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

Effets de solvants organiques sur le repliement de l'elastase pancreatique porcine etudies par la transition conformationnelle en fonction du PH

SIGLECNRS T Bordereau / INIST-CNRS - Institut de l'Information Scientifique et TechniqueFRFranc

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

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