in the AMDS study to see if ethanol is still hindered in the presence of sterol compounds.


Notes

{{Phospholipids Ethanol Phospholipids