Structural determinants of protein function Flashcards
What does the protein 3D shape determine?
How protein works in the cell
What do loop, coil and random coil structures share?
They have no regular defining properties in structure
Not Alpha-helices and Beta-sheets
What is the structure of loop and coil?
In line
Ordered (not mobile), but not in a systematic or regular way
What is the structure of loop and coil?
American Lines
Disordered, mobile, fluctuating set of structures
What % of protein is alpha helix?
31%
What % of protein is beta sheet?
28%
What is the remaining part of the protein structure?
Doesn’t repeat
Rest is non repetitive structure
What are the supersecondary structures (motifs)?
Greeks put in their hair
B alpha Beta Motif
Beta Hairpin motif
Alpha Alpha Motif
Helical supersecondary structures have?
looped together
4 Helix bundle motif
Describe the structure of Beta Supersecondary Structures
The chain is a N to a C with 4 sections.
Beta Hairpin motif
the second and third section folds so it is ordered 3,2,1,4
What are the different folds for Beta supersecondary structures?
Immunoglobulin fold
Beta-Barrel fold
Alpha/Beta Barrel (TIM barrel) fold
What is the structure of the immunoglobulin fold?
N to C Beta Hairpin motif 4 folds 1 is bound to 2 2 is bound to 5 4 to 3 3 to 6 6 to 7
What is the structure of the Beta barrel fold?
N to C beta hairpin motifs
1,2,3,4,5,6, 7, 8
Wiggly line
What is the structure of the Alpha/Beta Barrel (TIM barrel) fold?
N to C
Each is folded with itself in a beta hairpin motif
1,2,3,4,5, 6,7 ,8
So 1 is adjacent to 2
Define and give an example of Protein tertiary structure
How the secondary structural elements come together
Each protein structure is different (Unlike DNA)
Whale myoglobin (first structure solved): Oxygen carrier, allows whales to store oxygen for long periods while they are diving
Teritary structures that build protein structures may contain?
Alpha-helices and or Beta-sheets or neither
What are the features of the side chain location in tertiary structure?
Water is largely excluded from interior
Hydrophobic “non-polar” amino acids in the core: Shielded from the aqueous solvent (water)
Hydrophillic “charged” amino acids on the exterior- in contact with the water in the solvant
Uncharged polar amino acids often on surface, but can be found in the inside, but usually buried hydrogen bond donors form bonds with acceptors (sort of neutralizing the polarity)
What amino acids face protein interior?
Phe
lle
Leu
What amino acids face protein exterior?
Ala Asp Lys Gly Glu Asn Arg Gln
What are protein domains?
Large polypeptides (200 or more amino acids) Usually fold up into a group of globular domains
E.g. Glyceraldehyde-3-phosphate
What helps protein folding?
Proteins aren’t a tangled mess because they are hierarchically organised, with domains often divided into subdomains
Thing that need to end up close in 3D start close in 2D
What are the common DNA folds?
Helix-turn-helix
Zinc finger
Leucine zipper
What is the structure of Helix-turn-helix?
DNA-binding helix is connected to a Dimer-binding helix (loop de loop) by a turn shaped like a upside down mountain
Explain the Amino acid sequence for Helix-turn-helix motif
20 AA’s per chain
One Alpha helix for recognition of DNA then beta turn, then another Alpha helix
For DNA-binding helix-turn-helix motifs in the lac repressor (tetramer)
Helix-turn-helix: Sequence-specific binding due to?
Specific contacts between the recognition helix and major goove
What is the structure of the Zinc finger motif?
30 AA’s
Finger portion is a peptide loop cross-linked by Zn^2+ ion
Zn^2+ usually coordinated by 4 Cys, or 2Cys , 2 His
How does Zinc finger interact with DNA or RNA?
Binding is weak, so several zinc fingers often act in tandem
Binding can range from sequence specific to random
Explain the structure of Leucine Zipper Motif
Dimer of two amphipathic Alpha helices plus a DNA-binding domain
Each helix is hydrophobic on one side and hydrophillic on the other
Hydrophobic side is the contact between the two monomers
Apparently every seventh residue in helices is leu
What is the job of the Leucine Zipper motif?
The two helices wrap around each other in a gently coiled coil. The interacting Leu side chains and the conserved residues in the DNA-binding region are coloured to correspond to the sequence
What are EF hands and how do they bind calcium?
They are 40 AA’s forming a helix-loop-helix motif
present in > 100 proteins
Often found in multiple pairs, for example four in calmodulin (CAM)
Each EF hand binds to a single Ca^2+ ion
What is the first step in the activation of Calmodulin?
Calmodulin binds to four Calcium ions
What is the second step in the activation of Calmodulin?
Calmodulin changes conformation, resulting in an active complex
What is the third step in the activation of Calmodulin?
The two globular hands of the complex wrap around a binding site on a target protein
Src family kinases are a family of?
Non-receptor tyrosine kinases
SH2 and SH3 both play a part in?
Protein-protein interactions
Kinase catalytic domain contains?
The kinase active site
How is the kinase active site switched from inactive to active?
Through phosphorylation state, or protein interactions
How is Src inactivated?
Critical site phosphorylation site: Tyr527, CSK kinases (phosphorylates), or SHP-1 phosphorylase (dephosphorylates)
This inactivates Src through the interaction of P-tyr527 with the SH2 domain, which effectively folds Src up into a closed, accessible bundle.
How is Src activated?
Desphosphorylation of Tyr527 releases this bond, opening up the molecule to an active state
How does the Src family kinases interact with cellular cytosolic, nuclear and membrane proteins?
Modifying the proteins by phosphorylation of tyrosine residues
What does a Src-homolgy 2 domain compose of?
Comprises a central antiparallel Beta-strand surrounded by two Alpha-helices
Conserved AA contribute to pY recognition, variable AA recognise residues C-terminal to pY-provides specificity
What are the functions of SH2 domain?
modules of 100 AA
Widely distributed in metazoan proteins including PLCy (Phosphinositide phospholipase C, signaling) and Grb2 (Growth factor receptor-bound protein 2, signalling)
Recognise and bind pY-containing motifs of 4-7 amino acids (phosphopeptides)
Enable proteins with diverse functions such as Grb2 (adapter), PLCy (phospholipase) and Src (protein kinase) to interact with autophosphorylated domains of receptor tyrosine kinases. (RTKs).
What is the structure of the Sh3 domains?
60 AAs
Five Antiparallel Beta-strands form two perpendicular Beta sheets
Recognise pro-rich peptides with minimum sequence Pro-X-X-Pro
Found in various proteins that include Src (kinase), PLCy (phospholipase) and adapter proteins (Grb2)
Explain Protein folding
Molecular chaperones may be required to fold proteins, either newly synthesized or misfolded for a reason
Some chaperones bind to the amino terminus of the growing polypeptide chain during translation, stabilzing it in an unfolded configuration until synthesis is completed
What is the function of the E.coli chaperone: GroEl
it is bacterial protein which is a little folding machine
Takes unfolded or miss-folded proteins and refolds them
Its shape is like a rubbish bind with a lid
Two conformations of chaperones: Explain A
The hydrophobic patch attracts/binds incorrectly folded protein
it has a hydrphobic surfact that binds unfolded proteins
Lid closes with the client inside
Two conformations of chaperones: Explain B
Structural re-arrangment (uses ATP) exposing hydrphillic surface
Lid then opens and protein is released
What are the Macromolecular 4’ Structures?
Calcium Channel, GPCR and G protein
