Theoretical Studies of Antibody-Antigen Binding

抗体-抗原结合的理论研究

• 批准号: 9220477
• 负责人: Kim Sharp
• 金额: $ 17.5万
• 依托单位: University of Pennsylvania
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 1993
• 资助国家: 美国
• 起止时间: 1993-03-15 至 1995-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=9220477&HistoricalAwards=false
• 关键词: Theoretical; Studies; Antibody; Antigen; Binding

The proposed research is directed at understanding the physical and chemical basis of specific antibody-antigen binding. The experimental systems to be studied are three antibody/protein complexes and four antibody/hapten complexes for which high resolution X-ray structures and binding data re available, plus data on binding differences for point amino acid mutations and hapten analogue binding. The focus will be on two key aspects: 1) The role of solvation, which involves both electrostatic and hydrophobic interactions. 2)'Association entropy' effects, meaning the loss of translational/rotational entropy upon association, with the concomitant gain in vibrational entropy of the complex, and the change in conformational mobility of groups involved in the intermolecular contact. A combination of theoretical approaches will be used, the aim being to develop computationally feasible yet quantitative methods for calculating both differences in binding energy, and absolute binding energies. This will enable specific questions of biological importance to be addressed, including identifying the overall driving force for binding, contributions to specificity, the role of electrostatic complementarily, whether induced fitting is important, the intrinsic antigenicity of surface groups, and the effect of amino acids mutations and substitutions on binding energies. Electrostatics will be treated using a continuum treatment of solvent with an atomic detail representation of the molecule, using the Finite Difference Poisson-Boltzmann (FDPB) method. Dynamic aspects will be handled by a method which combines the FDPB method with molecular mechanics (FDPB/MD). Hydrophobic interactions will be treated using surface free energy relationships, modified to account for shape effects, calibrated on small molecule solvent transfer data. Translational and rotational entropies effects will be estimated from changes in the rotational and translational partition function upon binding. %%% The ability of an organism to produce molecules that bind specifically to certain 'target' molecules or parts of 'target' molecules, but not to other molecules, gives rise to the phenomenon of biological recognition at the molecular level. This process of molecular recognition underlies many fundamental biological processes including catalysis, gene transcription and the immune response. The design of drugs also involves creating or modifying molecules to recognize given biological target molecules. In physical terms recognition occurs because a molecule binds more tightly to its 'target' than to other molecules. It is known that the tightness of binding is determined by how much energy is released (the binding energy) when two molecules are brought together. it is also known that contributions to the binding energy come from the interaction of the two molecules with each other, the interaction of each molecule with its surroundings, especially water, and from the change in shape and mobility of each molecule upon binding. However it is not yet possible to calculate the binding energy accurately, even if the structure o the two molecules is known. This impedes both our understanding of what properties of molecules are necessary for recognition and the ability to design molecules to recognize a given target. The recognition of foreign antigens by antibodies is one of the key properties of an immune system, and one of the most studied examples of molecular recognition: The structures of at least seven antigen/antibody complexes are known at the atomic level, and their binding energies have been measured. Therefore these systems have been chosen for a detailed theoretical study of binding. The aim of the proposed research is to apply recently developed methods for simulating the behavior of molecules to the problem of calculating the different contributions to the antibody-antigen binding energy. The goal is to identify the properties of the antibodies important for tight binding and specificity, and to improve the ability to calculate binding energies.

提出的研究旨在了解特异性抗体-抗原结合的物理和化学基础。要研究的实验系统是三种抗体/蛋白质复合物和四种抗体/半抗原复合物，它们具有高分辨率的x射线结构和结合数据，以及点氨基酸突变和半抗原类似物结合的结合差异数据。重点将集中在两个关键方面：1)溶剂化的作用，它涉及静电和疏水相互作用。2)“关联熵”效应，即在关联时平移/旋转熵的损失，伴随着配合物的振动熵的增加，以及参与分子间接触的基团的构象迁移率的变化。将使用理论方法的组合，目的是开发计算上可行的定量方法来计算结合能和绝对结合能的差异。这将使具有生物学重要性的具体问题得以解决，包括确定结合的总体驱动力，对特异性的贡献，静电互补的作用，诱导拟合是否重要，表面基团的内在抗原性，以及氨基酸突变和取代对结合能的影响。静电将使用溶剂的连续处理和分子的原子细节表示，使用有限差分泊松-玻尔兹曼（FDPB）方法进行处理。动力学方面将通过结合FDPB方法和分子力学（FDPB/MD）的方法来处理。疏水相互作用将使用表面自由能关系进行处理，修改以考虑形状效应，并根据小分子溶剂转移数据进行校准。平动和旋转熵的影响将通过结合时旋转和动配分函数的变化来估计。生物体产生与某些“目标”分子或“目标”分子的某些部分特异性结合而不与其他分子结合的分子的能力，导致了分子水平上的生物识别现象。这种分子识别过程是许多基本生物学过程的基础，包括催化、基因转录和免疫反应。药物的设计还包括创造或修改分子以识别给定的生物靶分子。从物理角度来说，识别的发生是因为一个分子与“目标”的结合比与其他分子的结合更紧密。众所周知，结合的紧密程度是由两个分子结合时释放的能量（结合能）决定的。我们还知道，对结合能的贡献来自两个分子之间的相互作用，每个分子与周围环境，特别是水的相互作用，以及每个分子在结合时形状和迁移率的变化。然而，即使已知这两个分子的结构，也不可能精确地计算出结合能。这既阻碍了我们理解分子的哪些特性是识别所必需的，也阻碍了我们设计分子来识别给定目标的能力。抗体对外来抗原的识别是免疫系统的关键特性之一，也是分子识别研究最多的例子之一：至少有七种抗原/抗体复合物的结构在原子水平上是已知的，并且它们的结合能已经被测量。因此，选择这些体系进行结合的详细理论研究。提出的研究目的是应用最近发展的模拟分子行为的方法来计算抗体-抗原结合能的不同贡献。目的是确定对紧密结合和特异性重要的抗体的特性，并提高计算结合能的能力。