Poleto, M. D. | Search bioRxiv

bioRxiv2024

Structural dynamics of the methyl-coenzyme M reductase active site are influenced by coenzyme F430 modifications

Methyl-coenzyme M reductase (MCR) is a central player in methane biogeochemistry, governing methanogenesis and the anaerobic oxidation of methane (AOM) in methanogens and anaerobic methanotrophs (ANME), respectively. The prosthetic group of MCR is coenzyme F430, a nickel-containing tetrapyrrole derivative. Additionally, a few modified versions of F430 have been discovered, including the 172-methylthio-F430 (mt-F430) that functions with ANME-1 MCR. This study employs molecular dynamics (MD) simulations to unravel the intricacies of the active-site dynamics of MCR from Methanosarcina acetivorans and ANME-1 when bound to the canonical F430 compared to 172-thioether coenzyme F430 variants and substrates for methane formation. Overall, our simulations indicate that each MCR active site is optimized for a given version of F430 and support the importance of the Gln to Val substitution in accommodating the 172 methylthio modification. Notably, modifications in the 172 position disrupt the canonical coordination among cofactors in M. acetivorans MCR, implicating structural perturbations, but evidence of active site reorganization to maintain substrate positions suggest that the modified F430s could be accommodated in a methanogenic MCR. We additionally report the first quantitative estimate of MCR intrinsic electric fields pivotal in driving methane formation. Our results suggest that the electric field aligned along the CH3-S-CoM thioether bond facilitates homolytic bond cleavage, coinciding with the proposed catalytic mechanism. Structural perturbations, however, weaken and misalign these electric fields, emphasizing the significance of the active site structure in maintaining their integrity. In conclusion, our results deepen the understanding of MCR active-site dynamics, the enzymes organizational role in intrinsic electric fields for catalysis, and the interplay between active site structure and electrostatics. This work not only advances our comprehension of MCR functionality but also provides a foundation for future investigations employing sophisticated models to capture the complex electronic properties of MCR active sites quantitatively.

biophysics↗

bioRxiv2023

Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes

AbstractThe formation of G-quadruplexes (GQs) occurs in guanine-rich sequences of DNA and RNA, producing highly stable and structurally diverse noncanonical nucleic acid structures. GQs play crucial roles in regulating transcription, translation, and replication; and maintaining the genome, among others, thus changes to their structures can lead to diseases such as cancer. Previous studies using polarizable molecular dynamics simulations have shown differences in ion binding properties between telomeric and TERRA GQs despite architectural similarities. Here, we used volume-based metady-namics and repulsive potential simulations in conjunction with polarizable force fields to quantify the impact of ion binding on GQ dynamics and ion binding free energies. Furthermore, we describe how GQs exert electric fields on their surroundings to link dynamics with variations in electronic structure. Our findings provide new insights into the energetic, physical, and conformational properties of GQs and expose subtle, but important, differences between DNA and RNA GQs with the same fold.

biophysics↗