Lec 25 Flashcards
Lower A is _____ resolution
Higher
What are polyphen scores
Assign scores to tell the impact of genetic mutations on the protein structure and function
Tells whether a mutation is more or less pathogenic (disease causing)
based on if it’s a conservative, nonconservative mutation. If it changes a salt bridge that’s required etc.
Usually arg to lys we’d think is a conserved mutation because positively charged but it causes diseases why
What is it’s on the surface of the protein
Because arg can form many interactions at the same time but lysine can’t
Would have much of a role in causing a disease
What does polyphen take into account
It takes into account the PAM matrix and the 3D structure matrix
What is CPVT
A heart disease caused by a genetic mutation
Hard to diagnose because see nothing in the ECG
But if do a stress test , fast heart rate (tachycardia)
What do you need in order to understand the context of the mitation
Need to know the structural information of where the mutation is (ex. Alpha helix or beta sheet or loop) to see if it’s has an impact
Can you predict the 3D structure of protein from just the sequence
What can be used
This is the holy grail of biochemistry
Not yet but homology modelling is the best so far
HM only works well if the 3D structure of a homologous protein (similar to yours) is already found and you use that as a template to make yours
What is covariance in alpha fold and how can I help in figuring out structure
When doing MSA (multiple sequence alignments) with millions of proteins
You look at the highly conserved sequences and see if they are mutated in the other organism
If one amino acid changes in the sequence and another amino acid also changes near it (ex. The R and D in one turned into W and V in the other )
This means that the amino acids are mutating together and are interacting and close together in 3D.
What is the problem with finding covariance
If the sequence is highly conserved (not really changing) then you can’t really tell about covariance
If flexible hard to tell the 3D structure
Need a lot of mutation info of the protein
On a NOE z spectrum what does it mean if the residues are higher up on the x axis
What about lower
Higher means more stable structure
Lower means more unstable
What did the NOE z spectrum tell us about Calmodulin
Why
In the middle of the cam sequence it shows as flexible (lower NOE value, less stable)
But the crystal form shows as an alpha helix, which is not flexible
When we crystallize the structure for alpha fold, it can cause regions that are normally flexible to become rigid and more stable, which is why we see the helix and no loop
What is the message of the NOE z spectrum telling us about Calmodulin
You often need two different techniques to tell the structure of the protein
The alpha helix of cam rarely exists in solution
In NOE z spectrum about Calmodulin which do we see dip at the ends
The n and c term are flixble
How can alphafold be biased
It shows the calcium bound and apo state of cam as similar when it actually isn’t
It’s biased because it uses previous structures from the database to make the new protein
Why is the structur of apo cam hard to capture
How is it different from the alphafold prediction
Because it is very flexible and the lobes are moving a lot
Very diffent from alphafold because the linker region is actually a loop not a helix
In protien and ligands binding what is Koff and Kon
Kinetics constant that tell how the protein ligand complex comes apart (off) and comes together (on)
What are the equations for total protein and total ligand
P total = P free + PL (because p in both)
L total = L free + PL
What is Kon limited by and what is its range
What is the range of Koff
Limited by diffusion
Rate of 10^8 collision / sec at 1M concentration
10^6 (weak) to 10^-4 (strong)
What is the ligand leaving it’s binding site dependent on
The affinity (strength of the interaction) between the ligand and the binding site
What values of k off are better and why
Lower values (ex. 10^-4 sec -1)
Because If it take longer for ligand to come off, better and stronger interaction
What is the equilibrium constant for binding called
What is the formula
The KA : accosiation constant (how quickly the PL complex forms)
KA= Kon/Koff = [PL]/ P x L
How do you derive the Ka equation at equilibrium
Initially d[PL]/ dt = Kon [P][L] - Koff [PL]
At equallibtium , the change in PL is zero so
0 = Kon [P][L] - Koff [PL]
Kon [P][L] = Koff [PL]
So Kon/Koff = [PL]/ [P][L] = KA
What is KD
The dissociation constants
Inverse of KA so
Koff/Kon = [P][L] / [PL] = KD
1/KA
Why is the rate this: d[PL]/ dt = Kon [P][L] - Koff [PL]
Because the forward rate (formation of [PL]) depends on Kon times the concentration P and L
Minus however much is coming off
What is the Koff and Kon of ligands that bind tightly
What about ligands that bind weakly
Koff is low and Kon is high (Kon/Koff = KA)
Koff is high and Kon is low
What are the units of KD
Molarity
What is fractional saturation
What is the range
Y
Shows how much protein is bound to the ligand (fractional saturation of the protein)
0-1 (0% to 100%)
What is special about p total in each experiment
It’s constant in each experiment
We don’t normally know the free concentration of protein (just [P])
What is the fractional saturation equation
What is the assumption we make to get this equation
Y = [L] / KD + [L]
Assume that the free [L] = the total [L]
Why is fractional saturation important
During crystallization, want to know how much ligand gives you 99% saturation (just enough)
because you don’t want too much free ligand floating around and keep saturating the complex because that inhibits crystallization
Also for drug purposes to know how much drug is saturating the HSA protein
For purification
If the assumption [L] total does not = [L] free what happens
What is special about it
The fractional saturation equation to use changes
It’s a quadratic so need to use the - version of the quadratic
