Chapters 14 and 16

1. Chapters 14 and 16 Membrane Proteins Channels Fibrous Proteins Amyloid Fibrils

2. 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.

3. 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.

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

5. 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 b strands that form a channel through the membrane, and (d) a protein that is anchored to the membrane by one a helix parallel to the plane of the membrane.

6. Integral (Intrinsic) Proteins • penetrate the bilayer or span the membrane entirely • can only be removed from membranes by disrupting the phospholipid bilayer

7. 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.

8. 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

9. 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.

10. 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 membranes b. 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: • cytoplasmic (inner) side: • made in cytoplasm • b. extracellular (outer) side: • made in ER and undergo exocytosis

11. Solubilization and crystallization of membrane proteins

12. 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.

13. 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.

14. 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.

15. 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).

16. 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).

17. Porin Channels extracellular funnel • 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 b strands form an antiparallel b barrel that traverses the membrane. The long loop between b strands 5 and 6 (red) (eyelet) constricts the channel of the barrel. Two calcium atoms are shown as orange circles. Hydrophilic Hydrophobic periplasm

18. Each Porin Molecule has Three Channels Hydrophobic • 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.

19. 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?

21. 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.

23. 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.

27. 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.

28. Hydropathic Index

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

31. 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.

32. 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.

33. 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.

34. 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 a helices (keretin & myosin) • b sheet in amyloid fibers and silks

35. 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.

36. 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.

38. Types of Collagen

39. 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.

40. Formation of Hydroxyproline & Hydrolysine

41. Biosynthesis of Collagen

42. 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

43. 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.

44. 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.

45. 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).

49. 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-a-helical and vary greatly in size and sequence in different intermediate filaments.

50. 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).