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

2. Stabilization/destabilization forcesaffecting 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.

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 11-3

4. Surface residues: stability vs instability thermophilic CspB - 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. mesophilic CspB increased stability decreased stability 11-4 thermophilic thermophilic mesophilic

5. Protein biogenesis/degradationmachineries 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

6. protein-protein interactions “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. USA98, 4569. 11-6