More on proteins... Flashcards
- Temperature (heat), pH and solvent conditions can
be adjusted to unfold a
protein back into a more extended form.
When the unfolding conditions are reverted, many proteins
have enough
information stored in their sequence of amino acids to refold back to exactly
the same tertiary structure. Other proteins get stuck along the way (e.g. curdled
milk stays curdled after heat/cool treatment
The essence of correct protein
folding is the…
retention of partially
correct intermediates
Molten globules containing…
native secondary structure but
not tertiary structure are formed early in folding
-Molten refers to fluctuating nature of interactions between
secondary structures
-Globule refers to a condensed state
HYDROPHOBIC COLLAPSE
is the
driving force for
formation of molten globules
An unfolded polypeptide chain is often …
unstable in water
(in absence of denaturing agents) because many
nonpolar residues may come into contact with water.
-The hydrophobic groups tend to come together to avoid
water (hydrophobic collapse)
Nonpolar amino acids form a
hydrophobic core hidden from water
Amino acid residues have different
tendencies for forming (a)-helices,
(b)sheets or (b)turns
promote helix formation + other formations:
Some amino acid side chains (like glutamate,
alanine and leucine)
Proline and glycine do not favour helix
formation but have a tendency to form turns
Some amino acids favour b-strand formation
(like leucine, isoleucine, and valine)
Secondary structure prediction is
only about
60% accurate (but getting better.
Supersecondary structure:
In general more than 60% of
the
polypeptide backbone comprises
a-helices and b-sheets
The overall free energy change on
folding is
negative–so favorable.
Free energy is a balance of several
thermodynamic factors:
-Conformational entropy
-Enthalpy contribution
-Entropy contribution from hydrophobic
effect
Conformational entropy:
Unfavorable
energy favors random chains
conformation due to burying of
hydrophobic residues interacting with
water.
Enthalpy contribution:
Favorable
energy from intramolecular side
groups interaction.
Entropy contribution from hydrophobic
effect:
Favorable energy due to the
burying of hydrophobic R group
Local folding through…
nucleation of small clusters of residues due
to the hydrophobic effect
A General Order of Folding:
- Random polypeptide: hydrophobic residues stabilized by water forming a
cagelike structure, DS low. - Secondary structure starts to form:
-hydrophobic effect (hydrophobic residues buried inside the protein)
->favorable energy DS.
-release of water due to hydrophobic effect
->randomness conformational entropy increase (unfavorable energy DS).
- Secondary structure are formed, domains, protein folded: Intramolecular
side chain interactions create a negative enthalpy (favorable energy)
Motif:
-simple combinations of a few secondary structure
elements with specific geometric arrangement
- b-a-b and calcium calcium binding “hand” are examples
-A variety of structures are seen in globular protein
domains
-Looking at possible similarities can provide insight
into how structure and function are related
Domain:
polypeptide chain or part of polypeptide chain
that can fold independently into stable 3o structure
Many proteins have several compact…
compact globular regions. Each globular unit is called a domain.
- domains tend to have ~50 up to 200-300 amino acids
- less than 50 is difficult to fold stably
- more than 300 is difficult to fold correctly
A single domain is typically…
made of a single stretch of
primary sequence – there are many exceptions though
Tertiary folding is stabilized by
the same non-covalent interactions as found
in the secondary structures but involves amino-acid side chain interactions only not main chain atoms interactions.
- H-bonding
- ionic interactions
- van der Waals forces
- ‘hydrophobic’ interactions
disulphide linkages (Bonds)
covalent bonds that can stabilize protein tertiary structure
Salting Out:
The solubility of protein in an aqueous solution depends
on many factors, including:
- Size of protein
- Surface charge on protein
- Polarity of protein
- pH and ionic strength of the solution.