Secondary-structure prediction revisited: Theoretical β-sheet propensity and coil propensity represent structures of amyloids and aid in elucidating phenomena involved in interspecies transmission of prions

2019

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17Prions are pathogens which consist solely of abnormal isoform of prion protein (PrP Sc ) without any genetic material, 18 and they therefore depend on purely protein-based mechanism for diversification and maintenance of pathogenic 19 properties/information for strain diversity that has not been fully elucidated. According to the protein-only 20 hypothesis, pathogenic properties of prions are determined by conformations of the constituent PrP Sc , and 21 alterations to even a single residue can drastically change the properties when the residue is located at a critical 22 α Syn amyloid, whereas other hydrophobic amino acids 32 destabilized it. The stabilizing effect of methionine was attributable to the long side chain without Cβ branching. 33 The local structural model of PrP Sc also revealed unique effects of hydrophobic amino acids depending on regional 34 structures. Our study demonstrated specifically how and in what structure of in-register parallel β -sheet amyloids 35 hydrophobic residues can exert unique effects and provide insights into the molecular mechanism of strain 36 diversity of prions and other pathogenic amyloids. 37 38 65 high-resolution structural analyses [11][12][13][14][15][16]. 66 Not only by the Met/Val polymorphic codon 129, strain/species barriers of prions can be caused by 67 conservative replacements between different groups of hydrophobic amino acids. In experiments with 68 C-terminally-truncated Y145Stop mutant of human PrP and the counterparts of mouse and Syrian hamster PrPs, 69 whether residue 138 or 139 (in human numbering throughout unless otherwise noted) is isoleucine (Ile) or Met was 70 critical for efficient amyloid formation and cross-seeding among them [17][18]. In transmission of prions of sporadic 71 CJD homozygous for M129 to transgenic mice expressing human-mouse chimeric PrP, I138M substitution 72 substantially extended incubation periods [19]. M109 and M112 are influential on transmission efficiencies among 73 different hamster species [20][21]. In an experiment observing influences of systematically-introduced mutations of 74 mouse PrP on conversion efficiencies in scrapie-infected Neuro2a cells, Met at some positions, e.g., M213, were 75replaceable with other hydrophobic residues like Leu, whereas unreplaceable at other residues, e.g., M206 [22]. In 76 109 positive-value areas of (Pβ-Pα) and (Pβ-Pc) in residues 88-90 disappeared, making the C-terminal region solely 110 (Pα-Pc)-positive. Those alterations in predicted propensity profiles by the mutations were consistent with high 111 α -helix propensity of Met [34][35]. 112 MD simulation of α Syn(E61M) and α Syn(G84M) 113 MD simulations of homo-oligomer amyloids of α Syn(E61M) and α Syn(G84M) revealed that both the mutations

Section: Resultsmentioning

confidence: 99%

Conformation-dependent influences of hydrophobic amino acids in two in-register parallel β-sheet amyloids, an α-synuclein amyloid and a local structural model of PrP^Sc

2019

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“…To compare influences of Met and other hydrophobic amino acids on the local structures of αSyn amyloids, we introduced Met substitution at residues 61 (E61M) and 84 (G84M), where we previously investigated influences of isoleucine substitutions [24]. We first estimated intrinsic propensities of the mutant αSyn by secondary structure prediction algorithm [24][32][33]. They both raised local (Pα-Pc) values and the positive-(Pα-Pc) areas coalesced across the loop regions (Fig 1A, red circles, and 1B).…”

Section: Resultsmentioning

confidence: 99%

“…We used the same algorithm (http://cib.cf.ocha.ac.jp/bitool/MIX/) [32] as previously reported [24][33]. To clarify magnitude relations between two of the three conventional parameters, i.e., α-helix propensity (Pα), β-sheet propensity (Pβ), and coil propensity (Pc), we used their arithmetic differences as a new set of parameters, i.e., (Pβ-Pα), (Pβ-Pc) and (Pα-Pc) [24].…”

Section: Methodsmentioning

confidence: 99%

In silico evidence of unique behaviors of methionine in an in-register parallel beta-sheet amyloid, suggestive of its possible contribution to strain diversity of amyloids

2019

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17Mechanism of strain diversity of prions is a long-standing conundrum, because prions consist solely of abnormal 18 isoform of prion protein (PrP Sc ) devoid of genetic material. Pathogenic properties of prions are determined by 19 conformations of the constituent PrP Sc according to the protein-only hypothesis, and alterations to even a single 20 residue can drastically change the properties when the residue is located at a critical position for the structure of 21 PrP Sc . Interestingly, methionine (Met) is often recognized as the polymorphic or species-specific residues 22 34 Prion diseases are a group of neurodegenerative disorders which are characterized by accumulation of the 35 abnormal isoform (PrP Sc ) of prion protein (PrP) in the central nervous system [1]. Prion diseases have three 36 etiologies, i.e., sporadic, inherited and acquired, depending on how the causative PrP Sc starts propagation in the 37 body; in sporadic and inherited prion diseases, e.g., sporadic Creutzfeldt-Jakob disease (CJD) and fatal familial 38 insomnia (FFI), respectively, the causative PrP Sc are generated by spontaneous conformational conversion of 39 endogenous normal isoform PrP into PrP Sc without or with mutation in PRNP gene, which encodes PrP. Acquired 40 prion diseases are caused by intake of exogenous PrP Sc as infectious agents, prions, e.g. epidemic bovine 41 spongiform encephalopathy (BSE) in cattle [2] and chronic wasting disease (CWD) in cervids [3]. Prions behave 42 similarly as viruses, with high infectivity, existence of many strains, species/strain barriers, and adaptation to new 43 hosts, despite the lack of conventional genetic material. These virus-like properties of prions are explained by 44 hypothesis that pathogenic properties of prions are enciphered in the conformations of PrP Sc , i.e., protein-only 45 hypothesis [1][4]. 46 Indeed, pathogenic properties of prions and the consequent clinical features are greatly affected by the 47 48 fact that conformations of proteins are determined by the primary structures. For example, in sporadic CJD, PrP 49 deposition patterns, lesion profiles in the brain, clinical presentations, and apparent molecular sizes of 50 protease-resistant cores of PrP Sc are varied depending on whether the polymorphic codon 129 is methionine (Met) 51 or valine (Val) [5]. A pathogenic mutation D178N of human PrP reportedly causes either FFI or familial CJD in 52 association with Met129 or Val129, respectively [6]. The codon 129 polymorphism also determines susceptibility to 53 prion infections, i.e., species/strain barriers: a vast majority of new-variant CJD cases which resulted from 54 trans-species transmission of BSE to humans are homozygous for Met129 [7][8]; the polymorphic codon 132 of elk 55 PrP, either Met or leucine (Leu), which is equivalent to the codon 129 polymorphism of human PrP, also affects 56 susceptibility to CWD [9][10]. From the viewpoint of the protein-only hypothesis, effects of the polymorphisms are 57 mediated by structural alterations of the constitue...

“…On the other hand, the incompatibility between Pick’s Tau amyloid and 4R-Tau substrate by steric conflicts by the Cβ carbon of Val 30 0 demonstrated that strain barriers can be also posed by such local factors. We had hypothesized that conflicts between the local structures of the template amyloid and the corresponding local intrinsic propensity of the substrate peptide can cause a strain barrier, and that the intrinsic propensities are predictable by a secondary structure prediction algorithm [53][54]. Although the algorithm was originally designed for monomeric proteins, the singular structural feature of in-register parallel β-sheet amyloids could allow the application ( Fig 1A ).…”

Section: Insights From MD Simulations Of αSyn Amyloids: Significance mentioning

confidence: 99%

“…Although the algorithm was originally designed for monomeric proteins, the singular structural feature of in-register parallel β-sheet amyloids could allow the application ( Fig 1A ). By comparing the predicted propensities, i.e., β-sheet propensity (Pβ), α-helix propensity (Pα) and coil propensity (Pc), of PrPs from various species, we hypothesized that compatibility of β-arches between PrP Sc and PrP C contributes to species barriers ( Fig 2C ) [54]. Here we test the hypothesis the local conformations and the propensity of substrate with MD simulation, which enables observation of the influences exclusively of the conformations on behaviors of the peptides without any any interference from other factors or proteins.…”

Section: Insights From MD Simulations Of αSyn Amyloids: Significance mentioning

confidence: 99%

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

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...