Chemmama Ilan E, Chapagain Prem P, Gerstman Bernard S
Theoretical and Computational Biophysics Group, Department of Physics, Florida International University, Miami, Florida 33199, USA.
Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Apr;91(4):042709. doi: 10.1103/PhysRevE.91.042709. Epub 2015 Apr 15.
We investigate the propensities for amino acids to form a specific secondary structure when they are paired with other amino acids. Our investigations use molecular dynamics (MD) computer simulations, and we compare the results to those from the Protein Data Bank (PDB). Proper comparison requires weighting of the MD results in a manner consistent with the relative frequency of appearance in the PDB of each possible pair of amino acids. We find that the propensity for an amino acid to assume a secondary structure varies dramatically depending on the amino acid that is before or after it in the primary sequence. This cooperative effect means that when selecting amino acids to facilitate the formation of a secondary structure in peptide engineering experiments, the adjacent amino acids must be considered.
我们研究了氨基酸与其他氨基酸配对时形成特定二级结构的倾向。我们的研究使用分子动力学（MD）计算机模拟，并将结果与蛋白质数据库（PDB）中的结果进行比较。为了进行恰当的比较，需要以与PDB中每对可能的氨基酸出现的相对频率一致的方式对MD结果进行加权。我们发现，氨基酸形成二级结构的倾向会因一级序列中其前面或后面的氨基酸而有显著差异。这种协同效应意味着，在肽工程实验中选择氨基酸以促进二级结构形成时，必须考虑相邻的氨基酸。
