Computational redesign of protein-protein interaction specificity

Kortemme, Tanja; Joachimiak, Łukasz A.; Bullock, Alex N.; Schuler, Aaron D.; Stoddard, Barry; Baker, David

doi:10.1038/nsmb749

Cited by 283 publications

(269 citation statements)

References 42 publications

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“…Although all negative-design strategies optimize the difference in computed energy between the target and competing states, different groups have used a wide range of force fields, descriptions of the unfolded state, and optimization algorithms to achieve this end (7,8,10). For our studies, we used a force field that had been empirically optimized for protein design, implicitly considered the energy of the unfolded state to be constant, and used a combination of DEE and Monte Carlo search algorithms for global optimization.…”

Section: Predicted Vs Experimental Stabilitiesmentioning

confidence: 99%

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Specificity versus stability in computational protein design

Bolon

Grant

Baker

et al. 2005

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

133

123

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Protein-protein interactions can be designed computationally by using positive strategies that maximize the stability of the desired structure and͞or by negative strategies that seek to destabilize competing states. Here, we compare the efficacy of these methods in reengineering a protein homodimer into a heterodimer. The stability-design protein (positive design only) was experimentally more stable than the specificity-design heterodimer (positive and negative design). By contrast, only the specificity-design protein assembled as a homogenous heterodimer in solution, whereas the stability-design protein formed a mixture of homodimer and heterodimer species. The experimental stabilities of the engineered proteins correlated roughly with their calculated stabilities, and the crystal structure of the specificity-design heterodimer showed most of the predicted side-chain packing interactions and a mainchain conformation indistinguishable from the wild-type structure. These results indicate that the design simulations capture important features of both stability and structure and demonstrate that negative design can be critical for attaining specificity when competing states are close in structure space.adaptor protein ͉ protein engineering ͉ SspB H ighly specific recognition lies at the core of most cellular processes. The interaction of two partner proteins in a crowded intracellular environment depends on the equilibrium stability of the complex, which is determined by affinity and concentration, but is also controlled by the competing binding of either partner to other cellular macromolecules. Efficient protein recognition requires both stability and specificity. In natural systems, both parameters are subject to evolutionary optimization. Likewise in engineered systems, stability can be targeted for maximization, and known competing states or interactions can be minimized through the use of negative design. The biophysical tradeoff between stability and specificity in molecular recognition is a fascinating problem that has important implications in the development of practical tools for synthesizing and dissecting biological systems.Focusing on stability without explicit consideration of specificity has resulted in impressive protein-engineering feats, including full-sequence design of a zinc-finger protein that folds in the absence of metal (1), introduction of catalytic activity into previously inert protein scaffolds (2, 3), and the creation of a novel protein fold (4). These successes relied on positive design only. Positive design maximizes favorable interactions in the target conformation. Negative design, by contrast, maximizes unfavorable interactions in competing states and requires modeling of each unwanted conformation (5, 6).Protein-protein interactions have been successfully reengineered to alter binding specificity both by using and ignoring negative design (7-15). How is success possible in the absence of negative design? One possibility is that most changes that optimize the stability of a targe...

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Section: Predicted Vs Experimental Stabilitiesmentioning

confidence: 99%

“…Protein-protein interactions have been successfully reengineered to alter binding specificity both by using and ignoring negative design (7)(8)(9)(10)(11)(12)(13)(14)(15). How is success possible in the absence of negative design?…”

mentioning

confidence: 99%

Specificity versus stability in computational protein design

Bolon

Grant

Baker

et al. 2005

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

133

123

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“…Recently, several groups suggested that it is feasible to computationally redesign protein-protein interfaces by using native or homologous protein pairs (7)(8)(9)(10). For example, Reina et al (7) computationally reengineered a PDZ domain to bind novel peptide target sequences, and the designed protein showed affinity of two orders of magnitude higher than that of the WT interacting partners (7).…”

Section: Discussionmentioning

confidence: 99%

“…Havranek and Harbury (9) explicitly took negative design into account in protein-protein interface design. Kortemme et al (10) redesigned a DNase-immunity protein interface to specifically bind a new pair of interacting partners stronger than their WT counterparts.…”

Section: Discussionmentioning

confidence: 99%

“…Recent developments in structural bioinformatics have contributed greatly to our understanding of protein-protein interactions (1)(2)(3)(4)(5)(6). Several groups have addressed the feasibility of computational redesign of protein-protein interactions by using native or homologous protein-protein interfaces (7)(8)(9)(10). Because different protein backbones can perform similar functions (11), in the current study we explored the feasibility of designing nonnatural protein-protein interaction pairs using known protein scaffolds.…”

mentioning

confidence: 99%

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Nonnatural protein–protein interaction-pair design by key residues grafting

Liu

Zhu

et al. 2007

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

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Protein-protein interface design is one of the most exciting fields in protein science; however, designing nonnatural protein-protein interaction pairs remains difficult. In this article we report a de novo design of a nonnatural protein-protein interaction pair by scanning the Protein Data Bank for suitable scaffold proteins that can be used for grafting key interaction residues and can form stable complexes with the target protein after additional mutations. Using our design algorithm, an unrelated protein, rat PLC␦ 1-PH (pleckstrin homology domain of phospholipase C-␦1), was successfully designed to bind the human erythropoietin receptor (EPOR) after grafting the key interaction residues of human erythropoietin binding to EPOR. The designed mutants of rat PLC␦ 1-PH were expressed and purified to test their binding affinities with EPOR. A designed triple mutation of PLC␦ 1-PH (ERPH1) was found to bind EPOR with high affinity (K D of 24 nM and an IC50 of 5.7 M) both in vitro and in a cell-based assay, respectively, although the WT PLC␦ 1-PH did not show any detectable binding under the assay conditions. The in vitro binding affinities of the PLC␦ 1-PH mutants correlate qualitatively to the computational binding affinities, validating the design and the protein-protein interaction model. The successful practice of finding a proper protein scaffold and making it bind with EPOR demonstrates a prospective application in protein engineering targeting proteinprotein interfaces.de novo design of protein-protein interaction pair ͉ erythropoietin ͉ functional site grafting ͉ key residue at interface P rotein-protein interaction is critical in many biological processes ranging from cell differentiation to apoptosis; however, little is known about the general principles governing the specificity and binding affinity of protein-protein interactions. Recent developments in structural bioinformatics have contributed greatly to our understanding of protein-protein interactions (1-6). Several groups have addressed the feasibility of computational redesign of protein-protein interactions by using native or homologous protein-protein interfaces (7-10). Because different protein backbones can perform similar functions (11), in the current study we explored the feasibility of designing nonnatural protein-protein interaction pairs using known protein scaffolds.To reconstruct the function of a protein, one of the common strategies is grafting, i.e., transferring the functional epitopes from one protein to another. The critical step for protein grafting is to find suitable sites for functional epitope transfer. To this purpose, several computational methods have been developed including a geometric hashing paradigm (12), FITSITE (13), GRAFTER (14), and DEZYMER (15, 16). We have developed a strategy for protein-protein interface redesign by grafting discontinuous interaction epitopes to nonhomologous proteins (17-19). The erythropoietin (EPO)-EPO receptor (EPOR) system was used as an example for nonnatural protein-protein interaction-...

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Bioreduction

Parachin¹,

Carlquist²,

Gorwa-Grauslund³

2010

Encyclopedia of Industrial Biotechnology

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Bioreduction has emerged over the years as an alternative method to organic synthesis for the generation of chiral precursors of commercial interest. Bioreductions operate under mild conditions of pH and temperature with the help of highly regio‐ and enantio‐selective oxidoreductase enzymes. In this contribution, the different oxidoreductase families involved in bioreductions are exemplified and their main characteristics are presented. The wide spectrum of oxidoreductase substrates (including ketones, diketones, ketoesters, aldehydes, alkenes, and keto acids) is discussed and both preparative and industrial scale examples are reported. The advantages and disadvantages of using isolated enzymatic systems versus whole‐cell systems for bioreduction are discussed in terms of cost, specificity, stereoselectivity, and cofactor regeneration. The contribution is also reviewing strategies for improving the biocatalyst at the cell or enzyme level, which include process engineering, metabolic engineering as well as structure‐based and nonstructure‐based enzyme engineering. Finally, the potential role of metagenomics for isolating novel biocatalysts from different environments is discussed.

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Computational redesign of protein-protein interaction specificity

Cited by 283 publications

References 42 publications

Specificity versus stability in computational protein design

Specificity versus stability in computational protein design

Nonnatural protein–protein interaction-pair design by key residues grafting

Bioreduction

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