Structure elements and characterize of protein Flashcards
Methods of characterize a protein (6)
Absorbance
Fluorescence
Circular dichroism (Far and near UV)
NMR
Xray
SPR
Conserved substitutions
Amino acid replacement in a protein that changes a given amino acid to a different amino acid with similar biochemical properties.
Non conservative changes
A point mutation is a genetic mutation where a singel nucleotide is changed, deleted or inserted in a sequence of DNA or RNA.
Can lead to synonymous or frameshift mutation.
Secondary structure
α-helix
β-strand
Turns
Stabilized by H-bonds between peptide groups
Where the pro in helix?
At the beginning of helix
Side chain conformational restrictions
Val; Ile; Thr
α-helix dipole moment
peptide bonds have polarity which gives helices dipole moments.
Riges in grooves model
Helices often pack against each other according to ridges in grooves model.
Depending on actual amino acid sequence, ridges may formed of residues which are 3 to 4 amino acids apart.
NOT found in coiled coil but other motifs
310 helices are often found in proteins
regular α-helix is distorted by unfavourble residues
Rare α-helix
ψ and φ angels lie at the edges of the allowed region of the Ramachandran plot
Mixed β sheet
parallel + antiparallel β-strands
β turn four residues
Most common in protein
γ turn three residues
Links strands of antiparallel β sheet
Protein super-secondary structure
Motifs
If we think each secondary structure as a ¨ unit ¨ then a super secondary structure would comprised of at least two ¨ units ¨
Tertiary structure
The specific three-dimensional shape into which entire polypeptide chain if folded.
Two variants of ridges in grove model
1, if 2 helices with ridges 4 residues apart combine there is 50⁰ angle between helices.
2, one helix with ridges 4 residues apart + one helix with ridges 3 residues apart, there’s 20⁰ angle
