STRUCTURE AND AFFINITY--CALCULATING LIPID SELECTIVITY

结构和亲和力--计算脂质选择性

• 批准号: 2771066
• 负责人: THOMAS B WOOLF
• 金额: $ 11万
• 依托单位: JOHNS HOPKINS UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 1997
• 资助国家: 美国
• 起止时间: 1997-09-30 至 2002-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/2771066
• 关键词: chemical binding; computer simulation; fatty acid binding protein; intermolecular interaction; lipids; molecular cloning; molecular dynamics; mutant; protein structure function; retinoid binding proteins; site directed mutagenesis

DESCRIPTION: Molecular dynamics computer calculations are proposed to provide microscopically detailed relationships between the x-ray tertiary structures and the measured binding affinities in two members of the lipid binding protein superfamily. The lipid binding proteins (LBPs) are an ideal model system for studying the details of hydrophobic ligand recognition for three main reasons. First, there are a large number of LBPs with known tertiary structure. In all cases this has proven to be a beta-clam shell like structure with the ligand binding at an internal site. Second, there is excellent thermodynamic binding data available using the change in fluorescence of the acrylodan derivatized intestinal fatty acid binding protein (ADIFAB). Third, there is a rapidly increasing data set of single alanine mutants that are being characterized in terms of relative binding affinity for ligands and approached for structure determination. This allows pursuit of the proposals long-term goal: the ability to rationally predict the changes in binding affinity to a range of ligands for site-directed mutagenesis in the LBP family. This long-term goal would have important health benefits. In particular, the ability to rationally design a LBP family member with predictable binding affinity to fatty acids and/or retinoids, could lead to an important drug. These ambitious long-term goals will be approached through a series of short-term goals. The specific aims addressing the goals are to: (1) Determine the dynamical motions and the average properties of molecular dynamics simulations of intestinal fatty acid binding protein (I-FABP) and cellular retinol binding protein II (CRBP II) structures. (2) Develop qualitative methods for the prediction of the changes in binding affinity for site-directed mutants in I-FABP and CRBP II systems. (3) Calculate lambda coupled free energy changes for subset of site-directed mutants in I-FABP and CRBP II to improve the qualitative estimates for binding affinity of the second aim. These theoretical projects will complement ongoing NIH funded experimental work in the Sacchettini, Banaszak and Kleinfeld laboratories. A dialogue between the computational and the experimental will expand the range of connections in the LBP superfamily beyond what would be possible for any group acting in isolation.

描述：建议使用分子动力学计算机计算 提供 X 射线三级之间的微观详细关系 脂质的两个成员的结构和测量的结合亲和力 结合蛋白超家族。 脂质结合蛋白（LBP）是一种理想的 用于研究疏水配体识别细节的模型系统 三个主要原因。 首先，存在大量已知的 LBP 三级结构。 在所有情况下，这都被证明是贝塔蛤壳 与配体在内部位点结合的类似结构。 其次，有 使用变化可以得到出色的热力学结合数据 丙烯酰衍生的肠脂肪酸结合的荧光 蛋白质（ADIFAB）。 第三，单一数据集快速增长。 丙氨酸突变体的特征在于相对结合 配体的亲和力并用于结构测定。 这 允许追求建议的长期目标：能够理性地 预测与一系列配体的结合亲和力的变化 LBP 家族中的定点诱变。 这个长期目标将有 重要的健康益处。 尤其是合理设计的能力 与脂肪酸具有可预测的结合亲和力的 LBP 家族成员和/或 类视黄醇，可能会成为一种重要的药物。 这些雄心勃勃的长期目标将通过一系列措施来实现 短期目标。 实现目标的具体目标是：（1） 确定分子的动态运动和平均性质 肠脂肪酸结合蛋白（I-FABP）的动力学模拟和 细胞视黄醇结合蛋白 II (CRBP II) 结构。 (2) 开发 预测结合亲和力变化的定性方法 用于 I-FABP 和 CRBP II 系统中的定点突变体。 (3) 计算 定点突变体子集的 lambda 耦合自由能变化 I-FABP 和 CRBP II 用于改进结合亲和力的定性估计 的第二个目标。 这些理论项目将补充正在进行的 NIH 资助 Sacchettini、Banaszak 和 Kleinfeld 的实验工作 实验室。 计算与实验之间的对话 将扩大 LBP 超家族中的连接范围 对于任何孤立行动的团体来说都是可能的。