MEDICAL BIOLOGY AND

GENETICS

PROTEIN STRUCTURE AND FUNCTION

CHAPTER: 4

Prof. Dr. Esra ÇAĞAVİ

[email protected]
Office: North Campus, C Blok,1st Floor, Room 144,
School of Medicine, IMU
Office Phone: 216-681-5354
Lectures: T-Th 13:30-15:15
 Lecture Objectives

• Explain the main shape and structures of proteins

• Define various functions of proteinin our body

• Explain the major experimental approaches to

study proteins
Alberts • Bray • Hopkin • Johnson • Lewis • Raff • Roberts • Walter

Essential
Cell Biology
FOURTH EDITION

Chapter 4
Protein Structure and Function

Copyright © Garland Science 2014

Some general protein functions
Amino acids are the subunits of proteins
Amino acids in a protein are held together
by peptide bonds
The 20 amino acids found in proteins
Protein = Polypeptide
 Some amino acids can be post-translationally modified,
which is a critical switch for functional modulation and interaction with other proteins
Figure 2-87 Molecular Biology of the Cell (© Garland Science 2008)
Amino acid sequence à Protein shape and function
The shape of a protein is specified by its
amino acid sequence
 Amino acid sequence & distribution of polar and non-polar aa

Protein shape, folding and function

Conformation = Three dimensional arrangements of atoms

= Folded structure

Amino acid = aa
 Protein folding can be studied in a test tube by using
highly purified proteins.
What kind of information can you get?
Denaturation : unfolding, distrupting non-covalent interactions
holding the folded chain together

UREA

Denaturation Renaturation
Proteins fold into a conformation of lowest energy.
Molecular chaperons often assist in protein folding
Chaperon proteins assist in proper folding of
newly synthesized or denatured proteins

Which organelle is the main location of chaperons in the cell?

Proteins can be globular or fibrous, and they can
form filaments, sheets, rings or spheres
Protein conformation can be represented in a
variety of ways
Secondary structure of a polypetide chain: 1) Alpha-helix
•Alpha helix is generated when a single polypeptide chain twists
around itself to form a rigid cylinder
 Alpha-helices are abundant in proteins located in cell
membranes (trans-membrane proteins)

Figure 3-78a Molecular Biology of the Cell (© Garland Science 2008)

Alpha helices wrap around each other to form
stable structures of coiled coils.
Secondary structure of a polypetide chain: 2) Beta-sheets
Stacking of beta-sheets of some misfolded proteins
may lead to aggregates of amyloid fibers
Which disease do we see amyloid plaques in neurons leading to degeneration?

Prion diseases are caused by proteins whose misfolding is

infectious.Ex: Creutzfeldt-Jakob disease
Many proteins are composed of
separate functional domains
 Many proteins contain several domains often
connected each other by short, unstructured lengths
of polypeptide chains
At the beginning of time, there were many options
for a protein

The one with most stable structure, energetically

favorable folding and function was selected during
evolution

Through gene duplication and other gene

arrangements/mutations, its structure was
modified to enable new functions

Protein families formed

Proteins can be classified into many protein families by
using homology screens and sequence similarities
among different organisms.

Serine
Proteases
 We can be certain of a family relationship between two
proteins by comparing both:

1) Amino acid sequence

2) Three-dimensional structure (X-ray crystallography and
nuclear magnetic resonance-NMR)

Figure 3-13 Molecular Biology of the Cell (© Garland Science 2008)

The structure of a protein can be determined
by X-ray crystallography
Protein Domain: distinct structural unit that fold
independently of each other into stable and compact
structures.

- are modular units in which larger proteins are

built from

- contains 40-350 aa

- different domains are usually associated with

different functions
 Domain structure of a group of evolutionarily related
DNA binding protein
•More complex organisms tend to contain additional domains

Figure 3-19 Molecular Biology of the Cell (© Garland Science 2008)

 Sequence search can identify close relatives

Figure 3-14 Molecular Biology of the Cell (© Garland Science 2008)

Protein Identification
 The genome sequences of most common
experimental organisms are now known,
catalogues of all the proteins produced in those
organisms are available. The task of identifying
an unknown protein (or collection of unknown
proteins) thus reduces to matching some of the
amino acid sequences present in the unknown
sample with known catalogued genes. This task
is now performed almost exclusively by using
mass spectrometry in conjunction with computer
searches of databases.
Proteomics: is the characterization of all proteins in
the cell, including all protein-protein interactions and
all post-translational modifications.

In combination with the rapid purification techniques,

mass spectrometry has emerged as the most
powerful method for identifying unknown proteins and
mapping both the post-translational modifications of a
given protein and the proteins that remain associated
with it during purification.
 Mass spectrometry can be used to identify proteins by
determining the precise masses of peptides derived from them
Some proteins are formed as symmetrical assembly
of two different subunits
Identical protein subunits assemble into complex
structures
An actin filament is composed of
identical protein subunits
A single type of protein subunit can pack together to
form a filament, a hollow tube or a spherical shell
Many viral capsids are more or less spherical
protein assemblies
Collagen and elastin are abundant
extracellular fibrous proteins
Disulfide bonds help to stabilize extracellular proteins
The binding of a protein to another molecule is
highly selective
Ligand à from latin word “ligare” which means “to bind”

•Selectivity
•Specificity
•Affinity
Binding sites allow proteins to interact with specific
ligands. The surface conformation of a protein and
its binding site determines its chemistry.
An antibody is Y-shaped and has two identical antigen-
binding sites, one on each arm of the Y.
There are billions of different antibodies, each with a
different binding site.
Enzymes are powerful and highly specific catalysts
 Tightly bound small molecules add extra
functions to proteins

Retinal is a light-sensitive molecule covalently

attached to rhodopsin protein in our eyes.

A heme group is tightly, but non-covalently, attached

to each of the four polypeptide chains in hemoglobin
Tightly bound small molecules add extra
functions to proteins
 Protein function can be selectively disrupted
with small molecule inhibitors

Figure 8-27 Molecular Biology of the Cell (© Garland Science 2008)

The catalytic activities of enzymes are often
regulated by other molecules

feedback Feedback inhibition

activation
regulates the flow
through biosynthetic
pathways.
Feedback inhibition at multiple points regulate
connected metabolic pathways
Feedback inhibition triggers a conformational
change in an enzyme
Allosteric enzymes have two or more binding sites that interact
“allos” = other
“stereos” = solid or three-dimentional

OFF

ON

The equilibrium between two conformations of a protein is affected by

the binding of a regulatory ligand.
Protein activity is regulated by various ways
One of the most common form of post-translational
modification of a protein is Phosphorylation
A protein kinase catalyses the transfer of gamma-phosphate from ATP (or GTP)
to its protein substrates.
A protein phosphatase catalyses the transfer of the phosphate from a
phospho-protein to a water molecule

Protein Kinase

Protein Phosphotase

Together, these two families of enzymes act to modulate the activities of the
proteins in a cell, often in response to external stimuli.
Phosphorylation -Covalent addition of a phosphate group to
a protein- is a critical and major way to modify proteins and
their activity by causing a conformational change

à Ser, Thr, Tyr

Phosphorylation can either increase or decrease the
protein’s activity, depending on the site of
phosphorylation and the structure of the protein
 ***IMPORTANT: Two major intracellular signaling mechanisms

Figure 3-73 Molecular Biology of the Cell (© Garland Science 2008)

Ubiqutin addition can only be added on
Lysine (K) residues

Ubiqutination
Covalent and post-translational modifications also
control the location and interaction of proteins
Multisite protein modifications affect protein function
Combination of modifications on proteins alter its
behavior in the cell
GTP-binding proteins function as
molecular switches
An allosteric motor protein:
ATP hydrolysis allows motor
proteins produce directed
movements within cells by
changing conformation
The ABC (ATP-binding casette) transporter is a
protein machine that pumps large hydrophobic
molecules through a membrane
How do we study proteins?
Protein Purification
Protein Separation
Depending on the choice of matrix, proteins can be
separated according to:

•their charge (ion-exchange chromatography)

•their hydrophobicity (hydrophobic chromatography)

•their size (gel-filtration chromatography)

•their ability to bind to particular small molecules or

to other macromolecules (affinity chromatography).
•Proteins normally possess a net positive or negative
charge, depending on the mixture of charged amino
acid they contain.

•An electric field applied to a solution containing a

protein molecule causes a protein to migrate at a rate
that depends on its net charge on its size and shape.

•The most popular application of this property is SDS

polyacrylamide-gel electrophoresis (SDS-PAGE)
 Movie: SDS-PAGE electrophoresis

http://www.youtube.com/watch?v=bNm9l7j
V0MY
 General protein stain Specific protein blot

Figure 8-20 Molecular Biology of the Cell (© Garland Science 2008)

Western blotting
(immunoblotting)
 Movie: Western blot

http://www.dnatube.com/video/1511/Western
-blot
 GOOD LUCK AT THE EXAM!

Exam: Chapter 1, 2, 3 and 4

For next class: Chapter 5

DNA and Chromosomes