Enzyme Engineering by De Novo Design

Creative Enzymes provides comprehensive de novo enzyme design services, combining computational protein design, molecular modeling, and biophysical analysis to construct enzymes with entirely new structures and catalytic functions. Unlike conventional engineering methods that modify existing enzymes, de novo design starts from first principles—creating sequences that fold into desired architectures and perform specific catalytic roles. Our platform integrates structure prediction, folding simulations, and energy optimization algorithms, enabling the design of stable, functional biocatalysts for industrial, pharmaceutical, and research applications.

Background: How De Novo Enzyme Design Works

De novo enzyme design represents one of the most advanced frontiers in modern protein engineering. This approach aims to create new catalytic proteins from scratch, guided by an understanding of chemical reactivity, thermodynamics, and protein folding principles.

Unlike rational design or directed evolution, which modify natural scaffolds, de novo design builds customized protein backbones and novel active sites that do not exist in nature. By leveraging insights from sequence-to-structure relationships, statistical force fields, and quantum mechanical simulations, scientists can now predict how amino acid sequences fold and interact to catalyze desired reactions.

The key steps include:

• Theozyme Creation: Computationally model a minimal, idealized active site (the "theozyme") with amino acid residues positioned to stabilize the reaction's transition state.
• Scaffold Matching: Search a database of protein folds to find a "scaffold" that can structurally accommodate and support the designed theozyme.
• Computational Optimization: Use powerful software (like Rosetta) to design the rest of the protein sequence around the scaffold, optimizing it for stability and to precisely position the catalytic residues.
• Experimental Testing: Synthesize the genes for the top-ranked computational designs, express the proteins, and test them for the desired catalytic activity. Most initial designs fail, requiring iterative refinement.

During the de novo enzyme design process, major aspects include backbone sampling to explore feasible structural frameworks, scoring to evaluate stability and compatibility, sequence optimization to refine amino acid composition, and functional site design to tailor catalysis or specificity—together enabling the creation of novel enzymes with desired properties.

Figure 1. Major aspects of the de novo protein design. (Pan and Kortemme, 2021)

Creative Enzymes utilizes these state-of-the-art computational and experimental strategies to design enzymes capable of catalyzing unnatural reactions, operating under extreme conditions, or achieving higher efficiency than natural counterparts. This breakthrough capability opens possibilities for green chemistry, therapeutic development, and advanced material synthesis.

What We Offer: De Novo Enzyme Design

Creative Enzymes offers a one-stop de novo enzyme design service, combining computational prediction with experimental validation. Our team of structural biologists and computational chemists provides customized solutions for projects that require novel enzyme scaffolds, tailored active sites, or new catalytic mechanisms.

De Novo Design Services Workflow

# Required for the guaranteed packages but optional for custom services.

Methods for De Novo Enzyme Design

At Creative Enzymes, our de novo enzyme design services integrate state-of-the-art computational, biochemical, and molecular display technologies to create enzymes with entirely new catalytic functions. Depending on project requirements and desired outcomes, we employ one or a combination of the following approaches to ensure optimal structural and functional performance.

Table 1. Comparison of methods for de novo enzyme generation. (Golynskiy and Seelig, 2010)

Service Highlights

• Enzyme structure prediction and folding simulations using cutting-edge molecular dynamics and AI-assisted modeling.
• Energetic and thermodynamic analysis to evaluate conformational stability and reaction feasibility.
• De novo sequence generation guided by natural statistical force fields and quantum mechanics/molecular mechanics (QM/MM) models.
• Experimental validation and characterization, ensuring that designed enzymes achieve intended catalytic outcomes.

Through this integrated platform, Creative Enzymes delivers innovative, stable, and high-performance enzymes designed to meet even the most challenging application demands.

Contact Our Team

Why Partner with Creative Enzymes

Case Studies: De Novo Enzyme Design

Common Questions About De Novo Enzyme Design

• Q: What is the main difference between de novo enzyme design and rational design?

  A: Rational design modifies existing natural enzymes based on structural knowledge, while de novo design creates entirely new proteins from first principles. This allows greater freedom in defining new catalytic functions and structural architectures.

• Q: What kinds of reactions can be targeted by de novo enzyme design?

  A: De novo design can generate enzymes for both natural reactions (hydrolysis, oxidation, reduction) and unnatural reactions (carbon–carbon bond formation, polymerization, or synthetic chemical transformations).

• Q: How do you ensure the designed enzyme will function as expected?

  A: We combine computational energy calculations, AI-based structure prediction, and in vitro validation through expression and activity assays. This ensures each designed enzyme achieves its predicted catalytic activity and stability.

• Q: What data or input should clients provide?

  A: Clients should share reaction details, target substrates or products, desired conditions, and specific catalytic goals. Our scientists use this information to design an appropriate enzyme scaffold and catalytic site.

• Q: What is the typical project timeline?

  A: A full de novo design and validation project typically takes 10–16 weeks, depending on the reaction complexity, modeling depth, and required experimental verification.

• Q: Can de novo design be integrated with directed evolution or rational design?

  A: Yes. Creative Enzymes often combines de novo modeling with directed evolution or rational refinement to further optimize activity, selectivity, or stability after initial design validation.