MPL203T-18 Protein structure.pptx

© Ramaiah University of Applied Sciences
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Faculty of Pharmacy
Lecture No. 18
Course Leaders: Dr. Parasuraman.P
parasuraman.py.ph@msruas.ac.in

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Faculty of Pharmacy
Content
• Protein structure
• Levels of protein structure, Domains, motifs, and folds in
protein structure

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Faculty of Pharmacy
Lecture No. 18
• At the end of this lecture, student will be able to
– Describe the Levels of protein structure, Domains, motifs, and
folds in protein structure

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ACDEFGHIKLMNPQRSTVWY
primary structure
Principles of Protein Structure

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Different Levels of Protein Structure
NH2
Lysine
Histidine
Valine
Arginine
Alanine
COOH

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Common Secondary Structure Elements
• The Alpha Helix

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©M. S. Ramaiah University of Applied Sciences
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Properties of alpha helix
• 3.6 residues per turn, 13 atoms between H-bond donor and acceptor
• approx. -60º;  approx. -40º
• H- bond between C=O of ith residue & -NH of (i+4)th residue
• First -NH and last C=O groups at the ends of helices do not participate in H-
bond
• Ends of helices are polar, and almost always at surfaces of proteins
• Always right- handed
• Macro- dipole

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Alpha Helix

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Helical wheel
Residues i, i+4, i+7 occur on one
face of helices, and hence show
definite pattern of
hydrophobicity/ hydrophilicity

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Introduction to Molecular Biophysics
Association of helices: coiled coils
These coiled coils have a heptad repeat abcdefg with nonpolar residues at
position a and d and an electrostatic interaction between residues e and g.
Isolated alpha helices are
unstable in solution but are
very stable in coiled coil
structures because of the
interactions between them
The chains in a coiled-coil have
the polypeptide chains aligned
parallel and in exact axial
register. This maximizes
coil formation between chains.
The coiled coil is a protein motif that is often used to control oligomerization.
They involve a number of alpha-helices wound around each other in a highly
organised manner, similar to the strands of a rope.

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Introduction to Molecular Biophysics
The Leucine Zipper Coiled Coil
Initially identified as a structural motif in proteins involved in eukaryotic
transcription. (Landschultz et al., Science 240: 1759-1763 (1988).
Originally identified in the liver transcription factor C/EBP which has a Leu
at every seventh position in a 28 residue segment.

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Association of helices: coiled coils
The helices do not have to run in the same direction for this type of
interaction to occur, although parallel conformation is more common.
Antiparallel conformation is very rare in trimers and unknown in
pentamers, but more common in intramolecular dimers, where the two
helices are often connected by a short loop.
Chan et al., Cell 89, Pages 263-273.

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Since the dipole moment of a peptide bond is 3.5 Debye units, the alpha
helix has a net macrodipole of:
n X 3.5 Debye units (where n= number of residues)
This is equivalent to 0.5 – 0.7 unit charge at the end of the helix.
Basis for the helical dipole
In an alpha helix all of the peptide
dipoles are oriented along the
same direction.
Consequently, the alpha helix has
a net dipole moment.
The amino terminus of an alpha helix is positive and the
carboxy terminus is negative.

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Structure of human TIM
Two helix dipoles are seen to play
important roles:
1. Stabilization of inhibitor 2-PG
2. Modulation of pKa of active site
His-95.

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Faculty of Pharmacy
Helical Propensities
Ala -0.77
Arg -0.68
Lys -0.65
Leu -0.62
Met -0.50
Trp -0.45
Phe -0.41
Ser -0.35
Gln -0.33
Glu -0.27
Cys -0.23
Ile -0.23
Tyr -0.17
Asp -0.15
Val -0.14
Thr -0.11
Asn -0.07
His -0.06
Gly 0
Pro ~3

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Common Secondary Structure Elements
• The Beta Sheet

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Secondary structure: reverse turns

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Secondary Structure:
Phi & Psi Angles Defined
• Rotational constraints emerge from interactions with
bulky groups (ie. side chains).
• Phi & Psi angles define the secondary structure adopted
by a protein.

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The dihedral angles at Ca atom of every residue
provide polypeptides requisite conformational
diversity, whereby the polypeptide chain can fold into
a globular shape

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Ramachandran Plot

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Structure Phi (F) Psi(Y)
Antiparallel b-sheet -139 +135
Parallel b-Sheet -119 +113
Right-handed -helix +64 +40
310 helix -49 -26
p helix -57 -70
Polyproline I -83 +158
Polyproline II -78 +149
Polyglycine II -80 +150
Phi & Psi angles for Regular Secondary
Structure Conformations
Table 10
Secondary Structure

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Beyond Secondary Structure
Supersecondary structure (motifs): small, discrete, commonly
observed aggregates of secondary structures
 b sheet
 helix-loop-helix
 bb
Domains: independent units of structure
 b barrel
 four-helix bundle
*Domains and motifs sometimes interchanged*

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Common motifs

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Supersecondary structure:
Crossovers in b--b-motifs
Right handed
Left handed

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• Consists of two perpendicular 10 to 12 residue alpha helices
with a 12-residue loop region between
• Form a single calcium-binding site (helix-loop-helix).
• Calcium ions interact with residues contained within the loop
region.
• Each of the 12 residues in the loop region is important for
calcium coordination.
• In most EF-hand proteins the residue at position 12 is a
glutamate. The glutamate contributes both its side-chain
oxygens for calcium coordination.
EF Hand
Calmodulin, recoverin : Regulatory proteins
Calbindin, parvalbumin: Structural proteins

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EF Fold
Found in Calcium binding proteins such as Calmodulin

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•Consists of two  helices and a short extended amino acid chain between them.
•Carboxyl-terminal helix fits into the major groove of DNA.
•This motif is found in DNA-binding proteins, including l repressor, tryptophan
repressor, catabolite activator protein (CAP)
Helix Turn Helix Motif

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Leucine Zipper

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•The beta-alpha-beta-alpha-beta subunit
•Often present in nucleotide-binding proteins
Rossman Fold

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What is a Protein Fold?
 Compact, globular folding arrangement of the polypeptide chain
 Chain folds to optimise packing of the hydrophobic residues in the interior
core of the protein

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Common folds

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Tertiary structure examples: All-
Alamethicin
The lone helix
Rop
helix-turn-helix
Cytochrome C
four-helix bundle

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Tertiary structure examples: All-b
b sandwich b barrel

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Tertiary structure examples: a/b
placental ribonuclease
inhibitor
a/b horseshoe
triose phosphate
isomerase
a/b barrel

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Four helix bundle
•24 amino acid peptide with a hydrophobic surface
•Assembles into 4 helix bundle through hydrophobic regions
•Maintains solubility of membrane proteins

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Oligonucleotide Binding (OB) fold

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TIM Barrel
•The eight-stranded a /b barrel (TIM barrel)
•The most common tertiary fold observed in
high resolution protein crystal structures
•10% of all known enzymes have this domain

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Zinc Finger Motif

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Domains are independently folding structural units.
Often, but not necessarily, they are contiguous on the peptide chain.
Often domain boundaries are also intron boundaries.

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Domain swapping:
Parts of a peptide chain can reach into neighboring
structural elements: helices/strands in other domains
or whole domains in other subunits.
Domain swapped diphteria toxin:

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• Helix bundles
Long stretches of apolar amino acids
Fold into transmembrane alpha-helices
“Positive-inside rule”
Cell surface receptors
Ion channels
Active and passive transporters
• Beta-barrel
Anti-parallel sheets rolled into cylinder
Outer membrane of Gram-negative
bacteria
Porins (passive, selective diffusion)
Transmembrane Motifs

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Quaternary Structure
• Refers to the organization of subunits in a protein with multiple subunits
• Subunits may be identical or different
• Subunits have a defined stoichiometry and arrangement
• Subunits held together by weak, noncovalent interactions (hydrophobic,
electrostatic)
• Associate to form dimers, trimers, tetramers etc. (oligomer)
• Typical Kd for two subunits: 10-8 to 10-16M (tight association)
–Entropy loss due to association - unfavorable
–Entropy gain due to burying of hydrophobic groups - very favourable

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• Stability: reduction of surface to volume ratio
• Genetic economy and efficiency
• Bringing catalytic sites together
• Cooperativity (allostery)
Structural and functional advantages of
quaternary structure

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Quaternary structure of
multidomain proteins

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Faculty of Pharmacy
Summary
• It is the amino acid sequence (1940) that “exclusively” determines
the 3D structure of a protein
• The chemical nature of the carboxyl and amino groups of all amino
acids permit hydrogen bond formation (stability) and hence defines
secondary structures within the protein.
• While backbone interactions define most of the secondary
structure interactions, it is the side chains that define the tertiary
interactions
• The biological function of some molecules is determined by
multiple polypeptide chains – multimeric proteins

MPL203T-18 Protein structure.pptx

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