Control of repeat-protein curvature by computational protein design

Park, Keunwan; Shen, Betty; Parmeggiani, Fabio; Huang, Po-Ssu; Stoddard, Barry; Baker, David

doi:10.1038/nsmb.2938

Cited by 84 publications

(72 citation statements)

References 47 publications

(52 reference statements)

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“…Internal repeats were constrained to adopt the same primary sequence, side-chain, and backbone conformations by using symmetric sequence design and conformation sampling during all modeling moves. Symmetric structure prediction [18] and design has been used extensively in Rosetta [11] yielding atomic-accuracy predictions for large homomeric oligomers, designed cage-like assemblies or repeat proteins [12][13][14][15][19][20][21]. Our calculations were restricted to three internal repeats and two capping repeats.…”

Section: In Silico Designmentioning

confidence: 99%

“…Thereby, the peptide units fall out of register with the armadillo repeats. In importin-α, two separated negatively charged binding sites (major and minor binding site) are formed by repeats B-D and F-H, respectively, and can bind a bipartite nuclear localization sequences (NLS), with the typical sequence KRx [10][11][12] K+x+ ("+" denoting any positively charged residue [6]). Therein the two positively charged residue clusters are separated by a linker of 10-12 amino acids.…”

Section: Introductionmentioning

confidence: 99%

“…Using this template, the relative orientations between subsequent repeats were extracted and imposed as symmetric modeling constraints during backbone and side chain sampling simulations using the Rosetta software suite [11]. Similar design protocols have been used for the computational design of repeat proteins, first with sequence and structural information obtained from natural repeat protein families [12,13] and then for de novo designed repeat proteins with open [14] and closed [15] architectures. Using such approaches, typically >50% of the designed constructs can be expressed as soluble, folded, monomeric proteins and determined structures agree well with the design models (typical RMSD of Cα atoms 0.5 -2.5 Å).…”

Section: Introductionmentioning

confidence: 99%

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Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition

Reichen

Hansen

Forzani

et al. 2016

Journal of Molecular Biology

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Armadillo repeat proteins (ArmRP) recognize their target peptide in extended conformation and bind, in a first approximation, two residues per repeat. They may thus form the basis for building a modular system, in which each repeat is complementary to a piece of the target peptide. Accordingly, preselected repeats could be assembled into specific binding proteins on demand and thereby avoid the traditional generation of every new binding molecule by an independent selection from a library.Stacked armadillo repeats, each consisting of 42 amino acids arranged in three α-helices, build an elongated superhelical structure. Here, we analyzed curvature variations in natural ArmRPs, and identified a repeat pair from yeast importin-α as having the optimal curvature geometry to be complementary to a peptide over its whole length. We employed a symmetric in silico design to obtain a uniform sequence for a stackable repeat while maintaining the desired curvature geometry.Computationally designed armadillo repeat proteins (dArmRPs) had to be stabilized by mutations to remove regions of higher flexibility, which were identified by molecular dynamics (MD) simulations in explicit solvent. Using an N-capping repeat from the consensus-design approach, two different crystal structures of dArmRP were determined. Although the experimental structures of dArmRP deviated from the designed curvature, the insertion of the most conserved binding pockets of natural ArmRPs onto the surface of dArmRPs resulted in binders against the expected peptide with low nanomolar affinities, similar to the binders from the consensus-design series.

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Section: In Silico Designmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition

Reichen

Hansen

Forzani

et al. 2016

Journal of Molecular Biology

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“…We observe that ANK3 has a larger proportion of highly frustrated interactions, compared to the full consensus ANK4 in ( Figure 1A) not only in the Caps, but also in the internal repeats. This strategy was extended later on [32], using the Leucine Rich Repeat (LRR) family as a scaffold, for designing repeat proteins for which the curvature of the array could be rationally modified. The curvature is essential to tune the complementarity between the repeat protein and its target.…”

Section: Repeat Proteins Design: Regular and Highly Stable Moleculesmentioning

confidence: 99%

Telomerase and Cancer Research

de¹,

Junior²

2015

Biochem Mol biol J

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Repeat proteins are constituted by a variable number of copies of a given structural element that is tandemly repeated along a longitudinal axis. They mainly function as protein-protein interactors with binding interfaces that are not conserved along members of the same family but specific for each interacting pair. These proteins have been extensively used as scaffolds for protein design that are usually centered on the maximization of the stability of the repeat arrays. Although overall stability is important for obtaining molecules with enhanced solubility and expression, natural occurring repeatproteins have unstable characteristics that are relevant for their binding properties. Here we discuss the state of the art for repeat protein designs and the ideas of allowing energetic conflicts for introducing enhanced functionality in the arrays.

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“…Repeat proteins have applications that include their use as novel nanomaterials (12-14) and as scaffolds for molecular recognition (15, 16). These proteins may be designed using sequence consensus-based rules (17) or computational protein design methods (18,19). There are a number of families of beta-helical repeat proteins (20), from which we chose the pentapeptide repeat family, forming the repeat five residues (RFR)-fold, which has a square cross-sectional profile, as the basis for the design of a class of synthetic repeat proteins (21) (Fig.…”

mentioning

confidence: 99%

Synthetic beta-solenoid proteins with the fragment-free computational design of a beta-hairpin extension

MacDonald

Kabasakal

Godding

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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The ability to design and construct structures with atomic level precision is one of the key goals of nanotechnology. Proteins offer an attractive target for atomic design because they can be synthesized chemically or biologically and can self-assemble. However, the generalized protein folding and design problem is unsolved. One approach to simplifying the problem is to use a repetitive protein as a scaffold. Repeat proteins are intrinsically modular, and their folding and structures are better understood than large globular domains. Here, we have developed a class of synthetic repeat proteins based on the pentapeptide repeat family of beta-solenoid proteins. We have constructed length variants of the basic scaffold and computationally designed de novo loops projecting from the scaffold core. The experimentally solved 3.56-Å resolution crystal structure of one designed loop matches closely the designed hairpin structure, showing the computational design of a backbone extension onto a synthetic protein core without the use of backbone fragments from known structures. Two other loop designs were not clearly resolved in the crystal structures, and one loop appeared to be in an incorrect conformation. We have also shown that the repeat unit can accommodate whole-domain insertions by inserting a domain into one of the designed loops.computational protein design | synthetic repeat proteins | de novo backbone design | coarse-grained model D uring the course of evolution, natural proteins may be recruited to new unrelated functions conferring a selective advantage to the organism (1, 2). This accretion of new features and functions is likely to have left behind complex interlocking amino acid dependencies that can make reengineering natural proteins difficult and unpredictable (3). For this reason, we and others hypothesize that it is more desirable to design de novo proteins because these proteins provide a biologically neutral platform onto which functional elements can be grafted (4). Artificial proteins have been designed by decoding simple residue patterning rules that govern the packing of secondary structural elements, and this technique has been particularly successful for α-helical bundle proteins (5-7). An alternative approach is to assemble de novo folds from backbone fragments of known structures or idealized secondary structural elements and use computational protein design methods to design the sequence (4,(8)(9)(10). Both the computational and simpler rules-based design approaches have concentrated on designing proteins consisting of canonical secondary structure linked with loops of minimal length.A class of proteins that has attracted considerable interest is artificial proteins based on repeating structural motifs due to their intrinsic modularity and designability (11). Repeat proteins have applications that include their use as novel nanomaterials (12-14) and as scaffolds for molecular recognition (15, 16). These proteins may be designed using sequence consensus-based rules (17) or computational prot...

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Control of repeat-protein curvature by computational protein design

Cited by 84 publications

References 47 publications

Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition

Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition

Telomerase and Cancer Research

Synthetic beta-solenoid proteins with the fragment-free computational design of a beta-hairpin extension

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