Download Protein Structure

Protein Structure
Dr Vivek Joshi, MD
Peptides and Proteins
Peptide: A short polymer of amino acids joined by
peptide bonds; they are classified by the number of
amino acids in the chain.
 Dipeptide: A molecule containing two amino acids
joined by a peptide bond.
 Tripeptide: A molecule containing three amino acids
joined by peptide bonds.
 Polypeptide: A macromolecule containing many
amino acids joined by peptide bonds.


Protein: A biological macromolecule containing at
least 30 to 50 amino acids joined by peptide bonds.
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Levels of Organization Protein
Structure

Primary structure: The sequence of amino acids in a
polypeptide chain; read from the N-terminal amino acid to
the C-terminal amino acid.

Secondary structure: Conformations of amino acids in
localized regions of a polypeptide chain; examples are ahelix, b-pleated sheet, and random coil.

Tertiary structure: The complete three-dimensional
arrangement of amino acids in a polypeptide chain.

Quaternary structure: The spatial relationship and
interactions between subunits in a protein that has more
than one polypeptide chain.
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Levels of Organization in Protein
Structure (contd.)
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Four levels of protein structure
Primary Structure
◦ Order in which amino acids are joined
together
◦ AA sequence of the polypeptide chain
◦ Polypeptide backbone
◦ Includes the location of any disulfide bond
◦ Higher levels of protein structure are
decided by primary structure
◦ Amino acid sequence is specific –Coded by
gene
◦ Determines ‘Biological activity’ of the
protein
Stabilized by covalent bonds
Peptide Bond Formation
Peptide bond –
Amide linkage between the carboxyl group of one amino acid and the
a-amino group of another
A condensation reaction with liberation of water
Characteristics of the peptide bond

Shows Electronic resonance
Has a partial double bond character


No freedom of rotation

Rigid and planar-All 6 of the atoms O, C, N, H
are coplanar
Characteristics of the Peptide Bond

Generally a trans bond-Because of the steric interference of
the R-groups when in the cis position
 Uncharged but polar
Naming Peptides

Free amino end of the peptide chain (N-terminal) is written to the left

Free carboxyl end of the peptide chain (C-terminal) is written to the right

All amino acid sequences are read from the N- to the C-terminal end of the
peptide
Tyrosylglycylglycylphenylalanylleucine
Primary Structure

Amino acid sequence specifies 3D structure

The 20 amino acids can be linked in combinations specific for a given protein

Long chains of amino acids fold in a pattern dependent on the exact order of
amino acids

Different regions of the polypeptide chain may assume different conformations
as determined by the sequence of amino acids in that region

A genetic mutation leading to one incorrect amino acid substitution in a
protein comprising thousands of amino acids can result in that protein having a
different shape and little or even no biological activity-sickle cell disease
.
Secondary Structure

Defines the steric relationship between amino acids that are close to each other in the
primary amino acid sequence

Brought about by linking the carbonyl and amide groups of the peptide bonds by
means of hydrogen bonds (H-bonds)

Folding of polypeptide chain along a single axis
Kinds:
 Alpha helix
 Beta sheets
 Beta turns
Secondary Structure

Alpha helix

A rigid, rod-like structure

The lowest energy and most stable
conformation for a polypeptide chain

Forms spontaneously

Peptide bond planes are parallel to the
axis of the helix

Stability arises from the formation of the
maximum possible number of H-bonds

3.6 amino acid residues per 360°
turn (5.4 Å)

13 atoms/turn

1.5 Å rise/residue

R groups extend outward

Right-handed
Alpha helix
◦
H-bonds are formed between

Each carbonyl oxygen atom of a peptide bond and the hydrogen attached to
the amide nitrogen of the peptide bond 3.6 amino acid residues further along
the polypeptide chain

Each peptide bond forms 2 H-bonds:


One to the peptide bond of the 4th residue above

One to the peptide bond of the 4th residue below
Destabilized by the presence of proline

An helix breaker

Interrupts a-helical structure because

Its ring structure exerts geometric constraint

The nitrogen in the peptide linkage does not contain
the H atom required to form H-bonds
Alpha helix
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Secondary Structure

Beta pleated sheet

Composed of 2 or more peptide chains or segments of
polypeptide chains that are arranged either parallel or
anti-parallel to each other
C
N
N
C
Antiparallel
N
C
N
C
Parallel
Secondary Structure

Beta pleated sheet

the α-carbon and its R group side chain alternate slightly above and slightly
below the plane of the main chain of the polypeptide (ruffled or pleated
appearance)
Secondary Structure

Beta bend (reverse turn)
◦
◦
◦
◦
◦
Makes a tight 180° turn
Allows the polypeptide chain to abruptly reverse its direction
Helps to form a compact, globular shape
Surface of proteins-Charged residues
Generally composed of :
 Glycine – has the smallest R group
 Proline – causes a kink in the polypeptide chain

Combinations of secondary structures

Form the interior (core region) of globular proteins

Connected by loop regions at the surface of the protein

Zn finger motif-DNA
bab
Hairpin
aa
Supersecondary Structures (Motifs)
Tertiary structure






3-dimensional arrangement of all atoms in a single
polypeptide chain
The entire protein molecule coils into an overall threedimensional shape-Functional property to the protein
Spatial arrangement of amino acid residues that are far
apart in a linear sequence
Superfolding brings functional groups that are far apart near
to each other.
Correct folding is assisted by Chaperons
Incorrect folding-Altered protein-Prion disease
Tertiary Structure

Stabilizing interactions:
Covalent: disulfide bonds
Non-covalent
 Hydrogen bonds. Fine tunes the
tertiary structure by selecting the
unique native structure of a protein
 Ionic interactions. The association
of two ionic protein groups of
opposite charge is known as ion pair
or salt bridge.
 Hydrophobic interactions- The
major determinant of protein native
structure
The conformation or shape of the
protein is determined by:
◦ The nature of the interaction
of the different side chains
with the aqueous environment
◦ The interactions of the
different side chains with the
other side chains
Quaternary Structure

Refers to the spatial arrangement of the polypeptide chains of a multi-chain
protein(2 />2 polypeptide chains) and the nature of their contacts
Each polypeptide chain is a monomer/ subunit
Dimer, tetramer,

Oligomeric protein - protein with multiple subunits
Homooligomers – have identical subunits
Heterooligomers – have several distinct polypeptide chains

Non-covalent interactions hold the subunits together
 Hydrophobic, ionic, H-bond

Hemoglobin-2 a ,2 b

Immunoglobulin-2 Heavy ,2 Light chain

Creatine Kinase-Dimer

Lactate Dehydrogenase-Tetramer
Quaternary structure refers to the interaction among
protein subunits
Hemoglobin contains 2aand 2b subunits
Subunits may function independently or may work cooperatively
Hemoglobin – binding of oxygen to 1 subunit of the tetramer increases the affinity
of the other subunits to oxygen-Cooperative binding
Denaturation of Proteins
Denaturation: The process of destroying the native conformation
of a protein by chemical or physical means.
◦ Usually denaturation of protein refers to disruption of tertiary
and secondary structure, while primary structure remain
unaffected.
◦ It leads to loss of biological activity
◦ It decreases solubility and increases precipitability
◦ Some denaturations are reversible, while others permanently
damage the protein.
 Denaturing agents include:
◦ Heat, 6 M urea, detergents, Acids, Bases, Salts, Reducing
agents, Heavy metals, Alcohol

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Protein Turnover
 Older
proteins break down-Replaced by new one.
 Protein synthesis –Translation-Ribosomes
 Protein Breakdown
 Lysosomes-Proteases-Endocytosed protein
 Proteasomes-Cytoplasmic complexes-Older and abnormal protein
 Proteasomes are large protein complexes inside all eukaryotes and
in some bacteria.
 In eukaryotes, they are located in the nucleus and the cytoplasm.
 The main function of the proteasome is to degrade unneeded or
damaged proteins by proteolysis, a chemical reaction that breaks
peptide bonds.
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Proteasome-Ubiquitin pathway
Proteins are tagged for degradation by a small protein called ubiquitin. The
tagging reaction is catalyzed by enzymes called ubiquitin ligases. Once a
protein is tagged with a single ubiquitin molecule, this is a signal to other
ligases to attach additional ubiquitin molecules.
 The result is a polyubiquitin chain that is bound by the proteasome, allowing it
to degrade the tagged protein.
Protein Misfolding
Misfolded protein-Tagged and degraded within the cell.
Defect in this control system-Extracellular and
intracellular accumulation of misfolded proteins
Age
Disease
Prion Disease
Amyloidosis
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Prion Disease
Prion diseases are a family of degenerative brain disorders
observed in humans and numerous other mammals.
Some (but not all) cases originate by transmission from one
individual to another, however, no bacterial, viral, or parasitic agent
has been identified
Propagate by transmitting mis-folded protein
Protein does not itself self-replicate
Process dependent on presence of polypeptide in the host
Protein conformational disease
Transmitted by altering the conformation
Creutzfeldt-Jakob disease (CJD) in humans.
Prion-related Protein (PrP)

Encoded by the PrP gene of the mammal

Exists in 2 isoforms -identical primary structures and posttranslational modifications -different tertiary and quaternary
structures
#PrPc – PrP-sen (proteinase-sensitive)
Normal cellular protein
On the outer surface of neurons
Function still unclear
#PrPSc – PrP-res (proteinase-resistant)
Pathologic isoform
Invariably associated with TSEs or prion diseases
Prion-related Protein (PrP)
PrPc – Rich in a-helix

PrPSc – Consists mostly of b-sheets
Conversion of PrPc into PrPSc
 Involves alteration of ahelical structure into b-sheet-Aggregate-Amyloid
 Spontaneous
 Caused by infection
 Consumption of food, especially neural tissue, that contains PrPSc
Neurodegenerative diseases -Alzheimer's, Parkinson's, Huntington's
 Neuronal dysfunction - Induced by diffusible oligomers of misfolded proteins.
What bonds are broken and remade to go from a-helix to b-sheets?
Prion-related Protein (PrP)

Prions (Proteinaceous
infectious particle)
Infectious proteins that
contain no nucleic acid
Protein itself is capable
of acting like infectious
material and modifying
protein content of the
entire organism
Cause transmissible
spongiform
encephalopathies (TSE)
or prion diseases
Amyloidosis
 Normal Amyloid
precursor
protein-Abnormal
proteolytic cleavage-Long
Fibrillar protein consisting
of β-pleated sheetAmyloids
 Amyloid in Alzheimer’s
disease –Amyloid β(A β)Neurotoxic
 Thank
You