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Protein structure and function
Part - I
Marie-Véronique CLEMENT
Associate Professor
Yong Loo Lin School of Medicine
NUS Graduate School for Integrative Science and Engineering
Department of Biochemistry
National University of Singapore
8 Medical Drive, MD 7 #03-15
Singapore 117597
Tel: (65) 68747985
Fax: (65) 67791453
E-mail: [email protected]
From amino acids to protein:
N-terminus
terminates
by an amino group
Peptide bond
Amino acid
C-terminus
terminates by a
carboxyl group
A peptide: Phe-Ser-Glu-Lys (F-S-E-K)
The Shape of proteins:
Occurs
Spontaneously
Native conformation
determined by
different Levels
of structure
Four Levels of Structure Determine the
Shape of Proteins
Primary structure
The linear arrangement (sequence) of amino acids and the location of covalent (mostly
disulfide) bonds within a polypeptide chain. Determined by the genetic code.
Secondary structure
local folding of a polypeptide chain into regular structures including the a helix, b
sheet, and U-shaped turns and loops.
Tertiary structure
overall three-dimensional form of a polypeptide chain, which is stabilized by multiple
non-covalent interactions between side chains.
Quaternary structure:
The number and relative positions of the polypeptide chains in multisubunit
proteins. Not all protein have a quaternary structure.
Primary Structure of a protein:
determined by the nucleotide sequence of its gene
Bovine Insulin: the first sequenced protein
• In 1953, Frederick Sanger determined the amino acid sequence of insulin, a protein hormone
.
• This work is a landmark in biochemistry because it showed for the first time that a protein has
a precisely defined amino acid sequence.
• it demonstrated that insulin consists only of amino acids linked by peptide bonds between αamino and α-carboxyl groups.
• the complete amino acid sequences of more than 100,000 proteins are now known.
• Each protein has a unique, precisely defined amino acid sequence.
Primary Structure
Pro-insulin is produced
in the Pancreatic islet
cells
C-peptide
Pro-insulin protein
65/66
30/31
Human: Thr-Ser-Ile
Cow:
Ala-Ser-Val
Pig:
Thr-Ser-Ile
Chiken: His-Asn-Thr
Insuline
C-peptide
+ C peptide
Amino acid substitution in proteins from different species
Conservative
Substitution of an amino acid by another
amino acid of similar polarity
(Val for Ile in position 10 of insulin)
Non conservative
Substitution involving replacement
of an amino acid by another of
different polarity
(sickle cell anemia, 6th position of hemoglobin
replace from a glutamic acid to a valine induce
precipitation of hemoglobin in red blood cells)
Invariant residues
Amino acid found at the same position in
different species
(critical for for the sructure or function of the protein)
Protein conformation: most of the proteins fold into only
one stable conformation or native conformation
More than 50 amino acids becomes a protein
SECONDARY STRUCTURE
• Stabilized by hydrogen bonds
• H- bonds are between –CO and –NH
groups of peptide backbone
• H-bonds are either intra- or intermolecular
• 3 types : a-helix, b-sheet and triple-helix
What forces determine the
structure?
• Primary structure - determined by
covalent bonds
• Secondary, Tertiary, Quaternary structures all determined by weak forces
– Weak forces - H-bonds, ionic interactions, van
der Waals interactions, hydrophobic
interactions
Non covalent
interactions
involved in the
shape of proteins
Secondary structures:
a Helix:
a helix conformation was discovered 50 years ago in
a keratine abundant in hair nails, and horns
b Sheet:
discovered within a year of the discovery of
a helix.Found in protein fibroin the major
constituant of silk
The a helix:
result from hydrogen bonding, does not involve the side chain of the amino acid
bsheet:
result from hydrogen bonding, does not involve the side chain of the amino acid
Two type of b Sheet
structures
An anti paralellel
b sheet
A paralellel
b sheet
TRIPLE HELIX
• Limited to tropocollagen molecule
• Sequence motif of –(Gly-X-Pro/Hypro)n• 3 left-handed helices wound together to give a
right-handed superhelix
• Stable superhelix : glycines located on the
central axis (small R group) of triple helix
• One interchain H-bond for each triplet of aas –
between NH of Gly and CO of X (or Proline) in
the adjacent chain
Triple helix of Collagen
NONREPETITIVE STRUCTURES
• Helices/b-sheets: ~50% of regular
2ostructures of globular proteins
• Remaining : coil or loop conformation
• Also quite regular, but difficult to
describe
• Examples : reverse turns, b-bends
(connect successive strands of
antiparallel b-sheets)
The Beta Turn
•
•
•
(aka beta bend, tight turn)
allows the peptide chain to reverse direction
carbonyl O of one residue is H-bonded to the amide proton of a residue
three residues away
proline and glycine are prevalent in beta turns (?)
b-bulge
• A strand of polypeptide in a b-sheet may contain an “extra” residue
• This extra residue is not hydrogen bonded to a neighbouring strand
• This is known as a b-bulge.
Tertiary structure: the overall shape of a protein
or a telephone cord!!!
The secondary structure of a telephone
cord
A telephone cord, specifically the coil of a
telephone cord, can be used as an analogy
to the alpha helix secondary structure of a
protein.
The tertiary structure of a telephone cord
The tertiary structure of a protein refers to the
way the secondary structure folds back upon
itself or twists around to form a threedimensional structure. The secondary coil
structure is still there, but the tertiary tangle has
been superimposed on it.
Tertiary structure: the overall shape of a protein
Full three dimensional organization of a protein
The three-dimensional
structure of a protein
kinase