Protein and molecular recognition Flashcards
SH2 domains
- 100 amino acids
- two antiparallel beta strands surrounded by 2 helices
- phosphotyrosine binds as an extended strand
- there are conserved Arg/Lys residues that contribute to interact with the negative tyrosine
- variable residues contribute to specificity
- two binding pockets:
1. for the phosphotyrosine (conferring selectivity for the activate RTK/EGFR receptor)
2. for the downstream binding peptide (conferring sequence specificity to that protein)
Grb2
- one SH2 and two SH3 domains
- function– recruit Sos
Gbr2-Sos interaction
- the SH3 domain of Grb2 consists of 5 anti-parallel beta strands a a group of aromatic residues forming a hydrophobic patch
- the SH3 binds a left handed poly-proline helix (consensus=PxxP)
- the specificities of individual SH3 domains are different due to two charged variable loops
- as the binding surface of Grb2 is hydrophobic, the interactions between it and the hydrophobic Sos are strong and permanent !!
- 9 proline residues bind to a long groove in Grb2
Sos-Ras interaction
- binding is through a large interface– mainly hydrogen bonds and electrophilic interactions
- binding causes a change in the Ras nucleotide binding site (this releases GDP)
conformational changes in Ras
Ras has different conformations depending on which nucleotide is present;
the difference is because of conformational changes in two regions (“switch” 1 and 2) which form hydrogen bond with the “gamma” (third) phosphate of GTP
what does the GTPase activity of Ras require
- GAP
- inserts Arg residue in the active site to stimulate hydrolysis
Binding between Ras and Raf
- an intermolecular beta sheet (extending the anti-parallel beta sheet in both)
- Raf has NO direct contact with the GTP; Raf only contacts one of the switches which change conformation
Raf
- Ser/Thr kinase
- N terminal inhibitory domain loops back and blocks the catalytic domain normally
- Ras binds to inhibitory domain and displaces it, allowing activation
Fos and Jun
- DNA binding proteins causing transcription of growth factor responsive genes
- leucine zippers
bonds:
- hydrophobic interactions between the helices
- non-specific ionic interactions with phosphate backbone
- specific H bonds with base pairs (in the major groove)–>this gives the specificity of promoter interaction
binding specificity of antibodies
- determined by CDR sequence
- CDR3 is the most variable
- variability is achieved through recombination
FcgR (g=>gamma)
- it is a receptor on cell that binds the CH2 and CH3 constant domains of the antibody IgG
- leads to phagocytosis or cytotoxicity– mediated by the cell that expresses the receptor
FcRn
-is a receptor expressed in neonates that protects IgG from degradation
complement cascade and constant domains
- the constant domains of Ig are recognised by the first component of complement (C1q)
- conformational change and proteolysis leads to activation of the complement cascade and activation of the membrane attack complex
- the membrane attack complex forms pores in the cell and leads to lysis and inflammation response
what is the concept behind immunity to flu
- haemagglutinin binds sialic acid on target
- immunity comes from antibodies that block the site that binds to the sialic acid
human antibody fragments? their role?
- FAb–>(contain VL, CL, VH, and CH1)
- Fv–>(contains VL and VH)
- scFv–>(also contains VL and VH but with a peptide linker)
-used in drugs to bind to pathogens or toxins and simply block their function
