Bioc 192 Lecture 3

Elements of Protein Structure

Protein Display
Supersecondary Themes
Families of Protein Structure
Protein Folding & Disease

Educational Objectives

Explain what is meant by supersecondary structure and a structural domain.

Describe the interactions that stabilise the tertiary structure of a protein,
namely the various non-covalent interactions and disulfide bonds.

Appreciate that most proteins contain combinations of helices and sheets
that form distinctive patterns.

Understand and describe the common ways that protein structure is depicted.

Classify a given protein structure as being primarily
-helical,
/ or 
by studying its structure.

Understand the concept that the ultimate function of a protein is dictated
by its amino acid sequence and higher order structure

Understand the terms native and denatured when describing protein folding.

Describe Anfinsens experiment showing that the primary structure of a
protein determines secondary and tertiary level structures.

Appreciate that protein folding in vivo is often assisted by accessory proteins
(chaperones).

Outline the steps involved in folding a newly synthesised protein.

Provide examples of misfolded proteins and the diseases associated with
them.

Elements of Protein Structure

-helices
-strands
turns
random coils and loops

Protein crystallography is the source of most

protein structure information

X-rays
maths

maths

Protein display can be varied

Branden & Tooze, 1999

Protein Structural Shorthand

Helices shown as spirals (or cylinders)
Strands shown as arrows,
pointing from N to C
Turns and random coil, shown as loops

Protein Structure Shorthand

Alpha

Coil
Beta
Turn
Branden & Tooze, 1999

Protein Structure Shorthand

ribonuclease A
Alpha

Richardson
Diagrams

Protein Cartoons

Beta
Stryer, 4th
Edition

Protein Structure Shorthand

Easily visualize the main chain path of protein
Identify elements of secondary structure
Allows an appreciation of proteins as 3-D objects
Allows comparison to other proteins
Can add in key parts like metals or side chains

Building up Protein Tertiary Structure

Elements of secondary structure
Supersecondary structure
Protein domains
Complete protein structures

Supersecondary structure
Elements of secondary structure are
connected by turn or by regions of less
ordered structure called loops or coil to
make up supersecondary structure.
Combinations of helix and sheet are
common elements (or motifs) of
supersecondary structure

p95 Campbell and Farrell 6th ed.

Common motifs of
supersecondary structure

Helix - turn - helix

Beta hairpin
Greek key
Strand-helix-strand

Common motifs of
supersecondary structure
Helix - turn - helix
Simple Helix-turn-helix
DNA binding motif

EF hand proteins

Bind calcium
R hand
Thumb - helix F
Forefinger - helix E
Ca++ flexed 2nd finger

Both are common structural motifs

Branden & Tooze, 1999

Branden & Tooze, 1999

-hairpin

BPTI
bovine pacreatic trypsin inhibitor

Snake venom
endotoxin

Common
Anti-parallel
Length varies

Branden & Tooze, 1999

Greek Key

Greek Key

4 antiparallel strands
Branden & Tooze, 1999

 thinking about Greek key as

one long bent hairpin
4 antiparallel strands

Branden & Tooze, 1999

Strand, helix, strand

Branden & Tooze, 1999

R-handed, common

L-handed, uncommon

Protein Domains and motifs

Supersecondary structure elements combine to form domains
or motifs - independently folded regions that often possess a
specific binding function
Typically, a protein domain has a
hydrophobic core and the
hydrophilic parts of the protein are
arranged on the surface in contact
or near solvent.
Small proteins contain usually one
domain, larger proteins may be
multi-domained

Glyceraldehyde-3-phosphate dehydrogenase
p146 Voet, Voet and Pratt

Proteins can be grouped

into families based on tertiary
structure three examples
domain family
/ family
antiparallel family

 domain family
Four helix bundle

Branden & Tooze, 1999

 domain family

Four helix bundle

Branden & Tooze, 1999

 domain family
Globin Fold
Branden & Tooze, 1999

/ family

/ barrel

/ open twisted sheet

Branden & Tooze, 1999

/ family

Hydrophobic inside of barrel

Branden & Tooze, 1999

/ family

16 strand helix motif repeats

Branden & Tooze, 1999

anti-parallel family
anti-parallel barrel

Branden & Tooze, 1999

anti-parallel family

Retinal binding protein

Hydrophobic inside of barrel

Branden & Tooze, 1999

anti-parallel family

Hydrophobic inside of barrel

Branden & Tooze, 1999

Many More
Families of
Protein
Structure Exist

American
Scientist, 2002

Many types of structural motifs

and domains have been
described and are often
repeated in nature

Domains are often reused by nature and

combined with other domains to make proteins
with different functions.

Common Protein Domains

After Branden & Tooze, 1999

Protein Folding

Folding of Proteins
Proteins are synthesized as linear polymers that have to fold
into a 3-dimensional functional structure
Protein are made at the ribosome, and then they fold into their
active shape spontaneously
The only instructions needed are embedded in the aa
sequence
Essentially the sequence contains the instructions!
This was proven by a famous biochemist, Christian Afinsen, in
a series of experiments that led to a Nobel Prize

p105 Campbell and Farrell 6th ed.

The Afinsen Experiment in a Nutshell

Stryer, 4th Edition

Folding pathways
Protein folding is directed largely by its internal
hydrophobic residues, which form an internal core, while
hydrophilic residues are solvent exposed.
Not a random process
A likely sequence of events is:
(i)

Formation of short secondary structure

segments

(ii)

Nuclei come together, growing

cooperatively to form a domain

(iii)

Domains come together (but tertiary

structure still partly disordered)

(iv)

Small conformational adjustments to give

compact native structure

p114 Pratt and Cornely

Stabilisation of protein folding

Non-covalent interactions, while individually weak, in proteins
collectively make a significant contribution to protein
conformation stability
In some proteins additional covalent bonds (eg. disulfide bonds)
may be present that contribute to conformation stability

p100 Campbell and Farrell 6th ed.

Some protein folding is

assisted by chaperones
(a) chaperone-independent

(b) Chaperone-dependent eg Hsp70

(c) Chaperonin-dependent
eg GroEL-GroES
p356 Campbell and Farrell 6th ed.

Unfolding of proteins
Weakening of non-covalent interactions can lead to unfolding
and loss of biological function (denaturation)
May result from eg:
change in pH
heating
detergents (eg sodium dodecyl sulphate)
organic solvents
urea, guanidinium HCl

Unfolding of proteins
Correctly folded proteins may become denatured (unfolded)

Wiki Commons, Public domain, 2007

Protein Misfolding in Disease

Misfolding of Proteins

Proteins in living organisms that are folded normally

can sometimes change their shape and become
misfolded
Some misfolded proteins can cause other proteins to
change their shape as well, sometimes with disastrous
consequences

Misfolding of Proteins
In the brain three conditions have been indentified as being
due to a protein PrP that changes its shape and forms
aggregates that cause brain damage: bovine spongiform
encephalopathy (BSE), Creutzfeld-Jacob Disease (CSD), Kuru
The proteins that cause the problem are called prions for
proteins infectious agent
It is thought that the abnormal protein induces the normal
protein to misfold
> transformation
No treatment available, always fatal.

p105 Campbell and Farrell 6th ed.

Model for Prion Conformation

Misfolding of Proteins
Other diseases in which protein misfolding or aggregation is
thought to contribute to disease
Alzheimers Disease
Type 2 Diabetes
Prions are not involved in these ailments
Abnormally folded protein called amyloid is thought to
contribute