L1 - Protein structure & folding

Question 1

Different ways of illustrating protein structure?

Answer 1

Wire frame

Van der Waals surface

Protein backbone

Ribbon/cartoon

Molecular surface

Question 2

Wire frame illustration

Answer 2

Shows every bond with a colour at each end that denotes the element

Question 3

Van der Waals surface illustration

Answer 3

Atom radii & shows exposure of carbon on the outside

Question 4

Protein backbone illustration

Answer 4

Backbone trace

Shows some kind of symmetry about the central region where the active site is

Question 5

Ribbon/cartoon illustration

Answer 5

Represents the secondary structure

Red corkscrews – alpha helices

Yellow arrows – point from N terminus to C terminus – show the direction the polypeptide is going

Central domain is made of beta strands forming a barrel

Question 6

Molecular surface illustration

Answer 6

Different to the Van der Waals surface as its much smoother & much more representative of the active surface

Can see where the polarity is

Question 7

How can we determine protein structure?

Answer 7

X-ray crystallography

Nuclear magnetic resonance (NMR) spectroscopy

Question 8

X-ray crystallography

Answer 8

Diffraction patterns obtained from protein crystals are used to reconstruct the coordinates of atoms in the structure

Question 9

Nuclear magnetic resonance (NMR) spectroscopy

Answer 9

Magnetic interactions between atomic nuclei spreading through covalent bonds & space can be measured & used to determine connections & distances between protein atoms in the structure while in solution

Question 10

How can we know that proteins are dynamic?

Answer 10

Considered to resonate around a normal mode

Often a breathing structure by thermal interactions - Brownian motion hitting the proteins

Question 11

What are the non-polar amino acids?

Answer 11

Glycine 
Alanine 
Valine 
Cysteine 
Proline 
Leucine 
Isoleucine 
Methionine 
Tryptophan 
Phenylalanine

Question 12

What are the polar amino acids?

Answer 12

Serine 
Threonine 
Tyrosine 
Asparagine 
Glutamine

Question 13

What are the positively charged amino acids?

Answer 13

Lysine
Arginine
Histidine

Question 14

What are the negatively charged amino acids?

Answer 14

Aspartic acid

Glutamic acid

Question 15

What are the layers of protein structure?

Answer 15

Primary - amino acid sequence

Secondary - alpha-helices & beta-strands (turns, loops)

Tertiary - assembly of secondary structural elements

Quaternary - interactions between monomers

Question 16

Is the peptide bond planar?

Answer 16

Yes

All atoms are in 1 plane

Question 17

Is the polypeptide backbone flexible?

Answer 17

Can rotate around the alpha carbon

A protein structure has rigid links and isn’t like a piece of string

Links are joined together at the alpha carbons

Can rotate either side of the alpha carbon link

Question 18

What are torsion angles on bonds?

Answer 18

Formed by three consecutive bonds in a molecule and defined by the angle created between the two outer bonds

Question 19

How are torsion angles involved in rotation?

Answer 19

The ability to rotate can be defined – idea of torsion angles on bonds

Have 2: one that looks towards the C terminus (psi angle) and one that looks towards the N terminus (phi angle)

Question 20

What is a psi angle?

Answer 20

Torsion angle

Look from the alpha-carbon towards carbon

Question 21

What is a phi angle?

Answer 21

Torsion angle

Look from the nitrogen towards the alpha-carbon

Question 22

Are the majority of peptide bonds in trans or cis configuration?

Answer 22

Trans

Question 23

Why are the majority of peptide bonds trans?

Answer 23

Amide proton and the carbon oxygen are pointing in different directions

There is more space like this – they are trying to fight for the same space

Means they face opposite each other – this is defined by the omega angle

Question 24

What is the omega angle?

Answer 24

The torsion angle measured over the peptide bond, the chemical bond that connects two amino acids

Question 25

What are the 3 types of torsion angles?

Answer 25

Phi

Psi

Omega

Question 26

What degrees can an omega angle be?

Answer 26

can be 0 or 180 (+/- 10)

In trans its 180 degrees

In rare cases omega = 10 degrees for a cis peptide bond which usually involves proline

Question 27

How likely are you to get a cis conformation over a trans?

Answer 27

The cis conformation is present in about 1 in 1000 peptide bonds (Trans/Cis = 1000)

Question 28

Why is the configuration of proline more likely to be cis than other residues?

Answer 28

1 difference is in proline that doesn’t have the amide proton – amide proton is part of the side chain – changes the conformation of the peptide bond

Proline is trans 4 times more than cis (Trans/Cis = 4) – is a lot higher for other residues

Question 29

What is a Ramachandran diagram?

Answer 29

Is a way to visualise energetically allowed regions for backbone torsion angles psi against phi of amino acid residues in protein structure

Based upon the steric constraints to psi & phi so the side chain atoms do not overlap in space with other side chain or main chain atoms

Question 30

Principles of Ramachandran diagrams?

Answer 30

In allowed regions there are no atomic clashes

If we take the psi & phi angles you can define the structure of proteins

If you analyse the proteins, out of all the angles, you end up with only a very few possible

Because of problems with clashing, the proteins can only fold to about 10% of the possible conformations

Question 31

What does the Ramachandran diagram show us about the freedom of polypeptide chains?

Answer 31

The freedom for polypeptide chain is much less than at first apparent

The chain obeys simple rules when folding

Question 32

Why is the Ramachandran diagram for glycine different?

Answer 32

Has more rotational freedom

Big different is glycine that only has a H atom as its side chain – can explore a lot more of the plot

Glycine rich regions in proteins are very flexible & have lots of conformations – not accessible to other amino acids

Question 33

What are side chains chi torsions angles?

Answer 33

The side chain atoms of amino acids are named in the Greek alphabet according to this scheme

Potentially around each bond there is a torsion angle

Side chains can bring it lots of other complexity

The side chain torsion angles are named chi1, chi2, chi3…

Question 34

What are rotamers?

Answer 34

Rotamers are conformational isomers that differ by rotation about a single σ bond

Have certain places that are more common – some angles don’t occur

Low energy states are favorable

Question 35

What do conformational isomers tell us about protein structure?

Answer 35

Have preferred conformations – again proteins are less complex than thought to be

Question 36

H bonding patterns in the secondary structure?

Answer 36

The peptide group has dual H-bond capacity

H-bonds are weak, non-covalent interactions

They are directional & specific

Each peptide bond can form a H-bond in both directions

A network of interactions can hold the polypeptide in a strong & specific framework
• Alpha-helices
• Beta-sheets

Secondary structures form motifs & domains