BMSC 200 Module 4: Three Dimensional Structure of Proteins

helix dipole

• The net dipole of the helix will have a + charge at the N terminus and a - charge at the C terminus.
• They are stabilized by resides at each termini whose charge oppose the helix dipole.
• Asp and glu have a - charge at the N.
  • Lys, arg, and his have a + charge at the C.

amphipathic helics

• Residues separated by ¾ positions in the primary sequences on the same side of an a- helix.
• Residues separated by 2 resides will be on opposite sides of the helix.
• Positioning of hydrophobic/philic residues generates an amphipathic helix with polar/ non polar faces.

parallel and anti- parallel B sheet

• In parallel, strands run in the same direction.
• In anti- parallel, strands run in the opposite direction and are more stable due to geometry.

mixed B sheet

• B sheets can be parallel, anti, or mixed.
• Mixed contains both parallel and antiparallel strands.

amphipathic B sheet

Side chains that alternate above and below the polypeptide chain.

protein stability

• Weak interactions predominate the stability of the structure.
• Protein conformation with the lowest free energy is usually the one with max number of weak interactions.
• The stability of a protein reflects the difference in free energy of the folded and unfolded states.

folding

• Occupy at low energy with great stability.
• Rapid process, indicating proteins dont sample all folding patterns.

denaturation

• Disruption of native conformation with loss of biological activity.
• Energy required for denaturation is often small, only a few hydrogen bonds.
• It is cooperative and reversible.

quaternary structure

• Consists of multiple polypeptide chains.
• Involves copies of the same polypeptide or different.
• Usually associated through non- covalent interactions.
• They help stabilize subunits and prolong life, help facilitate combinations of structure/ function.

protein role

• Enzymes catalyze and store energy.
• They transport like hemoglobin (transports blood in bloodstream) and myoglobin (transport blood to the lungs).
• Physical cell support that supports organization and structure.
• Mechanical movement so being able for you to move around.
• Decoding cell info, the idea that your blueprint is DNA but it can only work with protein transcribers.
  • Insulin are hormones that help you regulate antibodies in your body.
• They are very diverse b/c of the 20 strands of amino acids.

protein size

• They are 100-1000 amino acids in length.
• The 51 is the transitional number to go from polypeptide to protein.
• The biggest protein is called Titin which has 34350 amino acids.

protein facts

• Function depends on its structure, the 3D structure is determined by amino acid sequences.
• Non covalent forces are the most important forces and the isolated protein exists in a small number of structural forms.

keratin

• It is the component of hair, wool, horns and nails.
• At the primary state, it has a repeating pattern where at positions A and D there are hydrophobic residues for every 7 positions.
• At the secondary structure, keratin forms an alpha helix so A and D end on the same face of he helix.
• The strength arises from covalent bonds and can link together to form DISULFIDE BONDS.

collagen

• Major protein of vertebrates and contains gly-X-Y where X is usually proline.
• At the secondary level, it forms left hand helixes of 3 residues/ turn.
• Vitamin C leads to the weakened structure of collagen and manifests in skin lesion but these enzymes performing modifications require Vitamin C.
• You can become hyperextensive and have stretchy skin as well. These include Osteogenesis imperfection, Marfan's syndrome, Stickler syndrome, and Ehlers- Danlos syndrome.

scurvy disease

Symptoms include bruises, tooth loss, wound healing, bone pain and bleeding from their mouth, nose and ears.

silk

• They are produced from insects and spiders which have to be flexible and strong.
• At the primary level, there is a 6 residue repeat of GSGAGA.
• At the secondary level, it is made from beta sheets and the polypeptides offer strength.
• Due to enticing properties, spider silk can be used for medical applications but the challenge is the availability for it.

prion disease

• Infectious disease based on misfolding a self- protein into a pathological confirmation.
• It is fatal and untreatable where you lose feeling in your body and become paralized.
• Increasing mechanisms associated with prion self- propagation are conserved in other proteinopathies such as Alzheimer's (B- amyloid), Parkinsons (a- synuclein), Huntington's (huntingtin), and ALS (superoxide dismutase)