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Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
Alpha domain structurs
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Alpha domain structurs

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Made for 3rd year Protein Engineering class

Made for 3rd year Protein Engineering class

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  • 1. Alpha-Domain Structures
  • 2. <ul><li>Alpha helices are very common in proteins. </li></ul><ul><li>Could a single alpha helix exist? </li></ul>Single alpha helix does not have a hydrophobic core, it is marginally stable in solution Two (or 3,4, etc) helices can pack together and form a hydrophobic core
  • 3. Coiled – coil (leucine zipper) <ul><li>The simplest way to join two alpha helices </li></ul><ul><li>In fibrous proteins (keratin, myosin) coiled-coil can be very long (hundreds of amino acids) </li></ul><ul><li>In globular proteins coiled-coils are much shorter (~10-30 aa) </li></ul>
  • 4. The heptad repeat <ul><li>d: Very often Leu (hence leucine zipper) </li></ul><ul><li>a: often hydrophobic </li></ul><ul><li>e, g: often charged </li></ul><ul><li>b,c,f: charged or polar </li></ul><ul><li>The above prefernces are strong enough to be predicted from sequence </li></ul>1 8 15 22 a b c d e f g Met Lys Gln Leu Glu Asp Lys Val Glu Glu Leu Leu Ser Lys Asn Tyr His Leu Glu Asn Glu Val Ala Arg Leu Lys Lys Leu
  • 5. Why a heptad ? <ul><li> helix: 3.6 residues per turn </li></ul><ul><li>3 10 helix: 3 residues per turn </li></ul><ul><li> helix in coiled coil is a bit distorted and has 3.5 residues per turn. </li></ul><ul><li>3.5x2=7, so two turns of helix form one heptad repeat </li></ul>
  • 6. Leu packs against Leu <ul><li>Every seventh residue in both  helices is a leucine, labeled “d”. </li></ul><ul><li>Due to the heptad repeat, the d-residues pack against each other along the coiled-coil. </li></ul><ul><li>Residues labeled “a” are also usually hydrophobic and participate in forming the hydrophobic core along the coiled-coil </li></ul>
  • 7. Interactions in coiled-coil <ul><li>Salt bridges can stabilize coiled-coil structures and are sometimes important for the formation of hetero-dimeric coiled-coil structures. The residues labeled “e” and “g” in the heptad sequence are close to the hydrophobic core and can form salt bridges between the two  helices of a coiled-coil structure, the e-residue in one helix with the g-residue in the second and vice versa. </li></ul>
  • 8. Helix-helix Packing <ul><li>The side chains of an  helix are arranged in  helix row along the surface of the helix </li></ul><ul><li>They form ridges separated by shallow furrows or grooves on the surface. </li></ul><ul><li> helices pack with the ridges with one helix packing into the grooves of the other and vice visa. </li></ul><ul><li>Ridges can be formed by the sidechains separated by four residues with an angle of 25 º (i +4) and by 3 residues with an angle of 45 º (i +3) to the helical axis. </li></ul>
  • 9. Helix-helix Packing <ul><li>By fitting the ridges of side chains from one helix into the grooves between side chains of the other helix and vice versa,  helices pack against each other. (a) Two  helices, I and II, with ridges from side chains separated by four residues marked in red and blue, respectively. In panel 4, the orientation of the helices has been rotated 50° in order to pack the ridges of one  helix into the grooves of the other. (b) In the red  helix, the ridges are formed by side chains separated by four residues and in the blue  helix by three residues. The  helices are rotated 20° in order to pack ridges into grooves, in a direction opposite that in (a). </li></ul>
  • 10. Knobs in Holes Model <ul><li>The positions of the side chains along the surface of the cylindrical  helix is projected onto a plane parallel with the helical axis for both  helices of the coiled-coil. </li></ul><ul><li>The side-chain positions of the first helix, the &amp;quot;knobs,&amp;quot; superimpose between the side-chain positions in the second helix, the &amp;quot;holes.&amp;quot; </li></ul>
  • 11. “ Knobs in holes” model in coiled-coil <ul><li>Leucines (“knobs”) of one helix sit in hydrophobic “holes” of other helix </li></ul>d a a d e
  • 12. “ Ridges in grooves model” <ul><li>Helices often pack each against other according to “Ridges in grooves” model </li></ul><ul><li>NOT found in coiled coil but other motifs </li></ul>Ridge Ridge Groove
  • 13. &nbsp;
  • 14. <ul><li>Depending on actual amino acid sequence, ridges may be formed of residues which are 3 or 4 amino acids apart </li></ul>
  • 15. Two variants of “ridges in grooves” model <ul><li>If 2 helices with ridges 4 residues apart combine, there is 50 o angle between helices </li></ul><ul><li>1 helix with ridges 4 residues apart + 1 helix with ridges 3 residues apart  20 o angle </li></ul>
  • 16. &nbsp;
  • 17. Four-helix Bundles <ul><li>Four-helix bundles frequently occur as domains in  proteins. </li></ul><ul><li>The arrangement of the  helices is such that adjacent helices in the amino acid sequence are also adjacent in the three-dimensional structure. </li></ul><ul><li>Some side chains from all four helices are buried in the middle of the bundle, where they form a hydrophobic core. </li></ul>
  • 18. Helices can be either parallel or anti parallel in four helix bundle <ul><li>In cytochrome b562 (a) adjacent helices are antiparallel, whereas the human growth hormone (b) has two pairs of parallel  helices </li></ul>
  • 19. Two leucine zippers can form a four helix bundle <ul><li>Two helices form leucine zipper </li></ul><ul><li>Two zippers pack as “ridges and grooves” </li></ul><ul><li>Note that usually two helices in 4hb do not make a leu zipper, this is just a special case </li></ul>Leu zipper
  • 20. Dimeric RNA-binding Protein Rop <ul><li>Each subunit of Rop comprises two  helices arranged in a coiled-coil structure with side chains packed into the hydrophobic core according to the &amp;quot;knobs in holes&amp;quot; model. </li></ul><ul><li>The two subunits are arranged in such a way that a bundle of four  helices is formed. </li></ul><ul><li>The RNA binding surface is located at the middle of the helices. </li></ul>RNA RNA
  • 21. Alpha-helical domains can be large and complex <ul><li>Bacterial muramidase </li></ul><ul><li>(involved in cell wall formation) </li></ul>
  • 22. Importin beta Involved in transporting (“importing”) proteins from cytosol to nucleus
  • 23. Globin fold <ul><li>One of the most important  structures </li></ul><ul><li>Present in many proteins with unrelated functions </li></ul><ul><li>All organisms contain proteins with globin fold </li></ul><ul><li>Evolved from a common ancestor </li></ul><ul><li>Humans: myoglobin &amp; hemoglobin </li></ul><ul><li>Algae: light capturing assembly </li></ul><ul><li>Contains 8  helices, forming a pocket for active site </li></ul>
  • 24. The Globin Fold has been Preserved During Evolution <ul><li>The 3D structures of globin proteins from different organisms (mammals, plants, and inserts) are solved and they share the same essential features of the globin fold. </li></ul><ul><li>The sequence homology is from 99 % to 16 %, which is very low. </li></ul><ul><li>How can amino acid sequences that are very different for proteins be very similar in their 3D structures? </li></ul>
  • 25. Evolution of Globins <ul><li>Arthur Lesk &amp; Cyrus Chothia in the UK have examined the residues that are structurally equivalent to positions in 9 known globin structures, that are involved in helix-heme contacts, and in the packing of the helices against each other. </li></ul><ul><ul><li>There are a total of 59 positions preserved, 31 buried in the middle of protein and 28 in contact with the heme group. </li></ul></ul><ul><ul><li>There is no conserved sequences nor size-compensatory mutations in the hydrophobic core formed by the 31 a.a. </li></ul></ul><ul><ul><li>Conclusion: The evolutionary divergence of globins has been constrained primarily by an almost conservation of the hydrophobicity of the residues buried in the helix-helix and helix-heme contact. </li></ul></ul>
  • 26. How do Proteins Adopt to Changes in the Size of Buried Residues? <ul><li>The mode of packing for the  helices are the same in all the globin structures </li></ul><ul><li>The same types of packing ridges into grooves occur in corresponding  helices in all these structures. </li></ul><ul><ul><li>The relative positions and orientations of the  helices change to accommodate changes in the volume of sidechains involved in the packing. </li></ul></ul><ul><ul><li>The structure of loop regions changes so that the movement of one helix is not transmitted to the rest of the structure to preserve the geometry of the heme pocket. </li></ul></ul>
  • 27. Myoglobin A B C D E F H G N C
  • 28. Hemoglobin <ul><li>Myoglobin is found in muscle cells as an internal oxygen storage </li></ul><ul><li>Hemoglobin is packed in erythrocites and transports oxygen from lungs to the rest of body </li></ul><ul><li>Myoglobin has a single polypeptide chain </li></ul><ul><li>Hemoglobin has 4 chains of two different types –  nd  </li></ul><ul><li>Both  and  chains have a globin fold and both bind heme </li></ul>
  • 29. Hemoglobin
  • 30. Sickle-cell anemia – a molecular disease <ul><li>Arises, when Glu 6 in  chains is mutated to Val </li></ul>
  • 31. Polymerization among hemoglobin molecules during sickle-cell anemia <ul><li>Mutated residue 6 gets inserted in a hydrophobic pocket of another hemoglobin molecule </li></ul>
  • 32. Mutant hemoglobin fibers in erythrocytes <ul><li>Mutant Normal </li></ul>Traffic jams can be caused in blood vessels by sickle shaped erythrocites
  • 33. Why is Glu 6 mutation preserved rather than eliminated during evolution? <ul><li>Mutation is predominantly found in Africa </li></ul><ul><li>Gives protection against malaria </li></ul><ul><li>Most mutation carriers are heterozygous, which have mild symptoms of disease, but still resistant to malaria – an evolutionary advantage </li></ul>
  • 34. &nbsp;

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