Perturbing the energy landscape for improved packing during computational protein design

Jack B Maguire; Hugh K Haddox; Devin Strickland; Samer F Halabiya; Brian Coventry; Jermel R Griffin; Surya V S R K Pulavarti; Matthew Cummins; David F Thieker; Eric Klavins; Thomas Szyperski; Frank DiMaio; David Baker; Brian Kuhlman

doi:10.1002/prot.26030

Perturbing the energy landscape for improved packing during computational protein design

Proteins. 2021 Apr;89(4):436-449. doi: 10.1002/prot.26030. Epub 2020 Dec 11.

Authors

Jack B Maguire¹, Hugh K Haddox^{2

3}, Devin Strickland⁴, Samer F Halabiya⁴, Brian Coventry^{3

5}, Jermel R Griffin⁶, Surya V S R K Pulavarti⁶, Matthew Cummins⁷, David F Thieker^{8

9}, Eric Klavins⁴, Thomas Szyperski⁶, Frank DiMaio^{2

3}, David Baker^{2

3

10}, Brian Kuhlman^{8

9}

Affiliations

¹ Program in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
² Department of Biochemistry, University of Washington, Seattle, Washington, USA.
³ Institute for Protein Design, University of Washington, Seattle, Washington, USA.
⁴ Department of Electrical and Computer Engineering, University of Washington, Seattle, Washington, USA.
⁵ Molecular Engineering PhD Program, University of Washington, Seattle, Washington, USA.
⁶ Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, USA.
⁷ Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
⁸ Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
⁹ Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
¹⁰ Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA.

Abstract

The FastDesign protocol in the molecular modeling program Rosetta iterates between sequence optimization and structure refinement to stabilize de novo designed protein structures and complexes. FastDesign has been used previously to design novel protein folds and assemblies with important applications in research and medicine. To promote sampling of alternative conformations and sequences, FastDesign includes stages where the energy landscape is smoothened by reducing repulsive forces. Here, we discover that this process disfavors larger amino acids in the protein core because the protein compresses in the early stages of refinement. By testing alternative ramping strategies for the repulsive weight, we arrive at a scheme that produces lower energy designs with more native-like sequence composition in the protein core. We further validate the protocol by designing and experimentally characterizing over 4000 proteins and show that the new protocol produces higher stability proteins.

Keywords: De novo protein design; Rosetta molecular Modeling program; computational protein design; energy landscape; energy optimization; massively parallel protein stability measurements.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Computational Biology / methods*
Databases, Protein
Hydrophobic and Hydrophilic Interactions
Protein Conformation*
Protein Engineering
Protein Folding*
Protein Stability*
Proteins / chemistry*

Substances

Proteins

Abstract

Publication types

MeSH terms

Substances

Grants and funding