Publication details

Different QM/MM Approaches To Elucidate Enzymatic Reactions: Case Study on ppGalNAcT2


JANOŠ Pavel TRNKA Tomáš KOZMON Stanislav TVAROŠKA Igor KOČA Jaroslav

Year of publication 2016
Type Article in Periodical
Magazine / Source Journal of Chemical Theory and Computation
MU Faculty or unit

Central European Institute of Technology

Field Physical chemistry and theoretical chemistry
Keywords QM/MM; glycosyltransferase; reaction mechanism; enzyme; DFT; Ab Initio MD
Description Hybrid QM/MM computational studies can provide invaluable insight into the mechanisms of enzymatic reactions that can be exploited for rational drug design. Various approaches are available for such studies. However, their strengths and weaknesses may not be immediately apparent. Using the retaining glycosyltransferase ppGalNAcT2 as a case study, we compare different methodologies used to obtain reaction paths and transition state information. Ab Initio MD using CPMD coupled with the String Method is used to derive the minimum free energy reaction path. The geometrical features of the free energy path, especially around the transition state, agree with the minimum potential energy path obtained by the much less computationally expensive Nudged Elastic Band method. The barrier energy, however, differs by 8 kcal/mol. The free energy surface generated by metadynamics provides a rough overview of the reaction and can confirm the physical relevance of optimized paths or provide an initial guess for path optimization methods. Calculations of enzymatic reactions are usually performed at best at the DFT level of theory. A comparison of widely used functionals with high-level DLPNO-CCSD(T)/CBS data on the potential energy profile serves as a validation of the usability of DFT for this type of enzymatic reaction. The M06-2X meta-hybrid functional in particular matches the DLPNO-CCSD(T)/CBS reference extremely well with errors within 1 kcal/mol. However, even pure-GGA functional OPBE provides sufficient accuracy for this type of study.
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