To FRET or Not to FRET: Bioinformatics and Fluorescence Spectroscopy suggest that Reduced Tryptophan to Heme Energy Transfer Facilitates Lignin Degradation in Class II Peroxidases

Abstract

A key step in the evolution of lignin-degrading enzymes is revealed by the observation that, unlike other heme-proteins studied to date, Class II peroxidases exhibit minimal energy transfer from tryptophan (Trp) to heme residues. Bioinformatics analyses and molecular dynamics simulations of Class II (MnP and VP) and Class III (horseradish peroxidase, HrP) structures indicate that the Trp residue in HrP has the highest orientational factor and fluorescence resonance energy transfer (FRET) efficiency. By contrast, Trp residues in MnP and VP display low FRET efficiency due to unfavorable orientation factors despite their proximity to the heme. Steady-state fluorescence experiments confirmed this low FRET efficiency, showing strong emission in MnP and VP but weak emission in HrP. This decreased Trp-to-heme energy transfer appears to minimize competition between direct FRET and long-range electron transfer (LRET), allowing electrons to flow from bulky lignin substrates to the heme center. Such a mechanism likely provided a selective advantage during the evolution of Class II peroxidases, facilitating efficient lignin degradation at the enzyme surface. HighlightsClass II peroxidases show reduced Trp-to-heme FRET compared with HRP MD simulations reveal unfavorable Trp-heme orientation in VP and MnP Low FRET correlates with strong Trp fluorescence in VP and MnP Reduced FRET favors long-range electron transfer (LRET) during lignin oxidation Findings suggest an evolutionary adaptation in lignin-degrading peroxidases O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=128 SRC="FIGDIR/small/697144v1_ufig1.gif" ALT="Figure 1000"> View larger version (36K): org.highwire.dtl.DTLVardef@f8b3a8org.highwire.dtl.DTLVardef@1db18a4org.highwire.dtl.DTLVardef@12ebf1dorg.highwire.dtl.DTLVardef@54712_HPS_FORMAT_FIGEXP M_FIG C_FIG