These are my notes from week 14 of MIT course 7.88j: Protein Folding and Human Disease, held by Dr. Jonathan King on May 14, 2015.

This was the final week of student presentations. Dr. King opened with a lecture on amyloids and prions. Colin Buss presented on Alzheimer disease. Guest lecturer Dr. Liliana Quintanar spoke about the role of metals in amyloid formation.

Amyloids and prions

When amyloid fibers in Alzheimer brains were characterized, it was assumed that the amyloid structure was unique to that disease. Over time, it became clear that more and more proteins were found in an amyloid state in disease. And then even later, it became clear that many proteins which are not known to form amyloid in vivo can do so under experimental conditions. All of these amyloids have similar cross-beta patterns on X-ray diffraction, suggesting some shared structural element in spite of a lack of any sequence homology. This has led to the idea that amyloid is not a modern anomaly, but may actually be a “common, ancetral” fold.


  • Transthyretin (TTR), in humans, binds retinol-binding protein (RBP), which binds retinol. TTR is thus in effect a carrier for retinol. TTR tetramers have to dissociate into partially folded monomers before forming amyloid, thus making TTR arguably the amyloidogenic protein with the best-characterized intermediate.
  • When Gajdusek first transmitted kuru to chimpanzees [Gibbs 1968], people on Dr. King’s campus circulated petitions to stop the research because they were worried that these experiments would select for particularly virulent kuru strains capable of spreading across primates.
  • The first iatrogenic transmission of CJD was reported in 1974 [Duffy 1974]. The more famous story is the one where electrodes used in a (then-undiagnosed) CJD patient in Zurich were treated with benzene, ethanol, and formadelhyde, yet still managed to accidentally transmit CJD to two patients with epilepsy in whom they were subsequently used. This incident was reported shortly after it occurred [Bernoulli 1977]. The same electrodes then transmitted CJD to a chimpanzee by 1979, and the researchers must have presented this at conferences as it seems to have become widely known at that time. But they waited another 16 years to see if another chimpanzee exposed to the gold wires used on the patient’s scalp would get sick. It never did, and the animal transmission experiments were finally written up in 1994 [Gibbs 1994].
  • Possibly the first functional amyloid discovered in humans is Pmel17, which generates melanin [Fowler 2006]. Another is CPEB, which was the topic of Eric Kandel’s keynote at Prion2014 Day 1.

Colin Buss: Alzheimer disease

A nice historical overview of AD can be found in [Holtzman 2011]. A useful review of AD neuropathology and what we know about the molecular basis of the disease is [Querfurth & LaFerla 2010].

APP has three alteratively spliced isoforms: APP695, APP751, and APP770 [Selkoe 2001]. APP695 was the first one to be cloned [Kang 1987].

Constitutive processing of APP yields three pieces: a soluble extracellular peptide of >100kDa called sAPP, a mebrane-associated ~11 kDa portion which includes Aβ, and the amyloid intracellular domain (AICD) [LaFerla 2002]. Alpha cleavage of APP was the first type of cleaveage to be discovered chronologically, and because alpha secretase cuts Aβ in half, people at first thought that Aβ must represent some off-pathway, non-physiological product [Esch 1990]. This view was challenged a few years later when beta cleavage was characterized [Haass 1992, Seubert 1993].

Alpha, beta, and gamma secretase activities were all characterized before the secretases themselves were discovered. The identification of gamma secretase was particularly challenging, as it eventually proved to be a complex with at least four limiting components [Kimberly 2003].

Some of the evidence for Aβ42, as opposed to Aβ40, being pathogenic comes from mouse models [McGowan 2005].

A review of some structural and functional studies of ApoE E4 is [Zhong & Weisgraber 2009].

Alzheimer disease is on the rise and new treatments are urgently needed†. A review of therapeutic strategies is [Citron 2010].

†A good citation on Alzheimer disease prevalence and economic costs is [Hurd 2013].

Liliana Quintanar: Copper-modulated amyloid aggregation

Several neurodegenerative diseases, including Alzheimer disease, Parkinson disease, and prion disease, are associated with elevated concentrations of metal ions [see e.g. Bush 2003]. Metal-protein interactions can be studied using several different methods including EPR, NMR, UV spectroscopy, and circular dichroism. NMR signal broadening by amino acid provides information on where the metal ion binds to the protein. One can also perform aggregation assays in the presence of metals. For instance, several metals, but especially Cu2+, accelerate the in vitro aggregation of alpha synuclein [Rasia 2005]. Two copper-binding sites in alpha synuclein have been identified [Binolfi 2010, reviewed in Binolfi 2012].

Aβ binds copper and zinc, particularly at D1, H6, H13, and H14. Aβ1-16 has been used as a model fragment for studying metal binding. See e.g. [Hureau 2012, Hureau & Dorlet 2012]. There are conflicting reports as to whether copper inhibits or promotes Aβ amyloid formation. Some of this may have to do with how you study it. In some paradigms you can see copper quench ThT fluorescence, yet amyloids are still visible on electron microscopy. There have been efforts to combine amyloid-binding small molecules with copper chelators to get bifunctional small molecules as potential anti-amyloid agents [Marquez 2014].