protein structure aimec

2. LEVELS OF ORGANIZATION-PROTEIN
STRUCTURE
• BY
• DR SHAMIM AKRAM
• AP BIOCHEM AIMC

3. MOLECULAR STRUCTURE OF PROTEINS
• PRIMARY STRUCTURE
• SECONDARY
• TERTIARY
• QUATERNARY

5. Level Of Protein Organization
 Primary Structure-The number and sequence of amino acids in the
protein -insulin
 Secondary Structure – Coiling of polypeptide chain about its axis with the
formation of  helices and  pleated sheets held by hydrogen bonding-
Collagen
 Tertiary Structure - Folding of helices and sheets influenced by R groups
forming 3D structure-Mb
 Quaternary Structure - The association of more than one polypeptide into a
protein complex influenced by R groups-Hb

7. +-
Protein
Secondary
Structure: 
Helix
C
O
C OH
H
C
H
C
O H
C N
H
H N
H H
H
C
H H HO
C
H
N
C
H
O
C N C
O
C
H
C N
O
C H
C
O
C
N
O
C
O
C
O
H
N
H
N
C HC
N

8. Protein Secondary
Structure:
 Helix
R
R
R
R
R
R
R
R
R
R
R
R
R
R
R groups stick out
from the  helix
influencing higher
levels of protein
organization

9. Secondary Structure -Helix

10. Secondary
Structure  Pleated Sheet
N
H
C
O
C
H
C N
C
O
N
H
C
O
C
H
C N
C
O
N
H
C
C C N
C
O
N
H
C
O O
C
H H
C N
C
O
H
N
C C
O
O
C
N
C
H
H
N
C C
O
O
C
N
C
H
H
N
C C
O
O
C
N
C
H
H
N
C C
OH
C
N
C
O

11. Secondary
Structure  Pleated Sheet
N
H
O
C
C C
H
N
C
O
N
H
O
C
C C
H
N
C
O
N
H
O
C
C C
H
N
C
O
N
H
O
C
C C
H
N
C
O
N
H
C
O
C
H
C N
C
O
N
H
C
O
C
H
C N
C
O
N
H
C
C C N
C
O
N
H
C
O O
C
H H
C N
C
O
H
N
C C
O
O
C
N
C
H
H
N
C C
O
O
C
N
C
H
H
N
C C
O
O
C
N
C
H
H
N
C C
OH
C
N
C
O

12. Protein Secondary
Structure:
 pleated sheet

13. Structure:
α helices and  pleated
sheets

14. Four Levels of Architectural Organization of
Proteins
• Primary Structure
It is the number
and sequence of
amino acids that
make up a protein
It is stabilized by
peptide bonds (non-
specific attractive
forces that occur
between adjacent –
COOH and NH2
groups)

16. Amino Acid Sequence Determines Primary
Structure-Naming the peptide
• The number and order of the amino acid residues in a polypeptide
constitute its primary structure.
• Amino acids present in peptides, called aminoacyl residues, are referred to
by replacing the ate or ine suffixes of free amino acids with yl (eg, alanyl,
aspartyl, tyrosyl). Peptides are then named as derivatives of the carboxy
terminal aminoacyl residue. For example, Lys-Leu-Tyr-Gln is called lysyl-
leucyl-tyrosyl-glutamine. The ine ending on the carboxy-terminal residue
(eg, glutamine) indicates that its α-carboxyl group is not involved in a
peptide bond.
• Three-letter abbreviations linked by straight lines represent an
unambiguous primary structure. Lines are omitted when using single-letter
abbreviations.

17. PEPTIDE BOND
• In a peptide molecule the amino acids are attached covalently to their
neighbouring acid by α-COOH gp. Of one amino acid with α-NH2 gp. of next
amino acid ,with elimination of one water molecule.
• CHARACTERISTICS OF PEPTIDE BOND
It is covalent bond
It is partial double bond i.e it is shorter than a single bond.
It is rigid bond (no rotation as it is shorter than a single bond,it would
require breaking the partial double bond).
It is planner (the 4 atoms of peptide bond are in same plan)
Always in trans configuration (both α-C on opp side)
-C=O & -NH are uncharged but polar, can form H-bonds

18. PEPTIDE BOND

21. Important peptides with primary structure
Dipeptide:urea,T3,T4
Tripeptide:TRH
Octapeptide:Angiotension II
Nanopeptide:oxytocin,vasopresin
Decaapeptide:Angiotension I
INSULINE: 51 A.A.

23. Vassopressin

24. Vasopressin

25. Vasopressin
• Vasopressin is also called ADH
(antidiuretic hormone)
• Vasopressin increases blood pressure
and inhibits diuresis.
• It constricts blood vessels rising the blood
pressure and affecting water and
electrolyte balance

26. Thyroxine
•
•
Thyroxine (T4) and Triiodothyronine (T3) represents
2 iodonated tyrosine residues on the same
polypeptide chain.
The synthesis of these hormones involves iodination
of the tyrosine ring, which concentrates iodide ion
from the blood serum .

27. Aspirin
The anti-
inflammatory and
analgesic
properties of
aspirin derive
from the
inhibition of
PGHS-2 or
prostaglandin H
synthetase-2.

28. Methods to determin primary structure
• Sangers method
• Edman’s method
• DNA sequence method

29. Secondary Structure of Proteins
•
•
•
• Refers to the steric (spacial)
relationship of amino acid
residues that are close to one
another in a linear sequence.
It is stabilized by hydrogen
bonding between carbonyl group
of 1 amino acid and the amino
group of another aminoacid 4
residue ahead.
The polypeptide chain can
change its orientation because
of free rotation around the
polypeptide backbone (-N-C-C).
The hydrogen bonding
produces a regular coiled
arrangement called helix.

30. Secondary Structureof Proteins
• α-Helix
• β-Pleated sheets
• β-Bends and turns
• Loops

31. Alpha Helix
• The polypeptide backbone of an α helix is twisted right-handed.
• A complete turn of the helix contains an average of 3.6 aminoacyl
residues, and the distance it rises per turn (its pitch) is 0.54 nm.
• The R groups of each aminoacyl residue in α helix face outward.
• Proteins contain only L-amino acids, for which a right-handed α helix is by
far the more stable, and only right handed α helices are present in
proteins.
• Since the peptide bond nitrogen of proline lacks a hydrogen atom, it is
incapable of forming a hydrogen bond with a carbonyl oxygen.
consequently, proline can only be stably accommodated within the first
turn of an α helix. When present elsewhere, proline disrupts the
conformation of the helix, producing a bend. Glycine, has small R gp. also
frequently induces bends within α helices.

35. Beta Sheet
• Portions of polypeptide chain(5-10 amino acid residues) from different primary
structural regions line up side by side just as a sheet of cloth just folded again and
again to form a β sheet, in which the R groups of adjacent residues project in
opposite directions.
• Unlike the compact backbone of the α helix, the peptide backbone of the β sheet
is highly extended. However, like the α helix, β sheets derive much of their
stability from hydrogen bonds between the carbonyl oxygens and amide
hydrogens of peptide bonds.
• However, in contrast to the α helix, these bonds are formed with adjacent
segments of the β sheet.
• Interacting β sheets can be arranged either to form a parallel β sheet, in which
the adjacent segments of the polypeptide chain proceed in the same direction
amino to carboxyl, or an antiparallel sheet, in which they proceed in opposite
directions.

37. β-Bends and turns
• Roughly half of the residues in a “typical” globular protein reside in α
helices or β sheets, and half in loops, turns, bends, and other
extended conformational features.
• Turns and bends refer to short segments of amino acids that join two
units of the secondary structure, such as two adjacent strands of an
antiparallel β sheet. A β turn involves four aminoacyl residues, in
which the first residue is hydrogen-bonded to the fourth, resulting in
a tight 180° turn. Proline and glycine often are present in β turns.

39. Loops
• Loops are regions that contain residues beyond the minimum number necessary to connect
adjacent regions of secondary structure.
• Irregular in conformation, loops nevertheless serve key biologic roles. For many enzymes, the
loops that bridge domains responsible for binding substrates often contain aminoacyl residues
that participate in catalysis.
• Helix-loop-helix motifs provide the oligonucleotide-binding portion of many DNAbinding
proteins such as repressors and transcription factors.
• Structural motifs such as the helix-loop-helix motif or the E-F hands of calmodulin that are
intermediate in scale between secondary and tertiary structures are often termed
supersecondary structures or motifs.
• Since many loops and bends reside on the surface of proteins, and are thus exposed to solvent,
they constitute readily accessible sites, or epitopes, for recognition and binding of antibodies.
• A domain(composed of many motifs in tertiary structure) is a section of the protein structure
sufficient to perform a particular chemical or physical task such as binding of a substrate or other
ligand.

40. BENDS-TURNS-LOOPS-SUPRASECONDARY STR
• Β-BENDS & TURNS:
Commonest,made up of 4 aminoacid residues mostly proline & glycine,
joins sec. structures, α-helix & β-sheets.
• LOOPS:
Also join adjacent sec.structure,but have more aminoacid residues.
• SUPRASECONDARY MOTIFS:
Formed e.g. where 2 B-sheets are joined by α-helix.
• Significance:
provide sites for binding of enzymes for activity.

41. FORCES HOLDING SECONDARY STRUCTURE
• Hydrogen bonding
• Hydrophobic interactions

42. SECONDARY STRUCTURE-COLLAGEN

43. TERTIARY STRUCTURE
• The term “tertiary structure” refers to the entire three-dimensional conformation
of a polypeptide. It indicates, in three-dimensional space, how secondary
structural features—helices, sheets, bends, turns, and loops —assemble to form
domains and how these domains relate spatially to one another.
• A domain (composed of many motifs in tertiary structure) is a section of the
protein structure sufficient to perform a particular chemical or physical task such
as binding of a substrate or other ligand.
• Simple proteins, particularly those that interact with a single substrate or other
ligand, such as lysozyme, or myoglobin, often consist of a single domain.
• By contrast, lactate dehydrogenase is comprised of two domains, an N-terminal
NAD+-binding domain and a C terminal binding domain for the second substrate,
pyruvate.

44. 3D Structure of Myoglobin
• Tertiary structure -
refers to the steric
relationship of amino
acid residue that are far
apart in the linear
sequenc.
• It also refers to how the
polypeptide chain is bent
or folded in 3
dimensions.
• It is stabilized by non-
covalent bonds,
hydrohobic bonds,
electrostatic bonds,
hydrogen bonding, Van
der Waals forces, and
covalent disulfide bonds.

47. FORCES HOLDING TERTIARY STRUCTURE
• Non-Covalent bonds
• Hydrophobic interactions
• Electrostatic forces
• H-bonds
• Covalent disulfide bonds
• Vander waal forces

48. Quaternary Structure
• Contains more than one polypeptide
chains stabilized by the same bonds as in
tertiary structure
• Quaternary level donates the way the
chains are packed together in a protein.
• Each chain in a protein is called a subunit
or domain (protomers).
• Proteins with more than 1 chain are called
oligomers.

49. Quaternary Structure
• Proteins containing multiple domains can also be assembled through
the association of multiple polypeptides, or protomers.
• Monomeric proteins consist of a single polypeptide chain. Dimeric
proteins contain two polypeptide chains,…oligomeric/multimeric.
• Homodimers contain two copies of the same polypeptide chain,
while in a heterodimer the polypeptides differ. Greek letters (α, β, γ,
etc) are used to distinguish different subunits of a hetero-oligomeric
protein, and subscripts indicate the number of each subunit type. For
example, α4 designates a homotetrameric protein, and α2β2γ, a
protein with five subunits of three different types.

50. Quaternary Structure
• Contains more than one polypeptide
chains stabilized by the same bonds as in
tertiary structure
• Quaternary level donates the way the
chains are packed together in a protein.
• Each chain in a protein is called a subunit
or domain (protomers).
• Proteins with more than 1 chain are called
oligomers.

52. THREE-DIMENSIONAL STRUCTURE
Determined by:
X-Ray Crystallography
Nuclear Magnetic Resonance Spectroscopy-NMR
Cryo–Electron Microscopy
Molecular Modeling

53. PROTEIN FOLDING
• Proteins are conformationally dynamic molecules that can fold into
their functionally competent conformation in a time frame of
milliseconds. Moreover, they often can refold if their conformation
becomes disrupted, a process called renaturation.
• Native Conformation of a Protein Is Thermodynamically Favored.
• Folding Is Modular (step by step)
• Auxiliary Proteins Assist Folding-Chaperones

54. CHAPRONES (HEAT SHOCK PROTEINS-HSP)
• The information needed for correct protein folding is present in primary
structure of the polypeptide.Many denatured proteins do not resume their
native conformation even when ideal conditions are restored.
• Explaination is the sp. Proteins chaprones needed for proper folding.
• These are specialized gp. of proteins that fascilitate in proper folding of
protein molecule( along with ATP hydrolysis) during synthesis of proteins.
• Two mech.:1- Chaprons bind hydrophobic regions of extended
polypeptide,preventing misfolding until folding is achieved.
• 2-Chaperonins unfold misfolded proteins actively(ATP hyd.)

55. PATHOLOGIC CONSEQUENCES OF PROTEIN
CONFORMATION-
• Sickle cell anemia and β-Thalassemia(AHSP absent)
• PROTEIN MISFOLDING
Alzheimer disease
Prions

56. PROTEIN MISFOLDING-Alzheimer disease
• Protein folding is a complex tral error process.Misfolded proteins are
tagged degraded withen the cell.This quality control system is not perfect
and aggregats may accumulate-Amyloidosis.
• Alzheimer disease:It is neurodegenerative disorder leading to cognitive
impairment with increasing Age.It is due to Aβ-a peptide 40-45 a.a.residue
in β-pleated sheet conformation-neurotoxic.
• 2nd cause is accumulation of neurofibrilary tangles in brain-defective Tau
protein is key compt of this.
Prion disease:The prion protein(PrP) is causative agent of Encephalpathies in
human & cattles due to change in 3-dimen.struc.α-helices present in
noninfectious prp are replaced by –sheetsin infectious form.

57. Prions
• The transmissible spongiform encephalopathies, or prion diseases,
are
• fatal neurodegenerative diseases characterized by spongiform
changes,
• astrocytic gliomas, and neuronal loss resulting from the deposition of
• insoluble protein aggregates in neural cells.