structural biology

49 Pages·2017·2.01 MB·English

by  Betul Cicek

6. Folding and flexibility

By Assist. Prof. Betul Akcesme
• “Prediction of three dimensional structure of a
protein from its amino acid sequence is the
major unsolved problem in structural
molecular biology”
Introduction
a polypeptide chain acquires its correct 3D structure to achieve the biologically
active native state
Some proteins folds spontaneously,
others require assistance such as enzymes
PROTEIN FOLDING
,chaperones)

CHAPERONS
1.Binds to partially folded polypeptide
prevents making unwanted bonding
- promotes the folding

MOLTEN GLOBULAR STATE
2. After a sequence acquires most of its
correct secondary structure, it has a
looser tertiary structure Molten globular state to native
state spontaneously
3. FINAL native state
How to predict the 3D structure from primary structure?
Major unsolved problem
native state protein is not static:

secondary elements, domains undergo small movements in space:
individual atoms or collectively;
Functional activities of protein : ligand binding trigger
conformation changes.
Globular proteins are only
marginally stable
Denatured state (unfolded) Native state (folded)
Energy difference: 5 – 15 kcal/mol
(a single H-bond: 2 – 5 kcal/mol)
Two major contributors to the energy difference: Enthalpy and Entropy

Decrease for
spontaneous process
energy of noncovalent interactions including the hydrophobic
interactions, hydrogen bonds, and ionic bonds.
ENTHALPY
These interactions are maximized to produce globular molecule in

native state
Covalent interactions ?
These non‐covalent interactions are therefore stronger and
more frequent in the native state and hence their energy
contribution, enthalpy, is much larger.
The enthalpy difference between native and denatured
states can reach several hundred kcal/mol.
ENTROPY
native state is order, denatured states is disorder –each denatured
structure is unique.

entropy between the native
ordered state and the
denatured state can also reach
Denatured state Native state
several hundred kcal/mol but
in the opposite direction to
the enthalpy difference.
FREE ENERGY difference between states are very small!
• Fig.6.22 from Mathews, van Holde & Ahern, Biochemistry, 3rd ed. (2000): Thermodynamics
of protein folding
• summary of overall interplay between DH and the -TDS components (both hydrophobic effect and
conformational entropy)

• A simple reaction profile for two state reaction. The reaction can be
described in terms entirely analogous to reaction kinetics where G is
the conformational stability of the folded protein (GU − GF). For
folding to occur the change in free energy must be negative
The marginal stability of the native state is biologically
and functionally important!

Globular proteins in correct quantities at appropriate times.

THEREFORE

It is equally important to be able to degrade proteins as it
is to be able to synthesize them.

Globular proteins in living cells usually have a rapid turnover ,which
means their native states is marginally stable.

Some enzymes need structural flexibility, which would be
inconsistent with a rigidly stabilized structure.