Down - Modifications

Question 1

[Modifications] What are the 4 types of chemical modification of amino acids and proteins?

Answer 1

PTMs in vivo

Nonspecific protein modification - protein aging through spontaneous damage

Non-protein modified AAs w. biological roles

In vitro chemical modifications

Question 2

[Modifications] What are the two main types of PTM modifications?

Answer 2

Main chain and side chain

Question 3

[Modifications] Give two examples of common N-terminal main chain modifications

Answer 3

Acetyaltion: Acetyl group bound between N and the carbonyl carbon. Reduce the charge and a bit bulkier

Cyclisation: Amino group in the backbone and in the residue makes cycle, one leave. No charged end and resistant to aminopeptidases

Question 4

[Modifications] Give an example of a common C-terminal modification

Answer 4

Amidation: Terminal Gly “sacrificed” thorugh hydroxylation > carboxyl group of Gly leave, leaving amino agroup behind. No charged end and resistant to carboxypeptidases

Question 5

[Modifications] Give some examples of side chain modifications (7)

Answer 5

Hyp ((4)-Hydroxyproline) & Hyl (Hydroxylysine): Extra OH on Pro/Lys

Super amino acid: Cross-linking of Lys, Hyl and His side chains

N-methylated lysine: 1, 2, 3. Less reactive and pH independent charge

Gla (γ-carboxyglutamic acid): Extra carboxyl group at end

Phosphorylation: On Ser/Thr. Kinase makes, phosphatase remove

Glycosylation: Addition of glycan (N or O). Improved solubility and protection.

GFP chromophore: Peptide sequence, fold itself to function

Question 6

[Modifications] Name some important cofactors in side chain modifications

Answer 6

Hyp/Hyl: α-ketoglutarate (“bounce O”) and vitamin C (convert enzyme into active)

Gla: Vitamin K (reactive alkoxide for activation)

Phosphorlyation: Phosphate group donor (ATP)

Question 7

[Modifications] What are the main differences between O- and N-linked glycosylation?

Answer 7

O: On OH Ser/Thr, directly on chain and during synthesis

N: On Asn, on carrier (dolichol, use phosphate) and added after

Question 8

[Modifications] Which are the three nonspecific protein modifications?

Answer 8

Spontaneous hydrolysis of Arg: Becomes citruline, same but no charge, recog as foreign

Glucose spontaneous reaction (glycation): Aldehyde in open form react with amino groups in N-terminals (permanent)

Nitration of Tyr (oxadative stress): Nitrate group added. Larger, more acidic, negative charge at neutral pH?

Question 9

[Modifications] Give examples of non-protein amino acids

Answer 9

Dopamine (Tyr), Histamine (His), Thyroxine (Tyr), Citrulline/ornithine (Arg)

Question 10

[Modifications] In vitro chemical modifciations can used to study proteins. How can unpaired Cys residues be studied?

Answer 10

Thiol group react directly with I-acetate, some sort of protection. Hydrolyze and detect these groups

Question 11

[Modifications] In vitro chemical modifciations can used to study proteins. How can one change the cleavage site of trypsin?

Answer 11

Remove charge from Lys and block Arg with butanedione - no recognition.
Reduce SS bonds, react free Cys with etyleneamine > Aec (analog to Lys) > recognition.

Question 12

[Modifications] How is labeling of proteins with photoaffinity done?

Answer 12

Light triggered crosslinking of molecules, based on azides and diazo compounds, with photo-induced elimination of N2