LEAPdb: a database for the late embryogenesis abundant proteins

<p>Abstract</p> <p>Background</p> <p>Late Embryogenesis Abundant Proteins database (LEAPdb) contains resource regarding LEAP from plants and other organisms. Although LEAP are grouped into several families, there is no general consensus on their definition and on their classification. They are associated with abiotic stress tolerance, but their actual function at the molecular level is still enigmatic. The scarcity of 3-D structures for LEAP remains a handicap for their structure-function relationships analysis. Finally, the growing body of published data about LEAP represents a great amount of information that needs to be compiled, organized and classified.</p> <p>Results</p> <p>LEAPdb gathers data about 8 LEAP sub-families defined by the PFAM, the Conserved Domain and the InterPro databases. Among its functionalities, LEAPdb provides a browse interface for retrieving information on the whole database. A search interface using various criteria such as sophisticated text expression, amino acids motifs and other useful parameters allows the retrieving of refined subset of entries. LEAPdb also offers sequence similarity search. Information is displayed in re-ordering tables facilitating the analysis of data. LEAP sequences can be downloaded in three formats. Finally, the user can submit his sequence(s). LEAPdb has been conceived as a user-friendly web-based database with multiple functions to search and describe the different LEAP families. It will likely be helpful for computational analyses of their structure - function relationships.</p> <p>Conclusions</p> <p>LEAPdb contains 769 non-redundant and curated entries, from 196 organisms. All LEAP sequences are full-length. LEAPdb is publicly available at <url>http://forge.info.univ-angers.fr/~gh/Leadb/index.php</url>.</p

Computational and Statistical Analyses of Amino Acid Usage and Physico-Chemical Properties of the Twelve Late Embryogenesis Abundant Protein Classes

Late Embryogenesis Abundant Proteins (LEAPs) are ubiquitous proteins expected to play major roles in desiccation tolerance. Little is known about their structure - function relationships because of the scarcity of 3-D structures for LEAPs. The previous building of LEAPdb, a database dedicated to LEAPs from plants and other organisms, led to the classification of 710 LEAPs into 12 non-overlapping classes with distinct properties. Using this resource, numerous physico-chemical properties of LEAPs and amino acid usage by LEAPs have been computed and statistically analyzed, revealing distinctive features for each class. This unprecedented analysis allowed a rigorous characterization of the 12 LEAP classes, which differed also in multiple structural and physico-chemical features. Although most LEAPs can be predicted as intrinsically disordered proteins, the analysis indicates that LEAP class 7 (PF03168) and probably LEAP class 11 (PF04927) are natively folded proteins. This study thus provides a detailed description of the structural properties of this protein family opening the path toward further LEAP structure - function analysis. Finally, since each LEAP class can be clearly characterized by a unique set of physico-chemical properties, this will allow development of software to predict proteins as LEAPs

sHSPdb: a database for the analysis of small Heat Shock Proteins

Background: small Heat Shock Proteins (sHSP) is a wide proteins family. SHSP are found in all kingdoms and they play critical roles in plant stress tolerance mechanisms (as well as in pathogenic microorganisms and are implicated in human diseases). Results: sHSPdb (small Heat Shock Proteins database) is an integrated resource containing non-redundant, full-length and curated sequences of sHSP, classified on the basis of amino acids motifs and physico-chemical properties. sHSPdb gathers data about sHSP defined by various databases (Uniprot, PFAM, CDD, InterPro). It provides a browser interface for retrieving information from the whole database and a search interface using various criteria for retrieving a refined subset of entries. Physicochemical properties, amino acid composition and combinations are calculated for each entry. sHSPdb provides automatic statistical analysis of all sHSP properties. Among various possibilities, sHSPdb allows BLAST searches, alignment of selected sequences and submission of sequences. Conclusions: sHSPdb is a new database containing information about sHSP from all kingdoms. sHSPdb provides a classification of sHSP, as well as tools and data for the analysis of the structure - function relationships of sHSP. Data are mainly related to various physico-chemical properties of the amino acids sequences of sHSP. sHSPdb is accessible at http://forge.info.univ-angers.fr/similar to gh/Shspdb/index.php

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

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