title: The VHSE-based prediction of proteasomal cleavage sites.
abstract: 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.
authors.affiliation: Key Laboratory of Dependence Service Computing in Cyber Physical Society, Ministry of Education, Chongqing, China ; College of Computer Science, Chongqing University, Chongqing, China.
authors.forename: Jiangan
authors.initials: J
authors.lastname: Xie
authors.forename: Zhiling
authors.initials: Z
authors.lastname: Xu
authors.forename: Shangbo
authors.initials: S
authors.lastname: Zhou
authors.forename: Xianchao
authors.initials: X
authors.lastname: Pan
authors.forename: Shaoxi
authors.initials: S
authors.lastname: Cai
authors.forename: Li
authors.initials: L
authors.lastname: Yang
authors.forename: Hu
authors.initials: H
authors.lastname: Mei
mesh_terms: D019295:Computational Biology; D015395:Histocompatibility Antigens Class I / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D008024:Ligands; D009842:Oligopeptides / Q000737:chemistry* / Q000378:metabolism; D011237:Predictive Value of Tests; D046988:Proteasome Endopeptidase Complex / Q000378:metabolism*; D059748:Proteolysis; D012107:Research Design; D060388:Support Vector Machine; D014764:Viral Proteins / Q000737:chemistry* / Q000378:metabolism
chemical_list: D015395:Histocompatibility Antigens Class I; D008024:Ligands; D009842:Oligopeptides; D014764:Viral Proteins; D046988:Proteasome Endopeptidase Complex
references.citation: J Immunol. 2002 Feb 15;168(4):1717-22
references.pmid: 11823502
references.citation: J Exp Med. 2000 Jan 17;191(2):239-52
references.pmid: 10637269
references.citation: Immunol Rev. 2005 Oct;207:19-30
references.pmid: 16181324
references.citation: Proc Natl Acad Sci U S A. 1996 Aug 6;93(16):8572-7
references.pmid: 8710912
references.citation: Biochim Biophys Acta. 1975 Oct 20;405(2):442-51
references.pmid: 1180967
references.citation: J Proteomics. 2009 Apr 13;72(3):567-73
references.pmid: 19084081
references.citation: J Mol Biol. 2000 May 5;298(3):417-29
references.pmid: 10772860
references.citation: Proc Natl Acad Sci U S A. 2012 Sep 11;109(37):14870-5
references.pmid: 22927375
references.citation: Nature. 2003 Dec 18;426(6968):895-9
references.pmid: 14685250
references.citation: Front Biosci (Landmark Ed). 2012 Jan 01;17:1904-16
references.pmid: 22201844
references.citation: Immunome Res. 2005 Oct 06;1(1):4
references.pmid: 16305757
references.citation: Appl Bioinformatics. 2003;2(3):155-8
references.pmid: 15130801
references.citation: Nucleic Acids Res. 2007 Jan;35(Database issue):D61-5
references.pmid: 17130148
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D1164-70
references.pmid: 21030437
references.citation: FEBS Lett. 2010 Apr 2;584(7):1393-8
references.pmid: 20040365
references.citation: Biopolymers. 2005;80(6):775-86
references.pmid: 15895431
references.citation: Mol Immunol. 1998 Jun;35(8):427-33
references.pmid: 9798647
references.citation: J Immunol. 2006 Sep 1;177(5):2741-7
references.pmid: 16920906
references.citation: Protein Eng. 2002 Apr;15(4):287-96
references.pmid: 11983929
references.citation: Immunity. 2000 Jan;12(1):107-17
references.pmid: 10661410
references.citation: J Exp Med. 2001 Jul 2;194(1):1-12
references.pmid: 11435468
references.citation: J Immunol. 2009 Dec 1;183(11):7379-87
references.pmid: 19917696
references.citation: Eur J Biochem. 1996 Jan 15;235(1-2):404-15
references.pmid: 8631360
references.citation: J Immunol. 2009 Nov 15;183(10):6069-77
references.pmid: 19841172
references.citation: Immunogenetics. 2001 Mar;53(2):87-94
references.pmid: 11345595
references.citation: Int Immunol. 2003 Jul;15(7):781-7
references.pmid: 12807816
references.citation: J Biol Chem. 2012 Oct 26;287(44):37371-82
references.pmid: 22930756
references.citation: Nat Rev Mol Cell Biol. 2001 Mar;2(3):179-87
references.pmid: 11265247
references.citation: Proc Natl Acad Sci U S A. 1998 Oct 13;95(21):12504-9
references.pmid: 9770515
references.citation: Int Rev Cell Mol Biol. 2008;267:59-124
references.pmid: 18544497
references.citation: Science. 1988 Jun 3;240(4857):1285-93
references.pmid: 3287615
references.citation: J Mol Biol. 2000 Jan 28;295(4):879-90
references.pmid: 10656797
references.citation: Arch Biochem Biophys. 2000 Nov 1;383(1):1-16
references.pmid: 11097171
references.citation: J Biol Chem. 2008 Jun 27;283(26):17891-7
references.pmid: 18424434
references.citation: J Mol Biol. 1999 Mar 5;286(4):1251-65
references.pmid: 10047495