1
Q
What are rotamers?
A
Rotamers - allowed arrangements of rotations in the side chain
2
Q
Why do we have non polar interactions at the surface?
A
- it needs to interact with other proteins so hydrophobic allows for interactions
- you want the protein to have marginal stability - you don’t want a brick
3
Q
What re the categories of proteins?
A
- Transmembrane
- Globular (water soluable)
- enzymees, antibodies
- focus of most lecture
- Fibrous
- elongated and generally soluablee
4
Q
What are the domain fold classes?
A
5
Q
How do we identify similarity in protein structure?
A
- superpose the structures, often just the C alpha atoms, and quantify on average the separation between equivalent positions
- quantified as root mean square deviation of equivalenced position
- Often need to introduce gaps
- Quuote RMS for number of atoms superposed out of how many
- RMS depends on number equivalenced
6
Q
Conservation and variation in homologous proteins
A
7
Q
Functional conservation and EC nomenclature
A
- the 4 digit EC nomenclature provides tool 3 difit code
- all 4 digits the same - same reaction on same substrate
- 3 digit the same - same reaction but different substrates
- <3 digits the same - quite different reactions
8
Q
What car the EC codes for different classes of anzxymes?
A
9
Q
How common is convergence of function?
A
- About 15% of enzyme active sites occur more than
once (i.e. mechanistic analogues)
- About 15% of enzyme active sites occur more than
- NB Sometimes one sees side-chains with similar
chemical properties (e.g. Asp in one enzyme and Glu
in another)
- NB Sometimes one sees side-chains with similar
10
Q
Convergence of fold
A
- some folds found very often between proteins with veery different functioons
- suggest favourable energetic arrangement and proteins have converged to somilar fold
- e.g. 4-α helical bundle , TIM (β/α)8 barrel
- But difficult to distinguish convergence and
divergence
- But difficult to distinguish convergence and
11
Q
What is a superfamily?
A
- a set of proteins that have all evolved directly from a common ancestor
- May have similar consequences that can be detected computationally but sometimes sequence similarity too remote to be detected
- may or may not have similar function
12
Q
Scop Hierarchical classification
A
13
Q
SCOP Topology
A
- domaisn classified in the same overall fold
- more or less the same secondary structure elements
- the same or siimilar connection topology
- sometimes with differing loop structures
SCOP families are manually constructed
A closer evolutionary relationship between proteins
Often similar function
Higher level of sequence identity (often >35% but not fixed)
14
Q
CATH domain classification
A
