IAPP, pt 2.

Secondary structure, intrinsic disorders, proIAPP:

Amyloidogenic Propensity of ProIAPP and IAPP in the Presence of Negatively Charged Lipid Bilayers
Suman Jha
Biophysical Journal, Volume 96, Issue 3, Supplement 1, February 2009, Page 93a
(only abstract is free available)


Our CD studies show that the secondary structure content of ProIAPP and IAPP is predominantly unordered with small amounts of ordered secondary structure elements as confirmed by ATR-FTIR spectroscopy. However, in the presence of anionic membranes, ProIAPP forms predominantly α-helices and loops that subsequently transform to intermolecular β-sheet structures. For comparison, IAPP forms intermolecular β-sheets largely via unordered and loop structures.

The ATR-FTIR and fluorescence spectroscopy studies performed also reveal that ProIAPP has a higher amyloidogenic propensity in the presence of negatively charged membranes, but is still less amyloidogenic than IAPP.

Amylin aka IAPP

On mechanism:
Intracellular amyloid-like deposits contain unprocessed pro-islet amyloid polypeptide (proIAPP) in beta cells of transgenic mice overexpressing the gene for human IAPP and transplanted human islets.

J. F. Paulsson . A. Andersson . P. Westermark .G. T. Westermark
Diabetologia (2006) 49: 1237–1246
http://www.springerlink.com/content/w824704516157312/fulltext.pdf

Fig. 8 Proposed sequence of events leading to islet amyloidosis.

a First, the processing of proIAPP is affected by factors such as high levels of NEFAs or glucose. Granules with amyloid-like fibres fuse and form an intracellular proIAPP amyloid-like deposit.

b Over time this aggregate enlarges and replaces most of the cell.

c This cell dies and the amyloid becomes extracellular and can act as a template for further amyloid formation.

d Amyloid is now made up by IAPP secreted from neighbouring beta cells. Formation of extracellular amyloid fibrils is preceded by the formation of toxic intermediates, which can interact with the cell membrane of surrounding cells and cause ionic influx, triggering the apoptosis cascade.

Formation of any amyloid fibril is a nucleationdependent process, and preformed fibrils may catalyse the conversion of a soluble protein to its fibrillar form. Human IAPP is a highly amyloidogenic peptide, and the release of insoluble intracellular aggregates into the extracellular space (e.g. by cell death) may stimulate the conversion of secreted IAPP. Consequently, elucidation of the initial step in amyloidogenesis, which may be an intracellular event, is particularly important.

Steered MD again

guys compared different pulling rates

Steered MD in GROMACS (pull code)

The pull code allows to apply a force between two centers of mass (for >1 groups). It appears to be useful to simulate protein penetration into lipid membrane (channel formation). Config must have a following lines:
pull_start = yes
pull_init1 = 0
pull = umbrella
pull_geometry = direction
pull_group0 = Protein
pull_group1 = POPC
pull_vec1 = 0 0 0.5
pull_k1 = 3000
pull_rate1 = 0.01 ; nm/ps Extreme parameters for extreme pulling

discussions: [1], [2]

b-Amyloid Ion Channels

Models of b-Amyloid Ion Channels in the Membrane Suggest That Channel Formation in the Bilayer Is a Dynamic Process: amyloid ion channel formation mechanism suggested (src)

Amyloid ion channels: oligomerization

results indicate that in lipid bilayers, a significantly higher percentage of these amyloids are oligomers (trimers and larger), while a small percentage of monomers and dimers are also present. On the contrary, soluble amyloid peptides are primarily monomers or dimers with a small percentage of higher-order oligomeric complexes. In the lipidic environment, thus, amyloid peptides undergo conformational changes favoring larger oligomeric complexes, although some large oligomeric complexes of soluble peptides can still retain their structure when inserted in a lipidic membrane (5, 23). A presence of large oligomeric complexes in membrane suggests that they could form supramolecular structures.


trimers are observed for amylin and Ab(1– 40), and tetramers are observed for ABri, amylin, Ab(1– 40), and a-synuclein

Also observed are pentamers for amylin and Ab(1– 40); hexamers for a-synuclein, SAA, ADan, amylin, and Ab(1– 40); and heptamers and octamers for a-synuclein and SAA.


Significantly, unlike earlier reports indicating amyloids’ tendency to form large fibrillar aggregates in solution, we confirmed that these peptides retained their globular structure over a period of several hours with no significant change in the size distributions and without significant aggregation, even at physiologically high concentrations.

multimeric peptide complexes have disk-like shapes with an outer diameter of 8–12 nm and often contain a central pore-like concavity with a diameter of 1–2 nm

Pentamers were mainly observed for amylin.

(src)

NOMAD: a Normal Mode Analysis Server.