Lecture 9 DA

Question 1

What is a limitation of x-ray crystallography?

Answer 1

It is just a snapshot of the crystal, at that moment in time. Crystals move and vibrate etc.

Question 2

Is the structure of a protein sufficient to determine its function?

Answer 2

Yes, but for some proteins only, like structural proteins.

Question 3

How are some amino acids important in correct biological activity in some proteins?

Answer 3

The active site of proteins with biological activity (ie enzymes) is formed by crucial amino acids.

Question 4

Do secondary structures of proteins form as the mRNA is translated, or once completely translated?

Answer 4

As it is being translated.

Question 5

What typically mediates complete folding of proteins?

Answer 5

Chaperones, but not always.

Question 6

How do chaperones bind to their target?

Answer 6

Via hydrophobic interactions.

Question 7

Where would evolution of amino acids be faster/slower, in the core, or on the surface?

Answer 7

Evolution is slower in core amino acids, whilst faster with surface ones.

Question 8

Are surface amino acids hydrophobic or -philic? What about core amino acids?

Answer 8

Core - hydrophobic

Surface - typically phydrophilic, but can be hydrophobic - ie clefts/active sites.

Question 9

What kind of architecture do proteins have?

Answer 9

Modular architecture.

Question 10

What kinds of proteins are the most difficult to crystallise and model? How are they typically crystallised?

Answer 10

Membrane spanning proteins. Easier to co-crystallise them with another protein that masks their hydrophobicity, and can be adjusted via algorithms for a pure dataset.

Question 11

What percentage of proteins are membrane spanning?

Answer 11

20%

Question 12

What percentage of drugs target a protein as its causative action?

Answer 12

50%

Question 13

The conformation of the backbone of amino acids is defined by what?

Answer 13

Phi and psi angles.

Question 14

Which amino acid has no angles of freedom? What about the most?

Answer 14

Proline - none

Glycine - most

Question 15

True or false

Most angles of phi and psi are allowed.

Answer 15

False

Question 16

What secondary structure can be found in each quadrant of the Ramachandran plot?

Answer 16

Top left - b-sheets
Top right - left-handed a-helix
Bottom left - right handed a-helix
Bottom right - NA

Question 17

Which secondary structure is most common?

Answer 17

Right handed a-helix

Question 18

What entirely dictates protein folding?

Answer 18

Primary sequence

Question 19

What is the Darwinian principle of protein evolution?

Answer 19

Proteins evolved from a common ancestor have similar folding.

Question 20

What does the algorithm based on Darwinian principles of protein evolution do?

Answer 20

Detects sequence similarity.

Question 21

What is the Boltzmann principle of protein folding?

Answer 21

Proteins search for conformational space, minimising their free energy.

Question 22

What does the algorithm based on Boltzmann principle of protein folding do?

Answer 22

simulates folding process.

Question 23

What is the function of ubiquitin?

Answer 23

Tags misfolded/unfolded proteins for digestion via a proteosome.

Question 24

When proteins are digested by a proteosome for being un/misfolded, what happens to them? How does this affect infection?

Answer 24

They go to the ER, and are put on MHC markers for display on the cell surface.
When infected, pathogen proteins will be displayed instead, allowing the immune system to be alerted.

Question 25

What is the primary repository for protein structures? What else does it contain? What tool can be used to search it?

Answer 25

Protein databank PDB.
Also contains DNA/RNA structures.
Searched with BLAST.

Question 26

Are new folds currently being found?

Answer 26

No

Question 27

Is there a finite number of folds, or is it infinite? Why?

Answer 27

Predicted to be finite, as there are a finite number of superfamilies.

Question 28

What does it mean if proteins have the same fold? What else points to this? Do they have sequence similarity?

Answer 28

Major structural similarity between the two.
Secondary structure must be in the same arrangement, with same overall topology.
Generally no sequence similarity.

Question 29

What does it mean if two proteins are in the same superfamily?

Answer 29

Probably common evolutionary origin, low sequence identity.

Question 30

What does it mean if two proteins are in the same family?

Answer 30

Clear evolutionary relationship, with moderate to high sequence similarity - >30% pairwise identity.

Question 31

Name and describe two protein structure comparison methods.

Answer 31

Protein sequence matching - applies dynamic programming to the problem of string matching, and uses a scoring scheme.
3D protein structure matching - uses algorithms similar to dynamic programming that finds optimal match between two shapes.

Question 32

How does the algorithm behind 3D protein structure matching work?

Answer 32

Looks at dihedral angles, phi and psi, and draws a distance matrix.

Question 33

How do some tools like DALI search for matching structures among proteins?

Answer 33

Splits searches into hexapeptides, and finds all matching hexapeptides.
Concatenates matching hexapeptides using simulated annealing.

Question 34

Name 4 modelling techniques.

Answer 34

Predicting secondary structures.
Homology modelling
Fold recognition
De novo prediction

Question 35

How can homologues sometimes be recognised when predicting secondary structures?

Answer 35

By similar patterns of secondary structures.

Question 36

Which modelling technique is generally the most accurate? What does it require?

Answer 36

Homology modelling. Requires a homolog with a known structure.

Question 37

What does de novo prediction use as the basis for its prediction?

Answer 37

The primary sequence is used.

Question 38

What are the steps of homology modelling (4)?

Answer 38

• Homologs of known structures are identified
• High quality alignment of the sequence in question with the protein of known structure.
• Run modelling algorithm. Different residues between the sequences are changed, and the consequence to overall structure evaluated.
• Model is evaluated for unacceptable stearic clashes (Ramachandran plot)

Question 39

What can be used to identify distantly related homologs?

Answer 39

Psi-BLAST

Question 40

How does fold recognition work (threading)?

Answer 40

Looks for a compatible fold for a given sequence.

Question 41

What is threading/fold recognition used in (3+)?

Answer 41

Profile matching, secondary structure prediction, alignments, etc

Question 42

When is the ab initio method used? What does it attempt to predict, and from what?

Answer 42

When the sequence cannot be assigned to a known fold.

It attempts to predict the structure from the primary sequence.

Question 43

How important is the ab initio method for fold predictions?

Answer 43

It is less important in fold predicting, but still important for refinement of strucure.

Question 44

Is it possible to obtain a high quality structure prediction from the primary sequence alone (with no reference protein/sequence)?

Answer 44

No.

Question 45

What is the thermodynamic hypothesis?

Answer 45

Protein is looking for the free energy minimum state.