Download Lattice Models of Protein Folding

Thermodynamic and Kinetic
Origins of Alzheimer's and Related
Diseases: a Chemical Engineer's
Perspective
Carol K. Hall
Department of Chemical & Biomolecular Engineering
North Carolina State University
http://turbo.che.ncsu.edu
Protein Folding: The ABCs
A. A protein is a chain of amino acid
residues arranged in a unique
sequence.
B. There are 20 possible sidechains.
C. Physiological proteins exist in the
folded or “native” state, the state
with the lowest free energy.
Villin headpiece protein
D. Proteins unfold into a “random coil” if
temperature raised or denaturant (urea,
GuHCl) added.
Unfolded
(high T or high denaturant)
E.
Folded
(moderate T or low denaturant)
Of all the forces thought to govern
protein folding, hydrophobicity and
hydrogen bonding are considered most
important.
•www.sas.upenn.edu
Amyloidoses: Diseases characterized
by the abnormal aggregation of proteins
into ordered structures, called “fibrils” or
“amyloid.”
Disease
Protein
Pick’s
tau
Alzheimer’s
A-beta
Parkinson’s
alpha synuclein
Prion disease (e.g. Mad Cow)
prion protein
Amyloid Lateral Sclerosis
TDP-43
( Lou Gehrig’s)
Huntington’s Disease
Huntingtin
Alzheimer’s Disease
• 100 years ago --Dr. Alois Alzheimer described
abnormal clumps in brain of deceased
dementia patient, Auguste D.
• Clinical symptoms: severe dementia, loss of
memory & motor skills----> death
• Late onset disease : 5-10% of 65-74 year olds,
50% of 85+ year olds
• 4.5 million Americans
• Costs $100 billion/year
• US Research Budget $650 million/year.
Structure of Amyloid Fibrils
AFM on fibrils of
A-ß protein
Fibrils are ordered
aggregates of peptides
characterized by crossbeta structure
-sheets in a
protofilament
Protofilament
structure
Issues in Amyloid
Disease Research
– Identity of toxic species--- early
oligomers or fibrils?
– Kinetics of fibril nucleation and growth
– Structure of fibrils
– Interactions with inhibitors
Objective
To develop a computational
tool that :
allows investigation
(particularly
visualization) of
spontaneous fibril
formation.
reveals the basic physical
principles underlying fibril
formation
.
•Six Blind Men and Elephant
Polyalanine– A Model System for
Studying Protein Fibrillization
•
Speculation - fibril formation is natural consequence of peptide
geometry, hydrogen-bonding capability and hydrophobic
interactions under slightly-denatured, concentrated conditions.
•
Polyalanine peptides form fibrils in vitro at high concentrations (C
> 1.5 mM) and high temperature (T > 40oC) (Blondelle et al.,
Biochem. 1997).
•
Peptide Sequence: KA14K
alpha-helix
beta-sheets in a fibril
Molecular Dynamics Simulations of
Protein Folding
Packages: Amber, CHARMm, ENCAD, ECEPP,
Discover, UNRES, etc.
Force fields: describe interactions between all
atoms on protein and in solvent at atomic
resolution
Desired Output:
“folding” trajectory of a protein
Limitation: very difficult to simulate folding of a
single protein even with the fastest computers
Implications : sacrifice details to study protein
aggregation
Discontinuous Molecular Dynamics
Traditional MD:
• Forces based on Lennard
Jones (LJ) potential.
• Follow particle trajectories
by numerically integrating
Newton’s 2nd law every
picosecond.
Discontinuous MD:
• Forces field based on squarewell potential.
• Follow particle trajectories
by analytically integrating
Newton’s 2nd law
• Particles move linearly
between collisons, capture or
bounce
PRIME (Protein Intermediate Resolution Model):
• United atom: NH, CaH, CO, R
R= CH3 for alanine
CH3
• Steric Interactions:
hard spheres with realistic
diameters
NH
• Pseudo-bonds maintain:
ideal backbone bond angles
trans-configuration
residue L-isomerization
CaH
CO
CH3,i
COi+1
COi
CHi
• Covalent bond and pseudo-bond
lengths set to ideal experimental
values
NHi
CHi+1
NHi+1
CH3,i+1
Smith and Hall. PROTEINS (2001) 44 344
Nguyen et al. Protein Sci (2004) 13 2909-2924
Model Forces: Hydrogen Bonding
Hydrogen bonds between backbone amine and carbonyl groups
are modeled with a directional square-well attraction of strength
eH-bonding.
COi
CHi
CH3,i
NHi
COj
CHj
NHj
Square-well attraction
Define reduced temperature as:
T*=kBT/ε H-bonding
Model Forces: Hydrophobic Interactions
• Solvent effects captured implicitly .
• Hydrophobic side chains cluster together to avoid water
• Hydrophobic interaction modeled as square-well attraction
between side chains.
• R= εhydrophobicity/εH-bonding
Folding of Single KA14K Chain
Nguyen,Marchut & Hall
Biophys. J (2004)
A Constant-Temperature Simulation:
48 Peptides at c=10.0mM, T*=0.14
Nguyen &
Hall, PNAS
(2005)
Equilibrium Simulations: 96 Peptides
• Use the replicaexchange method to
simulate 96-peptide
systems at different
temperatures and
peptide
concentrations.
• These trends
qualitatively agree
with experimental
data (Blondelle
1997)
Nguyen & Hall Biophys. J. (2004)
Fibril Structure: Intra-sheet Distance
• Intra-sheet distance: 4.92 ± 0.01A, comparable to
experimental values of 4.76A (Shinchuk et al.,
Proteins, 2005)
Fibril Structure: Inter-sheet Distance
• Inter-sheet distance: 7.52 ± 0.23A, comparable
to experimental values of 5.4A (Shinchuck et al.,
Proteins, 2005)
Fibril Structure: Peptide Orientation
Most peptides are in-register, same as
experimental results for the A-ß (10-35) peptide
(Benzinger et al., PNAS 1998)
Forming Various Structures versus t*
c=5mM, T*=0.14
 Amorphous aggregates
form instantaneously,
followed by ß-sheets,
and then fibrils after a
delay, called the lag
time.
all aggregates
 Appearance of a lag
time indicates that this
is a nucleated
phenomenon.
Nguyen & Hall, J. Biol. Chem (2005)
Fibril Formation in Seeded and
Unseeded Systems
at T*=0.14, c=2mM
• Adding a seed eliminates the fibril formation lag
time, as found experimentally.
In Conclusion---Technical
 First intermediate resolution simulations of
spontaneous “fibril” formation
 Our results qualitatively agree with
experimental data in general, and specifically
with those obtained by Blondelle et al.
(Biochemistry, 1997) on polyalanines.
 Next step: Extending PRIME to all 20 amino
acids. Which road to take?????
Acknowledgements
•
•
•
•
•
Dr.
Dr.
Dr.
Dr.
Dr.
Hung D. Nguyen
Alexander J. Marchut
Anne V. Smith
Hyunbum Jang
Andrew J. Schultz
• National Institutes of Health
• National Science Foundation