Computational Modeling and Design of Specific Protein-DNA Interfaces

蛋白质和DNA之间的序列特异性相互作用对于DNA的表达和维持至关重要。 基因组信息尽管全基因组测序项目产生了蛋白质-DNA的部件列表， 直接以潜在结合位点的形式和间接以推断蛋白质的形式 序列，这些数据并不直接说明这些部分之间的相互作用。我们的长期目标是 开发用于评估序列特异性结合偏好和亲和力的定量模型， DMA结合蛋白。这项研究背后的具体假设是，准确的建模和 蛋白质-DNA相互作用的工程化需要处理DMA和蛋白质柔性， 现实的评分功能。这是基于几项观察。首先，纯粹基于序列的模型 在预测结合偏好方面仅部分成功。第二，结构数据表明， 在蛋白质-DNA界面中明确定义的位置处的氨基酸可以参与上下文依赖的 由于构象自由的相互作用。因此，侧链的移动能力与常见的 由基于序列的方法做出的假设，即给定位置处的氨基酸具有单一模式， 行动上最后，对同源蛋白质-DNA复合物的晶体结构的检查揭示， 蛋白质和DNA序列的变化伴随着适度但重要的结构变化， 重新安排该提案的具体目标是为蛋白质生成一个物理模型， DNA相互作用，并通过实验测试该模型的预测： 1.构建一个物理模型，描述蛋白质-DNA界面特异性的基础。 2.使用物理化学和统计力学因素生成模型，用于预测 在双组分信号传导中发现的转录因子翼螺旋家族的结合位点 途径。 3.重新设计lAnil归巢核酸内切酶对靶基因的DNA结合和切割偏好 冈比亚按蚊是疟疾的主要传播媒介

Sequence-specific interactions between proteins and DMA are critical for the expression and maintenance of genomic information. Although genome-wide sequencing projects yield a parts list for protein-DNA interactions, directly in the form of potential binding sites and indirectly in the form of inferred protein sequences, these data do not directly speak to the interactions between these parts. Our long-term goal is to develop a quantitative model for assessing the sequence-specific binding preferences and affinities of DMA-binding proteins. The specific hypothesis behind this research is that accurate modeling and engineering of protein-DNA interactions requires treatment of both DMA and protein flexibility, and physically realistic scoring functions. This is based on several observations. First, purely sequence-based models are only partially successful in predicting binding preferences. Second, structural data indicate that a single amino acid at a well-defined position in a protein-DNA interface can participate in context-dependent interactions due to conformational freedom. Thus, a side chain's ability to move contradicts the common assumption made by sequence-based methods that an amino acid at a given position has a single mode of action. Finally, examination of crystal structures of homologous protein-DNA ^complexes reveals that changes in protein and DNA sequences are accompanied by modest but significant structural rearrangements. The specific aims in this proposal are designed to generate a physical model for protein- DNA interactions and to test experimentally the predictions made by this model: 1. To construct a physical model for describing the basis for specificity in protein-DNA interfaces. 2. To generate a model, using physical chemical and statistical mechanical considerations, for the prediction of binding sites for the winged helix family of transcription factors found in two-component signaling pathways. 3. To redesign the DNA binding and cleavage preference of the lAnil homing endonuclease to target genes in Anopheles gambiae, the primary vector for malaria.