标题：Protein structures-based neighborhood analysis vs preferential interactions between the special pairs of amino acids?
作者：Wang J;Cao Z;Yu J
作者机构：[Wang, J] Key Lab of Biophysics, Universities of Shandong, Dezhou University, Dezhou, 253023, China, Department of Physics, Dezhou University, Dezhou, 更多
通讯作者地址：[Wang, JH]Dezhou Univ, Shandong Univ, Key Lab Biophys, Dezhou 253023, Peoples R China.
来源：Journal of Biomolecular Structure and Dynamics
摘要：In the paper titled \"A stoichiometry driven universal spatial organization of. backbones of folded proteins: are there chargaff s rules for protein folding?\" (1), extensive statistic works were performed on 3718 structured proteins to exploit the potential inherent laws in protein folding problems. Subsequently, protein structure-based neighborhood analysis (see Figure 1 in Mittal et al. paper) was conducted to the backbones of these protein dataset. The results show that there are similar sigmoidal trends for neighborhoods of all the 20 amino acids, and all the sigmoidals were fitted as a generalized, single, sigmoidal equation (see Figure 2 in Mittal et al. paper). Based on the results, the total number of contacts made by amino acids was found to correlate excellently with average occurrence of that amino acid in the folded proteins shown in Figure 2E. Thereout the authors deduced that there is no any preferential interactions between amino acids, and protein folding is a direct consequence of a narrow band of stoichiometric occurrences of amino acids in primary sequences regardless of the size and the fold of a protein. In this connection, it should be noted that the preferential interactions between amino acids are the basis for introducing knowledge-based potentials, which in turn provide the underpinning for present day three-dimensional protein structure prediction by modeling and simulation (2-5).