H Y Zhang

Publications (2)9.97 Total impact

• Article: tRNA-dependent cysteine biosynthetic pathway represents a strategy to increase cysteine contents by preventing it from thermal degradation: thermal adaptation of methanogenic archaea ancestor.

  Ge Qu, Wei Wang, Ling-Ling Chen, Shao-Song Qian, Hong-Yu Zhang
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  ABSTRACT: Although cysteine (Cys) is beneficial to stabilize protein structures, it is not prevalent in thermophiles. For instance, the Cys contents in most thermophilic archaea are only around 0.7%. However, methanogenic archaea, no matter thermophilic or not, contain relatively abundant Cys, which remains elusive for a long time. Recently, Klipcan et al. correlated this intriguing property of methanogenic archaea with their unique tRNA-dependent Cys biosynthetic pathway. But, the deep reasons underlying the correlation are ambiguous. Considering the facts that free Cys is thermally labile and the tRNA-dependent Cys biosynthesis avoids the use of free Cys, we speculate that the unique Cys biosynthetic pathway represents a strategy to increase Cys contents by preventing it from thermal degradation, which may be relevant to the thermal adaptation of methanogenic archaea ancestor.
  Journal of biomolecular structure & dynamics 11/2009; 27(2):111-4. · 4.99 Impact Factor
• Article: Bioinformatic identification of the most ancient copper protein architecture.

  Hong-Fang Ji, Hong-Yu Zhang
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  ABSTRACT: Since copper ions participate in many cellular processes and are implicated in pathogenesis of many diseases, copper proteins have important biological significance. Thus, it is of interest to explore their origins, especially to address the following question: which is the most ancient architecture of copper proteins? In this paper, through analyzing the architectural features of copper proteins, we find that the fold-domain relationship of these proteins follows a power law, which can be explained by preferential attachment principle and implicates that the architecture of the most ancient copper proteins belonged to Cupredoxin-like (b.6) fold. According to the chronology of protein folds, this architecture originated rather late, which can be understood in terms of the low abundance of reducing amino acids (e.g., His, Cys and/or Met) in the primordial world, because these amino acids are required by copper proteins to bind copper ions.
  Journal of biomolecular structure & dynamics 11/2008; 26(2):197-201. · 4.99 Impact Factor