Lecture 1: Motifs of protein structure Flashcards
What are the levels of structure?
Tertiary structure tend to be the end of folding of a singular protein -> but it can still become part of a more complex structure
What secondary structures do you know? (note how they can be drawn)
Note: there is a limited combinations of psi and phi that can result in one of these structures (as previously shown in the Ramachandran plot)
What creates alpha helix?
Formation of C=O on position n and hydrogen bond N-H on position n+4 (every 4th aminoacid)
Moreover, since each C=O and N-H group create dipoles themselves and all hydrogen bonds face the same direction => they together contribute to electrical dipole of the entire structure
- Overall positive N-term and negative C-term
NOTE: 3.6 amino acids per turn, 5.4 height, side chains point outwards -> determine their function
What types of Helix structures can you think of? What determines it?
Depends on the position of the hydrogen bond
Alpha-helix - the one explained so far
- C=O from n, N-H on n+4
- 3.6 per turn
3(10)-helix
- N-H from n, C=O on n+3
- 3 per turn (triangular from above)
=> bigger chance of bad contacts, unstable, short
pi-helix
- N-H from n, to C=O on position n+5
- 4.4 per turn
- energetically unstable, very rare
- cavity in the middle (but still smaller than water)
What makes these different?
The proportion of hydrophobic and hydrophilic differs
- helices mostly composed of hydrophobic units would need to be placed in hydrophobic environment e.g. plasma membrane
- some helices can be amphipathic -> one side hydrophilic while the other hydrophobic
How are beta-sheets created? Where are the side chains?
Peptide chain, now posing as beta-strand, is placed next to other beta strands and becomes connected via hydrogen bonds between them
- side chains are on alternating sides
Unlike helices - it needs more backbones to interact with
How do we distinguish beta-sheets?
NOTE: Parallel are actually bended, zig zag style
What structures do we find between helices and sheets?
Between different structures we can find loops and turns (shorter loops connected to beta-sheets) => combination of the secondary structures forms motif
- e.g. helix-turn-helix, beta-alpha-beta-motif, hairpin (2 beta-sheets)
How do Harpin/Greek key motifs look like?
Various structured turns possible:
y-turn makes i and i+2 aminoacids connected via hydrogen bonds
Greek key:
- anti-parallele beta-sheets
What would be the most prominant way of combining parallel beta-sheets? Can you say more about it?
Beta-alpha-beta motif
- Most of the time motif is right handed
- Interactions of the sheet with helix mostlz hydrophobic
- C-term of 1. beta strand and N-term of helix involved in ligand or substrate binding
- helix is either above or below
Which motif is important for DNA binding?
Helix-turn-helix motif
- DNA has major and minor grooves -> interacts bases which creates specificity
- It can also occur in calcium binding motif
Fill in: secondary structures -> motifs -> …?
What are those? What clusters can you think of?
Domains
- conserved part of a given protein, that can exist, function and evolve independently of the rest of the protein
- could have been created by fusion of genes throughout evolution (but individual function is maintaned)
e.g. ligand-binding domains, DNA-binding domans, scaffolding domains
Let’s start with alpha structures
Look at an example of super-helical structure:
Bacterial muramidase
- involved in cell wall formation (peptidoglycan metabolism)
- 27 a-helices form 2 layered ring
- At C-terminal = superhelical twist
What happens to helices in solutions?
Helix alone in a solution = quite unstable secondary structure -> might be more beneficial to cooperate with another helix
- Two right-handed helices turn around each other to form left-handed coined-coil
How do amino acids within coiled coil look like?
- Every 7 aa = 2 rounds, amino acid pattern r
epeats = Heptad repeat- always the same polar.. sequence
- Hydrophobic center (a-a, d-d interaction)
- Surrounding ionic interaction (hiding the hydrophobic core)
- Outside polar amino acids
Look at how the hydrophobic parts stand against each other:
What is meant by the knobs and holes model?
Imagine we cut open the 2 helices and extend them to see their content -> in each lane there are gaps between the same amino acids (e.g. a line of d) that fit perfectly to the other helix (e.g. line of a)
Where do we encounter knobs and holes?
- Paraspeckles - nuclear structure formation involved in mRNA storage
- muscle protein myosin
- spectrina dn dystrophin linking actin molecules
- DNA and RNA binding
What is meant by “four helix bundle”?
= adjascent helices in primary structure (sequance) or in 3D
- different assemblies
- antiparallel e.g. helix-short loop-helix…
- parallel-antiparallel e.g. helix - long loop - helix - short loop
What structural characteristics are visible in this picture?
- Hydrophobic side chains packed tightly together
- Sometimes 2 pairs of coiled coils (knobs in holes)
- Results in an overal tilt angle of ~20 degrees
- packed in ridges in grooves model
How does the ridges in grooves model look like?
Group amino acids and find connecting lines = ridges
- between those ridges are grooves
- We can look at lines going from upper right to lower left - shown in the picture, that’s n and n+4
- BUT we can also draw lines from upper left to lower right, that being n and n+3
Look at these pictures:
- Great flexibility in how the ridges can group together
What is the globin fold? How can they differ? Where do we find it?
What can you say about hemoglobin?
- tetramer consists of 2 alpha- and 2 beta subunits
- each similar to myoglobin, each with heme pocket (co-factor ring, bind iron to ions in the middle)
- Very high concentration in red blood cells (completely crowded with this protein)
