Biology subjects

Robang, A. S.

Publications and source records attributed to Robang, A. S..

3 recordsLinked to original sources

bioRxiv2023

Design of parallel ????-sheet nanofibrils using Monte-Carlo search, coarse-grained simulations, and experimental testing

Peptide self-assembly into amyloid fibrils provides numerous applications in drug delivery and biomedical engineering applications. We augment our previously-established computational screening technique along with experimental biophysical characterization to discover 7-mer peptides that self-assemble into "parallel {beta}-sheets", i.e., {beta}-sheets with N-terminus-to-C-terminus {beta}-strand vectors oriented in parallel. To accomplish the desired {beta}-strand organization, we applied the PepAD amino acid sequence design software to the Class-1 cross-{beta} spine defined by Sawaya et al. This molecular configuration includes two layers of parallel {beta}-sheets stacked such that N-terminus-to-C-terminus vectors are oriented antiparallel for molecules on adjacent {beta}-sheets. The first cohort of PepAD identified peptides were examined for their fibrillation behavior in DMD/PRIME20 simulations, and the top performing sequence was selected as a prototype for a subsequent round of sequence refinement. The two rounds of design resulted in a library of eight 7-mer peptides. In DMD/PRIME20 simulations, five of these peptides spontaneously formed fibril-like structures with a predominantly parallel {beta}-sheet arrangement, two formed fibril-like structure with <50% in parallel {beta}-sheet arrangement and one remained a random coil. Among the eight candidate peptides produced by PepAD and DMD/PRIME20, five were synthesized and purified. All five assembled into amyloid fibrils composed of parallel {beta}-sheets based on Fourier Transform Infrared Spectroscopy, Circular Dichroism, Electron Microscopy, and Thioflavin-T fluorescence spectroscopy measurements.

bioengineering↗

bioRxiv2023

A Common Pathway for Detergent-Assisted Oligomerization of Aβ42

Amyloid beta (A{beta}) aggregation is a slow process without seeding or assisted nucleation. Sodium dodecyl sulfate (SDS) micelles stabilize A{beta}42 small oligomers (in the dimer-tetramer range); subsequent SDS removal leads to a 150-kD A{beta}42 oligomer. Dodecylphosphorylcholine (DPC) micelles also stabilize an A{beta}42 tetramer. Here we characterize the detergent-assisted oligomerization pathway by solid-state NMR spectroscopy and molecular dynamics simulations. SDS and DPC-induced oligomers have the same structure, implying a common oligomerization pathway. An antiparallel {beta}-sheet formed by the C-terminal region, the only stable structure in SDS and DPC micelles, is directly incorporated into the 150-kD oligomer. Three Gly residues (at positions 33, 37, and 38) create holes that are filled by the SDS and DPC hydrocarbon tails, thereby turning a potentially destabilizing feature into a stabilizing factor. These observations have implications for endogenous A{beta} aggregation at cellular interfaces.

biophysics↗

bioRxiv2022

Distinct neurotoxic TDP-43 fibril polymorphs can be generated by heterotypic interactions with α-synuclein

Amyloid aggregates of specific proteins form important pathological hallmarks in many neurodegenerative diseases, defining neuronal degeneration and disease onset. Recently, increasing numbers of patients show co-morbidities and overlaps between multiple neurodegenerative diseases, presenting distinct phenotypes. Such overlaps are often accompanied by co-localizations of more than one amyloid protein, prompting the question of whether direct interactions between different amyloid proteins could generate heterotypic amyloids. To answer this question, we investigated the effect of -synuclein (S) on TDP-43 aggregation inspired by their co-existence in pathologies such as Lewy body dementia and limbic predominant age-related TDP-43 encephalopathy. We previously showed that S and prion-like C-terminal domain (PrLD) of TDP-43 synergistically interact with one another to generate toxic heterotypic aggregates in vitro. Here, we extend these studies to investigate whether S induces structurally and functionally distinct polymorphs of PrLD aggregates. Using S -PrLD heterotypic aggregates generated in two different stoichiometric proportions, we show that S can effect PrLD fibril forms. The fibril samples have distinctive residue-level structural signatures in NMR spectra, dye-binding capability, proteinase K (PK) stability, and SDS-sensitive thermal stability. By gold nanoparticle labeling and TEM, we show the presence of both S and PrLD proteins within the same fibrils, and thus the existence of hetertypic hybrid fibrils. We also observe that S and PrLD co-localize in the cytosol of SH-SY5Y neuroblastoma cells, and show that the heterotypic PrLD fibrils selectively induce synaptic dysfunction in primary cortical neurons. These findings establish the existence of heterotypic amyloid polymorphs and provide a molecular basis for the observed overlap between synucleinopathies and TDP-43 proteinopathies.

biophysics↗