Protein Structure Exam

Question 1

What is a protein domain?

Answer 1

A protein domain is a distinct functional or/and structural units in a polypeptide chain (capable of folding as independent units)

Question 2

Can different domains of a protein have different function?

Answer 2

Yes, they could be either catalytic site, regulatory site or a binding site

Question 3

Do proteins of the same family have the same organization?

Answer 3

No, they can have different organization of same core domains

Question 4

What is the R-value?

Answer 4

The R-value is the quality of the atomic model, how well the simulated diffraction pattern matches experimentally observed one

Question 5

Are R-values above 0,6 good?

Answer 5

No, this represents totally random set of atoms. A good R-value would lie around 0.20

Question 6

What does R-free mean?

Answer 6

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

Question 7

What is the B-factor?

Answer 7

B-factor is measure of atomic vibrations, related to protein flexibility

Question 8

What is the best Ångstrom value for protein resolution?

Answer 8

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)

Question 9

Which parameters contribute to the B-factor?

Answer 9

The B-factor, measure of atomic vibration, contains contributions from; crystal defects/decay, data incompleteness, multiple conformations, model/refinement errors and occupancy

Question 10

What does the ramachandran plot show?

Answer 10

Tells us whether the protein being visualized and modelled, fits with what we know about protein chemistry (lot of outliers might be mistakes)

Question 11

What is B-factor also called?

Answer 11

B-factor is also referred to as the temperature factor, contributions from static and dynamic disorder (10-20 Å^2 is well determined)

Question 12

What is the R-factor a comparison between?

Answer 12

The value from R-factor is the disagreement between observations and calculated data

Question 13

What does resolution mean?

Answer 13

A measure of the amount and quality of the data

Question 14

What is R-value also called?

Answer 14

R-value, R-factor and R-work is synonyms for the same

Question 15

What is homologous proteins?

Answer 15

Proteins which derive from the same ancestral protein

Question 16

What is protein orthology?

Answer 16

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

Question 17

What is protein paralogy?

Answer 17

Occurs with duplication, still has the same function, but has more freedom; structure conserved and functions might vary

Question 18

Can mutations alter coding regions of a protein?

Answer 18

Yes, mutations can impact protein thermodynamic stability (misfolding and aggregation) on different layers; activity, local interaction, co-factor/metal binding and post translational modifications

Question 19

What does the Gibbs free energy mean?

Answer 19

Thermodynamic stability is measured in ΔΔG in kcal/mol indicating the change in Gibbs free energy between wild type and mutants global free energy

Question 20

What does a high Δ ΔG mean for a mutant?

Answer 20

That the mutant have a higher ΔΔG energy than the wild type, will be positive and highlight a possibly destabilizing mutation

Question 21

If you want to solve a large complex protein complex which technique would be most suitable?

Answer 21

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

Question 22

If we have a smaller protein (smaller than 50 kDa) which methods should we use?

Answer 22

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

Question 23

Is x-ray sensitive?

Answer 23

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

Question 24

What is the main purpose of the PDBminer?

Answer 24

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

Question 25

What is the purpose of CABSflex?

Answer 25

CABSflex analyzes the flexibility of protein structures, the dynamic behavior, how proteins move and change their conformation, creating an ensemble of a protein conformation representing the range of possible movements.

Question 26

What is the purpose of the FoldX tool?

Answer 26

FoldX provides protein stability prediction, calculating the free energy changes associated with protein folding. Can also provide informations in regards to protein-protein interaction, the stability of complexes formed between proteins or protein and DNA. it signifies with the energy calculations, the regions which need refinement.

Question 27

What is the purpose of MutateX?

Answer 27

Is the analysis of protein mutations, the mutational impact predictions allow insight into each substitutional effect. Showing how a mutation might affect protein performance. Mainly showing stability and functionality.

Question 28

What is the purpose of AlphaMissense?

Answer 28

AlphaMissense is prediction of missesense mutations effect on protein function and assess their potential pathogenicity.

Question 29

What is the purpose of docking?

Answer 29

Is prediction of preferred orientation and interaction of two molecules, typically a small molecule (ligand) and a protein (receptor) when they form a stable complex

Question 30

Can BLAST perform multiple sequence alignment?

Answer 30

No, because Basic Local Alignment Search Tool, is designed for identifying regions of similarity between sequences through local alignment.

Question 31

What is the Hidden Markov Models (HMMs)?

Answer 31

It is used in tools like HMMER, capturing more complex sequence patterns compared to simpler methods like blast. Build based on multiple sequence alignment (MSA) and model the probability of insertion and deletions at each site.

Question 32

Which method can be used to model long-range interactions in multiple sequence alignment (MSA)?

Answer 32

Attention mechanism, a model which can focus on specific parts of the input sequence when making predictions, thereby improving the accuracy and interpretability of the model.

Question 33

Which forces are a protein held together by?

Answer 33

Hydrophobic Force, salt bridges, H-Bonds, disulfide bridges and aromatic interactions

Question 34

What is the typical time-step for molecular dynamics simulations?

Answer 34

~ 10^-16 s

Question 35

What can FoldX be used to assess?

Answer 35

It can be used to assess the effect of mutations based on empirical field and include entropic terms

Question 36

What can FoldX be used to assess?

Answer 36

It can be used to assess the effect of mutations based on empirical field and include entropic terms

Question 37

What is docking?

Answer 37

Docking is testing of different ways a ligand, locating where the ligand most effectively interact with the protein in regards of chemical properties
- either random binding or choosing a specific area

Question 38

What does AlphaFold generate?

Answer 38

It generates high-accuracy models without using any explicit templates

Question 39

What does AlphaFold predict?

Answer 39

It can predict the structure of multi-domain proteins, and it also provides a predicted accuarcy of the mutual position of domains

Question 40

What is the advantages of LDDT (local distance difference test)

Answer 40

• it does not require a global superposition of the two structures
• it is local score
• it is normalized between 0 and 1

Question 41

What is the main driver in the predictive power of protein language models?

Answer 41

• ability to identify long-range interactions
• ability to take large models, hundreds millions of parameters

Question 42

What does Chothia and lesk plot show?

Answer 42

It reports the structural similarity between proteins in the same family, based on pairwise sequence similarity and valid for main chain atoms (not side chains)