Insights into Protein Sequence and Structure-Derived Features Mediating 3D Domain Swapping Mechanism using Support Vector Machine Based Approach.

Bioinformatics and Biology Insights
Khader ShameerR Sowdhamini

Abstract

3-dimensional domain swapping is a mechanism where two or more protein molecules form higher order oligomers by exchanging identical or similar subunits. Recently, this phenomenon has received much attention in the context of prions and neurodegenerative diseases, due to its role in the functional regulation, formation of higher oligomers, protein misfolding, aggregation etc. While 3-dimensional domain swap mechanism can be detected from three-dimensional structures, it remains a formidable challenge to derive common sequence or structural patterns from proteins involved in swapping. We have developed a SVM-based classifier to predict domain swapping events using a set of features derived from sequence and structural data. The SVM classifier was trained on features derived from 150 proteins reported to be involved in 3D domain swapping and 150 proteins not known to be involved in swapped conformation or related to proteins involved in swapping phenomenon. The testing was performed using 63 proteins from the positive dataset and 63 proteins from the negative dataset. We obtained 76.33% accuracy from training and 73.81% accuracy from testing. Due to high diversity in the sequence, structure and functions of proteins involved in d...Continue Reading

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Citations

Apr 5, 2012·Journal of Clinical Bioinformatics·Khader Shameer, Ramanathan Sowdhamini
Jan 26, 2012·Biochimie·Antonello MerlinoFilomena Sica
Jan 21, 2018·Heart·Khader ShameerPartho P Sengupta
Oct 1, 2011·Database : the Journal of Biological Databases and Curation·Khader ShameerRamanathan Sowdhamini
Mar 3, 2018·Acta Crystallographica. Section F, Structural Biology Communications·Clare HannonSimon E V Phillips
Jun 26, 2017·JACC. Basic to Translational Science·Kipp W JohnsonJoel T Dudley

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Software Mentioned

CD
3Dswap
custom Perl scripts
PyMol
Domain Identification ALgorithm ( DIAL )
JOY package
JOY
Protein Quaternary Structure server ( PQS )
Rasmol
LIBSVM

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