Comparison of the 2D ¹H-¹⁵N-HSQC spectra of Aβ₄₀(E22G) and Aβ₄₀(L17A/F19A/E22G).

<p>(A) 2D ¹H-¹⁵N-HSQC spectrum of Aβ₄₀(L17A/F19A/E22G) in 100 mM SDS solution. (B) Superimposition of 2D ¹H-¹⁵N-HSQC spectra of Aβ₄₀(L17A/F19A/E22G) (black) and Aβ₄₀(E22G) (light grey) in 100 mM SDS solution. Residues with noticeable chemical shift changes were labeled. (C) The effect of L17A/F19A replacements on the backbone resonances of Aβ₄₀(E22G). The weighted chemical shift differences ([(^HNΔ_ppm)²+(^NΔ_ppm/10)²]^1/2) were plotted as a function of residue number. ^HNΔ_ppm and ^NΔ_ppm were the ¹H^N and ¹⁵N chemical shift differences between Aβ₄₀(E22G) and Aβ₄₀(L17A/F19A/E22G), respectively.</p

The secondary structure contents estimated from the CD spectra of Aβ peptides.

<p>The secondary structure contents estimated from the CD spectra of Aβ peptides.</p

Comparison of the 2D ¹H-¹⁵N-HSQC spectra of wild-type Aβ₄₀ and Aβ₄₀(L17A/F19A).

<p>(A) 2D ¹H-¹⁵N-HSQC spectrum of Aβ₄₀(L17A/F19A) in 100 mM SDS solution. (B) Superimposition of 2D ¹H-¹⁵N-HSQC spectra of Aβ₄₀(L17A/F19A) (black) and wild-type Aβ₄₀ (light grey) in 100 mM SDS solution. Residues with noticeable chemical shift changes were labeled. (C) The effect of L17A/F19A replacements on the backbone amide resonances of wild-type Aβ₄₀. The weighted chemical shift differences ([(^HNΔ_ppm)²+ (^NΔ_ppm/10)²]^1/2) were plotted as a function of residue number. ^HNΔ_ppm and ^NΔ_ppm were the ¹H^N and ¹⁵N chemical shift differences between wild-type Aβ₄₀ and Aβ₄₀(L17A/F19A), respectively.</p

CD spectra of wild-type Aβ₄₀ and Arctic Aβ₄₀ variant in 100 mM SDS solution.

<p>(A) Superimposition of CD spectra of Aβ₄₀(L17A/F19A) (light grey) and wild-type Aβ₄₀ (black) in 100 mM SDS solution. (B) Superimposition of CD spectra of Aβ₄₀(L17A/F19A/E22G) (light grey) and Aβ₄₀(E22G) (black) in 100 mM SDS solution.</p

The predicted secondary structures of the α/β-discordant segments of double Ala-substituted Aβ peptides and their native forms.

<p>The secondary structure (upper row) for each amino acid residue was obtained by using the propensity-based prediction as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0154327#pone.0154327.g002" target="_blank">Fig 2</a> caption of ref. 27. Adopting the notation used in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0154327#pone.0154327.g002" target="_blank">Fig 2</a> caption of ref. 27, we denote the β-strands predicted with high and low probability by the symbols E and e, respectively. The symbols H and h were used for denoting the α-helical structures predicted with high and low probability, respectively.</p

Generation and Analysis of the Expressed Sequence Tags from the Mycelium of <i>Ganoderma lucidum</i>

<div><p><i>Ganoderma lucidum</i> (<i>G. lucidum</i>) is a medicinal mushroom renowned in East Asia for its potential biological effects. To enable a systematic exploration of the genes associated with the various phenotypes of the fungus, the genome consortium of <i>G. lucidum</i> has carried out an expressed sequence tag (EST) sequencing project. Using a Sanger sequencing based approach, 47,285 ESTs were obtained from <i>in vitro</i> cultures of <i>G. lucidum</i> mycelium of various durations. These ESTs were further clustered and merged into 7,774 non-redundant expressed loci. The features of these expressed contigs were explored in terms of over-representation, alternative splicing, and natural antisense transcripts. Our results provide an invaluable information resource for exploring the <i>G. lucidum</i> transcriptome and its regulation. Many cases of the genes over-represented in fast-growing dikaryotic mycelium are closely related to growth, such as cell wall and bioactive compound synthesis. In addition, the EST-genome alignments containing putative cassette exons and retained introns were manually curated and then used to make inferences about the predominating splice-site recognition mechanism of <i>G. lucidum</i>. Moreover, a number of putative antisense transcripts have been pinpointed, from which we noticed that two cases are likely to reveal hitherto undiscovered biological pathways. To allow users to access the data and the initial analysis of the results of this project, a dedicated web site has been created at <a href="http://csb2.ym.edu.tw/est/" target="_blank">http://csb2.ym.edu.tw/est/</a>.</p></div

Comparison of ¹³C^α secondary chemical shifts of double Ala-substituted Aβ peptides and their native forms.

<p>(A) The plots of ¹³C^α secondary chemical shifts of Aβ₄₀(L17A/F19A) (light grey) and wild-type Aβ₄₀ (black) as a function of residue. (B) The plots of ¹³C^α secondary chemical shifts of Aβ₄₀(L17A/F19A/E22G) (light grey) and Aβ₄₀(E22G) (black) as a function of residue.</p

A tail-to-tail arrangement of sense and <i>cis</i>-NAT gene pairs, <i>CCHL</i> (YMGL ESTG/ESTT 51764) and <i>TIM44</i> (YMGL ESTG/ESTT 51765).

<p>This figure presents an Ensembl-based visualization of the ESTs and ESTGenes/ESTTranscripts, YMGL ESTG/ESTT 51764 and YMGL ESTG/ESTT 51765, on top of <i>G. lucidum</i> genomic contig, contig00912. The former is annotated as cytochrome c heme lyase (<i>CCHL</i>) and the latter is annotated as mitochondrial import inner membrane translocase, subunit Tim44 (<i>TIM44</i>). The EST transcripts were built from overlapping ESTs-genome using a “cluster and merge” algorithm (see the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061127#s2" target="_blank">Materials and Methods</a> for details) and only the ESTs sharing identical splicing junctions were merged into an ESTTranscript. The orientation of each transcript was inferred by fitting splicing junctions to the consensus GT-AG pattern. YMGL ESTG/ESTT 51764 and YMGL ESTG/ESTT 51765 are on opposite strands and their 3′ regions corresponding to putative untranslated regions that overlap with each other (as indicated by the non-shaded area in each transcript). These two transcripts show a tail-to-tail arrangement between the sense and <i>cis</i>-natural antisense transcripts.</p

<i>G. lucidum</i> genes and their ESTs involved in the biosynthesis of triterpenoids.

<p>EC number: Enzyme commission number.</p><p>The 5^th-day, 14^th-day, 18^th-day, and 30^th-day columns list the numbers of ESTs derived from the <i>G. lucidum</i> mycelia cultivated for corresponding days.</p>*<p>: Derived from the monokaryotic strain, BCRC 37180.</p><p>E_value: The NCBI BLASTP E-value reported for the most similar gene in the non-redundant (NR) database for each putative protein.</p

Conformational changes of Aβ₄₀ using far ultraviolet circular dichroism spectra.

<p>(A) Aβ₄₀, (B) Aβ₄₀(L17A/F19A), (C) Aβ₄₀ (E22G), (D) Aβ₄₀(L17A/F19A/E22G) peptides at various incubated times. The concentration of Aβ peptides was 60 µM at pH 7.0 and 37°C.</p