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The transport of solutes across the cell membrane is essential for metabolic processes, like maintaining cell size and volume, generating the action potential, exchanging nutrients and gases, etc. Membrane transport can be either passive or active. It can be simple diffusion, facilitated, or mediated transport aided by transport proteins such as transporters and channels.
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Transporters are essential membrane transport proteins with functions related to cell nutrition, homeostasis, communication, etc. Approximately 7% of all genes in the human genome code for transporters or transporter-related proteins.
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Generative Landscapes and Dynamics to Design Functional Multidomain Artificial Transmembrane Transporters.

Fernando Montalvillo Ortega1, Fariha Hossain2, Vladimir V Volobouev2

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We developed a new method combining latent generative landscapes (LGL) and molecular dynamics (MD) to design functional artificial proteins. This approach successfully created novel copper transporters with native-like activity, revealing sequence-structure-function relationships.

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Area of Science:

  • Protein engineering and computational biology.
  • Synthetic biology and biophysics.

Background:

  • Designing functional artificial proteins is complex due to interconnected factors like fold, dynamics, and function.
  • Evolutionary patterns encode constraints that can guide protein sequence design.

Purpose of the Study:

  • To develop and validate an integrated computational and experimental workflow for designing novel, functional artificial proteins.
  • To explore uncharted protein sequence space and understand sequence-structure-function relationships.

Main Methods:

  • Utilized the latent generative landscape (LGL) framework to learn evolutionary patterns and predict functional protein sequences.
  • Employed molecular dynamics (MD) simulations to analyze protein dynamics and structural properties.
  • Integrated LGL and MD with biochemical characterization for comprehensive protein assessment.

Main Results:

  • Successfully designed and characterized two artificial multidomain ATP-driven transmembrane copper transporters.
  • The designed proteins exhibited native-like functionality.
  • The integrated approach effectively revealed intricate relationships between protein sequence, structure, and function.

Conclusions:

  • The combined LGL and MD workflow enables effective exploration of protein sequence space for designing functional proteins.
  • This integrative strategy is powerful for uncovering fundamental principles governing protein behavior.
  • Artificial proteins with desired functions can be engineered by leveraging evolutionary insights and biophysical simulations.