3.

Structure and function

of proteins

Secondary Structure
and Fibrous Proteins
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Structure of peptide bond

Prof. G. Gilardi - Biological Chemistry

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 Criteria to obtain 2ary structure:
Must have correct geometry
Bond length
Bond angles
Must have maximum productive
interactions
H-bonds with correct geometry

3D structure of myoglobin
Prof. G. Gilardi - Biological Chemistry
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Elements of 2ary structure:
helices i

i+1

i+2

i+3

i+4
310-helix -helix -helix
Prof. G. Gilardi - Biological Chemistry
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 Elements of 2ary structure:
-strands (parallel and antiparallel)

Parallel -strand: note H-bonding pattern.

Both parallel and antiparallel give -sheets
Prof. G. Gilardi - Biological Chemistry
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Antiparallel -strand: note H-bonding pattern.
Prof. G. Gilardi - Biological Chemistry
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Prof. G. Gilardi - Biological Chemistry
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Ramachandran
plot:

Example of sterically
non-allowed conformation
for = 0; = 0

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Experimental Ramachandran
plot for BPTI

BPTI = Bovin Pancreatic

Trypsin Inhibitor

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 Study of protein 2ary structure

Circular dichroism:

Prof. G. Gilardi - Biological Chemistry

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 Fibrous proteins
Proteins can be broadly classified as:
Globular = functional (enzymes, Ab etc)
Myoglobin
Hemoglobin
Cyt c
Fibrous = structural
Keratins
Fibroin
Collagen
Elastin

Prof. G. Gilardi - Biological Chemistry

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 Keratins: -keratin
Hair, nails, skin
> 300 residues, wholly -helical
Pairs of chains in coiled coil conformation
Every 4th aa is hydrophobic; because the turn
is 3.6 aa, there is a strip of hydrophobic aa that
tend to associate different strands
This forms resistant twisted cables
Can be flexible
Rigidity can be introduced by disulphide
bridges between cys
Permanent waves is hair: reduction and
reoxidation of S-S

Prof. G. Gilardi - Biological Chemistry

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 Fibroin
Silk, spider webs
Anti-parallel -sheets
Sequence:

Almost every other aa is Gly

This lies between Ala or Ser
It makes the sheets to fit
together
Bonded chains are stretched,
hence the material is inextesible,
but it is flexible because the
interaction between sheets are
weak van der Waals interactions Prof. G. Gilardi - Biological Chemistry
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 Collagen
Most abundant protein
Tropocollagen:
triple helix
Each chain ~ 1000 aa
Repeats Gly-Pro-(Pro/HPro)
Each molecule 300 nm long, overlaps for
64 nm with the neighbour
Aged collaged contains Lys that becomes
oxidised to aldehyde derivatives that can
give aldon condensation and dehydration
to produce cross-links (rigidity):

Prof. G. Gilardi - Biological Chemistry

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 Collagen
synthesis

Good example for post-

translational
modification:
Stage 1: translation
Stage 2: hydroxylation of
Pro and Lys
Stage 3: glycosylation

Prof. G. Gilardi - Biological Chemistry

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 Elastin

Ligaments and arteries need to

be flexible
Rich in Gly, Ala, Val
Very extended, more like a
random coil
The also contain frequent Lys
Here Lys are designed to hold
together 4 chains in desmosine
cross-links
Desmosine

Prof. G. Gilardi - Biological Chemistry

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 Outline of what
you must now know:

Nature and properties of the peptide bond;

Drawing of all the possible elements of II-ary structure
with H-bonding patterns;
Drawing and discussing the Ramachandran plot;
Principles of circular dichroism as technique to study II-
ary structure;
Examples of fibrous proteins with specific information of
their architecture;

Prof. G. Gilardi - Biological Chemistry

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 Possibili domande

Discutere, con luso esauriente di formule, il legame peptidico e

lorganizzazione della struttura secondaria delle proteine
Descrivi in termini di formule e grafici i vari tipi di eliche, foglietti
beta e turns nella struttura delle proteine.
Descrivi il ruolo del grafico di Ramachandran nel capire il ruolo
del legame peptidico nel determinare la struttura secondaria.
Cheratine, Fibroina, Collagene ed Elastina: discuti la struttura-
funzione di queste proteine.
Descrivi in termini di formule e grafici i vari tipi di eliche, foglietti
beta e turns nella struttura delle proteine.

Prof. G. Gilardi - Biological Chemistry

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