Protein structure can be described at several levels of organization. The primary structure is the amino acid sequence, while the secondary structure describes local patterns like alpha helices and beta sheets formed by hydrogen bonds. Tertiary structure refers to the overall 3D shape of a single polypeptide chain. Quaternary structure involves the arrangement of multiple protein subunits. Together these organizational levels allow proteins to carry out their diverse functions in the cell.

1. Protein Structure
- Sailee Gurav
(M.Sc. Biochemistry
Part -1)

2. 
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It‟s completely defined & predictable.
Each amino acid in one of these giant
macromolecules is located at a specific site
within the structure , giving the protein the
precise shape.
It can be described at several levels of
organization , each emphasizing a different
aspect & each dependent on different types
of interactions.

5. 
It‟s simply the sequence of the amino acid
polymer.

1 dimensional.

By convention, written from amino end to
carboxyl end.

It is important as it is the foundation in which
ultimately the higher structures of the protein
are determined, and thus the function of the
protein.

7.  It is a local, regularly occurring structure in
proteins and is mainly formed through hydrogen
bonds between backbone atoms.
 Pauling & Corey studied the secondary
structures and proposed 2 conformations.
The α helix and β sheets.

8. Right-handed coiled or spiral
conformation (helix)
3.6 residues per turn stabilized by
hydrogen bonds
Hydrogen bonding between
C' = O of residue n and NH of
residue n + 4
All C'O and NH groups are joined
by H-bonds.
Except: Terminal NH and C'O
groups

9. 
α-helix is tightly packed

Almost no free space within the
helix

Amino acid side chains are on the
outside of the helix

Roughly point “downwards”

Resembles branches of a
Christmas tree

Most common location of α helices
is along the protein periphery

One side facing the solution
(exterior)

One side facing hydrophobic
interior

10. α-helix
Also called the 4₁₃
π-helix
Very loosely coiled Hbonding pattern n + 5
Raerly found in nature.
310-helix
Very tightley coiled Hbonding pattern n+3 rarely
found in nature

12. 
Beta sheets are another major structural element in globular proteins
containing 20–28 % of all residues

The basic unit of a beta sheet is a beta strand with approximate
backbone dihedral angles phi = -120 and psi = +120

Two types: anti-parallel and parallel strand.

Due to the extended nature of the chain, no significant intra-segment
hydrogen bonds and van der Waals interactions between atoms of
neighboring residues.

Sometimes called the beta "pleated" sheet since sequentially
neighboring Ca atoms are alternately above and below the plane of
the sheet

13. Main-chain NH and O atoms within a b
sheet are hydrogen bonded to each other.
The amino acids in successive strands have
alternating directions (anti-parallel).

14. 
Antiparallel beta sheets are considered
intrinsically more stable than parallel
sheets due to the more optimal
orientation of the interstrand hydrogen
bonds

15. 
Different types
 Hairpin loops – often between anti-parallel beta strands
 Omega loops – beginning and end close (6-16 residues)
 Extended loops – more than 16 residues

Secondary structures are joined together by additional
structures called loops.

These patterns are called motifs

Defining motifs-small, specific combinations of secondary
structure elements

16. A supersecondary structure is a compact
three-dimensional protein structure of
several adjacent elements of secondary
structure that is smaller than a protein
domain or a subunit

18. 
Tertiary structures is defined as the overall arrangement of polypeptide
chains in three-dimensional space, describing how secondary structures
arrange into supersecondary structures that in turn arrange into domains
and domains into tertiary structures.

Components:
 Motif : a recognizable subcomponent of the fold – several motifs
usually comprise a domain
 Fold: used differently in different contexts – most broadly a
reproducible and recognizable 3 dimensional arrangement
 Domain: a compact and self folding component of the protein that
usually represents a discreet structural and functional unit

19. 
Tertiary structures can be divided into three main
classes:
a domain
b domains
a/b domains
 The domain is the unit of tertiary structure

21. 
In globular proteins
 Tertiary interactions are frequently stabilized by sequestration
of hydrophobic amino acid residues in the protein core
 Consequent enrichment of charged or hydrophilic residues
on the protein's water-exposed surface.

In secreted proteins
 disulfide bonds between cysteine residue helps to maintain
the protein's tertiary structure

24. They describes the arrangement of sub-units in a
protein consisting of more than one polypeptide
chain, where the sub-units may be identical or
different.
 The sub-units in a quaternary structure are held
together by non-covalent interactions where the
„contact regions‟ between the sub-units resemble the
interior of tertiary structure proteins as being
hydrophobic.
 These structures cannot have mirror image superpositioning resulting in symmetrical distribution of
the sub-units in the quaternary structure.


27. Poly proline -II helix in proteins:
Structure & Function.
The polyproline type II (PPII) helix in recent years has
emerged clearly as a structural class not only of fibrillar
proteins but also of the folded and unfolded proteins.
 The left-handed, extended PPII helix represents the only
frequently occurring regular structure .
 Natively unfolded proteins have a high content of the
PPII helices identified by spectroscopic methods.
 PPII is favorable for protein-protein and protein-nucleic
acid interactions and plays a major role in signal
transduction and protein complex assembly.


28. 
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PPII helices do not necessarily contain proline,
but proline has high PPII propensity.
PPII helices are involved in transcription, cell
motility, self-assembly, elasticity, and bacterial
and viral pathogenesis, & has an important
structural role in amyloidogenic proteins.
PPII helices are not always assigned in
experimentally solved structures, & they are
rarely used in protein structure modeling.

29. 
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Lehninger Principles Of Biochemistry,
Fourth Edition.
Biochemistry, by Voet & Voet, 3rd edition.
Harper’s Illustrated Biochemistry, 26th
edition.
Biochemistry , by Dr.U.Satyanarayana.
www.ncbi.nlm.nih.gov/
biochemistrycourse.blogspot.in/