Biochemistry

1. Tertiary Structure of
Protein
By
Mrs Sanchita Choubey
(M.Sc., PGDCR, Pursuing Ph. D)
Assistant Professor of Microbiology
Dr. D Y Patil Arts Commerce and Science College Pimpri, Pune

2. Protein structure: overview
Structural Element
• Primary Structure
• Secondary Structure
• Super-secondary
Structure
• Domain
• Tertiary Structure
• Quaternary
Structure
Description
AminoAcidSequenceof Protein
Helices,Sheets,Turns/Loops
Associationof SecondaryStructures
Self-containedStructural Unit
3D Arrangmentsof AllAtomsInA
Polypeptide Chain OR
FoldedStructureof WholeProtein
•IncludesDisulfideBonds
AssembledComplex (Oligomer)
•Homo-oligomeric(1 Protein Type)
•Hetero-oligomeric(>1 Type)

3. Tertiary Structure
Several important principles:
•
•
•
•
Secondary structures form wherever
possible (due to formation of large
numbers of H-bonds)
Helices & sheets often pack close
together
Backbone links between elements of
secondary structure are usually short
and direct
Proteins fold to make the most stable
structures (make H-bonds and
minimize solvent contact

4. H- bonds
Form in all
proteins. H-atom
of the peptide link
is attracted to the
oxygen of another
peptide link.
Ionic bonds
If some of the amino
acids in the proteins
have carboxylic acid or
amine side groups, an
ionic bond can form.
Covalent bonds
In a very small number of
proteins, sulfur-sulfur
covalent bonds (also
called cystine bonds or
are
disulfide bridges)
present.
While backbone interactions define most of 2ndry structure
interactions, it is side chains that define tertiary interactions

5. Protein-solvent interactions
hydrophilic amino acids (D, E, K, R, H, N, Q)
-these amino acids tend to interact extensively with solvent in context of
the folded protein; the interaction is mostly ionic and H-bonding
-there are instances of hydrophilic residues being buried in the interior of
the protein; often, pairs of these residues form salt bridges
hydrophobic amino acids (M, I, L, V, F, W, Y, A*, C, P)
-these tend to form ‘core’ of protein, i.e., are buried within folded protein;
some hydrophobic residues can be entirely (or partially) exposed
small neutral amino acids (G, A*, S, T)
- less preference for being solvent-exposed or not

6. Types of non-covalent interactions
interaction
ionic
(salt bridge)
nature
electrostatic
bond
length
1.8-4.0 Å
(3.0-10 Å
for like
charges)
“bond”
strength
1-6
kcal/mol
hydrophobic entropy - 2-3
H-bond
van der Waals
2.6-3.5
2.8-4.0
2-10
<1
H-bonding
attraction/
repulsion
 4.5-7.0 1-2
example
positive: K, R, H,
N-terminus
negative: D, E,
C-terminus
hydrophobic side chains
(M,I,L,V,F,W,Y,A,C,P)
H donor, O acceptor
closely-spaced atoms; if
too close, repulsion
F,W,Y (stacked)
aromatic-
aromatic
aromatic-amino
group
H-bonding 2.9-3.6 2.7-4.9 N-H donor to F,W,Y
these all contribute to some extent to protein structure & stability;
- important to understand extremophilic (or any other) proteins

7. Disulfide bonds
• a covalent modification; the oxidation reaction can either be intramolecular
(within the same protein) or inter-molecular (within different proteins, e.g.,
antibody light and heavy chains). The reaction is reversible.
Inside of cells maintained in a
reduced environment by
presence of many "reducing“
agents, such as tripeptide g-glu-
cys-gly (glutathione)
- most disulfide-bonded proteins are extracellular (e.g. lysozyme contains
four disulfide bonds); cysteines are usually in reduced form
- cellular enzymes (protein disulfide isomerases) assist many proteins in
forming proper disulfide bond(s)

8. Proteins have the capacity to fold and become active based on the
information contained in their amino acid sequence.
Thermodynamically spontaneous
Proteins fold in buffered water
type of interaction
hydrophobic group burial
hydrogen bonding
ion pairs/salt bridges
disulfide bonds
total contribution
~ 200 kcal/mol
small??
<15 kcal/mol
4 kcal/mol per link
Typical net protein stabilities are 5- 20 kcal/mol--> so even
minor interactions can make a difference!
Hydrophobic interactions are major stabilizing force of globular proteins
H- bonds and ionic interactions are optimized in specific structures that are
thermodynamically most stable
Contributions to Protein
Stability

10.  Tertiary Structure more conservative than Primary Structure
 Natural variation from species-to-species tends to favor changes in surface
(and therefore polar) groups.
 Structure is determined globally and redundantly.
Upto 30% of the amino acids in some proteins have been changed to
alanine with little change in the folded structure.
 So protein structure comparison important
• Protein family: proteins with significant primary sequence similarity, and/or
with demonstrably similar structure and function
• Super families: two or more families with little primary sequence similarities
make use of the same major structural motif and have functional similarities