Mechanistic Insights into the Specificity of Glycosaminoglycan Interactions withRegulatory Proteins

在本项目中，我们计划以定量的方式研究糖胺聚糖（GAG）与调节蛋白相互作用的特异性。特别是，我们将研究蛋白质对GAG的识别是否仅以非特异性静电或高度特异性相互作用（如盐桥和氢键）的模式为特征的问题。我们计划通过实验和理论相结合的方法，详细研究白细胞介素-8作为一种常见的调节蛋白与一些带负电荷的分子，如GAG、肽、核酸或聚合物之间的相互作用。在实验上，我们将特别应用核磁共振方法。在计算方面，我们将开展对接研究和分子动力学模拟。在项目的第二部分，我们计划通过这两种技术来研究组织蛋白酶与GAG的相互作用。组织蛋白酶B具有高表面正电荷的特点，因此与带负电荷的分子的非特异性相互作用是可以预料的。我们计划测试除了这种非特异性相互作用外，高度特异性相互作用是否也会引起高仿射GAG与蛋白质的结合。我们将通过实验和计算工具来研究络合物的结构。实验技术将在德国进行，而计算研究将由波兰合作伙伴进行。申请人多年来与几个共同出版物进行了卓有成效和成功的合作。

In the project, we plan to study the specificity of the interaction between glycosaminoglycans (GAG) with regulatory proteins in a quantitative fashion. In particular, we will work on the question whether or not the recognition of GAG by proteins is characterized just by an unspecific electrostatics or by a pattern of highly specific interactions, such as salt bridges and hydrogen bonds. We plan to study in detail the interaction between interleukin-8, a common regulatory protein, with a number of negatively charged molecules such as GAG, peptides, nucleic acids or polymers by a combination of experimental and theoretical methods. Experimentally, we will particularly apply NMR methods. Computationally, we will carry out docking studies and molecular dynamics simulations. In the second part of the project, we plan to study the interaction of cathepsins with GAG by means of both techniques. Cathepsin B is characterized by a high positive surface charge, such that the unspecific interaction with negatively charged molecules is to be expected. We plan to test if in addition to such unspecific interaction, also highly specific interactions give rise to high affine GAG binding to the protein. We will study the structure of the complex by experimental and computational tools. The experimental techniques will be carried out in Germany, while the computational studies will be carried by the Polish collaboration partner. The applicants have been engaged in a fruitful and successful collaboration for many years with several common publications.