Understanding the Key Roles of pH Buffer in Accelerating Lignin Degradation by Lignin Peroxidase

Abstract

pH buffer plays versatile roles in both biology and chemistry. In this study, we unravel the critical role of pH buffer in accelerating degradation of the lignin substrate in lignin peroxidase (LiP) using QM/MM MD simulations and the nonadiabatic electron transfer (ET) and proton-coupled electron transfer (PCET) theories. As a key enzyme involved in lignin degradation, LiP accomplishes the oxidation of lignin via two consecutive ET reactions and the subsequent C−C cleavage of the lignin cation radical. The first one involves ET from Trp171 to the active species of Compound I, while the second one involves ET from the lignin substrate to the Trp171 radical. Differing from the common view that pH = 3 may enhance the oxidizing power of Cpd I via protonation of the protein environment, our study shows that the intrinsic electric fields have minor effects on the first ET step. Instead, our study shows that the pH buffer of tartaric acid plays key roles during the second ET step. Our study shows that the pH buffer of tartaric acid can form a strong H-bond with Glu250, which can prevent the proton transfer from the Trp171-H •+ cation radical to Glu250, thereby stabilizing the Trp171-H •+ cation radical for the lignin oxidation. In addition, the pH buffer of tartaric acid can enhance the oxidizing power of the Trp171-H •+ cation radical via both the protonation of the proximal Asp264 and the second-sphere H-bond with Glu250. Such synergistic effects of pH buffer facilitate the thermodynamics of the second ET step and reduce the overall barrier of lignin degradation by ∼4.3 kcal/mol, which corresponds to a rate acceleration of 10 3 -fold that agrees with experiments. These findings not only expand our understanding on pH-dependent redox reactions in both biology and chemistry but also provide valuable insights into tryptophanmediated biological ET reactions.

O–O Bond Formation and Oxygen Release in Photosystem II Are Enhanced by Spin-Exchange and Synergetic Coordination Interactions

“…Thus, it is possible that our calculated barrier for Tyr161 radical reduction could be slightly underestimated, while the barrier for O 2 release is slightly overestimated. For the Tyr161 reduction, the neglect of some non-adiabatic effect on electron transfer may lead to the slight underestimation of the QM/MM calculated barrier . For the O 2 release process, the further inclusion of dynamic effects may facilitate the O 2 release process, which is worthwhile to investigate in our future work.…”

“…For the Tyr161 reduction, the neglect of some non-adiabatic effect on electron transfer may lead to the slight underestimation of the QM/ MM calculated barrier. 107 For the O 2 release process, the further inclusion of dynamic effects may facilitate the O 2 release process, which is worthwhile to investigate in our future work.…”

Insight into the activation mechanism of carbonic anhydrase(ii) through 2-(2-aminoethyl)-pyridine: a promising pathway for enhanced enzymatic activity

“…Despite the extensive research conducted on the B3LYP functional 91,92 it is important to keep in mind that different exchange-correlation functionals can cause inconsistencies when studying biological reactions. 81,93 The percentage of Hartree-Fock varies depending on the hybrid functional used and is not a universal value [94][95][96] so there is a likelihood of failure in specific cases. [97][98][99] Here, we have tested several wellknown functionals, including B3PW91, oB97X-D, and CAM-B3LYP, 68 for their energetics of the concerted reaction.…”

Industrial-Scale Engineering of Nano {RuO2/TiO2} for Photocatalytic Water Splitting: The Distinct Role of {(Rutile)TiO2–(Rutile)RuO2} Interfacing

“…2,3 Interfacing noble-metal nanoparticles, e.g., such as Au, Pt, Pd, or Ag, onto TiO 2 4 can provide significant benefits, including formation of a Schottky barrier 5 or the stimulation of a Localized Surface Plasmon Resonance effect, especially in the case of Au or Ag 6 onto TiO 2 . Alternatively, the use of heterojunctions of ntype with an appropriate p-type semiconductor, 7−9 e.g., TiO 2 / CuO, 10 or with transition metal oxides such as IrO 2 11 and RuO 2 , 12 offers a promising strategy for successful electron−hole (e − /h + ) separation and visible-spectrum response. RuO 2 , a functional semimetal widely used in industry, exhibits unique features including good chemical stability, 13 electrical conductivity, 14 and exceptional diffusion barrier properties.…”