Protein Structural Elements Flashcards
(34 cards)
What are the 9 hydrophobic amino acids?
glycine (Gly) alanine (Ala) valine (Val) leucine (Leu) isoleucine (Ile) proline (Pro) phenylalanine (Phe) methionine (Met) tryptophan (Trp)
How many residues needed to get around a turn of a right handed alpha helix?
3.6 residues
How do you draw a helical wheel?
- every 100 degrees place a residue
What is an EF hand?
helix-loop-helix structural domain or motif found in a large family of calcium-binding proteins
What is calmodulin?
is a calcium-binding protein found in the cytoplasm of all eukaryotic cells
What is the structure of calmodulin?
2 EF hands that interact
What happens when calcium binds to Calmodulin?
- EF hands change conformation
- one EF hand has a higher affinity for Ca than the other so one has a stronger affinity and once that has bound, it increases the other ones affinity like in O2 in haem
- Hydrophobic residues are exposed on the surface rather than in the middle like usual
- Protein changes conformation
What variations of signalling can be done with the binding of Ca2+ to CaM.
- Ca2+ binding modulates conformation and either activates or inhibits target protein
- Ca2+ binding dissociates the protein to free active site for phosphorylation or associates the protein, inhibiting it
What are β pleated sheets?
- patterns in the primary structure
- Beta sheets consist of beta strands connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet
What are the differences between parallel and anti parallel beta sheets?
parallel: hydrogen bonds are slightly straight hydrogen bonds are not parallel but at an angle anti parallel: H bonds are completely straight H bonds are parallel Twists more than the parallel
What are some common β strand motifs?
Hairpin
- hairpin is β strands antiparallel to each other
β meander / Beta barrel (which is a repetition of hairpin motif)
- makes a pore in the membrane allowing things to go in and out
β Propeller
β-α-β
- active site in loop 1
- right handed is dominant
α/β barrels (TIM barrels)
- alpha helix sits on the outside, beta sheets in the middle
- e.g. pyruvate kinase
- >10% of enzymes contain α8β8 barrels
What is the structure of pyruvate kinase?
- made of 4 domains
- each domain made of repeated alpha/beta barrels
What is divergent evolution? Inc example
Divergent evolution occurs when two separate species evolve differently from a common ancestor
- TIM barrels and Beta barrels diverged from a common ancestor
What is convergent evolution?
Convergent evolution occurs when species have different ancestral origins but have developed similar features.
Describe the immunoglobulin fold.
The immunoglobulin fold consists of a pair of β sheets, each built of antiparallel β strands, that surround a central hydrophobic core. A single disulfide bond bridges the two sheets.
Compare the constant and variable domains of immunoglobulins.
three loops present at one end of the structure form a potential binding surface. These loops contain the hypervariable sequences present in antibodies and in T-cell receptors. Variation of the amino acid sequences of these loops provides the major mechanism for the generation of the vastly diverse set of antibodies and T-cell receptors expressed by the immune system.
What other polypeptide helices occur other than right handed α helices?
3(10) helix: - 3 residues/turn - pitch = 6.0A - short, distorted segments - H bonds every 3 amino acids - thinner + longer than right handed α helices π helix: - 4.4 residues/turn - pitch = 5.2A - lack of van der Waals - H bonds every 5 amino acids - shorter + fatter than right handed α helices
Why don’t L-amino acids form left handed helices?
- the side chains and CO groups do not fit in the space
How do amino acids sequences affect the stability of α helices?
side chains 3 or 4 residues apart in the a.a. seq will interact so:
- bulky residues 3/4 residues apart in seq destabilise α helix formation
- residues of the same charge will repel and also destabilise α helix formation
proline breaks/ kinks α helix
Why does proline create kinks in α helices?
- doesn’t have free backbone rotation
- steric hindrance
- N doesn’t form H-bonds
What conformation are all non-proline amino acids usually in?
Trans configuration
Why is there a steric clash when proline is in the a configuration?
It can exists in both configurations as clashes in both
- if in trans configuration backbone clashes with N
- restriction around phi angle
- if in cis, clash between 2 Cα’s
What sort of helices does Poly-Proline form?
PPII (seen more in nature) and PPI
What sort of helices are present in Collagen?
- 3 PPII helices come together
- glycine, proline and hydroxy proline make 45% of the amino acids
- mediate protein interactions
