دورية أكاديمية
Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions
| العنوان: | Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions |
|---|---|
| المؤلفون: | Xiaoliang Pan, Richard Van, Jingzhi Pu, Kwangho Nam, Yuezhi Mao, Yihan Shao |
| سنة النشر: | 2023 |
| مصطلحات موضوعية: | Biophysics, Biochemistry, Sociology, Computational Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Information Systems not elsewhere classified, free energy contributions, enzyme mechanistic studies, ab initio <, reaction free energy, chorismate mutase reaction, individual residue contributions, free energy barrier, reaction coordinate, readily obtained, mutant design, highly desirable, enzymatic reactions |
| الوصف: | In enzyme mechanistic studies and mutant design, it is highly desirable to know the individual residue contributions to the reaction free energy and barrier. In this work, we show that such free energy contributions from each residue can be readily obtained by postprocessing ab initio quantum mechanical molecular mechanical (ai-QM/MM) free energy simulation trajectories. Specifically, through a mean force integration along the minimum free energy pathway, one can obtain the electrostatic, polarization, and van der Waals contributions from each residue to the free energy barrier. Separately, a similar analysis procedure allows us to assess the contribution from different collective variables along the reaction coordinate. The chorismate mutase reaction is used to demonstrate the utilization of these two trajectory analysis tools. |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | unknown |
| العلاقة: | https://figshare.com/articles/journal_contribution/Free_Energy_Profile_Decomposition_Analysis_for_QM_MM_Simulations_of_Enzymatic_Reactions/24538964Test |
| DOI: | 10.1021/acs.jctc.3c00973.s001 |
| الإتاحة: | https://doi.org/10.1021/acs.jctc.3c00973.s001Test https://figshare.com/articles/journal_contribution/Free_Energy_Profile_Decomposition_Analysis_for_QM_MM_Simulations_of_Enzymatic_Reactions/24538964Test |
| حقوق: | CC BY-NC 4.0 |
| رقم الانضمام: | edsbas.F0B51E68 |
| قاعدة البيانات: | BASE |
| DOI: | 10.1021/acs.jctc.3c00973.s001 |
|---|