Principles of molecular recognition

Molecular recognition importance

Specific interactions between molecules enable signalling, structure, and controlled cellular processes.

Complementary binding surfaces

Protein binding partners have matching shape and chemical properties allowing stable interactions.

Average buried surface area in protein–protein interactions

About 1500 Ų, but varies widely depending on the complex.

Types of interactions in molecular recognition

Hydrogen bonds, van der Waals forces, electrostatics, and the hydrophobic effect.

Hydrophobic contributions

Common in permanent interactions

stabilises complexes in aqueous environments.

Hydrophilic surfaces in transient interactions

Keep binding partners soluble when not part of the complex.

Key features of molecular recognition

high specificity

optimal affinity

tight regulation

Specificity importance

DNA-binding proteins must recognise correct sequences to activate specific genes.

Affinity definition

Strength of binding between two molecules, usually quantified by KD.

Dissociation constant KD

Ratio of koff / kon; lower KD = higher affinity.

Fraction bound equation

Fraction of protein bound = [Ligand] / (KD + [Ligand]).

Surface plasmon resonance (Biacore)

Technique for measuring kon, koff, and KD in real time.

Growth factor signalling example

Ligand binds receptor → dimerisation → phosphorylation → recruitment of Grb2 and SOS → Ras activation.

Role of SOS

Converts Ras-GDP to Ras-GTP by facilitating GDP release.

Molecular recognition control via conformational change

Ligand binding alters protein shape to allow or prevent interactions.

EGFR activation mechanism

EGF binding causes the receptor domains to close, forming a dimerisation interface.

SH2 domains

Bind phosphorylated tyrosines in specific peptide sequences.

SH2 specificity

Determined by a second pocket that recognises amino acid side-chains adjacent to phosphotyrosine.

Grb2 SH2 role

Binds phosphorylated EGFR via two binding pockets, enabling recruitment of SOS.

SH3 domains

Bind proline-rich sequences and mediate protein–protein interactions.

Grb2–SOS interaction

SH3 domain of Grb2 binds a proline-rich region on SOS with high specificity.

Ras–Sos conformational change

SOS binding opens Ras nucleotide pocket causing GDP release.

Ras activation mechanism

After GDP release, abundant cytoplasmic GTP binds Ras, activating it.

Ras–Raf interaction

Ras-GTP undergoes switch-region changes allowing Raf binding and MAP kinase activation.

Fos–Jun DNA binding

α-helices insert into the DNA major groove to recognise specific base sequences.

DNA binding interactions

Mainly electrostatic and hydrogen bonding with bases in the major groove.

Co-immunoprecipitation

Technique to identify interacting proteins using antibodies and pulldown.

Affinity tags

Engineered peptide tags allow purification of protein–protein complexes without specific antibodies.

Interactome definition

Complete map of molecular interactions within a cell or system.

Summary of recognition control

Shape/chemical complementarity can be modulated by phosphorylation or conformational change.