Dynamics and disorder

What timescale is bond stretching and angle bending?

ps-fs

what timescale is side chain/loop motion?

ns-ps

What timescale is folding of small peptides?

microseconds to nanoseconds

What timescale is protein folding and domain motion?

ms

How do disorder affect the protein?

sequence conservation, faster mutation rate and tolerates more mutations, enriched in eukaryotes vs prokaryotes

What is gibbs free energy determined by?

hydrophobic effect, hydrogen bonds, electrostatic interactions and conformational entropy

What is the order of least to most disorder protmoting amino acids?

W, F, Y, I, M, L, V, N, C, T, A, G, R, D, H, Q, K, S, E, P

What are properties of disordered protein-ligand binding?

lacks secondary or tertiary structure, highly flexible, conserved sequence, MoRFs and fly-casting as model, favours hydrophobic interactions, high specificity low affinity, enriched in eukaryotes, faster mutation rate

What are the properties of ordered protein ligand binding?

secondary, tertiary, Quaternary structure, favour polar interactions, segmented interface, small number of partners, high specificity, high affinity, no major structural change

what are MORFs?

molecular recognition features

how do disordered proteins flycast?

since greater capture radii, and chain flexibility, so disordered protein partially weakly binds to partner from large distance and reel in bindin partner while completing folding simultaneously enhancing binding speed

What is one-to-many signalling?

one protein is responsible for multiple transcriptional regulations

What is many-to-one signalling?

many amino acid polymers can bind to the same enzyme

How is binding driven in folded proteins?

enthalpy driven (H-bonds and electrostatic interactions)

why is binding weaker in disordered proteins?

They have to fold to entropy apposes enthalpy so low gibbs, so interactions are weaker

Why is specificity still high if binding is weaker?

since they are uncoupled

What are the mechanistic consequences of disordered-ligand binding?

multiple conformers, so different rates, the domination can also change with temperature

How can you detect disorder?

NMR, crystallography, circular dichroism, fluorescence spectroscopy, single molecule detection

How can crystallography detect disorder?

through lack of density, and a high B-factor indicates mobility and dynamics

How does circular dichroism detect disorder?

random coil shows disorder AKA CD signal vs wavelength plot, goes down then up and then plateaus

How does fluorescence spectroscopy detect disorder?

Use Trp fluorescence emission by looking for red shifts and intensity changes upon denaturation. REES can be used to report on equilibrium distribution of conformational states

How does NMR work for detecting disorder?

can label proteins with different isotopic labels and pick out specific interactions from specific residues to see how protein has changed

How does single molecule detection detect disorder?

low resolution so it doesn't tell you which parts are folded, but does show how many conformational states it can occupy and the interconversions of different energy levels.

What is a downside of using NMR for protein disorder detection?

isotropic labelling is very expensive and requires technical capability