Recurrence quantification analysis reveals interaction partners in paramyxovirlidae envelope glycoproteins

被引:15
作者
Giuliani, A
Tomasi, M
机构
[1] Ist Super Sanita, Tossicol Comparata & Ecotossicol Lab, I-00161 Rome, Italy
[2] Ist Super Sanita, Cell Biol Lab, I-00161 Rome, Italy
来源
PROTEINS-STRUCTURE FUNCTION AND GENETICS | 2002年 / 46卷 / 02期
关键词
signal analysis; bioinformatics; nonlinear methods; membrane fusion; protein-protein interaction;
D O I
10.1002/prot.10044
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The paramyxovirus envelope fuses with the host cell membrane by cooperative interaction of two transmembrane glycoproteins: the hemagglutinin neuraminidase (HN) and the fusion (F) glycoprotein. The interaction appears to be finely regulated, as both proteins must derive from the same viral species to obtain a functional interaction. Because HN and F do not form stable complexes, this interaction is poorly characterized. This article demonstrates that a modification of a classical bioinformatic method based on the co-evolution of interacting partners can detect the specificity of the HN and F interaction. The proposed approach relies on a relatively new nonlinear signal analysis technique, recurrence quantification analysis (RQA), applied to the hydrophobicity sequences of viral proteins. This technique is able to shed light on the interaction between RN and F proteins in the virus-cell fusion and, more generally, permits the quantitative comparison of nonhomologue protein systems. On the contrary, the same co-evolution approach, based on the classical sequence alignment procedure, was unable to discriminate interacting partners from the general strict correlation existing between the evolution of viral proteins as a whole. The cooperation between HN and F in the fusion process is thus demonstrated by a bioinformatic, purely sequence-dependent, perspective. Proteins 2002;46:171-176. (C) 2001 Wiley-Liss, Inc.
引用
收藏
页码:171 / 176
页数:6
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