Brigita Urbanc, Luis Cruz, Shouyong Peng, Jose Borreguero, Alfonso Lam Aggregation phenomena relevant to Alzheimer’s Disease: Statistical physics approach Sijung Yun Collaborators: Brigita Urbanc, Luis Cruz, Shouyong Peng, Jose Borreguero, Alfonso Lam Advisor: H.E. Stanley

Outline Alzheimer’s disease & Aβ- protein Simulation of Aβ-proteins folding and aggregation My research topic is computer simulation of protein folding and its aggregation. The protein that I chose to study is related to Alzheimer’s disease. So in the beginning, I am going to talk about the Alzheimer’s disease. And the relationship between Alzheimer’s disease and Amyloid beta protein. Mainly, there are two kind of amyloid beta protein, which is Ab40 & Ab42. For Ab42, 42 means that there are 42 amino acids. If you take out the last two amino acids from Ab42 protein, then it becomes Ab40. But they have very different characteristics. One of the differences is aggregation. Prepare two test tubes. Put many Ab40 protein in one test tube, and put many Ab42 in the other test tube. And wait for a few days. Then you will see that Ab42 proteins get together, and form a fibril( which you can think as a fiber). But Ab40 proteins almost remain individually without aggregation. Why is this aggregation property important to

Alzheimer’s disease is related to Amyloid β-proteins(Aβ) Over 50% for the people over 85 years old Increasing forgetfulness, etc. Clinically, a dementia characterized by fibril made of amyloid β-proteins(Aβ) and tangles made of τ-protein in brain Amyloid β-proteins(Aβ) come in two forms: Aβ40: 1DAEFR 6HDSGY 11EVHHQ 16KLVFF 21AEDVG 26SNKGA 31IIGLM 36VGGVV Aβ42: 1DAEFR 6HDSGY 11EVHHQ 16KLVFF 21AEDVG 26SNKGA 31IIGLM 36VGGVV 41I42A Oligomers of Aβ-40 and Aβ-42 are neurotoxic Oligomers of Aβ-42 are more neurotoxic than that of Aβ-40 Pictures of plaque and tangles.

What did we do? Why? We used “Discrete Molecular Dynamics” for the study of oligomerization of Aβ-40 and Aβ-42 in atomic detail Why? Experiment cannot show how Aβ-40 protein and Aβ-42 protein oligomerize in atomic detail Conventional molecular dynamics cannot study oligomerization (too much CPU time)

Discrete Molecular Dynamics(DMD) Conventional Molecular Dynamics Discrete Molecular Dynamics

DMD with hydrophobic interaction Hydrophobicity is the driving force of the protein folding and aggregation Hydrophobicity appears as “the effective attraction” between hydrophobic particles Hydrophilicity appears as “the effective repulsion” between hydrophilic particles Hydrophobic attraction Distance(Å) P.E. 3.07Å 7.5 Å Hydrophilic repulsion Distance(Å) P.E. 3.07Å 7.5 Å

Finally, Statistical analysis Running DMD Simulation Motivation to study 8 sets(or trajectories) not one set. Prepare 8 sets of 32 proteins for each Aβ40 and Aβ42 Get 8 trajectories for each Aβ40 and Aβ42 Finally, Statistical analysis

Simulation results (1) Oligomer Size distribution Explain about concentration Ref) Bital et al. (2003) Proc. Natl. Acad. Sci. USA 100(1) 330-5

How to read a contact map (35,18) (39,36) 1DAEFR 6HDSGY 11EVHHQ 16KLVFF 21AEDVG 26SNKGA 31I I GLM 36VGGVV 41I 42A

Simulation results(2) How “monomers” fold as time goes on 1DAEFR 6HDSGY 11EVHHQ 16KLVFF 21AEDVG 26SNKGA 31I I GLM 36VGGVV 41I 42A Monomers fold from “C terminal region”(Around 40 or 42) to “N terminal region”(around 1)

Simulation results (3) “Pentamers” of Aβ-40 and Aβ-42 Explain about concentration “N terminal”(Around 1) of Aβ42 is more stretched than that of Aβ40 Ref) Urbanc B, Cruz L,Yun S, Buldyrev SV, Bitan G, Teplow DB, Stanley HE, (2004) Proc. Natl. Acad. Sci. USA 101 17345-17350

Ongoing work: Adding Coulombic interaction Some amino acids are charged. Negatively charged amino acids: D-, E- Positively charged amino acids: R+, K+ 1D-AE-FR+ 6HD-SGY 11E-VHHQ 16K+LVFF 21AE-D-VG 26SNK+GA 31I I GLM 36VGGVV 41I 42A

Analysis ongoing: When electrostatic interaction is added Sharper  better defined structure

Conclusions “Monomers” fold from C terminal to N terminal N terminals of Aβ-42 oligomers are more stretched out than those of Aβ-40 oligomers Simulation shows there is a significant difference between aggregation of Aβ-40 and Aβ-42 Simulation gives insights why Aβ-40 and Aβ-42 aggregate differently; Reason; The hydrophobicity of 41th and 42th amino acids causes the structural difference in folding

Primary structure of Aβ(1-42) 1D-AE-FR+ 6HD-SGY 11E-VHHQ 16K+LVFF 21AE-D-VG 26SNK+GA 31I I GLM 36VGGVV {41I 42A} (Hydrophobic) I:Ile V:Val L:Leu F:Phe C:Cys M:Met A: Ala (Neutral in hydrophobicity) S:Ser T:Thr W:Trp P:Pro Y:Tyr G:Gly (Hydrophilic) R+:Arg K+:Lys D-:Asp E-:Glu N:Asn Q:Gln H:His

Simulation additional results Prediction of secondary structure of monomers (no electrostatic interaction) Initial 103 Steps 104 Steps 105 Steps Black: Aβ40 Red: Aβ42