PREDICTION OF STRUCTURES OF BIOACTIVE PEPTIDES BY USING HOMOLOGY APPROACH

In silico study for prediction of structures of bioactive peptides by using homology approach and different bioinformatics tools as Basic Local Alignment Search Tool (BLAST) Swiss Model workspace repository and template were applied. The homology model comprises four main steps find out the homology model against query protein identification of structural template(s) alignment of target sequence and template structure(s) model building and model quality evaluation. The feasible structures of antimicrobial antithrombotic casein derived immunomodulatory and mineral binding peptides were designed. Antimicrobial peptide seq8 (NP_446175.1) was analyzed by using above stated methodology and found that 3E6U chain D showed homology with this sequence. Like this methodology was followed for all query bioactive peptide sequences.


INTRODUCTION
Bioactive peptides have been defined as specific protein fragments that have a positive impact on body functions and conditions and may ultimately influence health (Kitts and Weiler 2003). According to Fitz-Gerald & Murray (2006) bioactive peptides have been defined as 'peptides with hormone-or drug-like activity that eventually modulate physiological function through binding interactions to specific receptors on target cells leading to induction of physiological responses. Most of these bioactivities are encrypted within the primary sequence of the native protein and peptides require to be released through one of the following ways: Hydrolysis by digestive enzymes such as trypsin and pepsin (FitzGerald et al 2004Korhonen & Pihlanto-Leppala 2006 Food processing (Van-Beresteijn et al 1994) and Through hydrolysis by proteolytic

Material and methods
The comparison of nucleotide or protein sequences from the same or different organisms is a very powerful tool in molecular biology. By finding similarities between sequences scientists can infer the function of newly sequenced genes predict new members of gene families and explore evolutionary relationships now the whole genomes are being sequenced sequence similarity searching can be used to predict the location and function of protein-coding and transcription-regulation regions in genomic DNA. Basic Local Alignment Search Tool (BLAST) is the tool most frequently used for calculating sequence similarity. BLAST comes in variations for use with different query sequences against different databases. The way most people use BLAST is to input a nucleotide or protein sequence as a query against all (or a subset of) the public sequence databases pasting the sequence into the textbox on one of the BLAST web pages. This sends the query over the Internet the search is performed on the NCBI servers and the results are posted back to the person's browser in the chosen display format. However many biotech companies genome scientists and bioinformatics personnel may want to use "stand-alone" Blast to query their own local databases or want to customize BLAST in some way to make it better suit their needs. Stand-alone BLAST comes in two forms the executables that can be run from the command line or the Standalone WWW BLAST Server which allows users to set up their own in-house versions of the BLAST Web pages.

SWISS-MODEL Workspace
The SWISS-MODEL Workspace is a web-based integrated service dedicated to protein structure homology modeling. It assists and guides the user in building protein homology models at different levels of complexity. Building a homology model comprises four main steps: identification of structural template(s) alignment of target sequence and template structure(s) model building and model quality evaluation. These steps can be repeated until a satisfying modeling result is achieved. Each of the four steps requires specialized software and access to up-to-date protein sequence and structure databases. Protein sequence and structure databases necessary for modeling are accessible from the workspace and are updated in regular intervals. Software tools for template selection model building and structure quality evaluation can be invoked from within the workspace. A personal working environment (workspace) where several modeling projects can be carried out in parallel is provided for each user. This help file provides references and illustrate the use of the individuals tools available from within the SWISS-MODEL Workspace.

SWISS-MODEL Repository
The SWISS-MODEL Repository is a database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL. The repository is developed at the Biozentrum Basel within the Swiss Institute of Bioinformatics. The repository currently contains three-dimensional models for sequences from the UniProt knowledge base. The content of the repository is updated on a regular basis incorporating new sequences taking advantage of new template structures becoming available and reflecting improvements in the underlying modelling algorithms. The current data status is given on the entry page.
The steps of structure prediction of protein are specified as firstly we opt the protein sequence of bioactive peptide from our database i.e. IBPD. Then investigate the protein data bank (PDB) by using BLASTp. After BLASTp and selection of best match form BLASTp results we had done the homology modelling by swiss modal workplace swiss modal repository. Finally we unearth the achievable three dimensional protein models.

Results and discussion
The feasible structures of proteins of unknown structures of bioactive peptides were designed by via bioinformatics tools and software packages and online servers available through different websites. To know about the functions and mode of action it is necessary to study the structures of the peptides. The application of computational chemistry will result in the creation of structure and sequence databases that will enable etc. and so on. An antimicrobial seq8 (NP_446175.1) was analyzed by swiss model for structure prediction and found that this seq was found best similarity with 3E6uD as the e-value was 0.00e-1bit score 91.479. It is again noted that when above stated seq was further analyzed by swiss repository template identification tool same