L1 - Protein structure & folding Flashcards
Different ways of illustrating protein structure?
Wire frame
Van der Waals surface
Protein backbone
Ribbon/cartoon
Molecular surface
Wire frame illustration
Shows every bond with a colour at each end that denotes the element
Van der Waals surface illustration
Atom radii & shows exposure of carbon on the outside
Protein backbone illustration
Backbone trace
Shows some kind of symmetry about the central region where the active site is
Ribbon/cartoon illustration
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
Molecular surface illustration
Different to the Van der Waals surface as its much smoother & much more representative of the active surface
Can see where the polarity is
How can we determine protein structure?
X-ray crystallography
Nuclear magnetic resonance (NMR) spectroscopy
X-ray crystallography
Diffraction patterns obtained from protein crystals are used to reconstruct the coordinates of atoms in the structure
Nuclear magnetic resonance (NMR) spectroscopy
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
How can we know that proteins are dynamic?
Considered to resonate around a normal mode
Often a breathing structure by thermal interactions - Brownian motion hitting the proteins
What are the non-polar amino acids?
Glycine Alanine Valine Cysteine Proline Leucine Isoleucine Methionine Tryptophan Phenylalanine
What are the polar amino acids?
Serine Threonine Tyrosine Asparagine Glutamine
What are the positively charged amino acids?
Lysine
Arginine
Histidine
What are the negatively charged amino acids?
Aspartic acid
Glutamic acid
What are the layers of protein structure?
Primary - amino acid sequence
Secondary - alpha-helices & beta-strands (turns, loops)
Tertiary - assembly of secondary structural elements
Quaternary - interactions between monomers
Is the peptide bond planar?
Yes
All atoms are in 1 plane
Is the polypeptide backbone flexible?
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
What are torsion angles on bonds?
Formed by three consecutive bonds in a molecule and defined by the angle created between the two outer bonds
How are torsion angles involved in rotation?
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)
What is a psi angle?
Torsion angle
Look from the alpha-carbon towards carbon
What is a phi angle?
Torsion angle
Look from the nitrogen towards the alpha-carbon
Are the majority of peptide bonds in trans or cis configuration?
Trans
Why are the majority of peptide bonds trans?
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
What is the omega angle?
The torsion angle measured over the peptide bond, the chemical bond that connects two amino acids
What are the 3 types of torsion angles?
Phi
Psi
Omega
What degrees can an omega angle be?
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
How likely are you to get a cis conformation over a trans?
The cis conformation is present in about 1 in 1000 peptide bonds (Trans/Cis = 1000)
Why is the configuration of proline more likely to be cis than other residues?
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
What is a Ramachandran diagram?
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
Principles of Ramachandran diagrams?
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
What does the Ramachandran diagram show us about the freedom of polypeptide chains?
The freedom for polypeptide chain is much less than at first apparent
The chain obeys simple rules when folding
Why is the Ramachandran diagram for glycine different?
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
What are side chains chi torsions angles?
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…
What are rotamers?
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
What do conformational isomers tell us about protein structure?
Have preferred conformations – again proteins are less complex than thought to be
H bonding patterns in the secondary structure?
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
