The disposition of the LZCC protein residues in wenxiang diagram provides new insights into the protein–protein interaction mechanism

Abstract

Wenxiang diagram is a new two-dimensional representation that characterizes the disposition of hydrophobic and hydrophilic residues in α-helices. In this research, the hydrophobic and hydrophilic residues of two leucine zipper coiled-coil (LZCC) structural proteins, cGKIα(1-59) and MBS(CT35) are dispositioned on the wenxiang diagrams according to heptad repeat pattern (abcdefg)(n), respectively. Their wenxiang diagrams clearly demonstrate that the residues with same repeat letters are laid on same side of the spiral diagrams, where most hydrophobic residues are positioned at a and d, and most hydrophilic residues are localized on b, c, e, f and g polar position regions. The wenxiang diagrams of a dimetric LZCC can be represented by the combination of two monomeric wenxiang diagrams, and the wenxiang diagrams of the two LZCC (tetramer) complex structures can also be assembled by using two pairs of their wenxiang diagrams. Furthermore, by comparing the wenxiang diagrams of cGKIα(1-59) and MBS(CT35), the interaction between cGKIα(1-59) and MBS(CT35) is suggested to be weaker. By analyzing the wenxiang diagram of the cGKIα(1-59.)·MBS(CT42) complex structure, most affected residues of cGKIα(1-59) by the interaction with MBS(CT42) are proposed at positions d, a, e and g of the LZCC structure. These findings are consistent with our previous NMR results. Incorporating NMR spectroscopy, the wenxiang diagrams of LZCC structures may provide novel insights into the interaction mechanisms between dimeric, trimeric, tetrameric coiled-coil structures.

Predicting protein structural classes based on complex networks and recurrence analysis

“…Moreover, introducing complex networks to biological systems can provide an intuitive vision and useful insights. Actually, various graph approaches have been successfully used to analyze many important biological problems, such as enzyme-catalyzed reactions [60][61][62][63], protein folding kinetics and folding rates [64,65], inhibition of HIV-1 reverse transcriptase [66,67], non-steady drug metabolism systems [68], evolution of biological sequences [69], and using Wenxiang graphs [70] to analyze protein-protein interactions [71,72]. This is mainly because the local and global properties of complex networks are useful for recognizing complicated interconnections and the information flow between different components in extended systems.…”

Wavelet images and Chou’s pseudo amino acid composition for protein classification

“…The graphical analysis via the ''cellular automaton image'' (Wolfram 1984) has also been applied to study hepatitis B viral infections (Xiao et al 2006) and HBV virus gene missense mutation (Xiao et al 2005), as well as representing complicated biological sequences (Xiao et al 2005) and providing assistance in the identification of various important protein attributes (Xiao et al 2006(Xiao et al , 2011Xiao and Chou 2007). Recently, the Wenxiang diagram (see Chou et al 1997 and the web-server at http://icpr.jci.edu.cn/bioinfo/wenxiang) has been used to study protein-protein interactions and provided very useful insights (Zhou 2011).…”

iAMP-2L: A two-level multi-label classifier for identifying antimicrobial peptides and their functional types

“…To address this problem, let us carry out a graphical analysis. Using graphic approaches to study biological systems can provide an intuitive vision and useful insights for helping analyze complicated relations therein, as indicated by many previous studies on a series of important biological topics, such as enzyme-catalyzed reactions [71][72][73], protein folding kinetics and folding rates [74], inhibition of HIV-1 reverse transcriptase [75], inhibition kinetics of processive nucleic acid polymerases and nucleases [76], protein sequence evolution [77], drug metabolism systems [78], and recently using wenxiang diagrams or graphs [79] to analyze protein-protein interactions [80].…”