Protein Structure

(in a nutshell)

Guy Ziv
December 26th , 2006

Myoglobin (1958)
Proteins

 From the Greek “proteios” meaning

“of first importance”
 The basic building blocks of almost all life
 Constitutes the majority of the cell, and perform nearly all
enzymatic activities
 Composed of 20 naturally occurring amino-acids

varying moiety
called “side chain”
Protein Synthesis In-vivo

1. Transcription:
DNA  messenger RNA (mRNA)
2. Translation:
mRNA  Linear chain of a.a.
(Ribosome)
3. Folding: Peptide bond
Linear chain  Structure

Protein chains have direction N-terminal → C-terminal

X-Rays crystallography –
the tool of structural biology

 Why X-ray?
Wavelength of visible light: ~500 nm
Bond lengths in proteins: ~0.15 nm
Typical X-ray wavelength: ~0.15 nm
 X-ray are (weakly) scattered by electrons
 Diffraction from a single molecule is weak
so use a crystal:
– Multiple copies of the molecule increases diffraction
– Crystalline structure imposes constraints on diffraction
pattern
Diffraction occurs at particular angles

 Diffractionspots
are the result of
constructive
interference
from multiple
scatterers θ
satisfying
Bragg’s Law:
λ = 2 d sinθ θ

θ
θ
Bragg planes intersect the unit cell in
particular “indices”

0,0 k

h=1, k=1 h=4, k=-2

Each Spot Represents a Unique Set of
Bragg Planes

Points in k-space
(Fourier Space)
h=2, k=1, l=3

h=10, k=3, l=8 detector

λ = 2 d sinθ

θ 1 θ 2 θ 3
Modern X-Ray Crystallography
Need good crystals for better resolution,
which is difficult in proteins (need right conditions)
and sometimes nearly impossible
Early 1950’s (e.g. membranal proteins)

High resolution details are faint – requires

good experimental apparatus

Recorded intensity give only the magnitude

but not the phase of the complex “form factor”

Error in density map lead to un-realistic

atom assignment, requiring iterative refinement
process
Historical perspective to
Pauling and Corey paper series

 X-ray crystallography, invented in the beginning

of the 20’th century, has been used to solve
structures of some amino-acids, synthetic
polymers (poly-glu) and small organic molecules
 Some fibrous materials such as wool and
α-keratin are sufficiently crystalline to give
diffraction patterns
 Evidence suggested that these proteins’
structure involve mainly translation and rotation
Pauling and Corey

Robert Corey (1897-1971)

Linus Pauling (1901-1994)
Pauling and Corey papers series –
PNAS April 1951

1. Pauling, L., Corey, R.B. and Branson H. R. The Structure of Proteins:

Two Hydrogen-Bonded Helical Configurations of the Polypeptide
Chain. PNAS, 37, 205-211, (1951).
2. Pauling, L. & Corey, R. B. Atomic Coordinates and Structure Factors for
Two Helical Configurations of Polypeptide Chains. PNAS, 37, 235-240,
(1951).
3. Pauling, L. & Corey, R. B. The Structure of Synthetic Polypeptides.
PNAS, 37, 241-250, (1951).
4. Pauling, L. & Corey, R. B. The Pleated Sheet, A New Layer
Configuration of Polypeptide Chains. PNAS, 37, 251-256, (1951).
5. Pauling, L. & Corey, R. B. The Structure of Feather Rachis Keratin.
PNAS, 37, 256-261, (1951).
6. Pauling, L. & Corey, R. B. The Structure of Hair, Muscle, and Related
Proteins. PNAS, 37, 261-271, (1951).
7. Pauling, L. & Corey, R. B. The Structure of Fibrous Proteins of the
Collagen-Gelatin Group. PNAS, 37, 272-281, (1951).
8. Pauling, L. & Corey, R. B. The Polypeptide-Chain Configuration in
Hemoglobin and Other Globular Proteins. PNAS, 37, 282-285, (1951).
Pauling and Corey papers series –
PNAS April 1951

1. Pauling, L., Corey, R.B. and Branson H. R. The Structure of Proteins:

Two Hydrogen-Bonded Helical Configurations of the Polypeptide
Chain. PNAS, 37, 205-211, (1951).
2. Pauling, L. & Corey, R. B. Atomic Coordinates and Structure Factors for
Two Helical Configurations of Polypeptide Chains. PNAS, 37, 235-240,
(1951).
3. Pauling, L. & Corey, R. B. The Structure of Synthetic Polypeptides.
PNAS, 37, 241-250, (1951).
4. Pauling, L. & Corey, R. B. The Pleated Sheet, A New Layer
Configuration of Polypeptide Chains. PNAS, 37, 251-256, (1951).
5. Pauling, L. & Corey, R. B. The Structure of Feather Rachis Keratin.
PNAS, 37, 256-261, (1951).
6. Pauling, L. & Corey, R. B. The Structure of Hair, Muscle, and Related
Proteins. PNAS, 37, 261-271, (1951).
7. Pauling, L. & Corey, R. B. The Structure of Fibrous Proteins of the
Collagen-Gelatin Group. PNAS, 37, 272-281, (1951).
8. Pauling, L. & Corey, R. B. The Polypeptide-Chain Configuration in
Hemoglobin and Other Globular Proteins. PNAS, 37, 282-285, (1951).
 Linus Carl Pauling
The Nobel Prize in Chemistry 1954

"for his research into the nature

of the chemical bond and its
application to the elucidation
of the structure of complex
substances"
Determinants of helical structure

superposition

Resonant partial double bond character of

peptide bond induces planar arrangement of
atoms
Distances and angles
Between atoms
All hydrogen bonds should be satisfied,
i.e. distance N-O of about 2.7Å and angle
between C = O and H – N less then ~30°
Building a model –
similar to building with LEGO blocks

 Start assembling monomers

(amino-acids) with fixed
translation and rotation
 Look for configurations which
have no steric hindrance (i.e.
clashes)
 Calculate N-H…O=C distances
and
angles (3-d trigonometry..)
2 models satisfies all constraints
The α-helix – one of the two common
structural elements in proteins

 Completes one turn every 3.7

N residues
C  Rises ~5.4 Å with each turn

O i  Has hydrogen bonds between

the C=O of residue i and the
N-H of residue i+4
 Is right-handed

i+4
Alpha-helices appear a lot in trans-
membranal proteins

membrane
1pv6.pdb

E.g. Lactose permease (LacY)

Why did Pauling and Corey succeed
where others failed?

 Understanding the importance of hydrogen

bonds
 Taking into account the planar peptide bond
 Better knowledge of covalent bond lengths
and angles
 MOST IMPORTANTLY – they were NOT
crystallographers, and did not consider only
models with integer number of residues per
turn!
Proof came 7 years later…

John Cowdery Kendrew

The Nobel Prize in Chemistry 1962

Kendrew, J. C., Bodo, G., Dintzis, H. M. Parrish, R. G., Wyckoff, H.,

and Phillips, D. C. A Three-Dimensional Model of the Myoglobin Molecule
Obtained by X-ray Analysis. Nature, 181, 662 (1958).
 Hierarchy of Protein Structure

Linear chain made of 20 possible

Alpha-helices, beta-sheets, turns
amino acids

Motifs, domains

Oligomers, complexes
The Protein Data Bank (www.pdb.org)
The PDB contains over 40,000
structures (as of December 2006)

NMR - Nuclear magnetic resonance

Allows structure determination based on
distance and angular constraints in solution
Proteins’ Structure is Dynamic

 Fluctuations
exists in all proteins
 Conformational changes ↔ Function

Adenylate kinase
An enzyme that catalyzes
the production of ATP from ADP
Protein Folding – still an open
question

 1954 Christian B. Anfinsen proved that the

protein structure is determined by it’s
sequence
Protein  Denatured (unfolded)  Protein
+ Urea Dilution
RNase
enzyme

 1969 “Levinthal paradox” – For a 100 a.a.

sequence there are 9100 possible
configurations. If sampled randomly every
nanosecond, it will take longer then the age
of the universe to fold a single protein
Protein folding – research continues

 Late 1980’s - Wolynes et al. present the

“Energy Landscape” or “Folding Funnel” model
for protein folding Entropy

Energy
Native
(folded) state

 2006– There is still no precise understanding

how proteins fold fast (up to µsec!), reliably and
accurately to their native structure