A novel method for enzyme design

Zhu, Xiaolei; Lai, Luhua

doi:10.1002/jcc.21050

Cited by 15 publications

(12 citation statements)

References 23 publications

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“…Then a scaffold protein or a scaffold‐protein library should be selected for active site searching. The scaffold library26 which contains 223 ligand‐binding proteins is recommended for enzyme design. We suggest that the residues in the substrate binding pockets are identified first and only these residues are set to be mutable.…”

Section: Methods and Algorithmsmentioning

confidence: 99%

“…Our case studies focus on the hotspots match searching for target protein binding design. The design protocol was first applied to the work of influenza hemagglutinin binding protein design using the same scaffold library that created by Fleishman et al 17 Similar to this scaffold library and the scaffold libraries11, 26 built for screening in enzyme design, a new scaffold protein library called the SimpleScaffold library was created. Only the proteins existing as monomers with 90 to 200 amino acids and without cofactor binding were collected from the protein data bank (PDB) 4.…”

Section: Introductionmentioning

confidence: 99%

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

Lai¹

2012

Proteins

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Proteins perform their functions mainly via active sites, whereas other parts of the proteins comprise the scaffolds, which support the active sites. One strategy for protein functional design is transplanting active sites, such as catalytic sites for enzyme or binding hot spots for protein-protein interactions, onto a new scaffold. AutoMatch is a new program designed for efficiently elucidating suitable scaffolds and potential sites on the scaffolds. Backrub motions are used to treat backbone flexibility during the design process. A step-by-step checking strategy and cluster-representation examination strategy were developed to solve the large combinatorial problem for the matching of active-site conformations. In addition, a grid-based binding energy scoring method was used to filter the solutions. An enzyme design benchmark and a protein-protein interaction design benchmark were built to test the algorithm. AutoMatch could identify the hot spots in the nonbinding protein and rank them within the top five results for 8 of 10 target-binding protein design cases. In addition, among the 15 enzymes tested, AutoMatch can identify the catalytic active sites in the apoprotein and rank them within the top five results for 13 cases. AutoMatch was also tested for screening scaffold library in designing binding proteins targeting influenza hemagglutinin, HIV gp120, and epidermal growth factor receptor kinase, respectively. AutoMatch, and the two test sets, ActApo and ActFree, are available for noncommercial applications at http://mdl.ipc.pku.edu.cn/cgi-bin/down.cgi.

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Section: Methods and Algorithmsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Lai¹

2012

Proteins

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“…A method for designing a new de novo protein was developed where one could search suitable scaffolds directly in the Protein Data Bank (PDB) [65]. Triose phosphate isomerase enzyme was used for the authentication of this method.…”

Section: Rational Computational Designmentioning

confidence: 99%

Computational Approaches for Rational Design of Proteins With Novel Functionalities

Tiwari¹,

Singh²,

Singh³

et al. 2012

Computational and Structural Biotechnology Journal

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Proteins are the most multifaceted macromolecules in living systems and have various important functions, including structural, catalytic, sensory, and regulatory functions. Rational design of enzymes is a great challenge to our understanding of protein structure and physical chemistry and has numerous potential applications. Protein design algorithms have been applied to design or engineer proteins that fold, fold faster, catalyze, catalyze faster, signal, and adopt preferred conformational states. The field of de novo protein design, although only a few decades old, is beginning to produce exciting results. Developments in this field are already having a significant impact on biotechnology and chemical biology. The application of powerful computational methods for functional protein designing has recently succeeded at engineering target activities. Here, we review recently reported de novo functional proteins that were developed using various protein design approaches, including rational design, computational optimization, and selection from combinatorial libraries, highlighting recent advances and successes.

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“…[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

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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.

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A novel method for enzyme design

Cited by 15 publications

References 23 publications

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

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

Computational Approaches for Rational Design of Proteins With Novel Functionalities

A computational method for design of connected catalytic networks in proteins

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