Protein structure and its details

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/