Development of an integrated structural biology platform specialized for sub-100 kDa protein complexes to support biologics discovery and rational engineering

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Abstract Background Developing a biologic medicine requires successful decision making during selection and optimization in addition to the pool of candidates at early research stages. Knowing structural information and binding patterns between drug target and discovery candidates greatly increases the probability of success. Methods With the cryo-EM resolution revolution and rapid development of computational software, we have evaluated and integrated various tools in structural biology and the computation field and established a highly cost-effective platform which allows us to obtain fast and accurate structural information for nearly all our biologics projects with a close to 100% success rate and as fast as weeks turn-around time. Results Here we report four case studies selected from 38 different protein structures and share how we integrate cryo-EM structure determination, computational structure modeling, and molecular dynamics simulation. With proper decision making and strategic planning, the platform allows us to obtain quality results within days to weeks, including sub-100 kDa complexes which are usually considered a challenge due to their small size. Conclusions Our utilization of this differential approach and multiple software packages allows us to manage priorities and resources to achieve goals quickly and efficiently. We demonstrate how to effectively overcome particle orientation bias by altering complex composition. In several of our examples, we use glycan density to facilitate interpretation of low-resolution 3D reconstruction and epitope mapping. Protein information plays an important role in our cryo-EM projects, especially in cases where we see significant challenges in obtaining high-resolution 3D maps.