Elucidating the dynamical and structural molecular factors at the origin of non-enzymatic protein-protein and protein-DNA cross-links

项目摘要 非酶促蛋白质-蛋白质和蛋白质-DNA交联是有害的翻译后 与许多严重病理学相关的修饰，包括癌症转移， 姐妹、视网膜病、慢性肾衰竭、皮肤和骨骼疾病、衰老、糖尿病、阿尔茨海默氏病、Par- 金森氏症和心血管疾病然而，治疗策略的发展是hin- 我们对它们的形成缺乏了解。我们建议填补这一知识空白 使用基于本征电场计算的计算方法。我们的目标是确定 非酶促反应形成的结构和动力学分子因素 蛋白质-蛋白质和蛋白质-DNA交联。我们的研究重点是糖介导的交联， 由糖化反应引发，因为它已被证明发生在广泛的系统中。 我们假设蛋白质（或DNA）水化层的部分耗尽暴露了侧 链（或核碱基）与周围的碳水化合物。这促进了糖化反应， 还原糖（葡萄糖）与游离胺基反应。糖化蛋白质和DNA 增强了形成加合物的能力，改变了它们的生物功能。我们的研究旨在 以提供糖介导的交联形成的分子解释，并可分为 分为三个推力;其中每一个都有可能扩展到一个独立的研究方向。 首先，我们建议表征健康和病理的水化层的密度， 蛋白质和DNA链已知聚集（胶原蛋白，弹性蛋白和α-突触核蛋白）， 旋转水平。我们对矿化胶原蛋白系统的初步数据表明， 由环境的性质而不是吸附位点的性质控制， 通过实验观察。这表明，密度泛函理论协议，我们德- 本研究开发的方法适用于表征大分子与水的相互作用。 其次，我们建议在脱水和水合生物分子中模拟碳水化合物的反应性， cules，作为非酶糖化反应的代表。我们的方法的新颖之处在于引入- 在经典的分子动力学模拟中使用内禀函数导出精确的反应性信息 电场作为键形成的度量。我们的初步数据验证了这种可行性 研究并包括开发允许这种计算的开源代码。 最后，我们建议将我们的原子数据整合到蛋白质的微观动力学模型中- 蛋白质和蛋白质-DNA交联过程。通过这个模型，我们的目标是预测关键的 密度、位置、协同性和与已知病理相关的交联强度， 逻辑，为确定治疗干预点铺平道路。

Project Summary Non-enzymatic protein-protein and protein-DNA cross-links are deleterious post-translational modifications that have been associated with many severe pathologies, including cancer metasta- sis, retinopathy, chronic renal failure, skin and bone disorders, aging, diabetes, Alzheimer’s, Par- kinson’s and cardiovascular diseases. However, the development of therapeutic strategies is hin- dered by our poor understanding of their formation. We propose to address this gap in knowledge using computational methods based on intrinsic electric field calculations. Our goal is to identify the structural and dynamical molecular factors at the origin of the formation of non-enzymatic protein-protein and protein-DNA cross-links. We focus our study on sugar-mediated cross-links, initiated by glycation reactions, as it has been shown to occur in a broad range of systems. We hypothesize that partial depletion of the protein (or DNA) hydration layer exposes side chains (or nucleobases) to surrounding carbohydrates. This facilitates glycation reactions whereby reducing sugars (glucose) react with the free amine groups. Glycated proteins and DNA then have enhanced ability to form adducts, altering their biofunction. Our proposed research seeks to provide a molecular interpretation of sugar-mediated cross-link formation and can be divided into three thrusts ; each of which with the potential to expand into a standalone research direction. First, we propose to characterize the density of the hydration layer of healthy and pathological proteins and DNA strands known to aggregate (collagen, elastin and α-synuclein) at the quan- tum level. Our preliminary data on mineralized collagen systems show that water adsorption is controlled by the nature of the environment rather than the nature of the adsorption site, consistent with experimental observations. This suggests that the density functional theory protocol we de- veloped for this study is suitable for the characterization of macromolecule-water interactions. Second, we propose to model carbohydrate reactivity in dehydrated and hydrated biomole- cules, as a proxy for non-enzymatic glycation reactions. The novelty of our approach is to intro- duce accurate reactivity information in classical molecular dynamics simulations using intrinsic electric fields as a metric for bond formation. Our preliminary data verify the feasibility of such study and include the development of an open-source code that allows this type of calculations. Finally, we propose to integrate our atomistic data into a microscopic kinetic model of protein- protein and protein-DNA cross-linking processes. With this model, we aim to predict the critical density, location, cooperativity and strength of cross-links that are associated with known patho- logies, paving the way towards the identification of therapeutic points of intervention.