PROTEINS
PROTEINS
Traditional Architecture
Form
fits
function
Wood, brick, nails, glass
Materials
Temperature, earthquakes
Environmental Factors
How many people?
Population Factors
Molecular Architecture
Amino acids, cofactors
Temperature, solubility
# partner proteins, # reactants
How many doors and windows?
Portals
Spanish, Victorian,
Motifs/Styles
Conserved domains or protein folds
Architect
Evolution
Passages for substrates
1950's blocky science building
Julia Morgan
and reactants
Levels of Protein Structure
Primary structure = order of amino
acids in the protein chain
Charged and polar R-groups tend
to map to protein surfaces
Non-polar R-groups tend to be
buried in the cores of proteins
Myoglobin
Blue = non-polar
R-group
Red = Heme
Amino Acids Are Joined By
Peptide Bonds In Peptides
- a-carboxyl of one amino acid is joined to
a-amino of a second amino acid (with
removal of water)
- only a-carboxyl and a-amino groups are
used, not R-group carboxyl or amino
groups
Chemistry of peptide bond formation
The peptide bond is planar
This resonance
restricts the number
of conformations in
proteins -- main
chain rotations are
restricted to f and y.
Primary sequence reveals important
clues about a protein
• Evolution conserves amino acids that are important to protein
structure and function across species. Sequence comparison
of multiple “homologs” of a particular protein reveals highly
conserved regions that are important for function.
• Clusters of conserved residues are called “motifs” -- motifs
carry out a particular function or form a particular structure that
is important for the conserved protein.
motif
DnaG
E. coli
small hydrophobic
DnaG
S. typ
large hydrophobic
DnaG
B. subt
polar
gp4
T3
positive charge
gp4
negative T7
charge
...EPNRLLVVEGYMDVVAL...
...EPQRLLVVEGYMDVVAL...
...KQERAVLFEGFADVYTA...
...GGKKIVVTEGEIDMLTV...
...GGKKIVVTEGEIDALTV...
: : : :
* *
*
:
:
Secondary structure = local folding
of residues into regular patterns
The a-helix
• In the a-helix, the carbonyl
oxygen of residue “i” forms a
hydrogen bond with the
amide of residue “i+4”.
• Although each hydrogen
bond is relatively weak in
isolation, the sum of the
hydrogen bonds in a helix
makes it quite stable.
• The propensity of a peptide
for forming an a-helix also
depends on its sequence.
The b-sheet
• In a b-sheet, carbonyl
oxygens and amides form
hydrogen bonds.
• These secondary
structures can be either
antiparallel (as shown) or
parallel and need not be
planar (as shown) but can
be twisted.
• The propensity of a peptide
for forming b-sheet also
depends on its sequence.
Why do Secondary Structures form
Tertiary structure = global folding of
a protein chain
Tertiary structures are quite varied
Quaternary structure = Higher-order
assembly of proteins
Examples of other quaternary
structures
Tetramer
SSB
Allows coordinated
DNA binding
Hexamer
Filament
DNA helicase
Recombinase
Allows coordinated DNA binding
Allows complete
and ATP hydrolysis
coverage of an
extended molecule
Quaternary Structures
Classes of proteins
Functional definition:
Enzymes:
Accelerate biochemical reactions
Structural:
Form biological structures
Transport:
Carry biochemically important substances
Defense:
Protect the body from foreign invaders
Structural definition:
Globular:
Complex folds, irregularly shaped tertiary structures
Fibrous:
Extended, simple folds -- generally structural proteins
Cellular localization definition:
Membrane:
In direct physical contact with a membrane; generally
water insoluble.
Soluble:
Water soluble; can be anywhere in the cell.
Protein Overview
Need to understand physical principles underlie the passage
from sequence
to structure
to dynamics
QuickTime™ and a
Sorenson Video 3 decompressor
are needed to see this picture.
Function
LEVINTHAL PARADOX
100 a.a in general
If there are 10 states/a.a
10100
conformations
Three Folding Problems
• Computational: Protein structure prediction from an
amino acid sequence.
• .Folding speed: “Levinthal paradox” the kinetic
question how can a protein fold so fasts
• The folding code: The ”thermodynamic” question of
how a native structure results from interatomic forces
acting on an amino acid sequence
What if proteins misfold?
• Diseases such as Alzheimer's disease, cystic fibrosis,
BSE (Mad Cow disease), and even many cancers are
believed to result from protein misfolding.
• When proteins misfold, they can clump together
("aggregate"). These clumps can often gather in the
brain, where they are believed to cause the symptoms
of Mad Cow or Alzheimer's disease.
Experimental Structure Prediction
• Electron Microscopy:
Structural information for large macromolecules at low resolution
• NMR (Nuclear Magnetic Resonance) Spectroscopy:
A solution of protein is placed in a magnetic field and the effects
of different radio frequencies on the resonance of different atoms
in proteins.
• X-ray crystallography:
The beam of x-rays are passed through a crystal of protein.
Atoms in the protein crystal scatter the x-rays, which produce a
diffraction pattern on a photographic film.
Pros and Cons
• None of them is high throughput technology
• NMR
–
–
–
–
Size of protein limited (about 200 residues)
Protein must be soluble
can provide the structure in near physiological condition
can provide informations about dynamics
• X-ray Crystallography
– Must be able to crystallize protein
– Accurate
X-ray crystallography
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
NMR
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
Why Predict Protein
Structures?
High Resolution Structures
better than 3Å
To eliminate protein
structure determination
To speed up drug
discovery
From a computational point of view:
‘Protein folding problem’
Sequence --------------> Structure
Dill & Chan
Function
A fundamental paradigm of protein science:
The amino acid sequence encodes the structure; the structure determines the
What is a molecular
dynamics simulation?
• Simulation that shows how the atoms in the
system move with time
• Typically on the nanosecond timescale
• Atoms are treated like hard balls, and their
motions are described by Newton’s laws.
Molecular Dynamics Theory
MD as a tool for minimization
Energy
Molecular dynamics
uses thermal energy
to explore the energy
surface
State A
State B
Energy minimization
stops at local minima
Folding Energy Landscape
The Folding @ Home initiative
(Vijay Pande, Stanford University)
http://folding.stanford.edu/
The Folding @ Home initiative