Rational design of alpha-helical tandem repeat proteins with closed architectures

By Lindsey Doyle, J. Hallinan, Jill Bolduc, F. Parmeggiani, David Baker, Barry L. Stoddard, Philip Bradley. 2015

123 citations recorded by the source corpus.

Tandem repeat proteins, which are formed by repetition of modular units of protein sequence and structure, play important biological roles as macromolecular binding and scaffolding domains, enzymes, and building blocks for the assembly of fibrous materials. The modular nature of repeat proteins enables the rapid construction and diversification of extended binding surfaces by duplication and recombination of simple building blocks. The overall architecture of tandem repeat protein structures—which is dictated by the internal geometry and local packing of the repeat building blocks—is highly diverse, ranging from extended, super-helical folds that bind peptide, DNA, and RNA partners, to closed and compact conformations with internal cavities suitable for small molecule binding and catalysis. Here we report the development and validation of computational methods for de novo design of tandem repeat protein architectures driven purely by geometric criteria defining the inter-repeat geometry, without reference to the sequences and structures of existing repeat protein families. We have applied these methods to design a series of closed α-solenoid repeat structures (α-toroids) in which the inter-repeat packing geometry is constrained so as to juxtapose the amino (N) and carboxy (C) termini; several of these designed structures have been validated by X-ray crystallography. Unlike previous approaches to tandem repeat protein engineering, our design procedure does not rely on template sequence or structural information taken from natural repeat proteins and hence can produce structures unlike those seen in nature. As an example, we have successfully designed and validated closed α-solenoid repeats with a left-handed helical architecture that—to our knowledge—is not yet present in the protein structure database.

Subfields: Molecular Biology

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Citations in the corpus

Hallucinating symmetric protein assemblies (2022, background): “With the exception of parametrically designed structures (11, 12), design strategies involve rigid body docking of characterized monomers into higher order symmetric structures, followed by interface optimization to generate low-energy assembled states (13–17).”
Identifying well-folded de novo proteins in the new era of accurate structure prediction (2022, methodology): “For the second dataset (“Monomer dataset”), we have curated a selection of 518 de novo proteins from several studies and spanning a wide range of folds (α, β, and mixed α/β) that were designed to be stable monomers without function (Kuhlman et al., 2003; Koga et al., 2012; Brunette et al., 2015; Doy”
Recent advances in de novo protein design: Principles, methods, and applications (2021, background): “By modulating the curvature, alpha tandem repeat proteins can form closed toroid structures (68).”
De novo protein design, a retrospective (2020, background): “Baker and coworkers have developed generalized computational methods to engineer cyclic and superhelical arrays formed from helix–loop–helix motifs (Brunette et al., 2015; Doyle et al., 2015).”
Protein sequence design with a learned potential (2020, background): “Computational protein design has emerged as powerful tool for studying the conformational space of proteins, and has allowed us to expand the space of known protein folds [1, 2, 3, 4, 5, 6], create variations on existing topologies [7, 8, 9, 10, 11], and access the expansive space of sequences yet t”
Reconfigurable asymmetric protein assemblies through implicit negative design (2021, unknown): “To build the C3-symmetric hub, we used a previously published crystal structure of a 12-repeat toroid ring (33).”
Essentials of de novo protein design: Methods and applications (2018, methodology): “Nevertheless, this method has been widely studied and successfully applied to build folds of various degrees of complexity, ranging from miniproteins(38,39) to large folds of highly nonlocal character.(25,27,30,37) The basic workflow for fragment assembly starts by representing the target protein to”
The coming of age of de novo protein design (2016, background): “The effort to construct de novo proteins with ideal backbone arrangements has led to the design of proteins with internal symmetry in which a single idealized unit is repeated numerous times 39–41 (Fig.”