Application of the Fuzzy Oil Drop Model Describes Amyloid as a Ribbonlike Micelle

Roterman, Irena; Banach, Mateusz; Konieczny, Leszek

doi:10.3390/e19040167

Cited by 26 publications

(57 citation statements)

References 55 publications

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“…Tetrapeptides shown in Table 2 were sections of the chain, which were important for the overall synergy that led to the formation of the complex structure of the bioactive protein form. This was especially visible in the case of proteins undergoing amyloid transformation, where a different model was chosen for shaping mutual relations, leading from the form of a spherical micelle to the form of a linear bands the presence of which is recognized in ribbon-like micelle [26]. This required a change in the organization system of the entire chain and thus the choice of a different synergy system.…”

Section: Discussionmentioning

confidence: 99%

“…The late intermediate structure-the fuzzy oil drop model-assumes that the spatial structure of proteins is obtained by the micellization mechanism [26]. So far, the presence of hydrophobicity distributions consistent with a three-dimensional (3D) Gaussian distribution has been shown, that is, the maximum concentration of hydrophobicity occurs in the center and decreases, as it moves away from the center until reaching a level of close to zero on a protein surface [27].…”

Section: Introductionmentioning

confidence: 99%

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Model of Early Stage Intermediate in Respect to Its Final Structure

2019

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The model, describing a method of determining the structure of an early intermediate in the process of protein folding to analyze nonredundant PDB protein bases, allows determining the relationship between the sequence of tetrapeptides and their structural forms expressed by structural codes. The contingency table expressing such a relationship can be used to predict the structure of polypeptides by proposing a structural form with a precision limited to the structural code. However, by analyzing structural forms in native forms of proteins based on the fuzzy oil drop model, one can also determine the status of polypeptide chain fragments with respect to the assumptions of this model. Whether the probability distributions for both compliant and noncompliant forms were similar or whether the tetrapeptide sequences showed some differences at a level of a set of structural codes was investigated. The analysis presented here indicated that some sequences in both forms revealed differences in probability distributions expressed as a negative statistically significant correlation coefficient. This meant that the identified sections (tetrapeptides) took different forms against the fuzzy oil drop model. It may suggest that the information of the final status with respect to hydrophobic core formation is already carried by the structure of the early-stage intermediate.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Model of Early Stage Intermediate in Respect to Its Final Structure

2019

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“…5.5; Tables 5.4 and 5.5) is particularly prone to conformational changes resulting from its poor alignment with the theoretical hydrophobicity distribution. Such changes may provide the seed for amyloid transformation -although the issue is quite complex and requires further study [13,24]. Similarities -linear propagation -in the distribution of local hydrophobicity peaks (red) and troughs (blue) in an amyloid plaque (2MVX; a4 β-amyloid) and in the CR micelle.…”

Section: Hypothetical Amyloidogenesis Of V Domainsmentioning

confidence: 99%

“…The model proposed in [24] stipulates that β-structural fragments perpendicular to the fibril's axis exhibit the following properties:…”

Section: Hypothetical Amyloidogenesis Mechanism Affecting the V Domaimentioning

confidence: 99%

Possible Mechanism of Amyloidogenesis of V Domains

Banach

Kalinowska

Konieczny

et al. 2017

Self-Assembled Molecules – New Kind of Protein Ligands

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This chapter discusses complexation of Congo red by amyloid structures comprising immunoglobulin light chains, particularly the so-called Bence-Jones (BJ) proteins. According to the presented study, in BJ proteins the V domain is substantially less stable than the C domain. This conclusion is based on quantitative analysis of the protein's hydrophobic core, made possible by the fuzzy oil drop model. Results indicate that the V domain exhibits structural ordering characteristic of amyloid aggregates, i.e. linear propagation of local hydrophobicity peaks and troughs rather than a monocentric hydrophobic core (typically present in globular proteins). On this basis, the authors propose a hypothetical arrangement of V domains which leads to formation of an amyloid. Structural similarities between V domains in BJ proteins and other types of amyloid aggregates enable the authors to study the specific mechanism of Congo red complexation by amyloids.The proposed Congo red complexation mechanism builds upon the authors' previous experience with bioinformatics tools. The subject should be of interest to researchers specializing in protein folding studies and misfolding diseases.

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“…The hydrogen bonds between the backbones of the amyloid thermodynamically favor the in-register alignment [15]. Roterman et al regarded the in-register amyloid as a “ribbon-like micelle” whose exposed hydrophobicity at the stack ends enable endless elongation [16]. Efficient propagation of the amyloids may stem from those thermodynamic features of the in-register parallel β-sheet structures.…”

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Mechanisms of strain diversity of disease-associated in-register parallel β-sheet amyloids and implications about prion strains

Taguchi

Otaki

Nishida

2018

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18The mechanism of strain diversity of prions still remains unsolved, because the investigation of inheritance and 19 diversification of the protein-based pathogenic information demands identification of the detailed structures of abnormal 20 isoform of prion protein (PrP Sc ), while it is difficult to purify for analysis without affecting the infectious nature. On the other 21 hand, the similar prion-like properties are recognized also in other disease-associated in-register parallel β -sheet amyloids 22 including Tau and α -synuclein (αSyn) amyloids. Investigations into structures of those amyloids by solid-state nuclear 23 magnetic resonance spectroscopy and cryo-electron microscopy recently made remarkable advances, because of their 24 relatively small sizes and lack of post-translational modifications. We review the advances on those pathogenic amyloids, 25 particularly Tau and α Syn, and discuss their implications about strain diversity mechanisms of prion/PrP Sc from the 26 viewpoint that PrP Sc is an in-register parallel β -sheet amyloid. We also present our recent data of molecular dynamics 27 simulations of α Syn amyloid, which suggest significance of compatibility between β -sheet propensities of the substrate and 28 local structures of the template for stability of the amyloid structures. Detailed structures of the α Syn and Tau amyloids are 29 good surrogate models of pathogenic amyloids including PrP Sc to elucidate not only the strain diversity but also their 30 pathogenic mechanisms. 31 32 33Strain diversity is one of the most mysterious feature of prions. The strain-specific traits of prions are enciphered in 34 the structures of the abnormal isoform prion protein (PrP Sc ), and they are stably inherited over generations solely by 35 passaging the exact structures of the PrP Sc through template-directed refolding of the normal isoform prion protein (PrP C ), 36 where the template PrP Sc imprint the structural details onto the substrate PrP C . Moreover, the strain-specific pathogenic 37 information encoded in the conformation of the PrP Sc is reproducibly "translated" into the strain-specific clinicopathological 38 traits in the manifested diseases [1] [2]. This view is widely accepted as the protein-only hypothesis but detailed 39 mechanisms, e.g., specifically what structures of PrP Sc encodes the pathogenic information and how the information is 40 translated, remain a challenge to the current biology. Investigations of the storage, inheritance and diversification of the 41 protein-based pathogenic information demand identification of the structure-phenotype correlations, but it is very difficult 42 because detailed structures of the entire PrP Sc is not available yet due to its incompatibility with high-resolution structural 43 analyses, i.e., X-ray crystallography or nuclear magnetic resonance spectrometry (NMR). The incompatibility is attributable 44 to difficulty in purification without losing infectivity [3], difficulty in recapitulating bona fide prion...

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Application of the Fuzzy Oil Drop Model Describes Amyloid as a Ribbonlike Micelle

Cited by 26 publications

References 55 publications

Model of Early Stage Intermediate in Respect to Its Final Structure

Model of Early Stage Intermediate in Respect to Its Final Structure

Possible Mechanism of Amyloidogenesis of V Domains

Mechanisms of strain diversity of disease-associated in-register parallel β-sheet amyloids and implications about prion strains

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