Supporting Information for;
Human Islet Amyloid Polypeptide N-Terminus Fragment Self-Assembly: Effect of Conserved
Disulfide Bond on Aggregation Propensity
Author Affiliation;
Alexandre I. Ilitchev†, Maxwell Giammona†, Thanh D. Do†, Amy G. Wong‡, Steven K. Buratto†, JoanEmma Shea†, Daniel P. Raleigh‡§, Michael T. Bowers†*
† Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
‡ Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA
§ Research Department of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT,
United Kingdom
* Address reprint requests to Michael T. Bowers, Department of Chemistry and Biochemistry, University of California, Santa
Barbara, California 93106, USA. E-mail: bowers@chem.ucsb.edu. Phone: 805-893-2893. Fax: 805-893-8703.
S1
Arrival Time Distribution Fitting
Arrival time distributions for species with a specific collision cross-section were calculated from the ion
flux at the drift cell exit. All ions in the peak are presumed to be the result of periodic delta-function
packets, with no additional ions produced or lost due to reaction in the drift cell.1 The resulting ion flux
is modeled as follows;
(𝑧 − 𝑣𝑑 )2
𝑠𝑎
𝑧
𝑟02
Φ(0, 𝑧, 𝑡) =
(𝑣 + ) × [1 − exp (−
)] exp [−
]
4𝐷𝑇 𝑡
4𝐷𝐿 𝑡
4(𝜋𝐷𝐿 𝑡)1⁄2 𝑑 𝑡
Where z is the drift distance, t is drift time, s is the source packet density, a is the exit aperture area, r0 is
the radius of the initial ion packet, DL and DT are the longitudinal and transverse diffusion coefficients,
and vd is the drift velocity.
REMD Simulation Temperature Lists
Temperature lists (in Kelvin) are presented below;
Dimer: 275.00, 279.60, 284.25, 288.96, 293.72, 298.54, 303.43, 308.38, 313.39, 318.46, 323.60,
328.79, 334.06, 339.39, 344.79, 350.25, 355.80, 361.40, 367.06, 372.80, 378.61, 384.50, 390.47, 396.50.
Tetramer: 279.50, 282.68, 285.89, 289.13, 292.39, 295.68, 299.00, 302.34, 305.66, 309.06, 312.49,
315.96, 319.45, 322.97, 326.52, 330.10, 333.71, 337.35, 341.03, 344.73, 348.47, 352.23, 356.03, 359.87,
363.73, 367.64, 371.57, 375.53, 380.53, 384.58, 388.65, 392.76.
S2
Supporting Figure 1
Fig. S1 Injection energy (IE) studies of IAPP fragment z/n = +1/2 oligomer peaks. All samples are at
50μM and 7.4 pH. WT1-8ox is indicated in blue, WT1-8red is indicated in green, and C2S/C7S1-8 is indicated
in orange. All peaks are annotated by z/n, where z is the charge and n the oligomer number. The crosssections for all peaks are also noted. Lower injection energies favor higher order oligomers whereas
higher injection energies break down higher order oligomers and shift the distribution to smaller order
oligomers. The lowest injection energy, 20V, represents an approximation of the in-solution oligomer
distribution. WT1-8ox is primarily dimer, WT1-8red essentially contains no dimer, and C2S/C7S1-8 consists
of only a small amount of dimer in solution. Each peak is fit using the procedure described above.
S3
Supporting Figure 2
Fig. S2 AFM image of the WT1-8ox fragment incubated for 24 hours at 50μM and 7.4 pH (A) along with
a cross-section height profile (B). Fibril structures exhibit a “fraying rope” morphology, with a thick
core ~3nm in height, fraying at the edges terminating in smaller fibrils ~0.4nm in height. This is
indicative of a self-aggregation mechanism in which smaller fibrils bundle together to form larger ones.
S4
Supporting Figure 3
Fig. S3 Histogram of average height values (B) generated from particle analysis of globular aggregates
of WT1-8ox incubated for 5 minutes at 50μM and 7.4 pH (A). The AFM image is repeated with the masked
particles used for the analysis indicated in blue.
S5
Supporting Figure 4
Fig. S4 Mass spectra of oxidized wildtype 1-8 hIAPP fragment (A - blue) and reduced 1-8 hIAPP
fragment (B - green). (M) indicates monomeric m/z, (M – H + K) corresponds to monomeric m/z with a
potassium ion substitution in place of a hydrogen. Mass spectra clearly show complete reduction of the
oxidized species, with no visible unreduced species in (B). Data was obtained on home-built time-offlight mass spectrometer.
S6
Supporting Figure 5
Fig. S5 Convergence test for all simulated oligomers, with WT1-8ox indicated in blue, WT1-8red indicated
in green, and C2S/C7S1-8 indicated in orange. The final 150 ns of each trajectory was split in half and
the potential mean force (PMF) for each half was individually calculated. If the two halves show no new
major features the system has reached convergence.
References
1. Mason, E. A.; McDaniel, E. W. Transport Properties of Ions in Gases. Wiley: New York 1988.
S7