Binding affinity and conformational change predictions for a series of inhibitors with RuBisCO in a carbon dioxide gas and water environment by multiple computational methods

Meng, Yue; Liu, Ruiyuan; Wang, Leng; Li, Fang; Tian, Yiyi; Lu, Huizhe

doi:10.1016/j.molliq.2023.121478

Cited by 5 publications

(2 citation statements)

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“…AMD is an extended biased-potential MD method that permits the efficient study of biomolecular systems on time scales several orders of magnitude larger than using standard classical MD methods, while still maintaining a fully atomic representation of the system . AMD has been successfully applied in the study of slow time-scale functional dynamics in folded proteins . GaMD is a robust computational method for simultaneous unconstrained enhanced sampling and free energy calculations of biomolecules.…”

Section: Tunnel Engineering Of Lipasementioning

confidence: 99%

“…83 AMD has been successfully applied in the study of slow time-scale functional dynamics in folded proteins. 84 GaMD is a robust computational method for simultaneous unconstrained enhanced sampling and free energy calculations of biomolecules. It works by adding a harmonic boost potential to smooth the biomolecular potential energy surface and reduce energy barriers.…”

Section: Identification Of Tunnelsmentioning

confidence: 99%

See 1 more Smart Citation

Computer-Aided Tunnel Engineering: A Promising Strategy for Improving Lipase Applications in Esterification Reactions

Chong,

Qi,

et al. 2023

ACS Catal.

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Esterification is one of the most important reactions in organic synthesis and industrial applications. The applications of lipases in esterification are increasingly widespread and have high cumulative values. Mostly, in the catalytic cycle of lipases, the tunnel connecting the active site to the surface of a protein plays a significant role in ligand transport. As a unique conformational structure of a protein, the tunnel could regulate the catalytic performance of lipases via ligand transportation. Therefore, the tunnel of lipase can be designed accordingly to speed up the transportation of the ligand, also highlighting the importance of tunnel engineering in the industrial application of enzymatic esterification reactions. This article reviewed the characterizations of the tunnel structure and focused on the strategies of tunnel engineering, such as rational design and directed evolution. Additionally, tunnel engineering using computer-aided design techniques (e.g., CAVER, Molecular Dynamics simulations) to improve the catalytic functions of lipases, such as activity, substrate specificity, and stability, was also discussed in depth. Finally, this review provides future perspectives about tunnel-engineered lipases as biocatalysts in esterification reactions.

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Section: Tunnel Engineering Of Lipasementioning

confidence: 99%

Section: Identification Of Tunnelsmentioning

confidence: 99%