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RosettaSurf - a surface-centric computational design approach

View ORCID ProfileAndreas Scheck, View ORCID ProfileStéphane Rosset, View ORCID ProfileMichaël Defferrard, View ORCID ProfileAndreas Loukas, View ORCID ProfileJaume Bonet, View ORCID ProfilePierre Vandergheynst, View ORCID ProfileBruno E Correia
doi: https://doi.org/10.1101/2021.06.16.448645
Andreas Scheck
1Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
2Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
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Stéphane Rosset
1Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
2Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
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Michaël Defferrard
3Signal Processing Laboratory (LTS2), École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
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Andreas Loukas
3Signal Processing Laboratory (LTS2), École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
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Jaume Bonet
1Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
2Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
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Pierre Vandergheynst
3Signal Processing Laboratory (LTS2), École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
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Bruno E Correia
1Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
2Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
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  • For correspondence: bruno.correia@epfl.ch
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Abstract

Proteins are typically represented by discrete atomic coordinates providing an accessible framework to describe different conformations. However, in some fields proteins are more accurately represented as near-continuous surfaces, as these are imprinted with geometric (shape) and chemical (electrostatics) features of the underlying protein structure. Protein surfaces are dependent on their chemical composition and, ultimately determine protein function, acting as the interface that engages in interactions with other molecules. In the past, such representations were utilized to compare protein structures on global and local scales and have shed light on functional properties of proteins. Here we describe RosettaSurf, a surface-centric computational design protocol, that focuses on the molecular surface shape and electrostatic properties as means for protein engineering, offering a unique approach for the design of proteins and their functions. The RosettaSurf protocol combines the explicit optimization of molecular surface features with a global scoring function during the sequence design process, diverging from the typical design approaches that rely solely on an energy scoring function. With this computational approach, we attempt to address a fundamental problem in protein design related to the design of functional sites in proteins, even when structurally similar templates are absent in the characterized structural repertoire. Surface-centric design exploits the premise that molecular surfaces are, to a certain extent, independent of the underlying sequence and backbone configuration, meaning that different sequences in different proteins may present similar surfaces. We benchmarked RosettaSurf on various sequence recovery datasets and showcased its design capabilities by generating epitope mimics that were biochemically validated. Overall, our results indicate that the explicit optimization of surface features may lead to new routes for the design of functional proteins.

Author Summary Finely orchestrated protein-protein interactions are at the heart of virtually all fundamental cellular processes. Altering these processes or encoding new functions in proteins has been a long-standing goal in computational protein design.

Protein design methods commonly rely on scoring functions that seek to identify amino acid sequences that optimize structural configurations of atoms while minimizing a variety of physics-based and statistical terms. The objectives of the large majority of computational design protocols have been focused on obtaining a predefined structural conformation. However, routinely introducing a functional aspect on designer proteins has been more challenging.

Our results suggest that the molecular surface features can be a useful optimization parameter to guide the design process towards functional surfaces that mimic known protein binding sites and interact with their intended targets. Specifically, we demonstrate that our design method can optimize experimental libraries through computational screening, creating a basis for highly specific protein binders, as well as design a potent immunogen that engages with site-specific antibodies. The ability to create proteins with novel functions will be transformative for biomedical applications, providing many opportunities for the design of novel immunogens, protein components for synthetic biology, and other protein-based biotechnologies.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted June 16, 2021.
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RosettaSurf - a surface-centric computational design approach
Andreas Scheck, Stéphane Rosset, Michaël Defferrard, Andreas Loukas, Jaume Bonet, Pierre Vandergheynst, Bruno E Correia
bioRxiv 2021.06.16.448645; doi: https://doi.org/10.1101/2021.06.16.448645
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RosettaSurf - a surface-centric computational design approach
Andreas Scheck, Stéphane Rosset, Michaël Defferrard, Andreas Loukas, Jaume Bonet, Pierre Vandergheynst, Bruno E Correia
bioRxiv 2021.06.16.448645; doi: https://doi.org/10.1101/2021.06.16.448645

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