Correlations between designability and various structural characteristics of protein lattice models.
Correlations between designability and various structural characteristics of protein lattice models.
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蛋白质晶格模型的可设计性与各种结构特征之间的相关性。
DOI：
10.1063/1.2737042
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发表时间：
2007
期刊：
影响因子：
--
通讯作者：
V. Anh
中科院分区：
文献类型：
--
作者：
Jianyi Yang;Zuguo Yu;V. Anh
利用6种晶格类型（4 × 4、5 × 5和6 × 6方形晶格、3 × 3 × 3立方晶格、2+3+4+3+2和4+5+6+5+4三角形晶格）、3种不同大小的字母（HP、HNUP和20个字母）和2种能量函数，基于结构的随机抽样和蛋白质序列空间的共同偏置抽样（CBS）计算蛋白质结构的可设计性。然后对结构的稳定性（平均能隙）、可折叠性和可设计性三个量进行了计算，以阐明结构的可设计性。作者发现，无论使用何种晶格类型、字母大小和能量函数，都会出现高度可设计（首选）的结构。对于所有考虑的情况，局部相互作用减少了简并并提高了可设计性。可设计性对序列空间的格子类型、字母大小、能量函数和采样方法都很敏感。与随机抽样方法相比，CBS和Metropolis蒙特卡罗抽样方法都提高了设计性。可设计性、稳定性和可折叠性三者之间的相关系数大多大于0.5，表明三者之间存在较强的相关关系。但可设计性与可设计性之间的相关关系并不强，因为可设计性与能量无关。结果对可设计性原理在蛋白质三级结构预测等方面的实际应用具有指导意义。
Using six kinds of lattice types (4 x 4, 5 x 5, and 6 x 6 square lattices; 3 x 3 x 3 cubic lattice; and 2+3+4+3+2 and 4+5+6+5+4 triangular lattices), three different size alphabets (HP, HNUP, and 20 letters), and two energy functions, the designability of protein structures is calculated based on random samplings of structures and common biased sampling (CBS) of protein sequence space. Then three quantities stability (average energy gap), foldability, and partnum of the structure, which are defined to elucidate the designability, are calculated. The authors find that whatever the type of lattice, alphabet size, and energy function used, there will be an emergence of highly designable (preferred) structure. For all cases considered, the local interactions reduce degeneracy and make the designability higher. The designability is sensitive to the lattice type, alphabet size, energy function, and sampling method of the sequence space. Compared with the random sampling method, both the CBS and the Metropolis Monte Carlo sampling methods make the designability higher. The correlation coefficients between the designability, stability, and foldability are mostly larger than 0.5, which demonstrate that they have strong correlation relationship. But the correlation relationship between the designability and the partnum is not so strong because the partnum is independent of the energy. The results are useful in practical use of the designability principle, such as to predict the protein tertiary structure.
DOI：
10.1073/pnas.93.8.3341
发表时间：
1996-04-16
影响因子：
11.1
作者：
Govindarajan, S;Goldstein, RA
通讯作者：
Goldstein, RA
DOI：
10.1073/pnas.89.19.9029
发表时间：
1992-10-01
影响因子：
11.1
作者：
GOLDSTEIN, RA;LUTHEYSCHULTEN, ZA;WOLYNES, PG
通讯作者：
WOLYNES, PG