Lipid Bilayers: A Chemist’s View

Burke Group Literature Seminar

Hosted by Eric Woerly

Friday, September 11, 2009

Lipid Bilayer Dynamics/Function Lipid Membrane Biosynthesis/Assembly

Membrane Proteins Ion Transport Across Membranes

Lipid Membrane/Fatty Acid Oxidation

Lipid Bilayers: A Chemist’s View

Lipid Bilayer Dynamics/Function

Next group:

Lipid Membrane Biosynthesis/Assembly

EPG, DMK, JL, NM, HCT

TMA, SJL, JO, DSP, BCW

Sphingolipid Cholesterol

Glycerophospholipids

Phospholipid Bilayer Components

Fluid Mosaic Model Random Distribution

Raft Model Domain Forming

Superlattice Model Regular distributions

Some Factors Influencing Membrane Fluidity and Distributions: • Lipid composition

• Sterols

• Membrane proteins

• Gel/Liquid-crystalline phase Biochim Biophys Acta 2009, 1788, 12-23.

Membranes are fluid and allow for the lateral movement of its components

Flippase

Lipid Membrane Models

Flippases create asymmetry of lipid components across the membrane. Lipids on both the interior and exterior of the cell are important for

various functions such as molecular recognition and apoptosis.

How and Why Do Lipids Flip?

Arachadonic acid metabolites are important to reproductive function, gastric acid secretion, memory, nerve growth and regeneration, producing skeletal muscle, and many other biological processes.

X

Cyclogoxygenase enzymes are inhibited by ibuprofen, acetylsalicylic acid, acetominiphen, etc.

Lipids as Paracrine Hormone Precursors

X

Vitamin D deficient child before and after treatment

Sterols as Hormone and Vitamin Precursors

Lipid Membrane Biosynthesis/Assembly

EPG, DMK, JL, NM, HCT

Next group:

Membrane Proteins

CB, CJB, JAK, BEU, PW

Coenzyme A

Acyl Carrier Protein

Fatty Acid Synthesis Pathway

Fatty Acid Synthase

Fatty Acid Synthase

Fatty Acid Synthase

Fatty Acid Synthase

Fatty Acid Synthase Enzymes (cytosol)

Lipid Membrane Lipid Membranes

Membrane Biosynthesis and Assembly

Wakil, S. J., Biochemistry, 1989, 28, 4523-4530. Weisiger, R. A., J. Mol. Neurosci., 2007, 33, 42-44.

http://www.williamsclass.com/SeventhScienceWork/CellTheoryParts.htm

Palmitic acid in FABP shuttle

Membrane Biosynthesis and Assembly

Weisiger, R. A., J. Mol. Neurosci., 2007, 33, 42-44.

Protein Data Bank, Mammalian FABP structure.

Membrane Proteins

CB, CJB, JAK, BEU, PW

Next group:

Ion Transport Across Membranes

SGB, GRD, ID, SAD, MME, KCG

• Peripheral proteins

• Integral proteins

image reference: http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/M/MembraneProteins.gif

• Monotopic proteins

• Transmembrane proteins

Membrane Proteins

• Known glycoproteins: structural proteins, enzymes, membrane receptors, transport proteins, etc.

• Precise function of the bound sugar moiety not well understood

O-linked saccharides

N-linked saccharides

Wiley Encyclopedia of Chemical Biology

Glycoproteins

α-Helical

Bundle

β-Barrel

Wiley Encyclopedia of Chemical Biology

Classification of Membrane Proteins

• X-Ray Crystallography • Most important method for determining high-resolution structures • Membrane proteins are notoriously difficult to crystallize and require

special techniques

• NMR Techniques • Some utility for structure determination • Investigation of backbone dynamics and protein-ligand interactions • Sample preparation is a major challenge

• Site-Directed Spin Labeling

• Label the protein with a nitroxide probe • The EPR spectrum of the nitroxide side

chain then provides information about the local structure and dynamics

Characterization of Membrane Proteins

Lodish et al. Molecular Cell Biology

Bacteriorhodopsin

• Passive and active transport

• Ion channels

• Receptors

• Membrane trafficking

• Structural support

Functions of Membrane Proteins

• Transport proteins are affected by bilayer thickness

• The conformational change in the membrane protein perturbs the membrane – this energy contributes the energy difference between conformations

• Protein performance is best when the protein and the surrounding bilayer are matched

Annu. Rev. Biophys. Biomol. Struct. 2007, 36, 107.

Lipid Bilayer Thickness and

Protein Function

• One kind of molecule present in the bilayer can affect multiple proteins in several species

• This suggests that these molecules act by disrupting the protein-bilayer interaction

• Molecules like capsaicin can disrupt the thickness or bending modulus of the bilayer

Capsaicin

Nature 2009, 459, 379.

Lipid Bilayer Composition and

Protein Function

Ion Transport Across Membranes

SGB, GRD, ID, SAD, MME, KCG

Next group:

Lipid Membrane/Fatty Acid Oxidation

GLB, EKD, SF, PJS, EMW

ClC Aquaporin KcsA

MacKinnon Nature 2002, 415, 287-294 MacKinnon et al. Science 1998, 280, 69-77

Agre P et al. J. Struct. Biol. 1999, 128, 34–43

Membranes Spanning Proteins

IUPAC (2003): A compound which can carry specific ions through membranes of cells or organelles.

For crown ethers, complex formation depends on diameter of the ether along with the basicity of the oxygen atoms.

Crown ethers are a classic example of carrier ionophores

Dibenzo-18-crown-6 -polyether

Pedersen, C.J. J. Am. Chem. Soc. 1967, 89, 7017. Steinrauf L. K.; Pinkerton M.; Chamberlin J.W. Biochem. Biophys. Res. Commun. 1968, 33, 29.

Due to the ability of ionophores to carry ions, they can be found as antibiotics. Nigericin is an example of an ion transporter used as an antibiotic.

Nigericin

Ionophores

gramicidin A (gA)

most likely active channel

kinetically trapped inactive channel possible active channel inactive channel

gA channels

F3gA channels

new heterodimeric channels

60 s after gA + F3gA

12 min after gA + F3gA

break/reform

Ion Channel-Forming Peptides

Kovacs, F.; Quine, J.; Cross, T. A. Proc. Natl. Acad. Sci. USA 1999, 96, 7910. O’Connell, A. M.; Koeppe, R. E., II; Anderson, O. S. Science 1990, 250, 1256.

Na

Gap Junctions

• Self-assembly plasma protein

• Hexamer (Homo- and Hetero-oligomerization)

• Ability to open/close channel

• Hexamer connects with another cell’s hexamer to bridge both cells’ cytoplasm

• Ion selectivity for smaller and less electronegative molecules

• Self-assembly plasma inserting small molecule

• Octamer (Homo-oligomerization)

• Ability to open/close channel

• Ion channel bridges between cell’s cytoplasm and extracellular environment

Yeager, M.; Unger, V.M.; Falk, M.M. Curr. Opn. Struc. Bio. 1998 8, 517-524. Falk, M.M.; Kumar, N.M.; Gilula, N.B. J. Cell Bio. 1994 127, 343-355.

Veenstra, R.D. J. Bioener. and Biomem. 1996 28, 327-337. Ahmad, S.; Martin, P.E.; Martin, E.M.; Evans, W.H. Eur. J. Biochem. 2001 268, 4544-4552.

Gap Junctions vs. Amphotericin B

OC

bilayer

OC

protein

OC

total GGG Gramicidin A is a molecular force transducer

Lundbæk, J. A. J. Gen. Physiol. 2008, 131, 421-429. Andersen, O. S.; Ingólfsson, H. I.; Lundbæk, J. A. Ion Channels. In Wiley Encyclopedia of Chemical Biology,

Wiley & Sons, 2008. Images reproduced without permission.

Amphiphiles Affect Membrane Protein Function by Binding to Lipid Bilayers

Lipid Membrane/ Fatty Acid Oxidation

GLB, EKD, SF, PJS, EMW

1904: Franz Knoop determined that fatty acids were oxidized at the beta-carbon.

Early Studies

1904: Franz Knoop determined that fatty acids were oxidized at the beta-carbon.

Early Studies

1904: Franz Knoop determined that fatty acids were oxidized at the beta-carbon.

Early Studies

1904: Franz Knoop determined that fatty acids were oxidized at the beta-carbon.

Early Studies

Biological Pathway

Mechanism of Peroxidaton

• Malonaldehyde

• Marker for oxidative stress in clinical settings

• Hydroxy-alkenals

• Most intensely studied are 4-hydroxy-2-nonenal, 4-hydroxy-2-hexenal

• Modify protein structure

• Serve as subcellular messengers in gene regulatory and signal transduction pathways

Effects of Lipoperoxidaton