Bioinformatic studies on the group 2 allergens of Dermatophagoides farinae from China.

The present study aimed to characterize the group 2 allergens of the house dust mite Dermatophagoides farinae (Der f 2) from Hainan Island, a tropical region in Southeastern China. We cloned and sequenced cDNA coding for Der f 2 and found an additional region of 87 base pairs (bp) (from +77 to +163 bp) in our strain that was absent in the reference sequence (GenBank AB195580) used for primer design. However, the BLAST analysis identified the same sequence in strains reported from Reinbek, Germany, and Guangzhou, China. A phylogenetic tree was constructed using the Der f 2 nucleotide sequences from different regions or countries and showed that the Hainan sequence clustered with the strains from Reinbek and Guangzhou. Analysis of the translated amino acid sequence suggests that the encoded peptide is hydrophobic and extracellular with a cleavage site between the 17th and 18th amino acid residues and contains a strong trans-membrane helix from the 6th amino acid to the 24th amino acid, indicating a MD-2-related lipid recognition domain in this protein. Furthermore, the secondary structure of the pro-protein consists of 16.57% alpha helix, 32.57% extended strand and 50.86% random coil. In brief, we obtained a gene coding for Der f 2 and predicted the molecular characteristics of this protein using bioinformatics tools. Our analysis identified that this gene showed several significant differences to those reported previously.

Synonymous codon usage in different protein secondary structural classes of human genes: implication for increased non-randomness of GC3 rich genes towards protein stability.

The relationship between the synonymous codon usage and different protein secondary structural classes were investigated using 401 Homo sapiens proteins extracted from Protein Data Bank (PDB). A simple Chi-square test was used to assess the significance of deviation of the observed and expected frequencies of 59 codons at the level of individual synonymous families in the four different protein secondary structural classes. It was observed that synonymous codon families show non-randomness in codon usage in four different secondary structural classes. However,when the genes were classified according to their GC3 levels there was an increase in non-randomness in high GC3 group of genes. The non-randomness in codon usage was further tested among the same protein secondary structures belonging to four different protein folding classes of high GC3 group of genes. The results show that in each of the protein secondary structural unit there exist some synonymous family that shows class specific codon-usage pattern. Moreover, there is an increased non-random behaviour of synonymous codons in sheet structure of all secondary structural classes in high GC3 group of genes. Biological implications of these results have been discussed.

Building multiple sequence alignments with a flavor of HSSP alignments

Homology-derived secondary structure of proteins (HSSP) is a well-known database of multiple sequence alignments (MSAs) which merges information of protein sequences and their three-dimensional structures. It is available for all proteins whose structure is deposited in the PDB. It is also used by STING and (Java)Protein Dossier to calculate and present relative entropy as a measure of the degree of conservation for each residue of proteins whose structure has been solved and deposited in the PDB. However, if the STING and (Java)Protein Dossier are to provide support for analysis of protein structures modeled in computers or being experimentally solved but not yet deposited in the PDB, then we need a new method for building alignments having a flavor of HSSP alignments (myMSAr). The present study describes a new method and its corresponding databank (SH2QS--database of sequences homologue to the query [structure-having] sequence). Our main interest in making myMSAr was to measure the degree of residue conservation for a given query sequence, regardless of whether it has a corresponding structure deposited in the PDB. In this study, we compare the measurement of residue conservation provided by corresponding alignments produced by HSSP and SH2QS. As a case study, we also present two biologically relevant examples, the first one highlighting the equivalence of analysis of the degree of residue conservation by using HSSP or SH2QS alignments, and the second one presenting the degree of residue conservation for a structure modeled in a computer, which , as a consequence, does not have an alignment reported by HSSP.