Computational Modeling and Design of Specific Protein-DNA Interfaces

特定蛋白质-DNA 界面的计算建模和设计

• 批准号: 7320199
• 负责人: JAMES J HAVRANEK
• 金额: $ 8.3万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-08-02 至 2008-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7320199
• 关键词: Affinity; Amino Acid Sequence; Amino Acids; Anopheles gambiae; Base Sequence; Binding; Binding Sites; Chemicals; Complex; Computer Simulation; DNA; DNA Binding; DNA Sequence; DNA Sequence Rearrangement; DNA-Binding Proteins; DNA-Protein Interaction; Data; Family; Freedom; Gene Targeting; Genome; Genomics; Goals; Homing; Homologous Protein; Maintenance; Malaria; Mechanics; Methods; Modeling; Peptide Sequence Determination; Pliability; Positioning Attribute; Protein Engineering; Proteins; Research; Score; Side; Signal Pathway; Specificity; Structure; Testing; Water; Winged Helix; base; design; endonuclease; model design; physical model; preference; transcription factor; vector

DESCRIPTION (provided by applicant): Sequence-specific interactions between proteins and DNA 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 DNA-binding proteins. The specific hypothesis behind this research is that accurate modeling and engineering of protein-DNA interactions requires treatment of both DNA 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.

描述（由申请人提供）：蛋白质和 DNA 之间的序列特异性相互作用对于基因组信息的表达和维护至关重要。尽管全基因组测序项目产生了蛋白质-DNA相互作用的部分列表，直接以潜在结合位点的形式，间接以推断的蛋白质序列的形式，但这些数据并不能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一个定量模型来评估 DNA 结合蛋白的序列特异性结合偏好和亲和力。这项研究背后的具体假设是蛋白质-DNA 相互作用的精确建模和工程需要处理 DNA 和蛋白质的灵活性以及物理上真实的评分函数。这是基于一些观察结果。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。其次，结构数据表明，由于构象自由，蛋白质-DNA 界面中明确位置上的单个氨基酸可以参与上下文相关的相互作用。因此，侧链的移动能力与基于序列的方法做出的常见假设相矛盾，即给定位置的氨基酸具有单一的作用模式。最后，对同源蛋白质-DNA 复合物晶体结构的检查表明，蛋白质和 DNA 序列的变化伴随着适度但显着的结构重排。 该提案的具体目标是生成蛋白质-DNA 相互作用的物理模型，并通过实验测试该模型的预测： (1) 构建描述蛋白质-DNA界面特异性基础的物理模型。 (2) 利用物理化学和统计机械考虑因素生成一个模型，用于预测双组分信号传导途径中转录因子翼螺旋家族的结合位点。 (3) 重新设计lAnil归巢核酸内切酶对疟疾主要传播媒介冈比亚按蚊靶基因的DNA结合和切割偏好。