Simulations of Peptide Aggregation

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Simulations of Peptide Aggregation
Joan-Emma Shea Department of Chemistry and
Biochemistry The University of California, Santa
Barbara
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Protein and Peptide Aggregation
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PROTEIN AGGREGATION AND DISEASE
Parkinson
Alzheimer
Prion (Mad Cow)
Huntington
Proteins not associated with a specific disease
can also aggregate to form amyloid fibrils
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APPLICATION TO BIOMATERIALS
Use of peptides to form nanoscale-ordered
monolayers, COSB 2004, 14 480
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Time scales
Side-chain rotations
Loop closure
Protein aggregation
Protein folding
Folding of ?-hairpins
Helix formation
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MULTISCALE APPROACH
All-atom Molecular Dynamics (MD) With EXPLICIT
Solvent
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1. Dimerization Mechanisms of 4 tetrapeptides KXXE
Fibrils of KFFE
2. Design of Inhibitors of aggregation of the
Alzheimer Amyloid-beta (A?) peptide.
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KXXE peptides
? Tjernberg et al. , JBC 277 (2002) 43243
KAAE
KLLE
KVVE
KFFE
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PEPTIDE MODEL
CHARMM19 Force Field and Generalized Born
Implicit Solvent
R
ep1 kCal/mol, s1Å, R17Å
Confining Sphere
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Simulation protocol Replica Exchange MD6
replicas for monomer total simulation time 40
ns12 replica for dimers total simulation time
400 ns
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Heterogeneous dimers
E (kCal/mol)
RMSD (Å)
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Association temperature Ta
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What determines transition temperature Ta?
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Free energy as a function of interaction energy
and radius of gyration
T285K
Rg (Å)
U (kCal/mol)
U
U
U
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Free energy as a function of interaction energy
and radius of gyration
T285K
Most favorable
Rg (Å)
Interaction energy KFFE gt KLLE KVVE gt KAAE
DU (kCal/mol)
DU
Least favorable
U
U
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Entropy loss due to dimerization
Monomers, Rggt5A
?-strand
?
Random Coil
?
Helix
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Entropy loss due to dimerization
Monomers, Rggt5A
?-strand
?
Random Coil
?
Helix
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Entropy loss due to dimerization
Monomers, Rggt5A
Dimers, Rglt5A
?-strand
?
Random Coil
?
Helix
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Entropy loss due to dimerization
Monomers, Rggt5A
Dimers, Rglt5A
?-strand
?
Random Coil
?
?-strand basin more populated for monomer of KVVE
than KLLE ?SL gt ?SV
Helix
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Association temperature
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Kinetic accessibility of dimers
KFFE
KLLE
KLLE
KFFE
Rg (Å)
E (Kcal/mol)
E (Kcal/mol)
DOWNHILL DIMERIZATION FOR KFFE
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Different mechanisms of dimerization
KFFE
KLLE
Rg over C?
Rg over PHE atoms
Rg over LEU atoms
PHE-PHE come together first (stabilized by vdw
interactions), followed by the overall collapse
of the structure with formation of peptide
backbones contacts .
LEU side chain formation and overall collapse
with formation of peptide backbone interactions
occur simultaneously.
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CONCLUSIONS
1.
for dimerization of the KXXE peptides
2. Strong sequence dependence of free energy
landscapes for dimerization, with KFFE
experiencing a barrierless transition.
3. KFFE dimers are the most thermodynamically
stable and kinetically accessible.
4. Dimer trends match experimental trends
observed for fibrils.
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LARGER SYSTEMS OLIGOMERIZATION OF THE
ALZHEIMER AMYLOID BETA (A?) PEPTIDES
AMYLOID BETA (A?) PEPTIDES AGGREGATE TO FORM
TOXIC OLIGOMERS AND FIBRILS
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FRAGMENT 25-35 OF THE (A?) PEPTIDE APPEARS TO
BE TOXIC IN MONOMERIC, SMALL OLIGOMERIC AND
FIBRILLAR FORMS
Aß40 DAEFRHDSGYEVHHQKLVFFAEDV25GSNKGAIIGL35MVGGVV
NO STRUCTURE OF THE MONOMERIC PEPTIDE AVAILABLE
IN AQUEOUS SOLVENT
PEPTIDE ADOPTS A HELICAL STRUCTURE IN
APOLAR ORGANIC SOLVENT (SUCH AS
HEXAFLUOROISOPROPANOL HFIP)
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EFFECTS OF SOLVENT ON FREE ENERGY LANDSCAPE OF
THE MONOMER

• REPLICA EXCHANGE SIMULATION IN
• HFIP/WATER CO-SOLVENT
• PURE WATER
• GROMOS96 FORCE FIELD, EXPLICIT SOLVENT

• 40 REPLICAS, 16 NS EACH, TOTAL SIMULATION TIME
  OF 640 NS

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FREE ENERGY SURFACE IN HFIP/WATER
COSOLVENT HELIX STABILIZATION
T300 K
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HFIP DISPLACES WATER NEAR THE PEPTIDE, AND FORMS
A COAT AROUND THE PEPTIDE
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FREE ENERGY SURFACE IN PURE WATER FORMATION OF
COLLAPSED-COILS and b-HAIRPINS
T300K
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Possible importance of turn in toxicity of
monomer
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REPLICA EXCHANGE MD ON DIMERS IN
WATERHETEROGENEOUS DIMERS
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TWO TYPES OF ORDERED DIMERS
Experimentally two different protofilament of
diameters 1.41 /- 0.48 nm 3.58 /- 1.53 nm
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PEPTIDE INHIBITORS OF ALZHEIMER A? AGGREGATION
Alzheimers disease (AD) is a neurodegenerative
disease of the central nervous system.
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ALZHEIMER DISEASE IS CHARACTERIZED BY
THE PRESENCE OF NEUROFIBRILLAR TANGLES AND
AMYLOID PLAQUES IN THE BRAIN
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AMYLOID PLAQUES CONSIST OF AMYLOID BETA (A?)
PEPTIDES GENERATED FROM THE PROTEOLYTIC
CLEAVAGE OF THE APP TRANSMEMBRANE PROTEIN
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In healthy individuals, the A? peptides are
broken down and eliminated. In AD, these
peptides self-assemble into amyloid fibrils
Fibril
Amyloid Plaques
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Both small soluble oligomers and fibrils appear
to be toxic to cells.
Misfolded Protein
Fibril
Native Protein
Soluble Oligomer
Protofibrils
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N-METHYLATED PEPTIDE INHIBITORS

• N-methylated A?(16-20)m peptides can
• prevent the aggregation of full length A? peptide
  
• disassemble existing fibrils and possibly small
  oligomers.

16K(me)LV(me)FF
Aß40 DAEFRHDSGYEVHHQ16KLVFFA22EDVGSNKGAIIGLMVGGVV
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MODEL SYSTEM
Fragment A?(16-22) KLVFFAE aggregates to form
fibrils
Aß40 DAEFRHDSGYEVHHQ16KLVFFA22EDVGSNKGAIIGLMVGGVV
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A?(16-22) KLVFFAE PROTOFIBRIL
INITIAL STRUCTURE Two parallel bilayers
Peptides in layer antiparallel lys16 and glu22
point to solvent leu17, phe19, ala21 point
inside core
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A?(16-22) KLVFFAE PROTOFIBRIL
INITIAL STRUCTURE Two parallel bilayers
Peptides in layer antiparallel lys16 and glu22
point to solvent leu17, phe19, ala21 point
inside core
GROMOS96 FORCE FIELD EXPLICIT SPC WATER (23000
atoms) REACTION FIELD/ PME TWO 20 NS
SIMULATIONS
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REPRESENTATIVE A?(16-22) PROTOFIBRIL (LAST 7 NS
OF SIMULATIONS)
Distance between bilayers 0.93 nm (Tycko
0.99nm) Distance between peptides 0.44-0.52 nm
(Tycko 0.47 nm)
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Structure of N-methylated A?(16-20)m Inhibitor
Peptide
Replica Exchange Molecular Dynamics, 30
replicas, 20 ns per replica
A?(16-20)m more rigid than A?(16-22), with
?-strand content This pre-organization may allow
A?(16-20)m to successfully compete with free
A?(16-22) for binding to fibril.
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Interaction of A?(16-20)m Inhibitor Peptide with
protofibril
INITIAL STRUCTURE
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Interaction of A?(16-20)m Inhibitor Peptide with
protofibril
AFTER 50 ns
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POSSIBLE MECHANISM OF FIBRIL DISRUPTION
Inhibitor drifts from edge of fibril to side and
inserts in fibril (between strands 6 and 7) with
Lys pointing to solvent and hydrophobic residues
inserted in fibril.
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POSSIBLE MECHANISM OF INHIBITION OF FIBRIL GROWTH
Inhibitor forms hydrogen bond with fibril, with
antiparallel alignment, possibly preventing
additional A?(16-22) peptides from binding.
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DESTABILIZATION OF FIBRIL WHEN INHIBITOR
INSERTED IN FIBRIL
Inhibitor inserted in fibril affects the twist
of the fibril and the distance between strands.
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CONCLUSIONS AND FUTURE DIRECTIONS

• Results suggest possible mechanisms of fibril
• inhibition and disassembly
• Extend the simulations to consider other
  orientations
• of the inhibitor peptides
• Study and design new inhibitors

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ACKNOWLEDGEMENTS
Dr. P. Soto
Dr. G. Wei
Dr. A. Baumketner
Collaborator Prof. Stephen Meredith, University
of Chicago
Other group members M. Friedel, M. Griffin, A.
Jewett, W. B. Lee and E. Zhuang
Funding NSF Career, David and Lucile Packard
Foundation, A. P. Sloan Foundation, Army
Research Office.
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University of California Santa Barbara