Lecture 3-Structural Organization of Membrane Proteins (March 4) PDF

For lecture 6 (Monday, March 11) Posted on Courselink: 1. Czachorowski, M., Lam-Yuk-Tseung, S., Cellier, M. and Gros, P. Transmembrane Topology of the Mammalian Slc11a2 Iron Transporter (2009). Biochemistry 48(35): 8422-8434 2. Associated work sheet Read the paper and find answers to the questions o...

For lecture 6 (Monday, March 11) Posted on Courselink: 1. Czachorowski, M., Lam-Yuk-Tseung, S., Cellier, M. and Gros, P. Transmembrane Topology of the Mammalian Slc11a2 Iron Transporter (2009). Biochemistry 48(35): 8422-8434 2. Associated work sheet Read the paper and find answers to the questions on the worksheet. You can leave out the “sequence analyses” and the “homology modelling” sections of the paper (methods, results and discussion). The work sheet should guide you through the sections that are relevant to our discussions. Use for self study. You do not have to submit the work sheet to Courselink Dropbox. Over-winding – the 310 helix 3 amino acids per turn The C=O group of amino acid #1 hydrogen bonds with the NH of amino acid #4 (C=O of residue i H-bonding with NH of residue i+3) Side chains line up with each other unlike an α-helix Commonly seen as a C-terminal 310 cap on an a-helix e.g., Voltage sensitive K+ channel Allows the positively charged residues of the voltage sensing helix 4 of the K+ channel to align in a single line α-helix 310 helix J Gen Physiol. 2010;136(6):585-592. doi:10.1085/jgp.201010508 Under-winding - p helices C=O of residue i hydrogen bonds with NH of residue i+5 Pure p helices not found Could occur as a turn or two in the middle of an a-helix A pi helix in the middle of an α helix will lead to a pi bulge The extra residue in the pi helix bulges out with its C=O not having a corresponding NH to H-bond with This introduces a kink to the α helix pi bulges are very common in multi-spanning TM proteins Proline residues are not very common in the interior of protein secondary structure because: A. Proline side chain is charged and polar B. Proline cannot form any hydrogen bonds C. Proline’s amide N does not have a H and therefore cannot get involved in H bonding D. Proline’s carbonyl group is unable to act as a hydrogen bond acceptor. E. Proline’s side chain links to its amino N and sterically obstructs H bond formation 99.95% of peptide bonds are trans configuration. Proline: ~ 6% are found in the cis configuration. Many of the cis prolines are found in Beta Turns. Proline kinks a-helices R + H3N 1 H C C O H O N C C H R 1 R 1 C N H O C H N C H C O 2 C O – H CH2 CH2 The N atom of a proline residue in a peptide bond does not contain a H to allow H-bond formation. In addition, since the N atom of proline is linked to its side chain forming a rigid ring, the N-Cα bond is Proline unable to rotate. kink This causes the helix to have a kink if there is a proline in the middle of the helix. Proline kinks are seen in the middle of a membrane In membrane proteins proline kinks are important https://www.nature.com/ar ticles/srep29809/figures/1 in the tight packing of transmembrane helices Partially unwound helices a-helices in TM proteins can be partially unwound in the middle of the membrane Allows side chains to be placed more freely, and could expose backbone residues for interactions Used to induce kinks and form binding sites GLUT5 glucose transporter – 4ybq Partial helices Multi-spanning TM proteins sometimes contain helices that do not fully cross the bilayer Shorter helices can cross part of the bilayer and then turn back Sometimes part of the helix can be spanned as an extended loop 2 short helices can mimic one long one Aquaporin – 3M9I Helix packing Helices cannot pack well if they are parallel This is because ridges of side chains are oriented diagonally to the helix axis Helices prefer to pack at an angle to one another This does however mean that they can only pack well with a given neighbour for 3 – 4 turns before they diverge too far to interact well a-helices consist of a series of ridges and grooves The surface of an a-helix consist of a series of ridges (the side chains) and grooves One set of ridges are formed by residues 4, 8,12; 7,11,15,19 etc. and run at an angle of 250 to the axis of the helix. The second set of ridges are formed by residues 4 & 7; 8 & 11; 12,15,18 etc. and run at an angle of 450 to the helix axis. Helices pack well if the ridges of one helix pack against the grooves of another B & T Fig. 3.11 https://www.sciencedirect.com/science/article/pii/S0005273602005734#FIG6 Ridges into Grooves ▪ 4-4 packing The two helices are oriented with their long axes crossing at an angle of 50° (25°+25°). ▪ 3-4 packing The two helices cross at an angle of 20° (45°–25°). 200 is more common in membrane proteins as it is closer to parallel ▪ knobs-into-holes packing side chains in one helix (knobs) pack into the spaces between the side chains (the holes) in the other (alternate to ridges into grooves) GXXXG motifs Having the sequence GXXXG in an alpha helix will bring the two glycine residues to the same face of the helix The lack of a side chain on the two glycines will leave a groove for another helix to approach closely GXXXG motifs are very commonly found in single-spanning TM proteins that dimerize. Glycines are often conserved at specific points where the helices interact with each other Monotopic membrane proteins Monotopic membrane proteins have small hydrophobic domains that interact with only one leaflet of the membrane These interactions hold them tightly to the membrane. The amount of structure of a monotopic protein embedded in the membrane is variable Peripheral membrane proteins Peripheral membrane proteins commonly interact with the polar head groups of membrane lipids using electrostatic interactions and hydrogen bonds Some peripheral membrane proteins use calcium to mediate interactions Other peripheral membrane proteins bind to integral membrane proteins Schutters, K Reutelingsperger, C. (2010) Apoptosis V15, 9