Woolfson D N, Alber T
Department of Molecular and Cell Biology, University of California, Berkeley 94720-3206, USA.
Protein Sci. 1995 Aug;4(8):1596-607. doi: 10.1002/pro.5560040818.
An algorithm based on the profile method was developed that faithfully distinguishes between the amino acid sequences of dimeric and trimeric coiled coils. Normalized sequence profiles derived from nonhomologous, two- and three-stranded, coiled-coil sequences with unambiguous registers were used to assign dimer and trimer propensities to test sequences. The difference between the dimer and trimer profile scores accurately reflected the preferred oligomerization state. The method relied on two strategies that may be generally applicable to profile calculations--profile values of solvent-exposed residues and of amino acids that were underrepresented in the data-base were given zero weight. Differences between the dimer and trimer profiles revealed sequence patterns that match and extend experimental studies of oligomer specification.
开发了一种基于轮廓法的算法，该算法能准确区分二聚体和三聚体卷曲螺旋的氨基酸序列。从具有明确比对的非同源双链和三链卷曲螺旋序列中得出的标准化序列轮廓，用于确定测试序列的二聚体和三聚体倾向。二聚体和三聚体轮廓得分之间的差异准确反映了偏好的寡聚化状态。该方法依赖于两种可能普遍适用于轮廓计算的策略——溶剂暴露残基和数据库中代表性不足的氨基酸的轮廓值被赋予零权重。二聚体和三聚体轮廓之间的差异揭示了与寡聚体规格的实验研究相匹配并扩展的序列模式。
