Biochemistry

Dr. Tareq Alhindi

Lecture Notes (05) part 1

 The Three-Dimensional Structure of Proteins
Protein Structure and Function

Biologically active proteins are polymers consisting of

amino acids linked by covalent peptide bonds.

Many different conformations (3D structures) are

possible for a molecule as large as a protein. Of these
many structures, one or (at most) a few have
biological
activity; these are called the native conformations.
Protein folding normally occurs as the protein is
being synthesized in the crowded environment
within a cell, aided by other proteins.
 The Three-Dimensional Structure of Proteins
Protein Structure and Function
Proteins are capable of four levels of structural
arrangement: primary, secondary, tertiary, and
quaternary.
The exact arrangement that a protein has depends on the
specific chemical sequence of its amino acids and the
types of side groups that are present.

The 20 commonly occurring amino acids are the building

blocks that make up proteins. Ten to 10,000 amino acids
can be linked together in a head-to-tail fashion to form the
sequence of a protein.

The amino acid sequence (the primary structure) of a

protein determines its three-dimensional structure,
which, in turn, determines its properties.
 The Three-Dimensional Structure of Proteins
Protein Structure and Function
The primary structure of a protein is its unique sequence of amino acids.
Secondary structure, found in most proteins, consists of coils and folds in
the polypeptide chain.
They form as a result of hydrogen bonds between the repeating
constituents of the polypeptide backbone (not the amino acid side chains).

Tertiary structure is determined by interactions among various side chains

(R groups), and any prosthetic groups (groups of atoms other than amino
acids).
Quaternary structure results when a protein consists of multiple
polypeptide chains, called subunits.
Interaction between subunits is mediated by noncovalent interactions, such
as hydrogen bonds, electrostatic attractions, and hydrophobic interactions.
 The Three-Dimensional Structure of Proteins
Protein Structure and Function

A slight change in primary structure can

affect a protein’s structure and ability to
function.
Sickle-cell disease, an inherited blood
disorder, results from a single amino acid
substitution in the protein haemoglobin.

The abnormal hemoglobin molecules cause

the red blood cells to aggregate into chains
and to deform into a sickle shape.
 The Three-Dimensional Structure of Proteins
Site-directed mutagenesis analysis of GPAT6.
Protein Structure and Function

Using molecular-biology techniques, such as site-

directed mutagenesis, it is possible to replace any
chosen amino acid residue in a protein with
another specific amino acid residue.

The conformation of the altered protein, as well as

its biological activity, can then be determined. The
results of such amino acid substitutions range from
negligible effects to complete loss of activity,
depending on the protein and the nature of the
altered residue.

Yang, Weili, et al. Proceedings of the National Academy of Sciences 107.26 (2010): 12040-12045.
 The Three-Dimensional Structure of Proteins
Protein Structure and Function
The secondary structure of proteins is the hydrogen-bonded arrangement of
the backbone of the protein, the polypeptide chain.

Within each amino acid residue are two bonds with reasonably free rotation:
(1) The bond between the -carbon and the amino nitrogen of that residue
(2) The bond between the -carbon and the carboxyl carbon of that residue.

Two bonds coming from the alpha carbon can rotate, and secondary structure
can be described by the two angles, phi Φ and psi Ψ.

The angles (Φ) and (Ψ), frequently called Ramachandran angles (after their
originator Ramachandran), are used to designate rotations around the C-N and
C-C bonds, respectively.
 The Three-Dimensional Structure of Proteins
Protein Structure and Function

The conformation of a protein backbone can be

described by specifying the values of Φ and Ψ
for each residue (-180° to 180°).

The Φ and Ψ angles repeat themselves in

contiguous amino acids in regular secondary
structures.

Ramachandran plot
 The Three-Dimensional Structure of Proteins
Protein Structure and Function

Ramachandran plot analysis of

transketolase.

Red region indicates favored region, yellow

region for allowed and light yellow shows
generously allowed region and white for
disallowed region.
 The Three-Dimensional Structure of Proteins
Protein Structure and Function

The -helix is stabilized by hydrogen bonds parallel to the helix axis within the
backbone of a single polypeptide chain. Counting from the N-terminal end,
the C-O group of each amino acid residue is hydrogen bonded to the N-H
group of the amino acid four residues away from it in the covalently bonded
sequence.

There are 3.6 residues per turn (n = 3.6) and the helix has a pitch (the linear
distance between corresponding points on successive turns) (p) of 5.4 Å.

The helical conformation allows a linear arrangement of the atoms involved

in the hydrogen bonds, which gives the bonds maximum strength and thus
makes the helical conformation very stable.
 The Three-Dimensional Structure of Proteins
Protein Structure and Function

Proteins have varying amounts of -helical structures,

varying from a few percent to nearly 100%.

Since the hydrophilic polypeptide backbone is optimally

hydrogen-bonded to itself and hidden away at the core of
the α-helix, such regions of secondary structure are
commonly seen in proteins that traverse the cell
membrane, such as transmembrane receptors and
transport proteins.

In such cases, the side-chains, which project into the lipid

environment, are typically non-polar.
 The Three-Dimensional Structure of Proteins
Protein Structure and Function
Several factors can disrupt the α-helix.
The amino acid proline creates a bend in the backbone because of its cyclic structure. It
cannot fit into the α-helix because (1) rotation around the bond between the nitrogen and
the α-carbon is severely restricted, and (2) proline’s α-amino group cannot participate in
intrachain hydrogen bonding.
Side chains including strong electrostatic repulsion due to the proximity of several charged
groups of the same sign, such as groups of positively charged lysine and arginine residues or
groups of negatively charged glutamate and aspartate residues.
Another possibility is crowding (steric repulsion) caused by the proximity of several bulky
side chains.
In the -helical conformation, all the side chains lie outside the helix; there is not enough
room for them in the interior. The α-carbon is just outside the helix, and crowding can occur
if it is bonded to two atoms other than hydrogen, as is the case with valine, isoleucine, and
threonine.
 The Three-Dimensional Structure of Proteins
Protein Structure and Function

The peptide backbone in the β-sheet is almost completely

extended.
Hydrogen bonds can be formed between different parts
of a single chain that is doubled back on itself (intrachain
bonds) or between different chains (interchain bonds).
If the peptide chains run in the same direction (if they are
all aligned in terms of their N-terminal and C-terminal
ends), a parallel pleated sheet is formed. When
alternating chains run in opposite directions, an
antiparallel pleated sheet is formed. The three-dimensional form of the antiparallel b-pleated
sheet arrangement. The antiparallel orientation allows for
The hydrogen bonding between peptide chains in the -
maximum hydrogen bonding because the oxygen,
pleated sheet gives rise to a repeated zigzag structure;
nitrogen, and hydrogen are in a straight line.
hence, the name “pleated sheet”.
The Three-Dimensional Structure of Proteins
Protein Structure and Function

Ball-and-stick diagram showing the arrangement of

hydrogen bonds in (A) parallel and (B) antiparallel -pleated
sheets.