Generative Landscapes and Dynamics to Design Functional Multidomain Artificial Transmembrane Transporters

Abstract

Design and synthesis of functionally active artificial proteins is challenging, as it requires simultaneous consideration of interconnected factors, such as fold, dynamics, and function. These evolutionary constraints are encoded in protein sequences and can be learned through the latent generative landscape (LGL) framework to predict functional sequences by leveraging evolutionary patterns, enabling exploration of uncharted sequence space. By simulating designed proteins through molecular dynamics (MD), we gain deeper insights into the interdependencies governing structure and dynamics. We present a synergized workflow combining LGL with MD and biochemical characterization, allowing us to explore the sequence space effectively. This approach has been applied to design and characterize two artificial multidomain ATP-driven transmembrane copper transporters, with native-like functionality. This integrative approach proved effective in revealing the intricate relationships between sequence, structure, and function.

Synergizing latent generative landscapes and molecular dynamics, we design and validate several artificial multidomain transmembrane transporters in in vitro and in vivo assays.