Protein stability, protein-protein interactions 11-1 Protein stability, protein-protein interactions Protein stability - how proteins achieve stability under extreme conditions (class presentation) Protein-protein interactions - recent literature (presentations)

Stabilization/destabilization forces affecting proteins 11-2 Any of the forces/structures below could be stabilizing or destabilizing: hydrophobic…………… increased strength at higher temperatures H-bond…………………. mostly stabilizing; could decrease flexibility ionic…………………….. can be attractive or repulsive surface residues………. major contribution to protein stability internal residues………. major contribution to protein stability compactness………….. can affect stability or flexibility loops……………………. short loops increases stability at higher temperatures cavities…………………. presence and size can affect stability secondary structures…. e.g., β-sheets, α-helices more stable than coils quaternary structures… oligomeric structures can be more stable (esp. hetero.) ligand binding…………. e.g., nucleotides, cofactors, etc. membrane binding…… major effect(s) on protein stability protein modifications…. modulation of conformation, activity, stability, location others…………………... temperature, pH, salt, small molecules, pressure, etc.

Protein stability in different organisms 11-3 Protein stability in different organisms Terminology psychrophile mesophile thermophile hyperthermophile halophile acidophile barophile extremophiles cold-adapted; cold-loving (-2 ºC to ~15ºC) grows at moderate temperatures (~15ºC to ~45ºC) and conditions heat-loving; grows at >45ºC up to ~80ºC grows at >80ºC; limit so far is about 115ºC grows at high in concentrated salts (internal >1M!) grows under highly acidic conditions, i. e., ~ pH 0-pH 2) adapted to high pressures (e.g., underwater) those that grow under extreme conditions .....

Surface residues: stability vs instability 11-4 thermophilic - Mesophilic Bs-CspB and thermophilic Bc-Csp differ at 12 positions in 67 aa - variants at all positions were constructed and tested for stability Cold shock protein (Csp) from Bacillus caldolyticus. Perl et al. (2000) Nat. Struct. Biol. 7, 380. thermophilic CspB mesophilic CspB increased stability decreased stability thermophilic mesophilic

Protein biogenesis/degradation machineries in extremophiles 11-5 Question: how do organisms survive at extreme temperatures? Do they have more proteins devoted to protecting the organism, e.g., molecular chaperones? protein folding catalysts? proteases? Answer: the short answer is ‘it doesn’t appear to be the case’ intrinsic property of proteins

protein-protein interactions 11-6 “Here one should remember that any protein fails to execute its function unless it interacts with other biomolecules” - Takashi et al. (2001) Proc. Natl. Acad. Sci. USA 98, 4569.