Three dimensional structure of proteins Flashcards
At what wavelength do you measure proteins absorbance?
280 nm
At what wavelength do you measure DNA?
260 nm
What is needed to be able to measure absorbance of a protein?
Aromatic aa, mostly W but also Y and F.
What does fluoresence measure?
Stability and binding events
What does Far CD measure?
Secondary structure, can tell if a protein is folded or not
What does Near CD-measure?
Tertiary structure, proteins fingerprints
What is the perk with calorimetry?
It can be used with unpurified samples
What does ITC measure?
Ligand binding
What does DSC measure?
Unfolding of a protein
What does NMR measure?
Determines protein structure and changes in individual amino acids when binding a ligand
What does X-Ray do?
Determines protein structure of crystallized proteins
What does SPR measure?
Determines the dissociationg constant (Kd) by measuring the refractive index
What does identical residues mean when you are aligning two sequences from different species?
The compared spot in the sequence are the same residue
What does conserved substitution mean when you are aligning two sequences from different species?
The compared residues in the sequence have similar structure and the structure will therefor be similar. Not a drastic mutation
What does non-conservative changes mean when you are aligning two sequences from different species?
That the spot compared have significantly different aa, leading drastic change in structure
What is a ramachandran diagram used for?
The diagram is used to see if a secondary structure is likely to occur. Some residues are more likely to be eg an a-helix than others
What does propensity mean?
The tendency of an aa to be in a certain secondary structure
What does a propensity score above 1 indicate? And below 1?
> 1 => Prefered structure
< 1 => not a likely structure
What does the ridges in grooves model mean?
It means that helicies often pack against each other matcher their grooves into another helix ridges
How many residues does an a-helix have per turn?
3,6 residues
How many residues does an 310 helix have per turn?
3
How many residues does an pi-helix have per turn?
4,4
How many residues does a (anti)-parallell b-strand have per turn?
2
Where are 310 helicies found in proteins?
- Regular a-helix is distorted by unfavorable residues
- At the end of a regular helix
- Short sequences in helical conformation
