Proteins are central to nearly all biological processes and possess key properties that enable their wide range of functions.
Key Properties of Proteins
1. Linear Polymers with Defined
Structures
- Building
Blocks:
Proteins are linear polymers made of monomer units called amino
acids, linked end-to-end.
- Peptide
Bond:
Amino acids are linked by a peptide bond (or amide bond), formed by
linking the α-carboxyl group of one amino acid to the α-amino group of another, with
the loss of a water molecule. This bond is kinetically stable.
- Polypeptide
Chain:
A series of amino acids joined by peptide bonds forms a polypeptide
chain; each amino acid in the chain is called a residue.
- Directionality: A polypeptide chain has
directionality:
- N-terminal
(α-amino) end: The beginning of the chain.
- C-terminal
(α-carboxyl) end: The end of the chain.
- Protein
Structure Levels:
The amino acid sequence dictates the three-dimensional structure:
- Primary Structure: The specific sequence of linked amino acids
- Secondary
Structure: Local three-dimensional structure
formed by hydrogen bonds between amino acids near one another (e.g., α-helices,
β-sheets).
- Tertiary Structure: Overall long-range three-dimensional structure formed by long-range interactions between amino acids. Protein function depends directly on this structure.
- Quaternary
Structure: Exists in proteins composed
of several distinct polypeptide chains (subunits) that assemble into a
functional complex.
- Cross-links: Polypeptide chains can be
cross-linked; the most common are disulfide bonds, formed by the
oxidation of a pair of cysteine residues, resulting in a unit
called cystine.
2. Wide Range of Functional Groups
- Proteins
contain diverse functional groups including alcohols, thiols,
carboxylic acids, and basic groups.
- The
array and sequence of these chemically reactive groups account for
the broad spectrum of protein function, especially the catalytic activity
of enzymes.
3. Ability to Form Complex
Assemblies
- Proteins
can interact with each other and other macromolecules (e.g., DNA,
lipids) to form complex, synergistic assemblies or "macromolecular
machines."
- Examples
include machinery for DNA replication, signal transmission, and muscle
contraction.
4. Varying Rigidity and Flexibility
- Some
proteins are rigid (e.g., structural elements in the cytoskeleton
or connective tissue).
- Others
display flexibility and can act as hinges, springs, or levers.
- Conformational
changes
in flexible proteins enable the transmission of information and the
regulated assembly of larger complexes.
Amino Acids: The Building Blocks
- Structure: An α-amino acid consists of a
central α-carbon atom linked to:
- An
amino group (NH2)
- A
carboxylic acid group (COOH)
- A
hydrogen atom (H)
- A
distinctive R group (or side chain)
L and D isomers of amino acids
- Chirality: With four different groups
attached to the α-carbon, α-amino acids are chiral
(except glycine, whose R group is a single H atom, making it
achiral).
- Isomers: Chiral amino acids exist as L
and D isomers (mirror images). Only L amino acids are constituents of
proteins.
- Ionization
(Zwitterions):
In solution at neutral pH, amino acids exist predominantly as dipolar
ions (zwitterions), where the amino group is protonated (-NH3+)
and the carboxyl group is deprotonated (-COO-). The ionization
state varies with pH.
The ionization state of
amino acids under different pH conditions
- The
Set of 20:
All proteins are constructed from the same set of 20 common amino acids,
with side chains varying in size, shape, charge, hydrogen-bonding
capacity, hydrophobic character, and chemical reactivity.
Classification of Amino Acids (Based
on R Group)
The
20 common amino acids are categorized into four groups:
1. Hydrophobic Amino Acids (Nonpolar
R groups)
- Tend
to cluster together in the interior of water-soluble proteins (hydrophobic
effect).
- Aliphatic: Glycine (achiral, H
side chain), Alanine (CH3), Valine, Leucine,
Isoleucine (includes an additional chiral center), Methionine
(includes a thioether -S- group).
- Cyclic/Restricted: Proline (side chain
bonded to both the N and α-carbon atoms, forming a pyrrolidine ring, which
restricts conformation).
- Aromatic: Phenylalanine (purely
hydrophobic), Tryptophan (less so due to its NH group in the indole
ring).
2. Polar Amino Acids (Neutral R
groups, Uneven Charge Distribution)
- More hydrophilic
(water-loving) than hydrophobic amino acids.
- Hydroxyl
Groups (-OH):
Serine, Threonine (has an additional asymmetric center), Tyrosine
(aromatic ring). The -OH groups make them reactive.
- Carboxamide
Groups (-CONH2): Asparagine, Glutamine.
- Sulfhydryl
Group (-SH):
Cysteine (structurally similar to serine but with a more reactive
thiol group; pairs can form disulfide bonds).
3. Positively Charged Amino Acids
(Positive Charge at Physiological pH)
- Highly
hydrophilic.
- Lysine (primary amino group at
terminus).
- Arginine (guanidinium group at
terminus).
- Histidine (imidazole group; pKα near 6, can be uncharged or
positively charged near neutral pH, often found in enzyme active sites).
4. Negatively Charged Amino Acids
(Negative Charge at Physiological pH)
- Also
highly hydrophilic.
- Aspartic
acid and Glutamic
acid.
- Often
called Aspartate and Glutamate to emphasize their negatively
charged state (COO-) at physiological pH.
Significance of Amino Acid Sequence
The
amino acid sequence (primary structure) is profoundly important:
- Determines
Function:
Essential for elucidating a protein's function (e.g., enzyme catalytic
mechanism).
- Determines
3D Structure:
The sequence is the link between the genetic message (DNA/RNA) and the
resulting functional 3D structure.
- Disease: Alterations in a single amino
acid can cause severe diseases (e.g., sickle-cell anemia).
- Evolutionary
History:
Similar sequences indicate a common ancestor, allowing molecular
events in evolution to be traced.
Primary Structure: Geometry and Conformation of the Protein Backbone
The specific geometry of the
polypeptide backbone is crucial because it limits the number of possible
protein folds, allowing proteins to adopt a unique, functional three-dimensional
structure.
Key Features of the Peptide
Bond
The chemical nature of the peptide
bond (linking the carbonyl C and amino N)
imposes significant constraints on the backbone:
· Planar Structure: The peptide bond is
essentially planar. Six atoms lie in the same plane: α-carbon and
CO (from the first
amino acid) and NH, α-carbon
(from the second amino acid).
Planar structure of peptide bond · Partial Double-Bond Character: The bond
resonates between a single bond and a double bond, giving it partial
double-bond character.
o This
prevents rotation about the C-N peptide bond, constraining the conformation of the
peptide backbone.
o The
C-N bond
length (typically 1.32 Å) is intermediate between a single bond (1.49 Å)
and a double bond (1.27 Å).
· Uncharged: The peptide bond is uncharged,
which permits polymers to form tightly packed globular structures.
· Trans Configuration Preference: Two
configurations are possible for the planar peptide bond:
o Trans:
The two α-carbon atoms are on opposite
sides of the peptide bond. Almost all peptide bonds in proteins are trans due to fewer
steric clashes.
o Cis:
The two α-carbon atoms are on
the same side of the peptide bond.
o Exception:
The most common cis
peptide bonds are X-Pro
linkages, where the cyclic side chain of proline reduces the steric
difference between the trans
and cis forms.
Configurations of peptide bond Freedom of Rotation and Torsion
Angles
In contrast to the rigid peptide
bond, the adjacent single bonds allow rotation:
· Single Bonds: The bonds between the N and the Cα
atom, and between the Cα
and the CO atom, are
pure single bonds.
· Conformational Freedom: The rotation
around these two bonds per residue allows proteins to fold in many different
ways.
· Torsion Angles: These rotations are
specified by torsion angles:
o Phi
(Φ): Angle of rotation
about the bond between the nitrogen
(N) and the α-carbon (Cα) atoms.
o Psi
(ψ): Angle of rotation
about the bond between the α-carbon (Cα)
and the carbonyl carbon (CO)
atoms.
o The
Φ and ψ angles determine the path of the
polypeptide chain.
Rotation about bonds in a polypeptide chain
Ramachandran Plot and Steric Exclusion
Not all combinations of Φ and ψ angles are possible due to physical
limitations:
· Steric Clashes: Many combinations of Φ and ψ angles are forbidden because of steric
collisions (atoms physically occupying the same space).
· Ramachandran Plot: The allowed
combinations of Φ and ψ angles are visualized on a two-dimensional
plot called a Ramachandran plot.
· Limitation: Approximately three-quarters
of the possible Φ and ψ combinations are excluded simply by local
steric clashes.
· Thermodynamic Role: The rigidity of
the peptide unit and the restricted set of allowed Φ and ψ angles limit the number of possible
conformations for the unfolded protein. This reduction in conformational
flexibility is essential to overcome the unfavorable entropy of folding,
allowing proteins to fold into a unique, defined structure.
Ramachandran plot
Protein
Secondary Structure: Helices, Sheets, and Turns
Secondary structure
refers to the regular, local folded segments of a polypeptide chain, stabilized
by a regular pattern of hydrogen bonds between the peptide N-H and C=O groups of
amino acids that are near one another in the linear sequence.
1. The Alpha (α)
Helix
The α-helix
is a common, rod-like, coiled structure proposed by Linus Pauling and Robert
Corey.
· Structure: A tightly coiled backbone
forms the inner part of the rod, with side chains extending outward in a
helical array.
· Stabilization: Stabilized by intrachain
hydrogen bonds (within the same polypeptide strand).
· Hydrogen Bonding Pattern: The C=O group of each
amino acid forms a hydrogen bond with the N-H group of the amino acid situated four
residues ahead in the sequence (i
to i+4). This
pattern ensures that almost all main-chain C=O and N-H groups are hydrogen bonded (except
near the ends).
H-bonding pattern in a helix
· Geometry:
o Residues
per turn: 3.6 amino acid residues per complete turn.
o Rise
(Translation) per residue: 1.5 Å along the helix axis.
o Pitch
(Length of one turn): 3.6 residues x 1.5 Å / residue = 5.4 Å.
· Screw Sense:
o The
α-helices
found in proteins are right-handed (clockwise) because this orientation
is energetically more favorable due to less steric clash between the side
chains and the backbone.
Alpha helix
· Helix Destabilizers ("Helix
Breakers"):
o Proline:
Lacks an N—H
group for hydrogen bonding and its rigid ring structure prevents the necessary Φ
torsion angle.
o Amino
Acids with β-carbon
branching (Valine, Threonine, Isoleucine): Their bulkiness causes steric
clashes.
o Serine,
Aspartate, Asparagine: Their side chains can compete for the main-chain N—H and C═O groups,
disrupting the regular pattern.
· Occurrence: α-helices
are abundant; for example, they make up about 75% of the residues in ferritin.
Many proteins that span biological membranes also contain α-helices.
2. The Beta (β)
Pleated Sheet
The β-pleated
sheet (or β-sheet) is another common periodic structure,
markedly different from the rod-like α-helix.
· Components: Formed by two or more
polypeptide chains or segments called β-strands
lying next to one another.
· β-Strand
Structure: Each β-strand is almost fully extended (not
coiled).
o Distance
between adjacent amino acids: Approximately 3.5 Å (much longer than 1.5 Å in an α-helix).
o Side
chains of adjacent amino acids point in opposite directions (up and
down).
· Stabilization: Stabilized by interchain
hydrogen bonds (between the N—H and C═O
groups of adjacent strands).
· Arrangements: Adjacent β-strands
can run in two ways:
o Antiparallel
β-Sheet: Adjacent strands run
in opposite directions. The N—H
and C═O of
each amino acid are directly hydrogen bonded to the C═O and N—H groups of a partner on the adjacent
strand.
o Parallel
β-Sheet: Adjacent strands run
in the same direction. The hydrogen bonding is slightly more complex,
connecting each residue's N—H
to the C═O
of one residue on the adjacent strand, and its C═O to the N—H of an amino acid two residues farther
along.
· Shape: β-sheets
are structurally diverse; while they can be flat, most adopt a somewhat
twisted shape.
· Occurrence: They are important structural
elements, forming the basis of proteins like fatty acid-binding proteins.
β-sheets
typically contain 4 or 5 strands, but can have 10 or more.
Anti-parallel beta sheet
Parallel beta sheet
3. Turns and Loops
These elements facilitate the
compact, globular shape of proteins by reversing the polypeptide chain's
direction.
· Reverse Turn (or β-turn/Hairpin
Turn): A common structural element that causes an abrupt reversal in
the polypeptide chain's direction.
o Often
stabilized by a hydrogen bond between the C═O groups of residue i and the N—H
group of residue i+3.
· Loops (or Ω-loops): More elaborate structures responsible
for chain reversals.
o Lack
regular, periodic structures (unlike α-helices
and β-strands).
o Are
often rigid and well defined despite their lack of periodicity.
· Location and Function: Turns and loops
invariably lie on the surfaces of proteins and frequently participate in
interactions between proteins and other molecules.
Structure of a reverse
turn Tertiary
and Quaternary Protein Structure
1. Tertiary Structure: The
Overall Fold
Tertiary structure refers
to the overall course of the polypeptide chain; specifically, the
spatial arrangement of amino acid residues that are far apart in the
linear sequence, and the pattern of any disulfide bonds.
Features of Tertiary Structure
·
It represents the final, stable,
three-dimensional shape of a single polypeptide chain.
·
Example (Myoglobin): The oxygen-storage
protein in muscle is a single, compact polypeptide chain (153 amino acids) with
approximately 70% of the chain folded into eight α-helices
connected by turns and loops.
·
Driving Force: The Hydrophobic Effect
o In
an aqueous environment, protein folding is primarily driven by the
tendency of hydrophobic residues to be excluded from water (the
Hydrophobic Effect).
o Interior
Core: Consists almost entirely of nonpolar residues (e.g., leucine,
valine, methionine). Charged residues are excluded from the interior.
o Exterior
Surface: Consists of a mixture of polar and nonpolar residues.
·
Stabilizing Interactions:
o Hydrogen
Bonding: To bury a segment of the main chain in the hydrophobic interior,
all peptide N—H and C═O groups must be paired
by hydrogen bonding (achieved by forming α-helices
or β-sheets).
o Van
der Waals Interactions: These maximize stability when the nonpolar side
chains in the core are tightly packed to minimize empty space.
· Amphipathic Secondary Structures: Many α-helices
and β-strands are amphipathic, meaning they
have a hydrophobic face (pointing into the protein interior) and a polar
face (pointing into the surrounding aqueous solution).
·
Membrane Proteins (The
"Exception"): Proteins that span biological membranes, like porins
in bacterial outer membranes, are "inside out" because they function
in a hydrophobic environment. Their outside surface is covered largely
with hydrophobic residues to interact with the membrane's alkane chains, while
the interior often contains polar/charged residues surrounding a water-filled
channel.
Motifs and Domains
·
Motifs (Super-secondary Structures):
Certain combinations of secondary structure that are present in many
proteins and often exhibit similar functions.
o Example:
A helix-turn-helix unit, found in many DNA-binding proteins.
·
Domains: Compact globular units
into which a polypeptide chain can fold, ranging from 30 to 400 amino acid
residues.
o Domains
may be connected by flexible segments and may be shared among proteins with
different overall tertiary structures (e.g., the CD4 immune protein has four
similar domains).
3-D structure of myoglobin
2. Quaternary Structure:
Subunit Arrangement
Quaternary structure refers
to the spatial arrangement of multiple polypeptide chains (subunits) and
the nature of their interactions. It is the fourth level of protein
organization.
· Subunit: Each individual polypeptide
chain in a protein with quaternary structure is called a subunit.
·
Simple Structures:
o Dimer:
Two identical subunits (e.g., the Cro DNA-binding protein).
o Tetramer:
Four subunits.
· Complex Structures: Proteins can contain
more than one type of subunit, often in variable numbers.
·
Example (Hemoglobin): The oxygen-carrying
protein in blood is a α2β2 tetramer,
consisting of two α subunits and two β subunits. Subtle changes
in the arrangement of these subunits are critical for its function.
· Viral Coats: Viruses often utilize
quaternary structure to make the most of limited genetic information, forming
symmetric capsids using many copies of a few types of subunit (e.g., rhinovirus
coat uses 60 copies of each of four subunits).
The α2β2
tetramer of human hemoglobin
