Structural Properties of Initial States in Protein Folding from NMR Alignment Data

NMR 比对数据中蛋白质折叠初始状态的结构特性

• 批准号: 0236316
• 负责人: Andrei Alexandrescu
• 金额: $ 57.58万
• 依托单位: University of Connecticut
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-02-15 至 2008-01-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0236316&HistoricalAwards=false
• 关键词: Structural; Properties; Initial; States; Protein

Recent work has shown that proteins under extreme denaturing conditions retain a net alignment with respect to an NMR magnetic field when immersed in the asymmetric environment of liquid crystals or gels. The asymmetric shapes of these matrices impose weak steric restrictions on the molecular reorientation of solutes. The resulting time- and ensemble-averaged alignment leads to incomplete cancellation of NMR dipolar couplings. Dipolar couplings report on the orientation of individual bond vectors with respect to the molecular alignment frame. The objectives of this project are to further the understanding of the structural basis for net alignment in denatured proteins and to use the alignment information encoded in dipolar couplings towards a structural characterization of denatured states. The objectives will be addressed with two model systems. The first consists of the two proteins CspA and LysN, which share a native five-stranded beta-barrel structural motif but no detectable sequence similarity. Dipolar couplings will be used to investigate the extent to which native-like structure is conserved between the denatured states of the two proteins. The second model system is comprised of two polypeptides that adopt regular extended alpha-helical structures: the S-peptide, which corresponds to the first alpha-helix of the protein ribonuclease A; and the GCN4-p alpha-helical coiled-coil dimer. Dipolar couplings will be used to determine the persistence length of alpha-helical conformations in the denatured forms of the two polypeptides.The principal motivation of this work is to obtain an improved understanding of the structural basis of protein folding. Protein folding remains one of the most difficult and intriguing problems in biology today, and is essential for progress in structural genomics. The new experimental window on structure in denatured states afforded by NMR alignment data, will allow more accurate modeling of protein folding and of the factors responsible for the stability of proteins to unfolding. Modeling of protein folding requires information on denatured states in as much as structure in these initial states can favor or oppose folding to the functional native state. The structural characterization of denatured states additionally impacts mechanisms for denatured protein aggregation reactions, which can occur through illegitimate recombination of incompletely formed nascent structures. The delineation of structural building blocks that persist in denatured proteins provides insights into the mechanisms by which protein structures evolve, information that in turn could be useful in protein design. This project offers the opportunity for students to train in a rich, multidisciplinary approach to protein folding that combines protein chemistry, state of the art NMR experiments, and structure modeling.

最近的工作表明，在极端变性条件下的蛋白质保持一个净对齐相对于NMR磁场时，沉浸在液晶或凝胶的不对称环境。 这些矩阵的不对称形状施加弱空间限制溶质的分子重新取向。 由此产生的时间和整体平均对齐导致NMR偶极耦合的不完全取消。 偶极偶联报告了各个键矢量相对于分子排列框架的取向。 本项目的目标是进一步了解变性蛋白质的净对齐的结构基础，并使用偶极耦合编码的对齐信息对变性状态的结构表征。 这些目标将通过两个模型系统来实现。 第一种由两种蛋白质CspA和LysN组成，它们共享天然的五链β-桶结构基序，但没有可检测到的序列相似性。 偶极偶联将用于研究两种蛋白质的变性状态之间天然样结构的保守程度。 第二个模型系统是由两个多肽，采用规则的延伸的α-螺旋结构：S-肽，其对应于蛋白质核糖核酸酶A的第一个α-螺旋;和GCN 4-β α-螺旋卷曲螺旋二聚体。 偶极偶联将被用来确定在变性形式的两个polypeptide.The主要动机的α-螺旋构象的持久长度，这项工作是为了获得一个更好的理解蛋白质折叠的结构基础。 蛋白质折叠仍然是当今生物学中最困难和最有趣的问题之一，并且对于结构基因组学的进展至关重要。NMR比对数据提供的变性状态下结构的新实验窗口将允许更准确地建模蛋白质折叠和负责蛋白质稳定性展开的因素。蛋白质折叠的建模需要关于变性状态的信息，因为这些初始状态中的结构可以有利于或反对折叠到功能性天然状态。 变性状态的结构表征另外影响变性蛋白质聚集反应的机制，其可通过不完全形成的新生结构的非法重组而发生。 在变性蛋白质中持续存在的结构构建块的描绘提供了对蛋白质结构进化机制的见解，这些信息反过来可能对蛋白质设计有用。该项目为学生提供了一个丰富的，多学科的方法来训练蛋白质折叠，结合蛋白质化学，最先进的NMR实验和结构建模的机会。