, Micelles, Membranes

Architectures of

Membrane proteins

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 1 From molecules to polymers Structures assembled through molecular bricks  • Polimers – Polynucleotides  Nucleic (RNA, DNA) – Polipeptides  Proteins

• Micelles, Liposomes, Membranes

• Hybrid structures  Ribosomes, Peptidoglycans

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 2 From molecules to polymers Structures assembled through molecular bricks  • Polimers – Polynucleotides  Nucleic Acids (RNA, DNA) – Polipeptides  Proteins

• Micelles, Liposomes, Membranes

• Hybrid structures  Ribosomes, Peptidoglycans

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 3 Architectures of amphipathic

Amphipathic nature of phospholipids leads to two major architectures in polar (aqueous) :

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 4 Architectures of amphipathic lipids

Amphipathic nature of phospholipids leads to two major architectures in polar (aqueous) solvents: Micelle • Micelles: one layer exposed to

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 5 Architectures of amphipathic lipids /Vesicle Amphipathic nature of phospholipids leads to two major architectures in polar (aqueous) solvents: • Micelles: one layer exposed to solvent • Membranes (also vesicles/liposomes): two faces – leaflets – exposed to solvent

Bilayer membrane

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 6 Micelles or membranes? • Most phospho-/glyco-lipids prefer bilayer than micelle architectures. Why? • Bulkiness of two fatty chains does not allow fit of hydrophobic tails to interior of micelle. • Fatty acids’ salts (e.g. ) containing only one chain readily form micelles.

• Other phases, such as hexagonal (HII), cubic, and more complex also found.

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 7 Micelles or membranes? • Most phospho-/glyco-lipids prefer bilayer than micelle architectures. Why? • Bulkiness of two fatty acid chains does not allow fit of hydrophobic tails to interior of micelle. • Fatty acids’ salts (e.g. soaps) containing only one chain readily form micelles.

• Other phases,• suchMicelles as hexagonal limited in (H size,II), cubic, less thanand more ~20 complexnm. also found. • Bilayers can be macroscopic, up to ~106 nm. • …a reason for preference of latter in living organisms.

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 8 Micelles or membranes?

All of these phases are formed by different natural lipids under variable conditions

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 9 Self-assembly of amphipathic lipids

bilayers (as well as micelles) form spontaneously in polar solvents (self-assembly). • Process mainly driven by and by optimization of hydrophobic interactions among lipid tails. • Electrostatic and H-bonds interactions between polar heads and solvents contribute to stabilization. • Membranes are cooperative structures: – Tend to be extensive. – Tend to close on themselves (forming vesicles/compartments) as to avoid hydrophobic edges exposed to solvent. – Are self-sealing (holes thermodynamically unstable).

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 10 Self-assembly of micelles

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 11 Self-assembly of bilayers

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 12 Key features of membranes Common features to all membranes • Sheet-like structures 5-10 nm thick (3-4 nm hydrophobic core). • Contain lipids (phospho-, glyco-, sphingo-lipids, sterols), proteins and carbohydrates. • Amphipathic lipids self-assemble in aqueous environment, held together by cooperative non-covalent interactions, and act as a barrier to flux of polar molecules. • Asymmetric: inner and outer leaflet (faces) always differ. • 2D solutions of oriented proteins and lipids: in general can translate into membrane plane, but rotations across membrane infrequent. • Most electrically polarized, with negative potential inside (typically ~ -60 mV).

Different membranes have their peculiarities (e.g. plasma membrane is peculiar with respect to membranes of organelles) and associated proteins can be also highly specific of that membrane.

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 13 Composition of membranes

Asymmetry key feature of biological membranes (e.g. plasma)

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 14 Composition of membranes

Highly variable lipids mixtures, depending on function.

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 15 Composition of membranes

Highly variable protein/lipid mass ratio (from 1:5 to 4:1) depending on role of specific membranes:

• Myelin (membrane insulating certain nervous fibers) has low content of proteins (15-30%) because pure lipids are good insulators. • Plasma membranes contain ~50% of proteins (pumps, channels, receptors, enzymes). • Mitochondrial and chloroplasts internal membranes transduce energy, need proteins (~75% of proteins).

Type of proteins also vary with specific function of membrane.

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 16 Functions of biological membranes Biological membranes define inside vs. outside of any cell and of organelles in eukaryotic cells • Prevent leaking of intracellular material and penetration of unwanted compounds. • Selective permeability through membrane proteins (pumps and channels) floating in lipids sea. • Additional functions associated to other membrane proteins: energy storage, information transduction, receptor functions, enzymatic activity, etc…

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 17 Plasma membranes in some cells

• Plasma membranes present in all kinds of cells. • Differ in Gram- and Gram+ bacteria.

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 18 Plasma membranes in some cells

• Gram+ and archaea have one membrane surrounded by cell wall. • Gram- two membranes separated by periplasm (contains proteins, peptides, and carbohydrates) lying in between. • Outer membrane quite permeable to small molecules owing to presence of porins.

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 19 Plasma membranes in some cells

Differ in prokaryotic and eukaryotic cells • Eukaryotic cells (with exception of plant cells) do not have cell walls, and their cell membranes consist of a single . In plant cells, cell wall is on outside of plasma membrane.

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 20 Plasma membrane FM model

Fluid mosaic model • Fluid because membranes are 2D solutions of oriented lipids and proteins • Mosaic because they are a composition of different lipids and proteins

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 21 Plasma membrane FM model

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 22 Membrane proteins classification

• Most processes carried out by/in membranes are mediated by proteins. • Protein classification based on strength of interaction with lipid bilayer, reflecting degree of burial into membrane

© Biochemistry, J. Berg et al., 5th ed., 2001 Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 23 Membrane proteins classification

Integral membrane proteins (yellow) interact strongly with hydrocarbon chains of lipids • Can be removed by agents competing with hydrophobic interactions, such as or organic solvents (e.g. hexane, toluene). • Most integral proteins span entire lipid bilayer.

© Biochemistry, J. Berg et al., 5th ed., 2001 Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 24 Membrane proteins classification

Peripheral membrane proteins (azur) bound to hydrophilic heads of lipids by electrostatic interactions and/or H-bonds • Can be dissociated by mild means, such as highly concentrated ionic solvents (e.g. 1 M NaCl) • Some further stabilized by covalent anchor to hydrophobic chains

© Biochemistry, J. Berg et al., 5th ed., 2001 Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 25 Membrane proteins’ topologies • α-helices and β-barrels (β-sheet curled to form a hollow cylinder) preferred structures assumed by integral membrane proteins (embedded in lipid bilayer). • Intra-chain H-bonds in α-helices and β-sheets thermodynamically favored in hydrophobic environment, where no polar competitor molecules are present.

Porin Bacteriorhodopsin

Prostaglandin synthase

© Biochemistry, J. Berg et al., 5th ed., 2001 Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 26 Membrane proteins’ topologies • α-helices usually span entire bilayer perpendicularly to its plane (~20 AA in length). • Most residues non-polar, distribution optimized to enhance stability: – Hydrophobic/apolar AA points towards lipid chains – Polar/charged residues create functional networks

Bacteriorhodopsin

© Biochemistry, J. Berg et al., 5th ed., 2001

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 27 Membrane proteins’ topologies Propensity of α-helices to insert into hydrophobic bilayers estimated from hydropathy (HP) index, i.e. (per-residue) free energy of transfer of mono-AA α-helices from hydrophobic environment to water: – Empirically, HP ≥ 20 kcal/mol for 20 AA sequence to be found as TM α-helix. – In a HP plot, peak should correspond to TM helix.

© Biochemistry, J. Berg et al., 5th ed., 2001 Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 28 Membrane proteins’ topologies

• PHE, MET, ILE highest value of transfer free energy  favourable TM helix. • ARG, ASP, LYS, GLU most negative values  unfavourable TM helix. • However… – Peak in HP index does not imply a sequence will give a trans-membrane (TM) helix! – Only valid for α-helices, not applicable to β-barrel!

HP index of a porin (β-barrel)

© Biochemistry, J. Berg et al., 5th ed., 2001 Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 29 Membrane proteins’ topologies

• β-barrels formed by antiparallel curled β-sheets. • Outside residues mostly nonpolar, inside (water-filled) hydrophilic, realized through alternation of hydrophobic and hydrophilic AA along each strand.

H-bond

© Biochemistry, J. Berg et al., 5th ed., 2001 Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 30 Membrane proteins’ topologies

• Some proteins attached to bilayer surface and have hydrophobic anchors protruding into the lipid bilayer. • Integral proteins (very stable) although not membrane-spanning.

Prostaglandin synthase

© Biochemistry, J. Berg et al., 5th ed., 2001 Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 31 Membrane proteins’ topologies Some proteins covalently attached to membrane lipids by means of ester hydrophobic groups.

© Biochemistry, J. Berg et al., 5th ed., 2001 Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 32 Membranes are fluids Membranes are highly flexible and dynamic objects

Lipid dynamics include: 1. Chain conformational transitions and defect motions 2. Rotational diffusion around long axes 3. In-plane lateral diffusion (local and jumps) 4. Heads’ motions 5. Out-of-plane vibrations 6. Collective undulations

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 33 Membranes are fluids Lipid and proteins lateral diffusion • Lateral diffusion obeys Einstein rule: s = 4Dt • Diffusion coefficient of various (fluid) membranes ~ 1µm2s-1 (1/100 of water).

~ 2 µm in 1s  a lipid can go from one end to other of a bacterium in 1s! • Proteins lateral motilities can vary from very low to lipid-like values: - 10-4 µm2s-1 for fibronectin, a glycoprotein anchoring cells to extracellular matrix (ECM) through linkages with integrin, in turn linked to cytoskeleton (interaction with actin fibers). - 0.4 µm2s-1 for bacteriorhodopsin (fast movement essential for efficient signaling).

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 34 Membranes are fluids Lipid and proteins transverse diffusion (flip-flop) • Flip-flop of lipids occurs very rarely (once in several hours) • Flipping of proteins never been observed Very frequent and fast Very rare

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 35 Membranes are fluids Lipid and proteins transverse diffusion (flip-flop) • Transverse diffusion important mechanism involved in building-up new membranes from existing patches (in eukaryotes plasma membranes built from ER ones). • Flippase enzymes present in ER membrane of eukaryotes and in plasma membrane of prokaryotes transfer some of newly formed phospholipids to opposite . • Flippases do not bind all phospholipids equally well, thus two membrane leaflets end up having different distributions of (asymmetric!)

Membrane building in eukaryotes Flippase action Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 36 Membranes are fluids Fluidity depends on composition and presence of non-fatty-acids lipids • Membranes can exist in different phases: two extreme ones are gel (solid-like) and fluid liquid. • Gel to liquid transition can be caused by conformational changes in packing of phospholipids acyl chains from trans to gauche. • Membrane-mediated processes depends crucially on fluidity!

Gel phase Liquid phase

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 37 Membranes are fluids Fluidity depends on composition and presence of non-fatty-acids lipids • Transition from gel-like to fluid state occurs abruptly at melting

Tm

© Biochemistry, J. Berg et al., 5th ed., 2001 • Additional phases also found (ripple and different fluid-like ones) • Transitions among different phases depend on many factors including temperature, pH, ionic strength, pressure and membrane composition (e.g. saturated/unsaturated lipids ratio and content of molecules such as cholesterol)

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 38 Membranes are fluids Fluidity depends on composition and presence of non-fatty-acids lipids • Some phospholipids (e.g. PC) undergo two steps transition.

• First transition at few degrees below Tm, due to changes in vicinity of polar heads (e.g. increased interaction with solvent). • Two step transition consequence of simultaneous changes in lipid order and membrane curvature  lipids that exhibit a pre-transition temperature display additional (ripple). • Ripple phase partially disordered, displays periodic one dimensional undulations on surface of lipid bilayer (arising from periodic arrangements of linear ordered

and disordered lipid domains). Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 39 Membranes are fluids Fluidity depends on composition and presence of non-fatty-acids lipids

Tm depends on length of fatty acyl chains and on their degree of unsaturation:

• cis double bond induces bending, interfering with ordered packing  Tm is lowered.

• Long hydrocarbons interact more strongly than short ones. Each additional –CH2– group adds ~0.5 kcal/mol to free energy of interaction of two adjacent chains.

© Biochemistry, J. Berg et al., 5th ed., 2001 Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 40 Membranes are fluids Membrane fluidity regulation in bacteria • Bacteria regulate fluidity of their membranes by varying number of double bonds and length of fatty acyl chains. • Ratio of unsaturated to saturated fatty acyl chains in E. coli membrane increases from 0.35 to 1.6 as growth T is lowered from 42°C to 27°C. • Decrease in proportion of saturated residues

prevents membrane from becoming too rigid.

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 41 Membranes are fluids Fluidity regulation in animal eukaryotic cells • Cholesterol is key regulator of fluidity, allowing bilayers to adopt extra lamellar phase (liquid-ordered), intermediate between gel and fluid. • Opposite effects depending

on T being below or above Tm: - Inserting cholesterol in gel phase disrupts packing, reducing ordering of lipid chains. - In liquid phase rigid hydrophobic moiety of cholesterol intercalates between lipid chains, favoring trans conformation. • In liquid-ordered phase: - Lateral and rotational diffusion similar to liquid-disordered phase.

- Conformational order similar to solid-ordered.

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 42 Membranes are fluids Ordering effect of cholesterol in DPPC bilayer

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 43 Membrane flexibility: a model Flexibility and hetereogenity of membrane “particles” (different kinds of lipids and proteins) reflect on macroscopic shape and rigidity of bilayer

• Membrane geometry deformations include stretching, bending, shrinking or expansion, shearing.

• Free energy cost associated to membrane deformation can be roughly estimated by means of elastic continuum theory.

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 44 Membrane flexibility: a model Flexibility and hetereogenity of membrane “particles” (different kinds of lipids and proteins) reflect on macroscopic shape and rigidity of bilayer

• Stretching can be described by simple area function Δa(x1,x2), depending on position on plane (reflects possible inhomogeneity in membrane). • Compression and expansion can be described by simple thickness function w(x1,x2). • Shearing can be describe through angle θ formed by two sides of surface elements.

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 45 Membrane flexibility: a model Flexibility and hetereogenity of membrane “particles” (different kinds of lipids and proteins) reflect on macroscopic shape and rigidity of bilayer

• Bending can be described by simple height function h(x1,x2) from a reference plane. • For practical purposes, best plane is 1 2 tangent to point (x 0,x 0) of interest  quadratic expansion of h using Taylor series in local reference frame: 2 h(x1 , x2 ) = ∑κij xi x j i, j=1

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 46 Membrane flexibility: a model Flexibility and hetereogenity of membrane “particles” (different kinds of lipids and proteins) reflect on macroscopic shape and rigidity of bilayer

• Bending can be described by simple height function h(x1,x2) from a reference plane. • For practical purposes, best plane is 1 2 tangent to point (x 0,x 0) of interest  quadratic expansion of h using Taylor series in local reference frame: 2 h(x1 , x2 ) = ∑κij xi x j i, j=1 • Can be done for every point of even complex surfaces, by sub-dividing surface and introducing many local reference frames.

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 47 Membrane flexibility: a model Flexibility and hetereogenity of membrane “particles” (different kinds of lipids and proteins) reflect on macroscopic shape and rigidity of bilayer

• Curvature (bending) of membrane can be calculated from knowledge of h, namely from 2nd order derivatives which account for surface curvature matrix κ:

! $ 2 κ11 κ12 ∂ h κ = # & κ = # & ij x x " κ 21 κ 22 % ∂ i∂ j

• Diagonalization of κ corresponds to identify reference frame giving two principal axes of curvature.

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 48 Membrane flexibility: a model ΔG of membrane deformation as functional of shape functions Δa, h, w, θ • Area stretching modeled by means of spring network. • Deformation from reference area associated to increase in free energy: " %2 Ka Δa(x1, x2 ) Gstretch = ∫ $ ' da 2 # a0 & 2 Ka Δa • If relative areal strain Δa/a constant: Gstretch = 2 a0 2 • Ka stretch modulus: 55-70 kBT/nm ~ 230-290 mN/m

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 49 Membrane flexibility: a model ΔG of membrane deformation as functional of shape functions Δa, h, w, θ • Bending (deformation from planar surface) modeled by means of spring network. • Free energy as a functional of principal curvatures:

K 2 b ! # Gbend = da"κ1 (x1, x2 ) +κ 2 (x1, x2 )$ 2 ∫

• Kb bending rigidity: 10-20 kBT

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 50 Membrane flexibility: a model ΔG of membrane deformation as functional of shape functions Δa, h, w, θ • Change in thickness modeled by means of elastic network. • Deformation from reference thickness associated to increase in free energy:

" %2 Kt w(x1, x2 ) − w0 Gthickness = ∫ da$ ' 2 # a0 &

2 • Kt stiffness modulus: 60 kBT/nm .

• Shear deformation also quadratic in θ.

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 51 Vesicles Vesicles are closed spherical shells of lipids that can be used as tools to investigate elastic properties of membranes Two main experiments

Micropipette aspiration Membrane pulling

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 52 Vesicles Micropipette aspiration • Small pipette (~ 10 µm diameter d) used as a solution probe to grab vesicles. • Pressure difference Δp between micropipette and solution allows suction that deforms vesicle membrane.

• Knowledge of Δp and geometric parameters Rv, R1 (~d/2) and l allows determination of τ and of moduli Ka and Kb. • Laplace-Young relation gives pressures

Δp needed to maintain spheres of radii RV/R1: 2τ 2τ Δpout = Δpin = Δpin RV R1

• Since: Δp = Δpin − Δpout Δpout Δp R • We have: τ = 1 2 1−(R1 RV )

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 53 Vesicles Micropipette aspiration

Δp R1 • For each Δp measure geometric parameters and calculate τ τ =  2 1−(R1 RV ) • From τ calculate moduli Ka and Kb. Δa • E.g. Ka calculated recalling that τ corresponds to ΔG per surface area: τ = Ka a0 • Δa determined from expt. images, or…

• Approximated (assuming constant Rv upon suction) by:

2 2 Δa = 2π R1l + 2π R1 a0 = 4π RV 

2 Δa R1 (1+ l R1) τ = Ka = Ka 2 a0 2RV

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 54 Vesicles Micropipette aspiration 2 Δa R1 (1+ l R1) τ = Ka = Ka 2 a0 2RV

Slope of τ vs. Δa/a0 gives

the stretch modulus Ka

Typical values for pure phospholipid bilayers ~250 mN/m Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 55 Vesicles Micropipette aspiration

Two main limitations: • Formula linking tension to stretch modulus ignore thermal fluctuations in membrane (entropic effect). • This is valid only at high enough tensions ironing out spontaneous undulations. • Stress-stretch relationship in entropic regime

allows determination of bending constant Kb.

• Values obtained for ideal single-lipid membranes, not accounting lipid heterogeneity, membrane proteins and intra- and extra-cellular connections.

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 56 Vesicles Membrane pulling • Closely mimic real world situation, where formation of tubules (e.g. in ER and trans-

Golgi network) occurs driven by forces different than those arising from Δp.

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 57 Vesicles Membrane pulling • Closely mimic real world situation, where formation of tubules (e.g. in ER and trans- Golgi network) occurs driven by forces different than those arising from Δp. • Experiments with optical tweezers show that applying a force to a single point of membrane results in tether formation. • Forces are in range 5-20 pN for a variety of different membranes.

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 58 Vesicles Membrane pulling • Free energy of vesicle+tether system can be written as sum of four terms:

L G = 8πK + πK + 4πK bend b b r b Vesicle  Tether end Tether body

2 Ka (a − a0 ) Gstretch = 2 a0

# 4 3 2 & GpV = −Δp% π R + r π L( $ 3 '

Gload = − fL

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 59 Vesicles Membrane pulling • Minimizing sum of free energy terms with respect to geometric variables r, L

and R gives a relation between applied force and tension and constant Kb

f = 2π 2Kbτ

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 60 References • Books and other sources • Physical Biology of the Cell, R. Phillips et al., 2th ed., Chap. 11 • Biochemistry (5th ed.), Berg et al., Chap. 12

Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course. 61