In this study, we developed a sustainable biocatalytic process for sitagliptin production using an AI-driven 6D-grid protein engineering platform. By leveraging molecular interaction data, solvent effects, and a database of 1.39 million structural fragments, we identified high-performing R-transaminase variants while minimizing experimental screening. The engineered enzyme exhibited excellent solubility, stability, and scalability, achieving up to...
This study employed quantum mechanical dynamics (QMD) simulations to elucidate the catalytic mechanism of Bacillus safensis nitrilase (BsNIT) toward pentanedinitrile (PD). The results revealed a sequential conversion of PD to 4-cyanobutanoic acid and subsequently to pentanedioic acid through two water-mediated hydrolysis steps involving the catalytic triad (C164, K130, and E38). Key intermediates and transition states...
In this research article, we demonstrate direct conversion of glucose to D-tagatose, a low-calorie rare sugar, using an engineered Escherichia coli whole-cell system. Our study identifies a galactose-1-phosphate phosphatase (DdGal1Pase) with stringent substrate selectivity driven by distinct hydrogen-bond networks, enabling reversal of the Leloir pathway and glucose-based tagatose biosynthesis. This work provides a foundation for...
This study provides the first comprehensive computational investigation of the nitrilase from Bacillus safensis (BsNIT) and Spirosoma linguale DSM 74 (SINIT) for elucidation on the reaction mechanism for nitrile hydrolysis and nitrile hydration reaction respectively. Mechanistic analysis revealed critical catalytic events, including nucleophilic attack by Cys and water-mediated proton transfer by Glu, with covalent substrate...
In this study, we developed an AI-driven protein stability prediction framework that integrates AlphaFold-generated structures, molecular refinement, and deep learning techniques. Multiple machine learning and neural network architectures were evaluated, with a multi-input CNN model leveraging protein contact maps delivering the best performance. The framework enables efficient prediction of mutation-induced stability changes, reducing reliance on...
We’re excited to announce our latest publication in Nature Scientific Reports on proteins with double active sites, which could revolutionize enzyme design strategies. We have developed an AI-based tool which creates enzymes with multiple active sites, enhancing their functionality by incorporating diverse catalytic activities. For example, a transaminase enzyme can now also facilitate hydrolysis reactions....
Chlorogenic acids (CHLs) are known to competitively bind to translocase-I (T1) of the glucose-6-phosphatase (G6 Pase) system, thereby inhibiting the transport of glucose-6-phosphate (G6P). This competitive binding results in a consequential reduction in blood sugar levels. In this study, steered molecular dynamics (SMD) simulation is employed to investigate the interaction between T1 and G6P, aiming...
Engineering the utilization of non-native substrates, or synthetic heterotrophy, in proven industrial microbes such as Saccharomyces cerevisiae represents an opportunity to valorize plentiful and renewable sources of carbon and energy as inputs to bioprocesses. We previously demonstrated that activation of the galactose (GAL) regulon, a regulatory structure used by this yeast to coordinate substrate utilization...
LSFG is a novel method for engineering proteins by utilizing an atomistic grid-based computational method that analyzes and compares protein atomic compositions. By arranging a protein’s atoms into a fine 3D grid, this approach captures atomic-level details in highly localized regions, allowing comparison of specific protein regions even in the absence of structural similarity. Unlike...
Presented herein is a method for protein engineering that constructs a three-dimensional grid space around a protein. Different probes simulating amino acid interactions are placed within the grid. Pair Interaction Energy is calculated using the FMO technique for probe-protein interactions. An algorithmic process calculates the sum of PIEs, extending from each grid point to its...
