Publication: Predicting the Oligomeric States of Fluorescent Proteins
Issued Date
2015
Resource Type
Language
eng
Suggested Citation
Saw Simeon, Watshara Shoombuatong, Likit Preeyanon, Virapong Prachayasittikul, Chanin Nantasenamat (2015). Predicting the Oligomeric States of Fluorescent Proteins. Retrieved from: https://repository.li.mahidol.ac.th/handle/20.500.14594/2121
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Title
Predicting the Oligomeric States of Fluorescent Proteins
Abstract
Currently, monomeric fluorescent proteins (FP) are ideal markers for protein tagging. The
prediction of oligomeric states is helpful for enhancing live biomedical imaging. Computational
prediction of FP oligomeric states can accelerate the effort of protein engineering to create
monomeric FPs by saving time and money. To the best of our knowledge, this study represents
the first computational model for predicting and analyzing FP oligomerization directly from their
amino acid sequences. An exhaustive dataset consisting of 397 unique FP oligomeric states was
compiled from the literature. FP were described by 3 classes of protein descriptors including
amino acid composition, dipeptide composition and physicochemical properties. The oligomeric
states of FP was predicted using decision tree (DT) algorithm and results demonstrated that DT
provided robust performance with accuracies in ranges of 79.97-81.72% and 80.76-82.63% for
the internal (e.g. 10-fold cross-validation) and external sets, respectively. This approach was also
benchmarked with other common machine learning algorithms such as artificial neural network,
support vector machine and random forest. A thorough analysis of amino acid sequence features
was conducted to provide informative insights into FP oligomerization, which may aid in
engineering novel monomeric fluorescent proteins. The following differentiating characteristics
of monomeric and oligomeric fluorescent proteins were derived from DT: (i) substitution of any
amino acid to Glu led to the reduction of aggregated proteins and (ii) oligomerization of FP
appears to be stabilized by several hydrophobic contacts.