Role of Helix Formation in Mediating Protein-Protein Interactions

螺旋形成在介导蛋白质-蛋白质相互作用中的作用

基本信息

批准号：
7939916
负责人：
GEORGE I MAKHATADZE
金额：
$ 29.91万
依托单位：
RENSSELAER POLYTECHNIC INSTITUTE
依托单位国家：
美国
项目类别：
财政年份：
1998
资助国家：
美国
起止时间：
1998-05-01 至 2011-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7939916
关键词：
Address Affect Affinity Alzheimer&apos s Disease Amino Acid Sequence Binding Bioinformatics Biological Biological Models Biomedical Research Breast Calcium Calorimetry Cell Cycle Regulation Cells Characteristics Chimeric Proteins Circular Dichroism Spectroscopy Complex Computational Biology DNA Repair Degenerative Disorder Fluorescence Foundations Gene Silencing Genus Cola Goals Kinetics Lead Mediating Methods Modeling Molecular Conformation Mono-S Neoplasm Metastasis Neoplastic Cell Transformation Peptides Phosphorylation Play Post-Translational Protein Processing Process Property Prostate Proteins Relaxation Research Role S100 Proteins Shapes Site-Directed Mutagenesis Solutions Specificity Stress Response Signaling Structure Subgroup Syndrome System Thermodynamics Transcriptional Regulation Treatment Efficacy Ubiquitin Work biological systems cancer type computer studies design human disease molecular dynamics programs protein degradation protein protein interaction protein structure trafficking

项目摘要

Th Protein-target interaction is one of the most important processes occurring in biological systems. One subgroup of such interactions takes place with a dramatic change in the secondary structure: from unstructured (coil) when it is unbound to a very characteristic structure (helix) when it is in the bound state. A detailed statistical thermodynamics study of the factors that affect this transition (from coil to helix), and how these factors affect the interaction between the protein and its target is very important as deregulation can result in a serious malfunction of the biological machinery and ultimately can be lethal. We will use the interactions between ubiquitin and ubiquitin interacting motif (UIM) as a model system to study in structural, dynamics and thermodynamics details the ubiquitin-UIM complex formation. Ubiquitin is a very small protein, yet it performs a wide variety of regulatory functions in the cell including protein degradation, trafficking, cell-cycle control, DNA repair, transcription regulation and gene silencing, stress response and signaling. All these functions are in the form of post-translational modifications of proteins via mono- or poly- ubiquitinylation. The extent and importance of ubiquitinylation as a regulatory cellular mechanism is widespread, and by some estimates, is surpassed only by protein phosphorylation. Among numerous target sequences that bind ubiquitin, the UIM is perhaps the simplest. It is a short 20-amino acid sequence that undergoes a coil-helix transition upon binding to ubiquitin. Rules that affect specificity and affinity in this type of interaction will be crucial in computational biology and bioinformatics to better predict target sequences that can interact with ubiquitin. To achieve these goals we will use both experimental and computational approaches to study ubiquitin-UIM complex formation. Experimental methods will include site-directed mutagenesis, calorimetry, fluorescence and circular dichroism spectroscopies, structural and relaxation NMR analysis. The computational approach will involve molecular dynamics simulations to model the energetics of interactions. This will allow us to establish general rules that can be used to modulate protein-helix interactions by affecting some of the properties that govern the helix-coil transition in target sequences. Such rules will lay the foundation for rational design of therapeutically effective target sequences for ubiquitin.

蛋白质靶标相互作用是发生在生物系统。这种互动的一个子组发生在戏剧性二级结构的变化：从非结构化（线圈）不结合到非常当特征结构（螺旋）处于边界状态时。详细的统计热力学研究影响这种过渡的因素（从线圈到螺旋），以及这些因素如何影响蛋白质与其靶标之间的相互作用非常重要的是，由于放松管制可能会导致生物机械的严重故障最终可能是致命的。我们将使用泛素和泛素相互作用基序之间的相互作用（UIM）作为研究结构，动力学和热力学细节的模型系统泛素-UIM复合物的形成。泛素是一种很小的蛋白质，但性能细胞中各种各样的调节功能，包括蛋白质降解，贩运，细胞周期控制，DNA修复，转录调控和基因沉默，压力反应和信号传导。所有这些功能都是翻译后的形式通过单或泛素化修饰蛋白质。程度和程度泛素化作为调节性细胞机制的重要性是广泛的，并且通过一些估计值仅被蛋白质磷酸化超过。在众多目标中结合泛素的序列，UIM也许是最简单的。这是一个短20个氨基与泛素结合后经历线圈螺旋过渡的酸序列。规则在这种类型的互动中影响特异性和亲和力在计算生物学和生物信息学可以更好地预测可以与泛素相互作用。为了实现这些目标，我们将同时使用实验和计算研究泛素-UIM复合物形成的方法。实验方法将包括定向诱变，量热法，荧光和圆形二色性光谱，结构和松弛NMR分析。计算方法将涉及分子动力学模拟，以模拟相互作用的能量学。这将使我们能够建立可用于调节蛋白质螺旋的一般规则通过影响控制螺旋线圈过渡的某些属性来进行相互作用目标序列。这样的规则将奠定理性设计的基础泛素的有效靶序列。