Stefan Auer
University of Leeds
PhysicsChemistryCondensed matter physicsColloidNucleation
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Publications 25
We consider the nucleation of amyloid fibrils when the process occurs by direct polymerization of fully extended peptides (i.e., β-strands) into fibrils composed of successively layered β-sheets with alternating weak and strong hydrophobic surfaces. We extend our recently developed nucleation model (Kashchiev, D.; Cabriolu, R.; Auer, S. J. Am. Chem. Soc. 2013, 135, 1531–1539) to derive general expressions for the work to form such fibrils, the fibril solubility, the nucleation work, the equilibr...
11 CitationsSource
#1Andrey V. BrukhnoH-Index: 8
#2Piero RicchiutoH-Index: 3
Last. Stefan AuerH-Index: 18
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Characterization of the folding transition in polypeptides and assessing the thermodynamic stability of their structured folds are of primary importance for approaching the problem of protein folding. We use molecular dynamics simulations for a coarse grained polypeptide model in order to (1) obtain the equilibrium conformation diagram of homopolypeptides in a broad range of the chain lengths, N = 10, ..., 100, and temperatures, T (in a multicanonical ensemble), and (2) determine free energy pro...
3 CitationsSource
#1Piero Ricchiuto (University of Leeds)H-Index: 3
#2Andrey V. BrukhnoH-Index: 8
Last. Stefan AuerH-Index: 18
view all 3 authors...
In this study, we address the questions of how important is the kinetics in protein aggregation, and what are the intrinsic properties of proteins that cause this behavior. On the basis of our recent quantitative calculation of the equilibrium phase diagram of natively folded α-helical and β-sheet forming peptides, we perform molecular dynamics simulations to demonstrate how the aggregation mechanism and end product depend on the temperature, concentration, and starting point in the phase diagra...
27 CitationsSource
#1Piero Ricchiuto (University of Leeds)H-Index: 3
#2Andrey V. Brukhno (University of Leeds)H-Index: 8
Last. Stefan Auer (University of Leeds)H-Index: 12
view all 4 authors...
By using a generic coarse grained polypeptide model, we perform multicanonical molecular dynamics simulations for determining the equilibrium conformation state diagram of a single homopolypeptide chain as a function of the chain length and temperature. The state diagram highlights the thermal regimes of stability for various conformational patterns in polypeptides, including swollen, random and collapsed coils, globular structures, extended and bended α helices, and compact β bundles. Remarkabl...
8 CitationsSource
#1Andrey V. Brukhno (University of Leeds)H-Index: 8
#2Anna AkinshinaH-Index: 7
Last. Stefan Auer (University of Leeds)H-Index: 18
view all 5 authors...
We model cyclic voltammetry experiments on supported lipid films where a non-trivial dependence of the capacitance on the applied voltage is observed. Previously, based on a mean-field treatment of the Flory–Huggins type, under the assumption of strongly screened electrostatic interactions, it has been hypothesized that peaks in the capacitance-vs.-voltage profiles correspond to a sequence of structural or phase transitions within the adsorbed film. To examine this hypothesis, in this study we u...
18 CitationsSource
1 CitationsSource
#1Stefan AuerH-Index: 18
#2Mark A. MillerH-Index: 27
Last. Michele VendruscoloH-Index: 77
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We show that the interplay between excluded volume effects, hydrophobicity, and hydrogen bonding in a tubelike representation of a polypeptide chain gives rise to free energy landscapes that, in addition to a clear global minimum, are characterized by the general presence of a small number of metastable minima, which correspond to common structural motifs observed in proteins. The complexity of the landscape increases only moderately with the length of the chain. Analysis of the temperature depe...
36 CitationsSource
#1Stefan Auer (University of Cambridge)H-Index: 18
#1Stefan Auer (University of Leeds)H-Index: 12
Last. Michele Vendruscolo (University of Cambridge)H-Index: 77
view all 3 authors...
Despite the complexity and the specificity of the amino acid code, a variety of peptides and proteins unrelated in sequence and function exhibit a common behavior and assemble into highly organized amyloid fibrils. The formation of such aggregates is often described by a nucleation and growth mechanism, in which the proteins involved also form intermediate oligomeric aggregates before they reorganize and grow into ordered fibrils with a characteristic cross-β structure. It is extremely difficult...
82 CitationsSource
#1Tuomas P. J. Knowles (University of Cambridge)H-Index: 56
#2Wenmiao Shu (University of Cambridge)H-Index: 17
Last. Mark E. Welland (University of Cambridge)H-Index: 64
view all 7 authors...
Aggregation of proteins and peptides is a widespread and much-studied problem, with serious implications in contexts ranging from biotechnology to human disease. An understanding of the proliferation of such aggregates under specific conditions requires a quantitative knowledge of the kinetics and thermodynamics of their formation; measurements that to date have remained elusive. Here, we show that precise determination of the growth rates of ordered protein aggregates such as amyloid fibrils ca...
134 CitationsSource