Measurement of amyloid formation by turbidity assay—seeing through the cloud

Abstract

Detection of amyloid growth is commonly carried out by measurement of solution turbidity, a low-cost assay procedure based on the intrinsic light scattering properties of the protein aggregate. Here, we review the biophysical chemistry associated with the turbidimetric assay methodology, exploring the reviewed literature using a series of pedagogical kinetic simulations. In turn, these simulations are used to interrogate the literature concerned with in vitro drug screening and the assessment of amyloid aggregation mechanisms.

ThT 101: a primer on the use of thioflavin T to investigate amyloid formation

“…To support the conclusions of the assay, orthogonal methods such as CD spectroscopy, TEM, and Fourier transform infrared spectroscopy (FTIR) are widely applied. Another classical method to follow protein aggregation is to measure sample turbidity, a handy and low cost method reviewed by Hall and his colleagues [113].…”

Foreword to ‘Multiscale structural biology: biophysical principles and mechanisms underlying the action of bio-nanomachines’, a special issue in Honour of Fumio Arisaka’s 70th birthday

“…Within the phage-related area work on bacterial homologs of phage proteins (Uchida et al 2014), mechanistic action of the gp5 trimer in the cell puncturing device (Nishima et al 2011), and determination of the molecular architecture of the T4 phage neck region (Fokine et al 2013) (all reviewed in Arisaka and Kanamaru 2013). Further to this, being a Professor did not slow down Fumio's own experimental output, with his engagement in a range of collaborative projects on topics as diverse as receptor biology (Mio et al 2010), assembly of nanotechnology components (Yokoi et al 2010;Inaba et al 2012;Sanghamitra et al 2014), hemoglobin allostery (Arisaka et al 2011), crop protein analysis (Wadahama et al 2012;Sato et al 2015;Yamniuk et al 2015), autophagy (Araki et al 2013, amyloid analysis (Zhao et al 2016;Hall et al 2016), biopharmaceutical development (Iwura et al 2014a(Iwura et al , 2014b, AUC methodological development (Zhao et al 2015) and thermostable enzymes (Tamakoshi et al 2011;Chen et al 2011;Ozawa et al 2012) among many others (Huq et al 2010;Yamasaki et al 2010;Kanazawa et al 2010;Sawada et al 2011;Akita et al 2012;Nomura et al 2012;Ishii et al 2012;Nozawa et al 2013;Seio et al 2013;Takei et al 2014;Kumazaki et al 2014;Owa et al 2014;Iwura et al 2014aIwura et al ,...…”

A simple method for modeling amyloid kinetics featuring position biased fiber breakage

“…Amyloid, a fibril-like homopolymer capable of being formed from many different protein monomer building blocks, has been shown to exhibit both helical polymerization kinetics and steady state behavior capable of quantitative description using helical polymerization models of Oosawa and colleagues [3][4][5][6]. A number of important extensions to these models been developed over the last twenty years to better describe amyloid formation [7][8][9][10][11][12][13][14]. These extensions are based on a consensus chemical schema (Fig.…”