4.4 Protein Denaturing + Folding

native conformation

balance between enthalpic + entropic forces, driven by hydrophobic effect

denatured protein

when the tertiary + seconday strucutre is disrupted

ways to denature protein

-heat

-denaturants

-organic solvents

-detergents

-acid/bases

-mechanical forces

-disruption at air + water interface

chaotropes

denaturant, small molecules that work by disrupting h-bonds + interact with the protein surface

ex: urea, guanidium chloride

why was levinthal’s paradox, the theory that proteins fold thru random sequential search for correct structure proven wrong

proetin folding happens way to fast

what is protein folding considered 2-state only

it happens very abruptly bc partially unfolded proteins are very unstable, when one part of the structure is dirupted it destabilizes the remaining structure

cooperative folding

many parts of a protein fold simulatenously in an interconnected way rather than each region independently

two theories of protein folding

1: structural nucleation

2: thermodynamic folding funnel

1:strucutral nucleation

local structures begin to form, based on local prefrences

2:hydrophobic collapse

molten globule state forms, protein rapdily shrinks to dense blob

3: stabilization of secondary structure

final functional form of protein, alpha helicies + beta sheets are precise, internal side chains pack together + water is expelled from portein core

Hierarchical protein folding

1:structural nucleation

2:hydrophobic collapse

3:seconday strucutre stabilization

first step of 2-D folding funnel

burst phase, rapid hydrophobic collapse to molten globule

what conclusions can be drawn from Christain Anfinsens expirements

-protein can be denatured + fold again

-native state is the most thermodynamically stable

urea- chaotrope

guandium chloride

2-D folding funnel steps

1: burst phase

2: rearrangements to maximize enthalpic benefit + find native strucutre (noncovalent interactions)

Thermodynamic folding funnel

-depth = ΔG

-width =avalible conformation space for the protein chain

wells= semi-stable folding intermediates

context dependent structure leads us to believe that…

misfolding is possible, as several different conformations are possible in different contexts

amyloids

long highly ordered fibrils, beta sheets gros perpendicular to fibrils

protein misfolding diseases

-alzheimers disease

-huntington’s disease

-cystic fibrosis

-cataracts

-prion disease

molecular chaperones

-inhibit inappropiate interactions between potentially complementary surfaces + disrupt unsuitable liasions

When an organism like E. coli is grown at increased temperature, the expression of chaperone proteins increases.

From a Biochem 5613 perspective, briefly, why

an increase in energy (for example, increased temperature) will lead

to an increase in dynamic motion, and potentially protein unfolding. Chaperone proteins counteract this by

preventing aggregation, and assisting proteins in attaining the native fold. This helps organisms survive

increased temperatures

molten globule

nonpolar side chains are

buried, and not exposed to solvent – but the protein is not taking on a well-formed structure, and there is

significant dynamic motion in the protein interior, rather than the smaller motions (“breathing”) of a typical

protein. Often in the molten globule state, there is still water dispersed through the protein core, and the buried

salt bridges or hydrogen bonding interactions that define specificity in structure are not yet formed