Normed principal component analysis (PCA) of the three pools plus HSP12.

<p>The number in each cell indicates the number of properties that are significantly different (p-value <0.05) using the non-parametric Mann Whitney test.</p>a<p>HYDROPHI: mean hydrophilicity; TRANSM: mean transmembrane tendency.</p><p>Normed principal component analysis (PCA) of the three pools plus HSP12.</p

Boxplot representation of MW/length ratio, FoldIndex, mean bulkiness and mean flexibility, mean molar fraction of buried residues and mean molar fraction of accessible residues.

<p>P1: pool 1. P2: pool 2. P3: pool 3. C8: LEAP class 8. IDP: intrinsically disordered proteins. FS: fully structured proteins. HSP: HSP12.</p

Normed principal component analysis (PCA) of LEAP class 2, hydrophilins, HSP12, LEAP class 8 and WHy domain.

<p>The number in each cell indicates the number of properties that are significantly different (p-value <0.05) using the non-parametric Mann Whitney test.</p>a<p>HYDROPHI: mean hydrophilicity; TRANSM: mean transmembrane tendency; FI: FoldIndex; GRAVY: grand average of hydropathy; HYDROPHO: mean hydrophobicity (); BULKI: mean bulkiness.</p><p>Normed principal component analysis (PCA) of LEAP class 2, hydrophilins, HSP12, LEAP class 8 and WHy domain.</p

Principal component analysis of the three pools and HSP12.

<p>Abbreviations used: <b>(i) Physicochemical properties</b>: isoelectric point: pi, FoldIndex: gi, GRAVY: gr, net charge at pH 7: ch, mean hydrophilicity: hi, hydrophobicity (): ho, mean average flexibility: fl, mean bulkiness: bl, mean molar fraction of buried residues: br, mean molar fraction of accessible residues: ac, mean transmembrane tendency: tr, molecular weight/length: ml. <b>(ii) Ratio [(%amino acid X)/(% amino acid X Uniprot)]</b>: pctA.Unip: A, pctC.Unip: C, pctD.Unip: D, pctE.Unip: E, pctF.Unip: F, pctG.Unip: G, pctH.Unip: H, pctI.Unip: I, pctK.Unip: K, pctL.Unip: L, pctM.Unip: M, pctN.Unip: N, pctP.Unip: P, pctQ.Unip: Q, pctR.Unip: R, pctS.Unip: S, pctT.Unip: T, pctV.Unip: V, pctW.Unip: W, pctY.Unip: Y. <b>(iii) Amino acids combination</b>: [D+E]: c1, [K+R]: c2, [D+E+K+R]: c3, [D+E−K−R]: c4, [A+I+L+V]: c5, [F+W+Y]: c6, [N+Q]:c7, [S+T]: c8, [C+W]: c9, [R+E+S+P]: c10, [C+F+W+Y]: c11.</p

Principal component analysis of LEAP class 2, hydrophilins, HSP12, WHy domain and LEAP class 8.

<p>Abbreviations used: Hy: hydrophilins; W: WHy domain; 2: LEAP class 2; 8: LEAP class 8; HSP: HSP12. (i) Physicochemical properties: isoelectric point: pi, FoldIndex: gi, GRAVY: gr, net charge at pH 7: ch, mean hydrophilicity: hi, hydrophobicity (): ho, mean average flexibility: fl, mean bulkiness: bl, mean molar fraction of buried residues: br, mean molar fraction of accessible residues: ac, mean transmembrane tendency: tr, molecular weight/length: ml. (ii) Ratio [(%amino acid X)/(% amino acid X Uniprot)]: pctA.Unip: A, pctC.Unip: C, pctD.Unip: D, pctE.Unip: E, pctF.Unip: F, pctG.Unip: G, pctH.Unip: H, pctI.Unip: I, pctK.Unip: K, pctL.Unip: L, pctM.Unip: M, pctN.Unip: N, pctP.Unip: P, pctQ.Unip: Q, pctR.Unip: R, pctS.Unip: S, pctT.Unip: T, pctV.Unip: V, pctW.Unip: W, pctY.Unip: Y. (iii) Amino acids combination: [D+E]: c1, [K+R]: c2, [D+E+K+R]: c3, [D+E−K−R]: c4, [A+I+L+V]: c5, [F+W+Y]: c6, [N+Q]:c7, [S+T]: c8, [C+W]: c9, [R+E+S+P]: c10, [C+F+W+Y]: c11.</p

Schematic representation of the approach for the study of LEAPs, hydrophilins and [WHy domain/LEAP class 8].

<p>(A) PCA 1: principal component analysis of the three pools. PCA 2: principal component analysis of [WHy domain/LEAP class 8] <i>vs</i>. [hydrophilins/LEAP class 2]. IDP: intrinsically disordered proteins. (B) Distribution of hydrophilins-like LEAPs, control LEAPs, hydrophylins and other LEAPs. Red squares: pool 1 (hydrophilins-like LEAPs) retrieved from LEAPdb characterized by %Gly>6%, GRAVY<−1 and mean hydrophilicity>1. Blue rectangles: pool 2 (control LEAPs) retrieved from LEAPdb characterized by %Gly<6%, GRAVY>−1 and mean hydrophilicity<1. Green triangles: pool 3 (hydrophilins) characterized by 6,2<%Gly<16,8%, −1,86</p

Boxplot representation of isoelectric point, mean net charge at pH 7, mean hydrophilicity, mean normalized GRAVY, mean normalized hydrophobicity () and mean transmembrane tendency.

<p>P1: pool 1. P2: pool 2. P3: pool 3. C8: LEAP class 8. IDP: intrinsically disordered proteins. FS: fully structured proteins. HSP: HSP12.</p

Schematic representation of WHy domain.

<p>(A) WHy domain contains an invariant triplet NPN situated 25 amino acids after the beginning of the WHy domain. (B) Some LEAP class 8 sequences contain a second WHy domain whose consensus sequence is very similar to the first domain. (C) Alignment of WHy domain sequences. The amino acids consensus sequence around the invariant triplet NPN can be written as: [ALMNV].{0,4}[FILMVWY].[AFILMV].{1,3}[FLMVY].[AILV].NPN.{3,3}[ILV].[AFILVY].{2,4}[FILMVY].{1,2}[FLVWY].[ILV].</p

Fractional content (<i>i.e.</i>, the sum of residues normalized by protein chain-length) of some particular amino acids combinations.

<p>(A) Negatively charged residues (Asp + Glu). (B) Positively charged residues (Arg + Lys). (C) Strongest disorder promoting residues (Arg + Glu + Ser + Pro). (D) Strongest order promoting residues (Cys + Phe + Tyr + Trp). P1: pool 1. P2: pool 2. P3: pool 3. C8: LEAP class 8. IDP: intrinsically disordered proteins. FS: fully structured proteins. HSP: HSP12.</p

Binary^a representation of the physico-chemical properties distribution of « hydrophilins-like LEAPs » (pool 1), « control LEAPs » (pool 2), hydrophilins (pool 3), HSP12, WHy domain and LEAP class 8.

<p>These data are compared to two control datasets (IDP and FS datasets).</p>a<p>Values +1, 0 and −1 values mean that the physico-chemical properties considered is upper, equal or lower, respectively, than either the calculated median value for the seven datasets or a definite « natural » value (see the corresponding figures).</p>b<p>Mean molar fraction of buried residues.</p>c<p>Mean molar fraction of accessible residues.</p>d<p>Mean transmembrane tendency.</p>e<p>Mean net charge at pH 7.</p>f<p>Mean hydrophilicity.</p>g<p>Grand average of hydropathy.</p>h<p>Mean hydrophobicity.</p>i<p>Intrinsically Disordered Proteins dataset.</p>j<p>Fully Structured proteins dataset.</p><p>Binary^{<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109570#nt102" target="_blank">a</a>} representation of the physico-chemical properties distribution of « hydrophilins-like LEAPs » (pool 1), « control LEAPs » (pool 2), hydrophilins (pool 3), HSP12, WHy domain and LEAP class 8.</p