Graham Sandra E, Peterson Julian A
Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.
Methods Enzymol. 2002;357:15-28. doi: 10.1016/s0076-6879(02)57661-8.
It seems as if the algorithms and weighting matrices for multiple sequence alignments of the highly divergent members of the P450 gene superfamily have advanced to the point that unknown proteins can be aligned to structurally known members with reasonable accuracy. As stated earlier, the alignment tends to break down at gaps in the sequence alignments, but these regions can be improved manually. This type of alignment and analysis is especially useful for extracting and analyzing the various genome databases. Variations of the conservation analysis can be used to identify charged and uncharged residues that may be important in domain/domain interactions with redox partners or effector molecules (e.g., cytochrome b5). From these alignments and with comparative analysis within families and across P450 families, one can readily obtain an estimation of those residues that might be involved in substrate binding, in redox partner interaction, and in the catalytic mechanism.
对于细胞色素P450基因超家族中高度分化成员的多序列比对而言，其算法和权重矩阵似乎已经发展到这样一种程度，即未知蛋白质能够以合理的准确度与结构已知的成员进行比对。如前所述，比对往往会在序列比对的缺口处失效，但这些区域可以手动改进。这种类型的比对和分析对于提取和分析各种基因组数据库特别有用。保守性分析的变体可用于识别在与氧化还原伙伴或效应分子（如细胞色素b5）的结构域/结构域相互作用中可能重要的带电荷和不带电荷的残基。通过这些比对以及家族内部和跨细胞色素P450家族的比较分析，可以很容易地估计出那些可能参与底物结合、氧化还原伙伴相互作用和催化机制的残基。
