Structure and Affinity: Computing FABP-Lipid Selectivity

结构和亲和力：计算 FABP-脂质选择性

• 批准号: 6744140
• 负责人: THOMAS B WOOLF
• 金额: $ 27.13万
• 依托单位: JOHNS HOPKINS UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-05-01 至 2007-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6744140
• 关键词: alanine; alcohols; artificial intelligence; chemical models; fatty acid binding protein; fatty acid transport; fatty acids; gene mutation; intermolecular interaction; lipid bilayer membrane; molecular dynamics; protein structure function; site directed mutagenesis; thermodynamics; water

DESCRIPTION (provided by applicant): Physiological control of the concentration of free fatty acid levels is central to human physiology. Fatty acid binding proteins (FABPs), a large superfamily of proteins found abundantly in many cell types, have been shown to play a role in the organism's ability to control fatty acid levels by selectively binding fatty acids. The details of the ability of these proteins to select fatty acids, based on chain length, saturation state, and headgroup type, is not clear at a molecular level. This is despite the existence of two central ingredients required for such an explanation: highly detailed structures (Banaszak and Cistola) and excellent binding thermodynamics (Kleinfeld). We aim, through this grant proposal, to provide the third needed ingredient for a detailed molecular description of binding. That is, our overall goal is the ability to compute the selective binding of fatty acids within fatty acid binding proteins. We approach this goal through three specific aims. Our first aim is to understand the basis of fatty acid solvation in the homogenous solvents water and octanol. This will provide a reference point for the changes to a heterogeneous environment provided by the fatty acid binding protein and considered in the next two aims. In the second aim, we will directly compute the relative free energy differences underlying discrimination of fatty acids afforded by the intestinal fatty acid binding protein (I-FABP). In the third aim we will draw connections between our calculations and the site directed mutants that have been characterized in the Kleinfeld lab. Throughout these aims we will use alchemical mutagenesis calculations with a range of solvation models. In particular, we will be testing new models for solvation developed in the Roux lab. The work will further involve extending our own approaches to relative free energy calculations through dynamic importance sampling, analysis of non-equilibrium work events, extrapolations from histogram analysis and intelligent stepping algorithms along the alchemical reaction coordinate. If we succeed in our long term goal, we will have achieved the ability to rationally design new protein binding interactions enabling discrimination of particular fatty acids. The achievement of this goal would have implications for rational treatment of heart disease and other, e.g. digestive system related, human diseases that involve the control of free fatty acid levels.

描述（由申请人提供）：游离脂肪酸水平浓度的生理控制是人体生理学的核心。脂肪酸结合蛋白（FABPs）是在许多细胞类型中大量发现的一个大的蛋白质超家族，已被证明在生物体通过选择性结合脂肪酸来控制脂肪酸水平的能力中发挥作用。这些蛋白质根据链长、饱和状态和头基团类型选择脂肪酸的能力的细节在分子水平上尚不清楚。尽管存在这样一个解释所需的两个核心要素：高度详细的结构（Banaszak和Cistola）和出色的结合热力学（Kleinfeld）。我们的目标是，通过这项拨款提案，为结合的详细分子描述提供第三种所需的成分。也就是说，我们的总体目标是能够计算脂肪酸结合蛋白中脂肪酸的选择性结合。我们通过三个具体目标来实现这一目标。我们的第一个目的是了解脂肪酸在均相溶剂水和辛醇中的溶剂化基础。这将为脂肪酸结合蛋白提供的异质环境的变化提供参考点，并在接下来的两个目标中考虑。在第二个目标中，我们将直接计算肠道脂肪酸结合蛋白（I-FABP）提供的脂肪酸区分的相对自由能差。在第三个目标中，我们将把我们的计算与克莱因菲尔德实验室中已被表征的定向突变体联系起来。在这些目标中，我们将使用一系列溶剂化模型的炼金术诱变计算。特别是，我们将测试Roux实验室开发的溶剂化新模型。这项工作将进一步涉及通过动态重要性采样、非平衡功事件分析、直方图分析的外推以及沿着炼金术反应坐标的智能步进算法，扩展我们自己的相对自由能计算方法。如果我们成功实现了我们的长期目标，我们将获得合理设计新的蛋白质结合相互作用的能力，从而能够区分特定的脂肪酸。这一目标的实现将对心脏病和其他涉及控制游离脂肪酸水平的人类疾病的合理治疗产生影响，例如与消化系统相关的疾病。