Secondary Structure Flashcards
Protein Secondary Structure
The assignment of helices and sheets – the local spatial conformation of a polypeptide’s backbone.
What is the α-helix?
The α-helix is a coiled or spiral conformation in which every backbone carbonyl oxygen (C=O) group forms a hydrogen backbone amide (N-H) group of the amino acid four residues ahead of it in the helix.
What is the α-helix also known as?
3.613 helix
* 3.6 amino acids in each turn of the helix
* 13-member ring is formed by hydrogen bonding
What is the significance of the hydrogen bonding in the α-helix?
The sum of the hydrogen bonds in a helix makes it quite stable.
Each hydrogen bond is relatively weak in isolation
What were the two key developments in the modelling of the α-helix?
- The correct bond geometry, thanks to crystal structure determinations of amino acids and peptides
- Pauling’s prediction of planar peptide bonds; and his relinquishing of the assumption of an integral number of residues per turn of the helix.
What is the hydrogen bonding pattern in the α-helix?
The i + 4 -> i hydrogen bonding pattern is observed in the α-helix
What was the pivotal moment in the development of the α-helix model?
- In 1948
- Pauling drew a polypeptide chain of roughly correct dimensions on paper and folded it into a helix being careful to maintain planar peptide bonds.
- After a few attemps he produced a model with physically plausible hydrogen bonds
Who did Pauling work with to confirm his model of the α-helix before publication?
Corey and Branson
What was Linus Pauling awarded his first Nobel Prize for?
in 1954
“for his research into the nature of the chemical bond and its application to the elucidation of the structure of complex substances”.
What are β-strands?
- usually 5-10 amino acids in length,
- residues forming an almost fully extended zig-zag conformation.
What is the β-sheet?
- A structure formed by two or more β-strands
What are the three types of β-sheets?
- Parellel
- Anti-parallel
- Mixed
Parallel β-sheets
When β stretches are running in the same direction
from N-term to C-term
Anti-parallel β-sheets
Successive strands of alternating directions
N-term to C-term followed by C-term to N-term
Mixed β-sheets
Containing both parallel and anti-parallel strands
What are loops & turns in proteins?
Regions of proteins that connect segments of α-helices or β-strands
Characteristics of loops & turns
- Vary in length and shape
- Allow the polypeptide to fold into a compact tertiary structure.
- Present on the surface of polypeptides
- Rich in polar/charged aa
- Quite flexible
- Often form the active sites of enzymes
What is a β-turn or β-bend?
- Characteristic feature of many polypeptides
- A loop structure that achieves a 180˚ alteration in backbone direction over the course of 4 amino acid residues
- Most often found between two stretches of antiparallel β-strands.
How is β-turn or β-bend stabilised?
In part by the formation of a hydrogen bond between C=O of the first residue and NH of the fourth residue
What amino acids are most commonly associated with the α-helix?
- Glutamic Acid
- Methionine
- Alanine
- Leucine
Which amino acid is commonly associated with minimizing steric hindrance and why?
Glycine due to its small side chain.
Which amino acid is commonly associated with introducing a kink or bend in the polypeptide backbone?
Proline due to its unusual structure
What are domains?
tightly folded subregions of a single polypeptide connected to each other by more flexible or extended regions
What are motifs?
Motifs are building blocks of domains
Composed of a few stretches of secondary structure arranged in a specific 3-D conformation.
