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

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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.