Chapters 14 and 16

Membrane Proteins

Channels

Fibrous ProteinsAmyloid Fibrils

Membrane Structure• Biological membranes are bilipid layers. In a real cell the

membrane phospholipids create a spherical three dimensional lipid bilayer shell around the cell. However, they are often represented two-dimensionally as:

• The circle, or head, is the negatively charged phosphate group and the two tails are the two highly hydrophobic hydrocarbon chains of the phospholipid. The tails of the phospholipids orient towards each other creating a hydrophobic environment within the membrane. This leaves the charged phosphate groups facing out into the hydrophilic environment. The membrane is approximately 5 nm thick.

Membrane Properties• This bilipid layer is semipermeable, meaning that

some molecules are allowed to pass freely (diffuse) through the membrane.

• The lipid bilayer is virtually impermeable to large molecules, relatively impermeable to molecules as small as charged ions.

• It is quite permeable to lipid soluble low molecular weight molecules. It is substantially permeable to water molecules. Molecules that can diffuse through the membrane due so at differing rates depending upon their ability to enter the hydrophobic interior of the membrane bilayer.

Membrane Functions

• Forms selectively permeable barriers• Transport phenomena• Cell communication and signaling• Cell-cell adhesion and cellular attachment• Cell identity and antigenicity• Conductivity

Membrane-bound Proteins

• From left to right are (a) a protein whose polypeptide chain traverses the membrane once as an a helix, (b) a protein that forms several transmembrane helices connected by hydrophilic loop regions, (c) a protein with several strands that form a channel through the membrane, and (d) a protein that is anchored to the membrane by one helix parallel to the plane of the membrane.

Integral (Intrinsic) Proteins

• penetrate the bilayer or span the membrane entirely• can only be removed from membranes by disrupting the

phospholipid bilayer

Transmembrane proteins

• Transmembrane proteins can be divided into two classes, either (1) single-pass and (2) multiple-pass.

• Trans-membrane proteins have membrane spanning portions containing helically arranged sequences of 20-25 hydrophobic amino acids. Short strings of hydrophilic amino acids separate the hydrophobic sequences from each other.

•These hydrophilic stretches tend to be found exposed to the more aqueous•environments associated with the cytoplasm or the extracellular space.

Covalently Tethered Integral Membrane Proteins

• Tethered integral membrane proteins may be largely exposed to either the cytoplasm or aqueous extracellular space, but are covalently linked to membrane phospholipids or glycolipids

Glycoproteins• Many integral proteins are

glycoproteins covalently linked to sugars via asparagine, serine, or threonine.

• The sugars of glycoproteins are exclusively found on the extracellular side or topological equivalent of the membrane.

• Glycosylation begins in the lumen of the ER

• Carbohydrates are modified in Golgi complex.

Properties of Peripheral (Extrinsic) Proteins• do not penetrate the phospholipid bilayer• are not covalently linked to other membrane components• form ionic links to membrane structures

a. can be dissociated from membranesb. dissociation does not disrupt membrane integrity

• located on both extracellular and intracellular sides of the membrane and often link membrane to non-membrane structures

synthesis of peripheral proteins:a. cytoplasmic (inner) side:

made in cytoplasmb. extracellular (outer) side:

made in ER and undergo exocytosis

Solubilization and crystallization of membrane proteins

Bacteriorhodopsin• An electron density map to 7 Å resolution (a) was obtained and

interpreted in terms of seven transmembrane helices (b). In 1990, the resolution was extended to 3 Å, which confirmed the presence of the seven helices connected by loop regions and where the retinal molecule was bound to bacteriorhodopsin.

Photoisomerization of Rentinal• The light-absorbing pigment retinal

undergoes a conformational change called isomerization when it absorbs light. One part of the molecule rotates 180° around a double bond between two carbon atoms (green). The geometry of the molecule is changed by this rotation from a trans form to a cis form.

• Protons are pumped from cytosol to the extracellular space, creating a proton gradient.

• The generated proton gradient is used to produce ATP and to transport ions and molecules across the membrane.

The Bacteriorhodopsin Proton Channel and Bound Retinal.

• A to E are the seven transmembrane helices. Retinal is covalently bound to a lysine residue. The relative positions of two Asp residues, which are important for proton transfer, are also shown.

• Retinal is bound in a pocket in the middle of bacteriorhodopsin.

• It is covalently linked to Lys-216 with a positive charge

• Asp-96 and Asp-85 are located on both sides of the retinal.

The Photocycle of Bacteriorhodopsin

• The protein adopts two main conformational states, tense (T) and relaxed (R). The T state binds trans-retinal tightly and the R state binds cis-retinal. The structure of bacteriorhodopsin in the T state, shown in (a), with trans-retinal bound to Lys 216 via a Schiff base. A proton is transferred from the Schiff base to Asp 85 following isomerization of retinal and a conformational change of the protein, as shown in (b).

The Photocycle of Bacteriorhodopsin

• The structure of bacteriorhodopsin in the R state with cis-retinal bound (c). A proton is transferred from Asp-96 to the Schiff base and from Asp-85 to the extracellular space. A proton is transferred from the cytoplasm to Asp-96, as shown in (d).

Porin Channels

• The outer membrane of bacteria contain porin channels with beta barrels.

• Ribbon diagram of one subunit of porin from Rhodobacter capsulatus viewed from within the plane of the membrane. Sixteen strands form an antiparallel barrel that traverses the membrane. The long loop between strands 5 and 6 (red) (eyelet) constricts the channel of the barrel. Two calcium atoms are shown as orange circles.

periplasm

extracellular

funnel

Hydrophobic

Hydrophilic

Each Porin Molecule has Three Channels• Large extracellular molecules

are prevented from entering the channel due to the funnel size of the trimer.

• Further screening occurs at the entrance of the channel in the individual barrels.

• A molecule small enough to enter the central channel will then encounter the eyelet where the charged sidechains determine the size limitations and the ion selectivity of the pore.

Hydrophobic

K+ Channel• The membrane potentials of resting cells are determined

largely by K+, which is actively pumped into cells by an ATP-driven Na, K+ pump.

• Na+ and K+ can also move freely in and out through K+ leak channels.

• The K+ leak channels in the plasma membrane are highly selective for K+ ions by a factor of 104 over Na+, and have a throughput of 108 ions per second.

• Why do K+ channels have such high specificity with high levels of ion conductance?

The Potassium Channel• Schematic diagram for the

structure of a potassium channel viewed perpendicular to the plane of the membrane. The molecule is tetrameric with a hole in the middle that forms the ion pore (purple). Each subunit forms two transmembrane helices, the inner and the outer helix. The pore helix and loop regions build up the ion pore in combination with the inner helix.

Potassium Channel Selectivity Filter

• Diagram showing two subunits of the K+ channel, illustrating the way the selectivity filter is formed. Main-chain atoms line the walls of this narrow passage with carbonyl oxygen atoms pointing into the pore, forming binding sites for K+ ions.

The Ion Pore of the Potassium Channel

• The cytosolic side of the pore begins as a water-filled channel that opens up into a water-filled cavity near the middle of the membrane. A narrow passage, the selectivity filter, links this cavity to the external solution. Three potassium ions (purple spheres) bind in the pore. The pore helices (red) are oriented such that their carboxyl end (with a negative dipole moment) is oriented towards the center of the cavity to provide a compensating dipole charge to the K+ ions.

Hydropathic Index

Channel selectivity is determined by the conserved residues at the P-regions.

Glucose Transporters

• The thermodynamic downward movement of glucose across the plasma membrane of animal cells is mediated by several glucose transporters (GLUT1-5) composed of about 500 amino acids.

• The common structural themes of GLUT is the presence of 12 transmembrane segments.

The glucose binding site alternately faces the inside and outside of the cell when occupied by a sugar.

The Photosynthetic Reaction Center• The three-dimensional structure of a

photosynthetic reaction center of a purple bacterium was the first high-resolution structure to be obtained for a membrane-bound protein. The molecule contains four subunits: L, M, H, and a cytochrome. Subunits L and M bind the photosynthetic pigments, and the cytochrome binds four heme groups. The L (yellow) and the M (red) subunits each have five trans-membrane -helices A-E. The H subunit (green) has one such trans-membrane helix, AH, and the cytochrome (blue) has none. Approximate membrane boundaries are shown. The photosynthetic pigments and the heme groups appear in black.

Photosynthetic Pigments in a Reaction Center

• Schematic arrangement of the photosynthetic pigments in the reaction center of Rhodopseudomonas viridis.

• The twofold symmetry axis that relates the L and the M subunits is aligned vertically in the plane of the paper. Electron transfer proceeds preferentially along the branch to the right.

Fibrous Proteins• Fibrous proteins are built up from long fibers.• Fibrous proteins often form protofilaments or

protofibrils that assemble to structurally specific, high order filaments and fibrils.

• Dependent on the secondary structure of the individual molecules, fibrous proteins an be divided into three classes• The triple helix (collagen)• Coil-coil helices (keretin & myosin)• sheet in amyloid fibers and silks

Facilitated Diffusion of Glucose into Erythrocytes

• All the steps in the transport of glucose into cells are freely reversible, the direction of movement of glucose being dictated by the relative concentrations of glucose on either side of membrane. In order to maintain the concentration gradient across the membrane, the glucose is rapidly phosphorylated inside the cell to glucose 6-phosphate by hexokinase.

Collagen• Collagens are proteins that assemble into fibrous super-

molecular aggregates in the extracellular space, which comprise three polypeptide chains with a large number of repeat sequences Gly-X-Y where X is often proline and Y is often hydroxyproline.

• Hydroxyproline is formed by the post-translational modification of proline by prolyl hydroxylase.

• Each collagen polypeptide chain contains about 1000 amino acid residues and the entire triple chain molecule is about 3000 Å long.

Types of Collagen

The Collagen Helix • Each polypeptide chain in the collagen molecule folds into an extended polyproline type II helix with a rise per turn along the helix of 9.6 Å comprising 3.3 residues. In the collagen molecule, three such chains are supercoiled about a common axis to form a 3000-Å-long rod-like molecule. The amino acid sequence contains repeats of -Gly-X-Y- where X is often proline and Y is often hydroxyproline.

Formation of Hydroxyproline & Hydrolysine

Biosynthesis of

Collagen

Gly to Ala Mutation in Polyproline Type II Helix.

• Models of a collagen-like peptide with a mutation Gly to Ala in the middle of the peptide (orange).

• Each polypeptide chain is folded into a polyproline type II helix and three chains form a superhelix similar to part of the collagen molecule. The alanine side chain is accommodated inside the superhelix causing a slight change in the twist of the individual chains

Hydrogen Bonding in the Collagen Triple Helix

• In the regular collagen triple helix, the three chains are held close together by direct interchain hydrogen bonds between proline C=O groups and glycine NH groups.

Hydrogen Bonds in the Gly-Ala Mutation

• In the region around the alanine residues, the three polypeptide chains are forced apart by the alanine side chains. • Four water molecules are inserted in the interior of the triple helix to mediate hydrogen bonds between the polypeptide chains, which are displaced due to the alanine side chains in this region.

Intrachain Water Bridges in a Collagen-like Peptide

Space-filling models of intrachain water bridges observed in the crystal structure of a collagen-like peptide. The oxygen atoms of the water molecules are yellow and the hydrogen atoms are white. A bridge of three water molecules hydrogen bonded to two C=O groups and linked to other water molecules are shown in (a). Long bridges of water molecules establish a network that surrounds the triple helix shown in (b).

Domain Organization of Intermediate Filament Monomers

• The domain organization of intermediate filament protein monomers. Most intermediate filament proteins share a similar rod domain that is usually about 310 amino acids long and forms an extended helix. The amino-terminal and carboxy-terminal domains are non--helical and vary greatly in size and sequence in different intermediate filaments.

A Model of Intermediate Filament Construction• The monomer shown in (a)

pairs with an identical monomer to form a coiled-coil dimer (b). The dimers then line up to form an antiparallel tetramer (c). Within each tetramer the dimers are staggered with respect to one another, allowing it to associate with another tetramer (d). In the final 10-nm rope-like intermediate filament, tetramers are packed together in a helical array (e).

Myosin Molecule

• Schematic diagram of the myosin molecule, comprising two heavy chains (green) that form a coiled-coil tail with two globular heads and four light chains (gray) of two slightly differing sizes, each one bound to each heavy-chain globular head.

Silk Fibers of Spiders• Individual spiders generate up to seven distinct silk fibers by

drawing liquid crystalline proteins from a set of separate gland-spinneret complexes.

• The proteins, silk fibroins, are produced inside the glands from a family of homologous genes and stored as a highly concentrated (up to 50%) solution of mainly -helical proteins.

• This solution is passed through the spinning machinery of the spider and mixed with other components, producing a variety of different fibers in which the proteins have adopted a -structure.

• Sequence pattern of silk fibers:– Variable domains at both N & C-termini flank a large region

of repetitive short sequences of alternating poly-Ala (8 to 10) and Gly-Gly-X repeats (where X is usually S,Y,or Q) up to 800 residues.

Silk Fibers of Spiders• Spider fibers are composite

materials formed by large silk fibroin polypeptide chains with repetitive sequences that form sheets. Some regions of the chains participate in forming 100 nm crystals, while other regions are part of a less-ordered mesh-work in which the crystals are embedded. The diagram shows a model of the current concepts of how these fibers are built up, which probably will be modified and extended as new knowledge is gained.

Alzheimer's Disease• Alzheimer's disease is characterized by the deposition of

insoluble amyloid fibrils as amyloid plaques in the neurophil as well as the accumulation of neurofibrillary tangles in cell bodies of neurons.

• The amyloid fibrils are composed of the amyloid peptide (A), a 39-43 amino acid residue peptide produced by cleavage from a larger amyloid precursor protein, APP. The Apeptide is known to be present in unaffected individuals and is thought to have a normal physiological role. However, in Alzheimer's disease patients, the A peptide forms ordered aggregates which are deposited extracellularly as amyloid plaques or senile plaques in the neurophil, and as vascular deposits.

Alzheimer's Disease

• Alzheimer's disease is not the only disease in which amyloid fibrils are involved in the pathology. There is now a list of some 16 proteins which can form amyloid fibrils in various diseases. These proteins vary considerably in their primary structure, function, size and tertiary structure, and yet they appear to form amyloid fibrils, which show very few structural differences.– Immunoglobulin light chain– A-proteins precursor

Electron Micrograph of Amyloid Fibrils

• Electron micrograph of amyloid fibrils formed in water from Aβ1-42, stained with 0.1 % phosphotungstic acid showing long straight fibrils of 70 - 80 Å diameter as well as fibrillar aggregate background. Bar = 1000 Å.

Structure of Amyloid Fibrils

• Electron microscopy has shown that amyloid fibrils are straight, un-branching fibers of 70-120 Å in diameter and of indeterminate length. All amyloid fibrils stain with the dye Congo red and give a green birefringence when examined under cross-polarized light, and finally they reveal a cross-β fiber diffraction pattern which suggests aβ-sheet type structure for the fibrils.

Structure of Amyloid Fibrils

• A strong 4.8 Å reflection on the meridian corresponds to the hydrogen bonding distance between β-strands (shown on the right), and a more diffuse 10 - 11 Å reflection on the equator shows the inter-sheet distance of about 10.7 Å. A spacing of 9.6 Å would correspond to the repeat distance for an anti-parallel arrangement of β-strands.

Structural Studies of Amyloid Fibrils• Structural studies of amyloid fibrils from Alzheimer's disease brain

have proved extremely difficult due to the insolubility of the plaques. Examination of the structure of amyloid fibrils has concentrated on fibrils formed in vitro from synthetic peptides homologous to the Aβ peptide.

• However, synthetic amyloid fibrils are problematic to study using conventional structural techniques. Methods such as single crystal X-ray crystallography and solution nuclear magnetic resonance (NMR) cannot be used on fibrils since they are insoluble.

• X-ray fiber diffraction, electron microscopy (EM), solid state NMR, fourier transform infrared spectroscopy (FTIR) and circular dichroism (CD) have been used to examine amyloid structure.

The Structure of Soluble Aβ• Structure prediction studies have indicated that the last 10

residues at the C-terminal and residues 17 - 21 of Aβ show the greatest hydrophobicity, while the C-terminus (from residue 28) showed a high probability for β-sheet structure. Residues 9 - 21showed a lower probability for β-sheet. Two β-turns are predicted between residues 6 and 8, and residues 23 and 27.

Structural Studies of Soluble Aβ

• The structure of the Aβ peptide has been extensively studied in solution, although it is necessary to use organic solvents such as DMSO and TFE, and detergents such as SDS to keep Aβ soluble.

• NMR, CD and FTIR studies have shown that Aβ generally forms -helical conformation in organic solvents, whereas in aqueous buffers or in water it is predominantly β-sheet, although this can be affected by pH, concentration and incubation time.

Conformational Switching• A -sheet content is linked to insolubility and related to

neurotoxicity. The fibrillar state is associated with protease resistance. The A peptide undergoes a conformation switch from -helical to -sheet structure during amyloidogenesis.

• The N-terminus is thought to be important for initiating conformational switching. Introduction of a single amino acid substitution (V18A) in A1-40, which leads to an increased propensity for -helical conformation compared to wild type, was found to be related to a decreased ability to form amyloid fibrils. Substitution of residues Lys16 in A1-28 or Phe19 or 20 for Ala in 10 - 23 results in peptides unable to form amyloid-like fibrils

• A short peptide 14 - 23 is capable of forming amyloid fibrils in vitro and the region 11 - 24 is thought to play an important role in the conversion.

• Residues 25 - 35 have been implicated in neurotoxicity, and residues 34 - 42 are very hydrophobic and are thought to be situated in the transmembrane region in APP. Peptides of this region are extremely insoluble and have been implicated in nucleating amyloid fibril formation.

Structure of A Fibril Intermediates• Beta-sheet conformation is tightly linked to fibrinogenesis • It is thought that fibril formation proceeds via a nucleation

dependent mechanism, which is highly concentration dependent and proceeds via a partially folded intermediate.

• Purification of A1-42 peptide from the brain of an Alzheimer's disease patient yielded stable dimeric and trimeric forms, and monomers that were capable of forming fibrils in vitro

• Studies of the short A14-23 peptide suggest that fibril polymerization proceeds via the formation of dimers, then tetramers and finally oligomers, in which the charged residues form ion pairs and the hydrophobic residues form a hydrophobic core.

Amyloid Fibrils

• Shown to the left is the hierarchy of structure from the A peptide folded into a -pleated sheet structure through protofilaments to amyloid fibrils with -strands running perpendicular to the fiber axis and held together by hydrogen bonding.