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Jiang Y, Ding N, Shao Q, Stull SL, Cheng Z, Yang ZJ. Substrate Positioning Dynamics Involves a Non-Electrostatic Component to Mediate Catalysis. J Phys Chem Lett 2023; 14:11480-11489. [PMID: 38085952 PMCID: PMC11211065 DOI: 10.1021/acs.jpclett.3c02444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
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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Affiliation(s)
- Yaoyukun Jiang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Ning Ding
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Qianzhen Shao
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Sebastian L. Stull
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Zihao Cheng
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Zhongyue J. Yang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Data Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
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Yang ZJ, Shao Q, Jiang Y, Jurich C, Ran X, Juarez RJ, Yan B, Stull SL, Gollu A, Ding N. Mutexa: A Computational Ecosystem for Intelligent Protein Engineering. J Chem Theory Comput 2023; 19:7459-7477. [PMID: 37828731 PMCID: PMC10653112 DOI: 10.1021/acs.jctc.3c00602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Indexed: 10/14/2023]
Abstract
Protein engineering holds immense promise in shaping the future of biomedicine and biotechnology. This Review focuses on our ongoing development of Mutexa, a computational ecosystem designed to enable "intelligent protein engineering". In this vision, researchers will seamlessly acquire sequences of protein variants with desired functions as biocatalysts, therapeutic peptides, and diagnostic proteins through a finely-tuned computational machine, akin to Amazon Alexa's role as a versatile virtual assistant. The technical foundation of Mutexa has been established through the development of a database that combines and relates enzyme structures and their respective functions (e.g., IntEnzyDB), workflow software packages that enable high-throughput protein modeling (e.g., EnzyHTP and LassoHTP), and scoring functions that map the sequence-structure-function relationship of proteins (e.g., EnzyKR and DeepLasso). We will showcase the applications of these tools in benchmarking the convergence conditions of enzyme functional descriptors across mutants, investigating protein electrostatics and cavity distributions in SAM-dependent methyltransferases, and understanding the role of nonelectrostatic dynamic effects in enzyme catalysis. Finally, we will conclude by addressing the future steps and fundamental challenges in our endeavor to develop new Mutexa applications that assist the identification of beneficial mutants in protein engineering.
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Affiliation(s)
- Zhongyue J. Yang
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt
Institute of Chemical Biology, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
- Data
Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Qianzhen Shao
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Yaoyukun Jiang
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Christopher Jurich
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt
Institute of Chemical Biology, Vanderbilt
University, Nashville, Tennessee 37235, United States
| | - Xinchun Ran
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Reecan J. Juarez
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Chemical
and Physical Biology Program, Vanderbilt
University, Nashville, Tennessee 37235, United States
| | - Bailu Yan
- Department
of Biostatistics, Vanderbilt University, Nashville, Tennessee 37205, United States
| | - Sebastian L. Stull
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Anvita Gollu
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Ning Ding
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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