1. The Structure and Folding Behavior
of the Kinesin Motor Protein
of the Kinesin Motor Protein
Sally Q. Fisher and Carol A. Parish
Department of Chemistry
University of Richmond
Richmond, VA 23173
BECKMAN SYMPOSIUM AUGUST 13, 2011

2. BECKMAN SYMPOSIUM AUGUST 13, 2011
Microtubule
+ end- end
Anterograde
Cargo ❖ Motor protein
❖ Walks along microtubules in
hand-over-hand fashion
❖ Transports anterograde
cargoes
❖ Implications for diseases
such as Alzheimer’s,
Huntington’s and cancer
Kinesin-1

3. BECKMAN SYMPOSIUM AUGUST 13, 2011
Motor Head
Connecting Stalk
Cargo-Binding
Tail

4. BECKMAN SYMPOSIUM AUGUST 13, 2011

5. BECKMAN SYMPOSIUM AUGUST 13, 2011
Tetratricopeptide Repeat Proteins:
TPRs
❖ 34 amino acid unit
❖ Helix-loop-helix motif
❖ Found in binding proteins
❖ Three or more in tandem
form a superhelix with a
binding groove

6. BECKMAN SYMPOSIUM AUGUST 13, 2011
Molecular Dynamics

7. BECKMAN SYMPOSIUM AUGUST 13, 2011
Molecular Dynamics

8. Methods
• Desmond (D.E. Shaw Research)
• All atom representation
• Explicit solvent
• Standard force fields

9. TRP 4
LEU 7
GLY 8
TYR 11
ALA 20
PRO 32
ALA 27
TYR 24
CTPR: Designed Consensus
TPR
BECKMAN SYMPOSIUM AUGUST 13, 2011
AEAWYNLGNAYYK QGDY DEAIEYYQKALEL DPRS

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1 2
3
4
5
6
CTPR

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TPR1 TPR2 TPR3 TPR4 TPR5 TPR6
Fraction Helicity
Hydrogen Bond
Count

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Table. Global Backbone Average and Maximum RMSD
Relative to Starting Structure
Average (Å) Maximum
TPR1 3.248 ± 1.008 4.924
TPR2 0.831 ± 0.368 3.391
TPR3 0.925 ± 0.245 2.202
TPR4 0.761 ± 0.169 1.973
TPR5 1.627 ± 0.438 2.918
TPR6 0.949 ± 0.335 3.238
TPR1 TPR2 TPR3 TPR4 TPR5 TPR6
Per-Residue RMSDs

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TPR1
LRTLHNLVIQYAS QGRY EVAVPLCKQALED
res 1-13:
69.37 D
res 5-15:
40.75 D
+
-
N
C
❖ N-terminus-
destabilizing dipole

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TPR1
LRTLHNLVIQYAS QGRY EVAVPLCKQALED
res 1-13:
69.37 D
res 5-15:
40.75 D
❖C-terminus-
Hydrogen bonding
LRTLHNLVIQYAS QGRY EVAVPLCKQALED

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TPR1
LRTLHNLVIQYAS QGRY EVAVPLCKQALED
res 1-13:
69.37 D
res 5-15:
40.75 D
❖ Loop-
helix breaker
LRTLHNLVIQYAS QGRY EVAVPLCKQALED

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Exploring the Folding Behavior
❖ Unknown folding landscape
❖ Diffusion-collision model?
❖ Highly stable SS structural elements
❖ Rate determining transition involves docking of
monomers

17. QuickTime™ and a
GIF decompressor
are needed to see this picture.
amber03 + tip3p // 400 ns
simulation

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Exploring the Folding Behavior
❖ Regan- Multistate folding
❖ Simulations from the folded
ensemble
❖ Lattice model for folding
❖ 1-D Ising Model
Residue
Residue

20. QuickTime™ and a
GIF decompressor
are needed to see this picture.
charmm22star + tip3p_charmm // 200 ns
simulation
425 K

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Time
Residue 1
2
3
4
0 100 200

22. BECKMAN SYMPOSIUM AUGUST 13, 2011
Conclusions
❖ Verified by MD that the Kinesin-1
cargo-binding domain (P46824
sequence) is capable of adopting
six stable TPRs
❖ These TPRs, when connected in
tandem, are capable of forming a
super-helix similar to other
binding domains.
❖ The folding behavior is multi-state
and may be well described by
simple lattice models.

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Acknowledgements
❖ Carol Parish
❖ Meredith Weck and Lisa Gentile
❖ Jordan Cox and Joseph Gindhart
❖ Evan Wang and Phillip Geissler
❖ TeraGrid- TACC, NICS,
PSC
❖ D.E. Shaw Research
❖ Merck
❖ NSF
❖ Arnold and Mabel Beckman
Foundation