Lee Julian
Department of Bioinformatics and Life Science, Soongsil University, Seoul 156-743, Korea.
Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Aug;88(2):022710. doi: 10.1103/PhysRevE.88.022710. Epub 2013 Aug 14.
I compute exact partition function zeros of β hairpins, using both analytic and numerical methods, extending previous work [J. Lee, Phys. Rev. Lett. 110, 248101 (2013)] where only a restricted class of hairpins was considered. The zeros of β hairpins with an odd number of peptide bonds are computed and the difference of the distribution of zeros from those for an even number of peptide bonds is explained in terms of additional entropy of liberating the extra bond at the turn region. Upon the introduction of a hydrophobic core in the central region of the hairpin, the zeros are distributed uniformly on two concentric circles corresponding to the hydrophobic collapse and the transition to the fully folded conformation. One of the circles dissolves as the core moves toward the turn or the tip region, which is explained in terms of the similarity of the intermediate state with the folded or unfolded states. The exact partition function zeros for a hairpin with a more complex structure of native contacts, the 16 C-terminal residues of streptococcal protein G B1, are numerically computed and their loci are closely approximated by concentric circles.
我使用解析和数值方法计算了β发夹的精确配分函数零点,扩展了之前的工作[J. Lee, Phys. Rev. Lett. 110, 248101 (2013)],在之前的工作中仅考虑了一类受限的发夹。计算了具有奇数个肽键的β发夹的零点,并根据在转角区域释放额外键的附加熵解释了与具有偶数个肽键的发夹的零点分布差异。在发夹的中心区域引入疏水核心后,零点均匀分布在两个同心圆上,分别对应疏水塌缩和向完全折叠构象的转变。当核心向转角或末端区域移动时,其中一个圆消失,这可以根据中间状态与折叠或未折叠状态的相似性来解释。对具有更复杂天然接触结构的发夹,即链球菌蛋白G B1的16个C末端残基,进行了精确配分函数零点的数值计算,其轨迹由同心圆紧密近似。