Enzyme Rational Design & De Novo Design Services

CD Biosynsis delivers advanced Enzyme Rational Design & De Novo Design Services, leveraging high-resolution structural bioinformatics and computational chemistry to precisely tailor or create entirely new enzyme functions. Rational design uses molecular modeling to introduce targeted mutations for improving activity, stability, and substrate specificity based on existing enzyme structures. De Novo Design goes further, computationally creating a protein backbone to stabilize a desired transition state, resulting in a novel enzyme fold capable of catalyzing a non-natural reaction. Our services encompass Active Site Engineering, Allosteric Regulation Design, Fusion Protein construction, and Cofactor Engineering, offering the ultimate solution for generating biocatalysts that are optimized for industrial efficiency, chiral synthesis, and novel biological pathways.

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Precision Engineering for Optimal Biocatalytic Function

Rational design and de novo design represent the pinnacle of enzyme engineering, offering fine control over catalytic outcomes unattainable through random evolution alone. Rational design allows us to pinpoint specific residues for mutation based on predicted structural consequences (e.g., introducing a disulfide bond for thermostability or altering a pocket residue for substrate promiscuity). De novo design tackles chemical transformations for which no natural enzyme exists, constructing a protein scaffold to catalyze a target reaction from scratch. We integrate advanced computational tools—including molecular dynamics and free energy calculations—to predict the outcomes of design iterations, ensuring high experimental success rates and delivering high-performance, tailored biocatalysts.

Targeted Design and Novel Creation

Rational Active Site Engineering Advanced Design Modules De Novo Creation and Scaffold Design

Targeted Mutagenesis

Precision Control over Catalysis

Enzyme Active Site Engineering Service

Rational modification of residues within the active site to enhance catalytic rate (kcat), reduce Michaelis constant (Km), or precisely control enantioselectivity.

Surface Charge Engineering

Modifying surface residues to improve solubility, prevent aggregation, or enhance tolerance to extreme pH or salt concentrations.

Domain Swapping / Chimeragenesis

Computational grafting of functional domains from one enzyme to another to introduce novel traits like binding or dimerization capabilities.

Functional Refinement Modules

Controlling Enzyme Behavior and Input

Enzyme Allosteric Regulation Design Service

Engineering a new allosteric site to control enzyme activity via small molecule induction or inhibition, critical for pathway control.

Enzyme Cofactor Engineering Service

Rational mutation of the cofactor binding site to alter cofactor preference (e.g., from $\text{NADH}$ to $\text{NADPH}$) or improve regeneration efficiency.

Enzyme Fusion & Oligomerization Service

Designing interfaces for specific oligomer formation or fusion with other proteins (e.g., scaffolds or tags) to enhance stability or create multi-enzyme complexes.

Creation of Novel Catalysis

Building Function from Scratch

De Novo Enzyme Design

Computationally generating novel protein backbones and active sites to catalyze reactions for which no natural enzyme exists, typically targeting transition states.

Transition State Stabilization

Focusing design efforts on geometric and electronic complementarity to the target reaction's transition state to maximize catalytic power.

Design Validation

Final high-resolution molecular dynamics and stability calculations ensure the designed fold is both stable and functional prior to Gene Synthesis.

Rational Design and De Novo Creation Pipeline

A rigorous, structure-based path to a tailored biocatalyst.

Analysis and Targeting

Design and Modeling

Validation and Selection

Delivery

Structural Input: Use of crystal structure or high-quality homology model.

Mechanism Analysis: Identify residues involved in binding and catalysis.

Targeted Design: Apply Enzyme Active Site Engineering Service or other modules like Enzyme Cofactor Engineering Service.

De Novo Scaffold: Or, initiate De Novo Enzyme Design for novel reaction.

Enzyme Allosteric Regulation Design Service: Molecular dynamics and stability calculations on designed variants.

Enzyme Fusion & Oligomerization Service: Final selection and ranking of designed mutations/sequences.

Gene Synthesis: Synthesize the optimized gene sequences.
Delivery: Optimized gene, 3D structural model, and detailed rationale for each mutation.
Optional: Expression and initial characterization (see Enzyme Engineering services).

The Ultimate in Engineered Catalytic Control

Ultra-High Selectivity

Achieve unparalleled control over regio-, chemo-, and enantioselectivity via active site manipulation.

Novel Functionality

Create enzymes for non-natural reactions or design regulatory circuits via allosteric control.

Predictive Efficiency

Computational modeling reduces experimental variants to a highly selective, high-probability set.

Customizable Scaffolds

Utilize de novo design to build stable protein structures tailored to a specific catalytic need.

Client Testimonials on Rational and De Novo Design

"The Active Site Engineering Service delivered a variant with 10-fold improved enantioselectivity, a result we had failed to achieve through random directed evolution."

Dr. Samuel Liu, R&D Director

"The computational design of a novel allosteric site was successful, allowing us to turn the pathway enzyme on and off using a cheap small-molecule inducer."

Ms. Janet Chen, Lead Bioengineer

"We commissioned the De Novo Enzyme Design for a Diels-Alder reaction. The result was a stable, synthetic enzyme that showed measurable catalytic activity, a huge milestone."

Dr. Kenji Tanaka, Principal Scientist

"Their rational design approach for Cofactor Engineering successfully shifted our enzyme's preference from $\text{NADH}$ to $\text{NADPH}$, aligning perfectly with our chassis cell's metabolic profile."

Mr. Alex Johnson, Research Manager

"The Fusion & Oligomerization Service created a stable dimerized enzyme that was far more thermostable than the monomer, dramatically improving its industrial lifespan."

Dr. Maria Gomez, Group Leader

FAQs about Enzyme Rational Design & De Novo Design Services

Still have questions?

What is the difference between rational design and de novo design?

Rational design, exemplified by our Enzyme Active Site Engineering Service, modifies an existing natural enzyme structure. De Novo Enzyme Design creates an entirely new, synthetic protein fold from scratch to catalyze a target reaction.

Can you introduce a new regulatory mechanism?

Yes. Our Enzyme Allosteric Regulation Design Service uses computational methods to design a binding site for a chosen small molecule, allowing it to modulate enzyme activity.

What information is required to start a de novo design project?

The primary input is the chemical reaction you wish to catalyze, specifically the target transition state structure. No existing enzyme sequence or structure is required.

Can you alter cofactor usage?

Absolutely. Our Enzyme Cofactor Engineering Service uses rational design principles to mutate residues in the cofactor binding pocket to switch specificity (e.g., from $\text{NADH}$ to $\text{NADPH}$) or enhance cofactor binding affinity.

How much does Metabolic Engineering services cost?

The cost of Metabolic Engineering services depends on the project scope, complexity of the target compound, the host organism chosen, and the required yield optimization. We provide customized quotes after a detailed discussion of your specific research objectives.

Do your engineered strains meet regulatory standards?

We adhere to high quality control standards in all strain construction and optimization processes. While we do not handle final regulatory approval, our detailed documentation and compliance with best laboratory practices ensure your engineered strains are prepared for necessary regulatory filings (e.g., GRAS, FDA).

What to look for when selecting the best gene editing service?

We provide various gene editing services such as CRISPR-sgRNA library generation, stable transformation cell line generation, gene knockout cell line generation, and gene point mutation cell line generation. Users are free to select the type of service that suits their research.

Does gene editing allow customisability?

Yes, we offer very customised gene editing solutions such as AAV vector capsid directed evolution, mRNA vector gene delivery, library creation, promoter evolution and screening, etc.

What is the process for keeping data private and confidential?

We adhere to the data privacy policy completely, and all customer data and experimental data are kept confidential.