Team:Warsaw/Modelling/Structural

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Introduction

Because the native conformation of secretion peptide from hemolysin A is not determine we decided to use several computational structure prediction method to find the three-dimensional structure of this domain. Additionally we attempt to obtain the theoretical models of proaptoptotic fusion proteins and naturally occuring proteins which are used in our project.

Fundamental basis

Protein folding

Protein folding is the physical phenomena by which a polypeptide chain folds into highly specific and functional three-dimensional structure from random coil. Shortly after translation from mRNA each protein molecule exist as an unfolded chain with no characteristic conformation. However aminoacids interact with each other to create a well-defined three dimensional structure known as the native state. This resulting conformation is determined by the amino acid sequence.

Fusion proteins

Fusion proteins are proteins which are created by means the joining two or more genes which originally encoded separate polypeptide chain. Expression of that fusion gene results in a single polypeptide with functional properties derived from each of the proteins encoded by used genes. Recombinant fusion proteins are created artificially via DNA recombination for use in biological research or to produce altered proteins with new features.

In most cases the functionality of fusion proteins is not interrupted. It is possible due to intristic protein domains modularity. The fragment of polypeptide which corresponds to a given domain may be removed ar added to the rest of the molecule without destroying its native capabilities.

However it is highly recommended to predict the three-dimensional structure of fusion protein or the artificially attached domains. The knowledge of the spatial organisation of any given protein is an extremely useful prerequisite for the understanding of the function and for the rational modification of the proteins.

Methods

We choose following servers to compute the secondary structures and full models for proteins of interest.

[http://www.bioinfo.pl/ BioInfoBank Meta Server]

This server offers a set of structural models collected from the prediction servers are assessed using the powerful 3D-jury consensus approach.

[http://zhang.bioinformatics.ku.edu/I-TASSER/ TASSER]

I-TASSER server is an Internet service for protein structure and function predictions. Models are built based on multiple-threading alignments by LOMETS and iterative TASSER simulations.

[http://robetta.bakerlab.org/ Robetta]

Robetta is a full-chain protein structure prediction server. It parses protein chains into putative domains and models those domains either by homology modeling or by de novo modeling

[http://www.reading.ac.uk/bioinf/ModFOLD/ The ModFOLD Model Quality Assessment Server]

ModFOLD is a server which can provide a single score and a p-value relating to the predicted quality of a single 3D model of a protein structure and rankings for multiple 3D models for the same protein target according to predicted model quality. It also may do some predictions of the local quality within multiple models.