5. Beta Domains Antiparallel -structures comprise second large group of protein domain structures. Functionally, this group is the most diverse; enzymes, transport proteins, antibodies, cell surface proteins, virus coat proteins. 4 beta strands (with -loop- structure), there are 24 ways. more beta strands, the more theoretical arrangements. BUT! There are only a few observed structures.Common properties Built up from 4 to over 10 beta strands b strands are arranged in predominantly antiparallel fashion The strands usually form 2 twisted sheets that are joined together and packed against each other, resembling barrel or distorted barrel (=double b sandwich)4 different Domains: Up-and-down barrel Greek Keys Jelly roll barrels Beta helix domains ( quite new fold)1) Up-and-down barrels have a simple topology The simplest topology successive strand is added adjacent tothe previous strand until the last strand isjoined by hydrogen bonds to the firststrand and the barrel is closed. is similar to that in the /-barrel structures, EXCEPTthe strands are antiparallel and all the connections are hairpins ( not alpha helix) adjacent beta strands in the aminoacid sequence are also adjacent in the 3D structure Function:transporting the lipid alcohol vitamin A (retinol) from its storage site in the liver to vitamin-A dependent tissues Structure:The eight anti-parallel strands twist and curl Two sheets packed against each other. (green and blue, with red participating both).A retinol molecule is bound inside the barrel, between the two sheets, such that its only hydrophilic part (an OH tail) is at the surface of the molecule. The binding site is lined with hydrophobic residues, which provide a hydrophobic surrounding for the hydrophobic part of the retinol molecule.RBP: amino acid sequence reflects structure A large part (blue) of RBP beta strands are exposed to solvent. This is amazingly achieved by alternating hydrophobic and hydrophilic residues in those beta strands. Strands 1,2,3,4,5,6 form one sheet; strands 1,8,7,6,5 form another sheet; 1,5,6 are shared. The amino acid sequence of strands 2 3 4 of RBP clearly illustrate this arrangement.Membrane spanning -structures Porin channels are made by up and down -barrels. Sixteen strands form an antiparallel barrel that traverses the membrane. The loops at the top of the picture are extracellular, the short turns at the bottom face the periplasm.A 2nd example of up-and-down b barrel: neuraminidase Influenza virus 1. an RNA virus with an outer lipid envelope; 2. two viral proteins anchored in the membrane: neuraminidase & hemagglutinin (both transmembrane) Inside membrane region few residues; transmembrane region; Outside membrane: a stalk and a head piece Role of hemagglutinin , will be mentioned. Role of neuraminidase facilitate the release of progeny virions from infected cells by cleaving sialic acid residues from the carbohydrate side chains of the viral hemagglutinin and of the glycosylated cellular membrane proteinsNeuraminidase Here, up-and-down strands form six small sheets, instead of a barrel. Each sheet has 4 strands. The 6 sheets arranged like the blades of a 6-bladed propeller. Loop regions between the strands form the active site in the middle of one side of propeller. Active sites The 12 loops 6 connecting 6 propeller, 6 within each blade connecting 2nd and 3rd strands, form the active site.This is similar to the active site in the / barrel active site (on top of the barrels formed by loops on top)2) Greek key motifNotice that this is not up-and-down barrel since the red strands connects from n to n+3. They are not connected by hairpin loops. Red and green form a Greek key motif-crystallin as an example for greek key Transparency and refractive power of the lenses of our eyes Smootly changing concentration gradient of Lens specific proteins-crystallins3) The Jelly Role The top right picture is jelly roll motif Then imagine you have this antiparallel beta strand, interrupted by loops. Roll according to the jelly roll motif around the barrel, you get a jelly roll barrel. This is generalized Greek keyHemagglutinin of InfluenzaLike neuraminidase, hemagglutinin is another protein anchored in influenza virus lipid envelope.Role of hemagglutinin (glycosylated)mediate virus binding to host cells by recognizing and binding to sialic acid residues on glycoproteins of the cell membraneOne subunit of hemagglutinin HA1: the first 63 residues extends 100A long, then (residues 116-261) at the top, it forms an 8-stranded distorted jelly roll barrel. The remaining 70 residues return to the step region, running nearly antiparallel to the initial stretch of 63 residues. HA2: a hairpin loop of two alpha helices packed together. The second alpha helix is 50 residue long and 76A long, goes towards the membrane. At the bottom, there is a beta sheet of 5 antiparallel strands, with one strand from HA1. The last 20 residues (called fusion peptide) at the amino end of HA2 are associated with the activity by which the virus penetrates the host cell membrane to initiate infection. The hemagglutinin trimerThe receptor sites formed by the jelly roll domain.To start infection, hemagglutinin binds to sialic acid residues of glycosylated receptor proteins in the target cell surface. The virus gets into cell by endocytosis (plasma membrane folds inward to take substances into the cell). Antibodies in our immune system bind to this receptor binding site to prevent the virus entering our cellsBut the virus can mutate the receptor to escape this binding. This receptor is ideal drug target.The binding site of hemagglutinin The binding site is located at the tip of the subunit within the jelly roll structure. Beta strand 1 contains a long insertion, causing a bulge in strand 8 at the corresponding place. Yellow ball is binding site. A 2nd function of Hemagglutinin in the infection of host cells:aid in endosome and viral membrane fusion First function: binding to sialic acid residue It binds to the plasma membrane via the receptor, and is taken into the cells by endocytosis. vesicles containing bound viruses causes an accumulation of protons and a consequent lowering of the pH value inside the vesicles hemagglutinin to change conformation due to low pH Induce the fusion of the viral envelope membrane with the membrane of the endosome. Structural change at lower pH value Hemagglutinin undergoes a massive conformational change at lower pH value (