Layers: A molecular surface peeling algorithm and its applications to analyze protein structures.

Naga Bhushana Rao Karampudi,Ranjit Prasad Bahadur

doi:10.1038/srep16141

Naga Bhushana Rao Karampudi, Ranjit Prasad Bahadur

Open Access

https://doi.org/10.1038/srep16141

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Journal: Scientific reports	Publication Date: Nov 10, 2015
Citations: 5	License type: CC BY 4.0

Affiliation: Indian Institute of Technology Kharagpur

Abstract

We present an algorithm ‘Layers’ to peel the atoms of proteins as layers. Using Layers we show an efficient way to transform protein structures into 2D pattern, named residue transition pattern (RTP), which is independent of molecular orientations. RTP explains the folding patterns of proteins and hence identification of similarity between proteins is simple and reliable using RTP than with the standard sequence or structure based methods. Moreover, Layers generates a fine-tunable coarse model for the molecular surface by using non-random sampling. The coarse model can be used for shape comparison, protein recognition and ligand design. Additionally, Layers can be used to develop biased initial configuration of molecules for protein folding simulations. We have developed a random forest classifier to predict the RTP of a given polypeptide sequence. Layers is a standalone application; however, it can be merged with other applications to reduce the computational load when working with large datasets of protein structures. Layers is available freely at http://www.csb.iitkgp.ernet.in/applications/mol_layers/main.

Highlights

In a linear polypeptide, residues at distant positions interact and form a nucleus, which grows into a fully folded structure by wrapping the surrounding residues[20]
We have developed Layers, which identifies residue transition pattern from folded protein structures, extracts surface atoms and non-randomly samples the molecular surface
The residue transition pattern (RTP) based on peeled layers can be used to identify proteins with similar folding patterns

Summary

Introduction

Residues at distant positions interact and form a nucleus, which grows into a fully folded structure by wrapping the surrounding residues[20]. Viewing molecules as layers of atoms, it can be hypothesized that the surface layer is stabilized by the inner layers. We have developed an algorithm named Layers that peels atoms of molecules as layers from periphery to center. Layers identifies residue transition pattern (RTP), which may be used for the comparison of folding pattern between two molecules. It extracts molecular surfaces and protruding atoms at custom fineness by non-random sampling, which can be used for shape estimation and molecular surface comparison for protein recognition and ligand design. We present a comparison of surface layers extracted using Layers and Solvent Accessible Surface Area (SASA) method[21]

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Results

Conclusion