Transcript Lecture 21 - phys.protres.ru

PROTEIN PHYSICS
LECTURE 21
Protein Structures: Kinetic Aspects (3)
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Nucleation in the 1-st order phase transitions
Nucleation of protein folding
Solution of Levinthal paradox
Folding rate:
chain length and 3D fold (“contact order”)
Levinthal paradox
Native protein structure
reversibly refolds from
various starts, i.e., it is
thermodynamically
stable.
?
But how can protein
chain find this unique
structure - within
seconds - among zillions
alternatives?
However, the same problem – how to find one
configuration among zillions – is met by crystallization
and other 1-st order phase transitions.
1-st order phase transition:
rate of nucleation
The idea that protein folding includes nucleation,
as the other 1-st order phase transitions, gave a
clue to solve the Levinthal paradox
???
Before considering kinetics, let us recall basic facts on protein
thermodynamics (for 1-domain proteins, of 50–200 residues).
1) Protein unfolding is reversible, and it occurs as an “all-ornone” transition in single-domain proteins. This means
that only two states, native and denatured, are present
(close to the mid-transition) in a visible quantity.
2) “All-or-none” transition requires the amino acid sequence
that provides a large energy gap between the most stable
structure and the bulk of misfolded ones.
3) The denatured state is often the random coil.
4) Native structure, even under physiological conditions, is
only by a few kcal/mol more stable than the unfolded state
(i.e., it is not far from the mid-transition).
Let us consider sequential folding (or unfolding) of a chain
that has a large energy gap between the most stable fold
and the bulk of the other ones; and let us consider its
folding close to the thermodynamic mid-transition
sequential folding/unfolding
The same pathway: “detailed balance”
How fast the most stable fold will be achieved?
Note. Elementary rearrangement of 1 residue takes 1-10 ns.
Thus, 100-residue protein would fold within ms, if there were
no free energy barrier at the pathway…
Free energy barrier:
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=========
↓
Mid-transition
THIS
EXPLAINS
PROTEIN
FOLDING
TIMES:
↓
Nucleus:
not as small,
it comprises
20-60%
of the protein
Up to now, a vicinity of mid-transition has been considered.
When the globular state becomes more and more stable, this
accelerates folding at first (when the native structure is still the
only structure that is more stable than the denatured state),
but then a massive misfolding and subsequent rearrangement
of wrong folds can decrease the folding rate.
Quantitative consideration needs analysis of networks of
folding pathways.
This results in more accurate theoretical estimates of
folding rates, as well as positions of the folding nuclei.
,

The rate of 2-state folding
depends mainly on the
contact order,
while
the rate of 3-state folding
depends mainly on the
chain length.
Protein Structures: Kinetic Aspects

Protein folds spontaneously. How can it?
 Protein folding intermediates.
MG.
 Transition state &
folding nucleus.
 Solution of Levinthal paradox.
 Theory of folding rates: chain length and
“contact order”.