flexibility and interactions

what are loop motions?

movement and conformational flexibility of loops that connect secondary structures

where are loops commonly found?

protein surface

what are loop motions used for?

signalling, molecular recognition, binding

what is an example of loop motions?

substrate binding to triose phosphate isomerase enzyme

loop changes from open to closed stabilising the intermediate compound

what is domain motion?

large scale movements of domains in protein e.g. hinge bending/twisting

what is an example of domain motion?

enzymes undergoing conformational changes when substrates bind

what is a receptor?

macromolecule/protein/nucleic acid

what is a ligand?

smaller molecule/other macromolecule

describe receptor ligand interactions

receptor and ligand interact via non-covalent interactions (hydrogen bonding, electrostatic interactions, van der Waal’s) in a receptor-ligand complex

receptor and ligand also have shape complimentarity

what are some examples of receptor-ligand interactions?

• Transport of proteins and ligands e.g. SPP

• DNA/RNA binding with proteins e.g. TATA binding protein

• Hormone receptors and hormones e.g. oestrogen receptor

• Riboswitches and small ligands (regulating protein synthesis)

• Antibodies and antigens

• Enzymes and substrates

• Drugs

what is the TATA binding protein?

universal transcription factor that recognises and binds to the TATA box

what is the function of the TATA binding protein?

• binds to the minor groove in DNA causing a sharp kink in DNA (~80°)

• bend helps recruit other proteins, transcription factors and RNA polymerase, forming pre-initiation complex for transcription

what are the features of the TATA binding protein

• basic residues (lysine,K and arginine, R) on binding surface for electrostatic interactions with negatively charged phosphate backbone of DNA

• phenylalanine side chains insert themselves between base pairs of double helix

• two symmetrical asparagine side acids form hydrogen bonds at centre

what are karrikins?

molecules that link environmental events e.g. wildfires to biological responses in plants

how do karrikins work?

• karrikins are produced during forest fires

• sugars and cellulose from burning plant material undergo chemical transformations, releasing karrikin into air which then settles on ground

• rain solubilises karrikins and they enter soil and enter dormant seeds

• bind to KAI2 receptor protein in seeds initiating a signalling cascade which leads to seed germination

why are karrikins important after a wildfire?

triggering germination allows trees that have been burned to be replaced