Section 5-5 National Tsing Hua University

CHEM5980

Protein hierarchical structures

• Primary structures are sequence of

protein
• Secondary structures are α helix, β
sheet and turns.
• Domains are small regions of protein
capable of folding independently that
formed by interaction between α helix
and/or β sheet. Typically less than 100
amino acids.
• Tertiary structure is consist of one or
several domains.
• Quaternary structure is assembled from
multiple independent protein chains to
form complex structures. They are
usually nanometer sized machines.
 Section 5-5 National Tsing Hua University
CHEM5980

Protein domains
• Protein domains are modular units with specific arrangements of secondary
structures. Sometimes they are stable without the rest part of protein and with
original functions.
• Protein domains can be reused for different functions, this protein evolution can be
done by homologous recombination.
• Some domains are
popular in proteome,
but the extent may
be different from
organism to organism.
Common protein
domains in human
proteome are listed.
 Section 5-5 National Tsing Hua University
CHEM5980

Zinc finger domain

• Classical zinc finger C2H2 (2 Cys and 2 His) is the most common domain in human
proteome. It stabilize the folding by the coordination of a zinc ion.
• Classical zinc finger is about 25 amino acid residues with an α helix and a peptide
loop. One C2H2) variant has 2 cysteine residues on the loop and 2 histidine residues
on helix to coordinate to zinc ion.
• Classical zinc finger proteins bind DNA in major groove with specificity as nucleases
and transcription factors. Zinc finger is important in DNA sequence recognition. The
occurrence of zinc finger in human proteome indicates the importance of
transcription factor in human cells.
• A broader definition of zinc finger is
structural motif the bind zinc to stabilize the
structure. there are a number of unique
types of zinc fingers, each with a unique
architecture.
 Section 5-5 National Tsing Hua University
CHEM5980

Zinc finger domain

• Zinc finger domains share consensus
sequence (F/Y)-X-C-X2-5-C-X3-(F/Y)-X5-ψ-
X2-H-X3-5-H, where X is any amino acid
and ψ is hydrophobic residues. In the
presence zinc ion, the domain folds into
a compact ββα structure.
• From the crystal structure of Zif268 with
DNA provided the insight how zinc-
finger recognize DNA sequence. The
amino acid residue positioned -1, 3 and
6 on helix have good contact with
primary DNA strand, while position 2
interact with the complementary strand.
• Arg at -1 position binds to a pair of
hydrogen bonds to guanine. This
interaction is also stabilized by aspartate
at position 2.
• With the residues at these positions
change, different sequence can be
recognized.
Annu Rev Biophys Biomol Struct 2000, 29, 183
 Section 5-5 National Tsing Hua University
CHEM5980

Zinc finger domain

• Based on the known zinc-finger binding to DNA sequence, the specificity can be
predicted.

Annu Rev Biophys Biomol Struct 2000, 29, 183

 Section 5-5 National Tsing Hua University
CHEM5980

β-sandwich architectures
• Immunoglobulin domain composed of two face-to-face anti-parallel β sheets, which
consist of 3~4 β strands.
• The individual β strands connect back and forth in both sheets; as an example, one
sheet may contain β strand in order of strand 1, 2, 5 and 4 strand and the other
sheet has strands 3, 6, and 7.
• In immunoglobulins, the immunoglobulin domains are connected by flexible hinge
regions, which functions as joints for the arm. This morphology allows adjustable
bidentate adjustment to bind to antigen.

Immunoglobulin type G (IgG)

 Section 5-5 National Tsing Hua University
CHEM5980

β-sandwich architectures
• Immunoglobulin domains also present in proteins other
than immunoglobulin, such as muscle protein, in which
the immunoglobulin domain contribute to the its
resiliency property.
• Titin is the third abundant protein in muscle that limits
the range of motion of the sarcomere in tension. The
immunoglobulin domains unfold when the protein is
stretched and refold when the tension is removed

Circulation 2006, 113, 1922

 Section 5-5 National Tsing Hua University
CHEM5980

β-sandwich architectures
• Fibronectin is a glycoprotein of the extracellular matrix that binds components such
as collagen, fibrin, and heparan sulfate proteoglycans.
• Fibronectin type III domain is another popular in human proteome with anti-
parallel β sandwich structure.
• Olfactory cells adhesion molecule (OCAM) plays a role for compartmentalization of
synapses within the glomerular layer. OCAM binds to each other through a
immunoglobulin domain and provides cell adhesion. Both immunoglobulin domains
and Fibronectin type III domains (Fn3I and Fn3II) are available in OCAM.

OCAM

OCAM

http://www.ks.uiuc.edu/Research/fibronectin/index.old.html
 Section 5-5 National Tsing Hua University
CHEM5980

β-sandwich architectures
• Cadherin domain coordinate adhesion between cells through
protein complex anchored to internal cytoskeleton actin.
• The extracellular part of cadherin contains 5 cadherin folding
domains. The terminal domain can dimerize with another similar
domain from another cell.
• During dimerization, tryptophan residue on one cadherin domain
binds to hydrophobic pocket of the complementary domain and
results in β strand exchange.
• Cadherin requires calcium ion to support its structure although it
only weakly binds to cadherin.
• Losing cadherin on cancer cells are related to invasive tumor.
Ca2+
Trp
 Section 5-5 National Tsing Hua University
CHEM5980

WD domains
• WD domain is formed with 4-strand anti-parallel β sheet that with a orthogonal
twist over 40 amino acids and therefore called WD40 domain.
• The WD40 domain is composed of several repeats, a ~20-residue variable region of
is followed by a more common repeated set of residues.
• Blade-like WD40 domain is formed and fit together with other WD40 to form a
propeller-like structure with the 7 bladed beta propeller being most common.
• WD domain serve as diverse roles in cell signaling, including regulation of
transcription, cell-fate determination, trans-membrane signal transduction, vesicle
trafficking and others.

Trend Biochem Sci 2007, 32, 547

 Section 5-5 National Tsing Hua University
CHEM5980

Three-strand helix of collagen

• Collagen is the most abundant protein (25-35%) in human and can be found in
extracellular matrix.
• Collagen is exploited as key structure and support role in body, for instance, bone
and cartilage rely on the collagen for their strength. Other tissues such as nose and
outer ears consist largely on collagen.
• Collagen are form with a large number of Gly-Xaa-
Yaa tripeptide repeat, where Xaa and Yaa are usually
proline or 4-hydroxyproline.
• The collagen peptide chain interwind with two other
collagen chains to form a triple helix. This helix is
hold by hydrogen bonds formed between glycine N-
H to proline carbonyl in the other chain and so on.
• The 4-hydroxyproline is formed by post-translational
modification by enzyme, the stereoelectronic effect
from the hydroxyl group involves the helix stability.

stabilize destabilize
 Section 5-5 National Tsing Hua University
CHEM5980

7 transmembrane domains
• Seven-transmembrane domains are
characterized by the presence of seven α helix
that traverse the cell membrane.
• The helices of the seven transmembrane are
common element for signal transduction. These
helices form a basket for binding small molecules,
which functions as signaling messengers.
• Using Rhodopsin as example, this G-protein
receptor bind aldehyde ligand retinal and form
imine with its lysine residue. Then light transform
the trans C-C double bond into cis and change the
conformation as a signal for the receptor to
transmit into cell through G-protein.
• α helix bundles are common as protein domains,
these helices usually have hydrophobic amino acid
on the location in contact with other helix to drive
protein folding in aqueous solutions.
 Section 5-5 National Tsing Hua University
CHEM5980

Peptide-binding domains
• Sequence-selective peptide binding is often involved in protein communications.
SH2 and SH3 domains are examples toward this interaction.
• SH2 domain recognize a phosphate group on tyrosine, which is the result of a
signaling process. SH2 domain has antiparallel β sheet with a α helix at both top
and bottom.
• SH3 domains are β barrel and they recognize peptides with multiple prolines that
forms a helix structure, which has a three-fold symmetry viewing from the helical
axis.

SH2 SH3
 Section 5-6 National Tsing Hua University
CHEM5980

Higher levels of protein structure

• Protein tertiary structure is defined by the folding of a individual peptide chain.
Usually such structure are composed by several domains.
• Tyrosine kinase Src is an example that the combination of multiple domains from a
single peptide chain to elicit protein function.
• Binding of kinase domain to C-terminal peptide with phosphotyrosine residue to
keep enzyme inactive. Src activator can be unleashed by tyrosine residue
dephosphorylation.
• https://www.youtube.com/watch?v=kbI-1Y63Sfw
 Section 5-6 National Tsing Hua University
CHEM5980

Higher levels of protein structure

• Quaternary structure consist of non-covalent bonded
proteins that assemble into large complexes.
• Ferritin, a iron storage protein, is an example of
quaternary structure that is composed of 24 identical
4-helix bundles.
• The assembly of collagen begins with C-terminal
domain fold into globular structure and trimerize to
nucleate triple-helix.
• Isomerization of proline is catalyzed by prolyl cis-trans
isomerase to help helix formation.
• Enzyme cleave globular domain to allow collagen helic
to form fibril.
 Section 5-X National Tsing Hua University
CHEM5980

Diseases arise from protein misfolding

• Protein folding is crucial to maintain their functions, misfolding of certain essential
protein cause diseases.

Nat Rev Mol Cell Biol 2014, 15, 384

Section 5-X National Tsing Hua University
CHEM5980

Disease Models & Mechanisms 2014, 9

 Section 5-X National Tsing Hua University
CHEM5980

Mechanism of protein folding disease

Disease Models & Mechanisms 2014, 9

 Section 5-X National Tsing Hua University
CHEM5980

Mechanism of protein folding disease

Disease Models & Mechanisms 2014, 9

 Section 5-X National Tsing Hua University
CHEM5980

Mechanism of protein folding disease

AAT: α1-antitrypsin
Secreted protease inhibitor

Disease Models & Mechanisms 2014, 9

 Section 5-X National Tsing Hua University
CHEM5980

Mechanism of protein folding disease

Disease Models & Mechanisms 2014, 9

Section 5-X National Tsing Hua University
CHEM5980

Disease Models & Mechanisms 2014, 9

Section 5-X National Tsing Hua University
CHEM5980