1. Protein misfolding diseases (Alzheimer’s) Zeinab Mokhtari Introduction Alzheimer’s disease Monday, July-5-2010 Protein misfolding diseases Preventing amyloid aggregate formation References In the name of God

2. Protein folding Protein folding refers to the process by which a protein assumes its characteristic structure, known as the native state. The most fundamental question of how an aminoacid sequence specifies both a native structure and the pathway to attain that state has defined the protein folding field. 2

3. the first phase Understanding the mechanisms of protein folding and uncovering the fundamental principles that govern the folding transition the second phase What are the mechanisms of protein folding in a context, such as under the influence of other biological molecules in the cellular environment? Fig. 1. Growth of the Protein Folding Field. The average number of publications per year in protein folding field and the average number of publications per year that are dedicated to application Protein folding two predominant phases 3

4. Studying protein folding Anfinsen showing that proteins can fold spontaneously in vitro studies a milliseconds-to-seconds time scale Anfinsen showing that proteins can fold spontaneously in vitro studies a milliseconds-to-seconds time scale Levinthal o a random conformation search does not occur in folding o proteins fold by specific ‘folding pathways’ o well-defined partially-structured intermediate states Levinthal o a random conformation search does not occur in folding o proteins fold by specific ‘folding pathways’ o well-defined partially-structured intermediate states A small number of residues (folding nucleus) need to form their native contacts in order for the folding reaction to proceed fast into the native state. nucleation theory Protein folding 4

5. Protein engineering, nuclear magnetic resonance (NMR), mass spectrometry, hydrogen exchange, fluorescence resonance energy transfer (FRET), and atomic force microscopy (AFM) Computational methods  The Fold-Rate server (http://psfs.cbrc.jp/fold-rate/)http://psfs.cbrc.jp/fold-rate/  The Parasol folding server (http://parasol.tamu.edu/groups/amatogroup/foldingserver)http://parasol.tamu.edu/groups/amatogroup/foldingserver … The close interplay of computational and experimental efforts has advanced our knowledge of protein folding kinetics, including predicting the protein folding rate, identifying the kinetically-important residues, and characterizing the multiple pathways. Experimental methods Protein folding Studying protein folding 5

6. I.protein folding in vivo is usually assisted by molecular machinery, such as chaperones (in an ATP-dependent manner), and often involves small molecule cofactors. II.the concentrations of macromolecular solutes in cells can reach hundreds of grams per liter, but most in vitro studies are performed in buffered solution with <1% of the cellular macromolecule concentration. Two major differences between protein folding in vivo and in vitro : Protein folding 6

7. The thermodynamic stability of a protein is measured by the free-energy difference between the folded state and the unfolded state: ∆G = G unfold -G fold Experimentally, ∆G values can be obtained from denaturing experiments where the protein unfolds by increasing temperature or by adding denaturing agents such as urea and guanidinium HCl (GdHCl). Native State, one conformation Unfolded, many conformations Protein folding 7

8. While all the information needed for proteins to fold is encoded in their amino-acid sequence, there are many more elements that play a part in vivo. In a crowded cellular environment, surrounded by interacting proteins, nascent polypeptides face a formidable challenge in finding the correct interactions that result in a folded and functional protein. Protein folding 8

9. Molecular chaperones, recognize misfolded proteins and provide an environment conducive to the formation of the appropriate native contacts. Protein folding 9

10. Protein misfolding diseases (Alzheimer’s) Introduction Alzheimer’s disease Protein misfolding diseases Preventing amyloid aggregate formation References

11. Many diseases are now associated with protein aggregation and particularly with a form of ordered aggregate called the amyloid fibrils. Protein misfolding 11

12. Protein folding diseases:  excessive quantities of wrongly folded proteins collect in the form of uncontrolled piles of molecular rubbish (amyloidoses).  a small error in the genetic blueprint leads to incomplete folding of a protein, which affects its function. (P53 : the malfunctioning of central tumour suppressor could cause cancer. ) 12

13. Disease Pick’s Alzheimer’s Parkinson’s Prion disease (e.g. Mad Cow) Amyloid Lateral Sclerosis ( Lou Gehrig’s) Huntington’s Disease Protein tau APP alpha synuclein prion protein TDP-43 Huntingtin Protein misfolding diseases Protein misfolding amyloidoses 13

14. Protein misfolding diseases (Alzheimer’s) Zeinab Mokhtari Introduction Alzheimer’s disease Monday, July-5-2010 Protein misfolding diseases Preventing amyloid aggregate formation References

15. Alois Alzheimer and family,1910 Auguste D Alzheimer 15

16. Alzheimer 16

17.  Alzheimer’s is a progressive disease.  Age is the biggest risk factor.  We don’t know what causes it.  We can temporarily slow it’s progression.  We can’t cure it.  Caregivers and support groups are very important.  There is always hope for the future. Alzheimer Normal AD No one knows what causes AD to begin, but we do know a lot about what happens in the brain once AD takes hold. 17

18. 1. Recent memory loss affecting job 2. Difficulty performing familiar tasks 3. Problems with language 4. Disorientation to time or place 5. Poor or decreased judgment 6. Problems with abstract thinking 7. Misplacing things 8. Changes in mood or behavior 9. Changes in personality 10. Loss of initiative Alzheimer’s disease is an irreversible, progressive brain disease that slowly destroys memory and thinking skills. Alzheimer 18

19. Protein misfolding diseases (Alzheimer’s) Zeinab Mokhtari Introduction Alzheimer’s disease Monday, July-5-2010 Protein misfolding diseases Preventing amyloid aggregate formation References

20. The aggregation of β-amyloid (Aβ) peptide → Alzheimer’s disease (AD) Aβ-42 peptide is the key target in the finding of inhibitors of AD-related amyloid formation. low molecular weight drugs Aβ-42 monomer–monomer interactions preventing amyloid aggregate formation High temperature, low pH, and salt conditions Alzheimer 20

21. the effect of α-D-mannosylglycerate (MG) and its structural analogs on the inhibition of Alzheimer’s Aβ aggregate formation and neurotoxicity Thermal stress Freezing Thawing Drying MG MG strongly inhibits amyloid formation of Aβ-42 and its neurotoxicity in vitro. Alzheimer 21

22. ThT-induced fluorescence assay and AFM image analysis no inhibition effect inhibition effect Alzheimer 22 amyloid aggregates → new emission maximum

23. AFM images of Aβ42 (25 mM) samples incubated with control, α-D-mannosylglycerate, α-D- mannosylglyceramide, mannose, glycerol and methylmannoside at 100 mM concentration. Alzheimer 23 inhibition effect

24. carboxyl group Alzheimer 24

25. Sequence (Three-Letter Code) H - Asp - Ala - Glu - Phe - Arg - His - Asp - Ser - Gly - Tyr - Glu - Val - His - His - Gln - Lys - Leu - Val - Phe - Phe - Ala - Glu - Asp - Val - Gly - Ser - Asn - Lys - Gly - Ala - Ile - Ile - Gly - Leu - Met - Val - Gly - Gly - Val - Val - Ile - Ala - Thr - Val - Ile - Val - Ile - OH DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIATVIVI Sequence (One-Letter Code) covering the ‘‘hot spots’’ responsible for Ab fibrillation penta peptides such as KLVFF  electrostatic interactions between residues  hydrophobic interactions between highly apolar residues Alzheimer 25

26. 26 Some References peptides 29 (2008) 578 –584 Nanomedicine: Nanotechnology, Biology, and Medicine 1 (2005) 300– 305 Archives of Biochemistry and Biophysics 469 (2008) 4–19 Journal of Molecular Biology (2006) 362, 347–354 Biochimica et Biophysica Acta 1764 (2006) 443–451

27. Everything is okay in the end. If it's not okay, then it's not the end. 27