Carbon distribution to toxic effect in toxin proteins.

The role of hydrophobic force in biological function through the formation of several local macro-molecular structures is evident. Carbon is the element that contributes to biological function in living systems. We show that carbon distribution is related to protein activity using an example. The carbon distribution profile is foreseen to help undestand unfolded and misfolded regions of protein structures. The carbon distribution profile in a toxin protein that is found associated with the toxic shock syndrome is described in this study. The carbon profile provides insight to the association of specific residues responsible for toxicity.

CARd: Carbon distribution analysis program for protein sequences.

Carbon distribution is responsible for stability and structure of proteins. Arrangement of carbon along the protein sequence is depends on how the amino acids are organized and is guided by mRNAs. An atomic level revision is important for understanding these codes. This will ultimately help in identification of disorders and suggest mutations. For this purpose a carbon distribution analysis program has been developed. This program captures the hydrophobic / hydrophilic / disordered regions in a protein. The program gives accurate results. The calculations are precise and sensitive to single amino acid resolution. This program is to help in mutational studies leading to protein stabilisation.

Allotment of carbon is responsible for disorders in proteins.

Sequence stretches in proteins that do not fold into a form are referred as disordered regions. Databases like Disport describe disordered regions in proteins and web servers like PrDOS and DisEMBL, facilitate the prediction of disordered regions. These studies are often based on residue level features. Here, we describe proteins with disordered regions using carbon content and distributions. The distribution pattern for proteins with disordered regions is different from those that do not show disordered regions.

CARBANA: Carbon analysis program forprotein sequences.

There are lots of works gone into proteins to understand the nature of proteins. Hydrophobic interaction is the dominant force that drives the proteins to carry out the biochemical reactions in all living system. Carbon is the only element that contributes towards this hydrophobic interaction. Studies find that globular proteins prefer to have 31.45% of carbon for its stability. Taking this as standard, a carbon analysis program has been developed to study the carbon distribution profile of protein sequences. This carbon analysis program has been made available online. This can be accessed at www.rajasekaran.net.in/tools/carbana.html. This new program is hoped to help in identification and development of active sites, study of protein stability, evolutionary understating of proteins, gene identification, ligand binding site identification, and to solve the long-standing problem of protein-protein and protein-DNA interactions.

Role of large hydrophobic residues in proteins.

Large Hydrophobic Residues (LHR) such as phenylalanine, isoleucine, leucine, methionine and valine play an important role in protein structure and activity. We describe the role of LHR in complete set of protein sequences in 15 different species. That is the distribution of LHR in different proteins of different species is reported. It is observed that the proteins prefer to have 27% of large hydrophobic residues in total and all along the sequence. It is also observed that proteins accumulate more LHR in its active sites. A window analysis on these protein sequences shows that the 27% of LHR is more frequent at window length of 45 amino acids. The influenza virus and P. falciparum show a random distribution of LHR in its proteins compared to other model organisms.

Role of thymine in protein coding frames of mRNA sequences.

Distribution of thymine in protein coding mRNA sequences has been studied here. Our study suggest that thymine in protein coding sequences are not randomly distributed but with probability. Frame1 prefers to have definite amount of thymine. It is observed that the thymine content of frame 4 is also involved in protein coding. Frame 3 prefers to have least amount of thymine. However, frame 2 and frame 6 shows a variable degree of thymine content. The mRNA sequences of heterosexual animals, particularly, the human show a different distribution profile (less thymine in frame 1) compared to that of yeast and plants.

BIOFFORC: tool development for biological file format conversion.

UNLABELLED: The use of bioinformatics tools require different sequence formats at various instances. Every tool uses specific set of formats for processing. Sequence in one format is often required in another format. Thus, there is a need for sequence format conversion. A number of such tools are available in the public domain. Here, we describe BIOFFORC as a file format converter. The tool is developed with a graphical user interface in PERL. AVAILABILITY: http://www.winningpath.com/biofforc/