Automatch: Target‐binding protein design and enzyme design by automatic pinpointing potential active sites in available protein scaffolds

Lai, Luhua

doi:10.1002/prot.24009

Cited by 18 publications

(13 citation statements)

References 64 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Second, we used the native conformation of each key residue (E99, Y160, and M161) in 2L and the solution structure of DS119 (PDB ID: 2KI0) as inputs for our grafting method. We have previously developed an efficient program, AutoMatch, for transplanting functional residues onto any protein scaffolds . With the constraints to keep the grafted residues in native conformations, AutoMatch searched for the best combination of mutagenesis sites to accommodate E, Y and M on DS119.…”

Section: Resultsmentioning

confidence: 99%

“…We posit that in these three proteins the key residues can sample bigger conformational space and accordingly adjust their conformations when they approach TNFα. This difference suggests we should capture this feature and incorporate more backbone motions in AutoMatch calculations in addition to the backrub motion . It may also explain why RosettaDesign can significantly improve the binding affinity for Tbab2‐4 through finer sampling of the backbone conformations …”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Rational design of TNFα binding proteins based on the de novo designed protein DS119

et al. 2016

Self Cite

View full text Add to dashboard Cite

De novo protein design offers templates for engineering tailor-made protein functions and orthogonal protein interaction networks for synthetic biology research. Various computational methods have been developed to introduce functional sites in known protein structures. De novo designed protein scaffolds provide further opportunities for functional protein design. Here we demonstrate the rational design of novel tumor necrosis factor alpha (TNFa) binding proteins using a home-made grafting program AutoMatch. We grafted three key residues from a virus 2L protein to a de novo designed small protein, DS119, with consideration of backbone flexibility. The designed proteins bind to TNFa with micromolar affinities. We further optimized the interface residues with RosettaDesign and significantly improved the binding capacity of one protein Tbab1-4. These designed proteins inhibit the activity of TNFa in cellular luciferase assays. Our work illustrates the potential application of the de novo designed protein DS119 in protein engineering, biomedical research, and protein sequence-structure-function studies.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Rational design of TNFα binding proteins based on the de novo designed protein DS119

et al. 2016

Self Cite

View full text Add to dashboard Cite

show abstract

“…[1][2][3][4][5] Several approaches have been developed to generate new enzyme active sites by searching for placements of catalytically competent side-chain constellations in selected protein scaffolds or curated subsets of the Protein Data Bank containing up to several thousand protein structures. [6][7][8][9][10][11] Rosetta computational enzyme design calculations have proceeded by first generating an ideal active site, or theozyme, consisting of the reaction transition state surrounded by side-chain functional groups positioned so as to maximize transition-state stabilization. RosettaMatch is then used to search for geometrically compatible placements of these ideal active sites in protein scaffolds.…”

Section: Introductionmentioning

confidence: 99%

A computational method for design of connected catalytic networks in proteins

et al. 2019

View full text Add to dashboard Cite

Computational design of new active sites has generally proceeded by geometrically defining interactions between the reaction transition state(s) and surrounding sidechain functional groups which maximize transition-state stabilization, and then searching for sites in protein scaffolds where the specified side-chain-transitionstate interactions can be realized. A limitation of this approach is that the interactions between the side chains themselves are not constrained. An extensive connected hydrogen bond network involving the catalytic residues was observed in a designed retroaldolase following directed evolution. Such connected networks could increase catalytic activity by preorganizing active site residues in catalytically competent orientations, and enabling concerted interactions between side chains during catalysis, for example, proton shuffling. We developed a method for designing active sites in which the catalytic side chains, in addition to making interactions with the transition state, are also involved in extensive hydrogen bond networks. Because of the added constraint of hydrogen-bond connectivity between the catalytic side chains, to find solutions, a wider range of interactions between these side chains and the transition state must be considered. Our new method starts from a ChemDraw-like two-dimensional representation of the transition state with hydrogen-bond donors, acceptors, and covalent interaction sites indicated, and all placements of side-chain functional groups that make the indicated interactions with the transition state, and are fully connected in a single hydrogen-bond network are systematically enumerated. The RosettaMatch method can then be used to identify realizations of these fully-connected active sites in protein scaffolds. The method generates many fully-connected active site solutions for a set of model reactions that are promising starting points for the design of fully-preorganized enzyme catalysts.

show abstract

“…The automated searching program Dezymer was developed to construct metal-binding sites for rational design of nascent metalloenzymes [ 21 , 22 ]. Other newly developed programs for matching active sites onto protein scaffolds include vector matching [ 23 ], OptGraft [ 24 ], ScaffoldSelection [ 25 ], ProdaMatch [ 26 ], AutoMatch [ 27 ], and Saber [ 28 ]. However, the actual effectiveness of these programs to generate de novo enzymes has not been confirmed by experimental validation [ 23 – 28 ].…”

Section: Introductionmentioning

confidence: 99%

Use of an Improved Matching Algorithm to Select Scaffolds for Enzyme Design Based on a Complex Active Site Model

et al. 2016

View full text Add to dashboard Cite

Active site preorganization helps native enzymes electrostatically stabilize the transition state better than the ground state for their primary substrates and achieve significant rate enhancement. In this report, we hypothesize that a complex active site model for active site preorganization modeling should help to create preorganized active site design and afford higher starting activities towards target reactions. Our matching algorithm ProdaMatch was improved by invoking effective pruning strategies and the native active sites for ten scaffolds in a benchmark test set were reproduced. The root-mean squared deviations between the matched transition states and those in the crystal structures were < 1.0 Å for the ten scaffolds, and the repacking calculation results showed that 91% of the hydrogen bonds within the active sites are recovered, indicating that the active sites can be preorganized based on the predicted positions of transition states. The application of the complex active site model for de novo enzyme design was evaluated by scaffold selection using a classic catalytic triad motif for the hydrolysis of p-nitrophenyl acetate. Eighty scaffolds were identified from a scaffold library with 1,491 proteins and four scaffolds were native esterase. Furthermore, enzyme design for complicated substrates was investigated for the hydrolysis of cephalexin using scaffold selection based on two different catalytic motifs. Only three scaffolds were identified from the scaffold library by virtue of the classic catalytic triad-based motif. In contrast, 40 scaffolds were identified using a more flexible, but still preorganized catalytic motif, where one scaffold corresponded to the α-amino acid ester hydrolase that catalyzes the hydrolysis and synthesis of cephalexin. Thus, the complex active site modeling approach for de novo enzyme design with the aid of the improved ProdaMatch program is a promising approach for the creation of active sites with high catalytic efficiencies towards target reactions.

show abstract

Automatch: Target‐binding protein design and enzyme design by automatic pinpointing potential active sites in available protein scaffolds

Cited by 18 publications

References 64 publications

Rational design of TNFα binding proteins based on the de novo designed protein DS119

Rational design of TNFα binding proteins based on the de novo designed protein DS119

A computational method for design of connected catalytic networks in proteins

Use of an Improved Matching Algorithm to Select Scaffolds for Enzyme Design Based on a Complex Active Site Model

Contact Info

Product

Resources

About