Protein Structure Exam Flashcards
(42 cards)
What is a protein domain?
A protein domain is a distinct functional or/and structural units in a polypeptide chain (capable of folding as independent units)
Can different domains of a protein have different function?
Yes, they could be either catalytic site, regulatory site or a binding site
Do proteins of the same family have the same organization?
No, they can have different organization of same core domains
What is the R-value?
The R-value is the quality of the atomic model, how well the simulated diffraction pattern matches experimentally observed one
Are R-values above 0,6 good?
No, this represents totally random set of atoms. A good R-value would lie around 0.20
What does R-free mean?
R-free is unbiased, where the data is split to 90% refinement and 10% experimental to calculate the R-free value (test, train). Should lie around 0.2 or a little higher
What is the B-factor?
B-factor is measure of atomic vibrations, related to protein flexibility
What is the best Ångstrom value for protein resolution?
The lower the Å, the higher the resolution, therefore it is preferable to be low (very low Å, extremely precise electron density, can be almost perfectly reconstructed backbone)
Which parameters contribute to the B-factor?
The B-factor, measure of atomic vibration, contains contributions from; crystal defects/decay, data incompleteness, multiple conformations, model/refinement errors and occupancy
What does the ramachandran plot show?
Tells us whether the protein being visualized and modelled, fits with what we know about protein chemistry (lot of outliers might be mistakes)
What is B-factor also called?
B-factor is also referred to as the temperature factor, contributions from static and dynamic disorder (10-20 Å^2 is well determined)
What is the R-factor a comparison between?
The value from R-factor is the disagreement between observations and calculated data
What does resolution mean?
A measure of the amount and quality of the data
What is R-value also called?
R-value, R-factor and R-work is synonyms for the same
What is homologous proteins?
Proteins which derive from the same ancestral protein
What is protein orthology?
Orthologous proteins, have the same specificity in different organisms, e.g. bind the same ligand and similar DNA sites in related genomes
; structure and function very conserved
What is protein paralogy?
Occurs with duplication, still has the same function, but has more freedom; structure conserved and functions might vary
Can mutations alter coding regions of a protein?
Yes, mutations can impact protein thermodynamic stability (misfolding and aggregation) on different layers; activity, local interaction, co-factor/metal binding and post translational modifications
What does the Gibbs free energy mean?
Thermodynamic stability is measured in ΔΔG in kcal/mol indicating the change in Gibbs free energy between wild type and mutants global free energy
What does a high Δ ΔG mean for a mutant?
That the mutant have a higher ΔΔG energy than the wild type, will be positive and highlight a possibly destabilizing mutation
If you want to solve a large complex protein complex which technique would be most suitable?
Cryo-EM would be most suitable as it doesn’t rely on the formation of a crystal and it is less sensitive to motion as the NMR spectroscopy
If we have a smaller protein (smaller than 50 kDa) which methods should we use?
NMR is usually employed to smaller proteins, because of the slow molecular tumbling leads to rapid nuclear relaxation and thereby low detection sensitivity, resulting in difficulties obtaining information about local conformation and distances
Is x-ray sensitive?
X-ray require all conditions to be optimized, for it to be able to form a crystal. Therefore large complexes need to be very stable to be captured with this technique
What is the main purpose of the PDBminer?
To get structural information from protein data bank (PDB), providing information regarding features of domains, patterns, stored nucleic acids in the protein and visualization of the protein
