secondary structure - proteins

• why are all conformations for proteins not possible?

  • polypeptide folding is not random
  • peptide bond is quite rigid and so random sequence is limited in possibilities
  • peptide chains adopt specific secondary structures giving further limitations
• often secondary structures will form, deform, form and deform until it gets thee right secondary structure
• Rotations around the C alpha:

  • the two planes can rotate on either side of the C-alpha
  • N side rotates by angle Phi
  • CO side rotates by angle Psi
• Free rotations can only occur around the C alpha of an amino acid and rotation can not occur in the C-N bond as there is resonance stability
• only few of the angles of Psi and Phi result in stable conformations of the secondary structure

  the most common formation being:

  • right-handed alpha-helix
  • beta strands
• the angles of Psi and Phi that results in unstable conformations are due to the fact that there's stereo clashes and so not energetically favourable structures
• Any molecule which has a hydrogen atom attached directly to an oxygen or a nitrogen is capable of hydrogen bonding - so peptide bonds are ideal for hydrogen bonding
• A hydrogen atom attached to relatively electronegative atom (nitrogen) is a hydrogen bond donor
• An electronegative atom is a hydrogen bond acceptor
• hydrogen bonding in secondary structures

  A) hydrogen bond donor site

  B) hydrogen bond acceptor site

  
• h-bonds gives rise to several (periodic) features called secondary structures - alpha helix or beta sheets
• in the polypeptide chain, H is small so has a high charge density and so pulls electrons form the carbonyl group from a nearby amino acid and forms a hydrogen bond

  • the high charge density attracts a lone pair of electrons from oxygen which becomes the hydrogen bond acceptor - a dipole-dipole interaction
• what are turns?

  part of the secondary structure - used to break one structure and form the next/another structure
• how is the alpha helix formed?

  • Repeating values of Phi -57º and Psi -47º give a right handed alpha helix - its stabilised by intra-strand hydrogen bonding
  • CO of each residue is h-bonded to NH of the 4th residue ahead (6 carbons between each h-bond)
• what are the features of an alpha helix?

  • R groups are extended on the outside
  • Phi/Psi angles are -57º and -47º
  • one complete turn is every 3.6 amino acids
  • twists clockwise
  • peptide bonds are trans and planar
  • distance between the two c-alphas = 1.5Å

  
• what is a amphipathic helix?

  A helix with both hydrophobic and hydrophilic regions/properties
• what are the properties of an amphipathic helix?

  Hydrophilic amino acid side chains on one side of the helix and hydrophobic side chains on the other side

  Such alpha helices in some cases can be used to associate a protein or peptide to a membrane - reason why amphipathic helices are important
• Membrane association can happen with amphipathic helices - polar faces to the centre and non-polar faces towards the lipid bilayer
• what are the arrangement amphipathic helices can be arranged in membranes?

  • transmembrane - middle is non-polar
  • pore for transport - inside is polar and outside is hydrophobic so can allow ions to be transported through the aqueous channels

  
• a proteins helix content is variable-

  • myoglobin, haemoglobin - almost all alpha-helix
  • alpha-chymotrypsin - almost no alpha helix
• what are complex helices?

  Alpha-helices can wind around each other to form 'coiled coils' that are extremely stable (stiff for support)

  They are found in fibrous structural proteins such as keratin and myosin
• examples of globular proteins that are diagnostic markers are...?

  ferritin and transferrin
• what is ferritin and its properties?

  • an iron storage protein - stores and releases iron as demanded so also used as a delivery mechanism
  • water soluble + has 24 subunits with bundled of helices
  • ~4500 irron (Fe3+) ions are caged until needed
  • reduces toxicity as its kept hidden and caged + keeps it soluble
  • can be used as a diagnostic marker for IDA
  • works in synergy with transferrin
• what is transferrin and its properties?

  • iron transport protein - in blood plasma
  • each molecule binds two irons - Fe3+
  • delivers to tissues that have a transferrin receptor 1 (TfR1) e.g. delivers to erythroblasts in the bone marrow which then uses it to make haemoglobin
  • binding site has amino acids with electronegative atoms and bidentate carbonate H bonded to an arginine side chain and the N terminus
  • transferrin test can be done when looking at IDA

  
• how do ferritin and transferrin act like diagnostic markers?

  IDA is positive if:

  • serum iron test show low level of iron (this test alone is not sufficient to diagnose IDA)
  • serum transferrin test will show higher level of this protein. TIBC test will reflect lower transferrin saturation indicating the protein has yet spare capacity to bind more iron
  • serum ferritin test will show lower levels of this protein
• what is TIBC and what does it show?

  total iron binding capacity - how much of your transferrin is saturated with iron
• what can be used as alpha-helix breakers?

  Proline, Glycine, and Disulfide bonds.
• why are alpha-helix breakers used?

  • sometimes you need a mixture of structures or change from helix strand to beta sheet as its required for the function of protein
• where are alpha helix breakers found?

  in bends
• how does glycine act as an alpha helix breaker?

  • glycine is too flexible and so rotation is easy and helix loses rigidity
• how does proline acct as an alpha helix breaker?

  • proline is cyclic (imino acid) and has a fixed Phi angle so doesn't have a lot of free rotation
  • and so creates a kink in the helix
  • these residues often serve as alpha-helix breakers and found at the boundaries of alpha helices and in turns
• what are beta sheets?

  Secondary structure of proteins formed by hydrogen bonding between adjacent strands of amino acids.

  The peptide is in extended form of 5 or more residues
• what are the two types of beta sheets?

  Parallel and antiparallel.
• describe parallel beta sheets?

  • R groups point up and down
  • the strands are held by h-bonds between backbone >C=O and >N-H on different strands
  • H-bonds connects an amino acid (from strand one) in one chain with two from another chain
  • strands run in the same direction

  
• describe antiparallel beta sheets?

  • side chains alternatively up and down (trans configuration)
  • H-bonds connects each amino acid in one chain with another amino acid from another chain
  • strand run in opposite directions

  
• what makes the extended structure of a beta sheet appear pleated?

  alpha-carbon being tetrahedral and peptide bond being planar
• in beta sheets - R groups lie perpendicular to the sheets: stick out on either face of the sheet
• where do antiparallel beta sheets occur?

  In silk (fibroin) - its so smooth because every second amino acid is glycine and so all side chains on one face are hydrogen and most on the other side is Ala (CH3) = tight packing

  
• when do turns occur?

  generally occurs when the protein chain needs to change direction in order to connect two other elements of secondary structure
• when are B-turns used? and what red often present in them?

  To change direction in which sheets or helices run in.

  Proline and glycine often present in B-turns