Computational design of specific binding proteins using Leave-One-Out

使用留一法进行特异性结合蛋白的计算设计

基本信息

批准号：
8373084
负责人：
CHRISTOPHER BYSTROFF
金额：
$ 38.43万
依托单位：
RENSSELAER POLYTECHNIC INSTITUTE
依托单位国家：
美国
项目类别：
财政年份：
2012
资助国家：
美国
起止时间：
2012-09-20 至 2017-07-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8373084
关键词：
Address Affinity Algorithms Amino Acid Sequence Amino Acid Substitution Anthrax disease Appearance Authorization documentation Avian Influenza Binding Binding Proteins Biological Markers Biosensor Complement Computing Methodologies DNA Shuffling Dengue Virus Detection Development Diagnostic Disease Disulfides Elements Engineering Event Feedback Fluorescence Fluorescent Probes Foot-and-Mouth Disease Funding Genes Goals Green Fluorescent Proteins HIV In Vitro Individual Influenza A Virus, H5N1 Subtype Influenza Hemagglutinin Left Libraries Ligand Binding Memory Modification Monoclonal Antibodies Occupations Online Systems Pathway interactions Patient Self-Report Peptides Property Proteins Proteomics Protocols documentation Reporting Research Research Design Running Shapes Signal Transduction Site Specific qualifier value Specificity Speed Structure System Therapeutic Thermodynamics Time United States National Institutes of Health Validation Viral Proteins Work base cancer cell cluster computing cost design enzyme activity global health improved in vivo influenzavirus interest methicillin resistant Staphylococcus aureus microorganism new technology novel novel strategies parallel computing pathogen protein folding protein purification protein structure rapid detection receptor sensor software development therapeutic protein yeast two hybrid system

项目摘要

DESCRIPTION (provided by applicant): Computational design of specific binding proteins using Leave-One-Out The goal of this research is to be able to design a receptor protein for any protein target. Furthermore, we propose that the binding event will be signaled by the appearance of enzyme activity or fluorescence. The novel binding proteins will be able to sense and report the presence of a specific protein or peptide in a mixture of others, allowing the detection of disease agents or other proteins of interest both in vivo and in vitro. The new approach takes advantage of protein folding pathways. When proteins fold, they do so in a specified order of events, and the events can be predicted based on the structure of the protein. When a protein finishes folding, its activity is immediately turned on. If we leave out one small piece of the protein so that the folding cannot finish, then the protein sits in an inactive state ntil the missing piece appears. Using this Leave-One- Out strategy, partially folded proteins become sensors for their missing pieces. Using computational design algorithms, a new amino acid sequence can be substituted for the left out piece. This new sequence can be from anthrax, avian flu, a cancer cell marker or any other protein. Computational substitution of the amino acids surrounding this new sequence is made possible using massively parallel computing clusters and grid computing, and by dividing the design task into numerous smaller tasks based on what is known about protein folding and energy calculations. The final design is a protein that wraps around the target peptide, specifically identifying it by its complementary shape. Green fluorescent protein has been the subject of the first leave-one-out design studies and has yielded specific binding proteins that glow only when the target peptide is present. PUBLIC HEALTH RELEVANCE: Computational design of specific binding proteins using Leave-One-Out The results of this research could revolutionize protein diagnostics, replacing monoclonal antibodies as the current best means of specific protein identification. Computationally designed specific binding proteins could be used as protein therapeutics, biosensors, proteomic arrays, fluorescent probes, protein purification affinity agents, and many other applications.

描述（由申请人提供）：使用一对一的特定结合蛋白的计算设计本研究的目标是能够为任何蛋白质靶标设计受体蛋白。此外，我们提出结合事件将通过酶活性或荧光的出现来发出信号。新型结合蛋白将能够感知并报告其他混合物中特定蛋白或肽的存在，从而可以在体内和体外检测疾病剂或其他感兴趣的蛋白质。新方法利用蛋白质折叠途径。当蛋白质折叠时，它们会以指定的事件顺序进行，并且可以根据蛋白质的结构预测事件。当蛋白质完成折叠时，其活性会立即打开。如果我们遗漏了一小部分蛋白质，以使折叠无法完成，那么蛋白质处于不活跃状态下，出现了缺失的碎片。使用此保留的策略，部分折叠的蛋白质成为缺失的传感器。使用计算设计算法，可以将新的氨基酸序列代替为左侧的部分。这个新序列可以来自炭疽，禽流感，癌细胞标记或任何其他蛋白质。使用大量平行的计算群集和网格计算，并根据有关蛋白质折叠和能量计算的知识将设计任务分为许多较小的任务，可以使围绕该新序列的氨基酸进行计算取代。最终设计是一种蛋白质，可围绕靶肽包裹，特别通过其互补形状识别它。绿色荧光蛋白一直是第一个外出设计研究的主题，并且产生了仅在存在靶肽时发光的特定结合蛋白。公共卫生相关性：使用剩余的特定结合蛋白的计算设计，这项研究的结果可以彻底改变蛋白质诊断，从而取代单克隆抗体作为当前特定蛋白质鉴定的最佳手段。计算设计的特定结合蛋白可以用作蛋白质治疗剂，生物传感器，蛋白质组学阵列，荧光探针，蛋白质纯化亲和力剂以及许多其他应用。