The VHSE-based prediction of proteasomal cleavage sites

Prediction of proteasomal cleavage sites has been a focus of computational biology. Up to date, the predictive methods are mostly based on nonlinear classifiers and variables with little physicochemical meanings. In this paper, the physicochemical properties of 14 residues both upstream and downstre...

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Bibliographic Details
Published in:PloS one 2013-09, Vol.8 (9), p.e74506-e74506
Main Authors: Xie, Jiangan, Xu, Zhiling, Zhou, Shangbo, Pan, Xianchao, Cai, Shaoxi, Yang, Li, Mei, Hu
Format: Article
Language:English
Subjects:
Algorithms
Amino acids
Antigens
Bioengineering
Cleavage
Computational Biology
Computer applications
Computer science
Datasets
Downstream
Education
Histocompatibility Antigens Class I - chemistry
Histocompatibility Antigens Class I - metabolism
Humans
Hydrophobic and Hydrophilic Interactions
Hydrophobicity
Immunology
In vivo methods and tests
Laboratories
Ligands
Methods
Oligopeptides - chemistry
Oligopeptides - metabolism
Peptides
Physicochemical properties
Prediction models
Predictive Value of Tests
Properties (attributes)
Proteasome Endopeptidase Complex - metabolism
Proteasomes
Proteins
Proteolysis
Research Design
Residues
Substrates
Support Vector Machine
Support vector machines
Upstream
Viral Proteins - chemistry
Viral Proteins - metabolism
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Summary:Prediction of proteasomal cleavage sites has been a focus of computational biology. Up to date, the predictive methods are mostly based on nonlinear classifiers and variables with little physicochemical meanings. In this paper, the physicochemical properties of 14 residues both upstream and downstream of a cleavage site are characterized by VHSE (principal component score vector of hydrophobic, steric, and electronic properties) descriptors. Then, the resulting VHSE descriptors are employed to construct prediction models by support vector machine (SVM). For both in vivo and in vitro datasets, the performance of VHSE-based method is comparatively better than that of the well-known PAProC, MAPPP, and NetChop methods. The results reveal that the hydrophobic property of 10 residues both upstream and downstream of the cleavage site is a dominant factor affecting in vivo and in vitro cleavage specificities, followed by residue's electronic and steric properties. Furthermore, the difference in hydrophobic potential between residues flanking the cleavage site is proposed to favor substrate cleavages. Overall, the interpretable VHSE-based method provides a preferable way to predict proteasomal cleavage sites.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0074506