Periodic Reporting for period 1 - DesProtDNA (Computational design of proteins binding nucleosomal DNA with specificity for therapeutic applications)
Berichtszeitraum: 2017-04-01 bis 2019-03-31
The design of nucleosome-binding molecules specific for a DNA sequence remains an outstanding challenge. Nevertheless, nucleosomal DNA binding specificity is hard to achieve by repurposing currently existing chromatin-interacting proteins due to the lack of suitable natural templates. Recent advances in computational protein design provide a route to custom-tailor protein structures and interactions, and here we set out to design, for the first time, proteins customized to bind nucleosomal DNA with specificity. Such protein customization underlies the challenge of identifying and/or building a protein structure, its optimal placement around the DNA target site, and an amino-acid sequence that stabilizes the target protein-DNA complex.
DesProtDNA comprised three objectives. First, development of a general computational method to de novo design protein-DNA binding interfaces in the nucleosome with specificity. Second, experimentally validate the method by testing proteins designed to target a nucleosome with high-resolution structure available. Third, use the method to design proteins binding specific nucleosomal DNA sites involved in diseases. Additionally, the project aims to provide the researcher with new computational and experimental skills to implement new protein-DNA design schemes and validate them.
In conclusion, we have developed three different computational approaches that range from redesigning currently existing proteins to full de novo design to achieve optimal binding to nucleosomal DNA. The designed proteins have been experimentally characterized by expressing them recombinantly and assessing their binding properties. Novel nucleosome binding proteins have been obtained that where designed to target specific DNA sites and have binding interfaces similar as designed. Yet, further high-resolution structural information is necessary to confirm the actual binding mode of the designs. This is the first time proteins have been designed to bind the exposed face of nucleosomal DNA. Obtaining high-resolution structural conformation of our designs will lay the groundwork for developing new chromatin-based therapeutic strategies as well as innovative research tools for chromatin studies using our computational design method.
The computational approaches were tested with the design of proteins targeting the nucleosome containing the 601-sequence, which is a DNA sequence strongly favoring nucleosomes and for which there are high-resolution crystal structures available. The designed proteins expressed solubly at high levels, except for the repurposed TAL effectors, which may not tolerate these modifications as these are marginally stable. For the helical bundles designed with the first approach we identified three proteins binding more strongly to nucleosomes than to naked DNA (in the low micromolar range). We carried out sedimentation velocity experiments and found that the design complexes were monodisperse, and one design bound with a stoichiometry of 2 protein:1 nucleosome. Currently, electron microscopy experiments are carried out to further elucidate the structure of this complex. Smaller versions of the designed proteins and that preserve the same binding interface were also found to bind nucleosomes with similar affinity, further supporting that the proteins bind through the intended interfaces. On the other hand, proteins de novo-designed in the third approach seem the most promising to achieve the highest specificity. Binding assays indicate novel binding proteins forming lower molecular weight species, which may support formation of protein-nucleosome complexes with 1:1 stoichiometry. Currently, additional experiments to get more structural characterization of these designs are in process.
We have presented our work in several international conferences, and we are currently preparing a manuscript for publication.