ArticleThe journal of physical chemistry letters2023
Substrate Positioning Dynamics Involves a Non-Electrostatic Component to Mediate Catalysis.
Article in The journal of physical chemistry letters, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 10 citations in OpenAlex.
- MutexaGPT: an intuition-to-design translator for physics-based enzyme engineering.Nature computational science · 2026Article
- Deciphering the evolutionary origin of the enantioselectivity of short-chain dehydrogenases from plants toward 1-borneol.Nature communications · 2026Article
- MutexaGPT: An Intuition-to-Design Translator for Physics-based Enzyme Engineering.Research square · 2026Article
- Computational Method for the Detection of Communication Pathways in Enzymes that Correlate with Experimentally Defined Thermal Activation Networks.The journal of physical chemistry letters · 2026Article
- Correlated Motion-Based Residue Network Analysis Reveals the Distal Thermal Activation in Soybean Lipoxygenase.bioRxiv : the preprint server for biology · 2025Article
- The Role of the Unusual 2-Tyr-1-carboxylate Non-heme Iron Motif in the Mechanism of N,N-Dimethylformamidase.ACS catalysis · 2025Article
- Physics-based modeling in the new era of enzyme engineering.Nature computational science · 2025Review
- Digging out the Molecular Connections between the Catalytic Mechanism of Human Lysosomal α-Mannosidase and Its Pathophysiology.Journal of chemical information and modeling · 2025Article
- Direct asymmetric synthesis of β-branched aromatic α-amino acids using engineered phenylalanine ammonia lyases.Nature communications · 2024Article
- Article
- Mutexa: A Computational Ecosystem for Intelligent Protein Engineering.Journal of chemical theory and computation · 2023Review
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Substrate positioning dynamics (SPD) orients the substrate in the active site, thereby influencing catalytic efficiency. However, it remains unknown whether SPD effects originate primarily from electrostatic perturbation inside the enzyme or can independently mediate catalysis with a significant non-electrostatic component. In this work, we investigated how the non-electrostatic component of SPD affects transition state (TS) stabilization. Using high-throughput enzyme modeling, we selected Kemp eliminase variants with similar electrostatics inside the enzyme but significantly different SPD. The kinetic parameters of these mutants were experimentally characterized. We observed a valley-shaped, two-segment linear correlation between the TS stabilization free energy (converted from kinetic parameters) and substrate positioning index (a metric to quantify SPD). The energy varies by approximately 2 kcal/mol. Favorable SPD was observed for the distal mutant R154W, increasing the proportion of reactive conformations and leading to the lowest activation free energy. These results indicate the substantial contribution of the non-electrostatic component of SPD to enzyme catalytic efficiency.
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