Protein Structure
Gerardus Mulder
1802-1880
Elemental analysis of whole
proteins, coined the term protein.
Fibrin
Why study structure?
Structure helps us understand function
Many disorders are due to aberrant protein
structure
Sickle cell anemia
Can aid in design of therapeutics
Disruption of structure causes disruption of
function
denaturation
A proteins function depends on its
specific confirmation
A functional proteins consists of one or more
polypeptides that have been precisely twisted,
folded, and coiled into a unique shape.
It is the order of amino acids that determines
what the three-dimensional confirmation will be.
A proteins specific confirmation
determines its function.
In almost every case, the function
depends on its ability to recognize and
bind to some other molecule.
For example, antibodies bind to particular
foreign substances that fit their binding sites.
Enzyme recognize and bind to specific
substrates, facilitating a chemical reaction.
Neurotransmitters pass signals from one cell
to another by binding to receptor sites on
proteins in the membrane of the receiving cell.
Biology/Chemistry of Protein Structure
Primary Assembly
STRUCTURE
PROCESS
Secondary Folding
Tertiary Packing
Quaternary Interaction
Protein Assembly
occurs at the ribosome
involves dehydration
synthesis and
polymerization of amino
acids attached to tRNA:
NH +- {A + B A-B + H O} -COO -
3 2 n
thermodynamically
unfavorable, with E =
+10kJ/mol, thus coupled
to reactions that act as
sources of free energy
yields primary structure
Primary Structure
primary structure of human insulin
CHAIN 1: GIVEQ CCTSI CSLYQ LENYC N
linear
CHAIN 2: FVNQH LCGSH LVEAL YLVCG ERGFF YTPKT ordered
1 dimensional
sequence of amino
acid polymer
by convention, written
from amino end to
carboxyl end
a perfectly linear
amino acid polymer is
neither functional nor
energetically
favorable folding!
Frederick Sanger (1918-1997)
S-Q-D-A-G-M-Q-Q-G-A-D-M-D-Q-V-S-A
Sequenced insulin using
limited Proteolysis and
paper chromatography!
Dipeptides
Enzymatic
hydrolysis
Protein Folding
occurs in the cytosol tumbles towards
involves localized spatial conformations that reduce
interaction among primary E (this process is thermo-
structure elements, i.e. the dynamically favorable)
amino acids yields secondary structure
may or may not involve
chaperone proteins
The discovery of Secondary
Structure
Linus Pauling 1901-1994
Trained in theoretical physics, at
the center of early X-ray
crystallography
Recognized the importance of the
H-bond in stabilizing protein
structure
Published proposed -helix and -sheet in 1951
Secondary Structure
non-linear
3 dimensional
localized to regions of an
amino acid chain
formed and stabilized by
hydrogen bonding,
electrostatic and van der
Waals interactions
The secondary structure of a protein results
from hydrogen bonds at regular intervals along
the polypeptide backbone.
Typical shapes
that develop from
secondary structure
are coils (an alpha
helix) or folds
(beta pleated
sheets).
The structural properties of silk are due to beta
pleated sheets.
The presence of so many hydrogen bonds makes
each silk fiber stronger than steel.
Ramachandran Plot
Pauling built models based on the following
principles, codified by Ramachandran:
(1) bond lengths and angles should be
similar to those found in individual
amino acids and small peptides
(2) peptide bond should be planer
(3) overlaps not permitted, pairs of atoms
no closer than sum of their covalent radii
(4) stabilization have sterics that permit
hydrogen bonding
Two degrees of freedom:
(1) (phi) angle = rotation about N C
(2) (psi) angle = rotation about C C
A linear amino acid polymer with some folds
is better but still not functional nor
completely energetically favorable
packing!
Protein Packing
occurs in the cytosol (~60% bulk
water, ~40% water of hydration)
involves interaction between
secondary structure elements
and solvent
may be promoted by
chaperones, membrane proteins
tumbles into molten globule
states
overall entropy loss is small
enough so enthalpy determines
sign of E, which decreases
(loss in entropy from packing
counteracted by gain from
desolvation and reorganization
of water, i.e. hydrophobic effect)
yields tertiary structure
Protein Interaction
occurs in the cytosol, in close proximity to other
folded and packed proteins
involves interaction among tertiary structure
elements of separate polymer chains
may be promoted by chaperones, membrane
proteins, cytosolic and extracellular elements as
well as the proteins own propensities
E decreases further due to further
desolvation and reduction of surface area
globular proteins, e.g. hemoglobin,
largely involved in catalytic roles
fibrous proteins, e.g. collagen,
largely involved in structural roles
yields quaternary structure
Quaternary Structure
non-linear
3 dimensional
global, and across
distinct amino acid
polymers
formed by hydrogen
bonding, covalent
bonding, hydrophobic
packing and hydrophilic
exposure
favorable, functional
structures occur
frequently and have been
categorized
A proteins confirmation can change in response
to the physical and chemical conditions.
Changes in pH, salt concentration, temperature,
or other factors can unravel or denature a
protein.
These forces disrupt the hydrogen bonds, ionic
bonds, and disulfide bridges that maintain the
proteins shape.
Some proteins can return to their functional
shape after denaturation, but others cannot,
especially in the crowded environment of the
cell.
Usually denaturation is permanent
In spite of the knowledge of the three-
dimensional shapes of over 10,000
proteins, it is still difficult to predict the
confirmation of a protein from its primary
structure alone.
Most proteins appear to undergo several
intermediate stages before reaching their
mature configuration.
The folding of many proteins is protected by
chaperonin proteins that shield out bad
influences.