PLAT domain protein 1 (PLAT1/PLAFP) binds to the Arabidopsis thaliana plasma membrane and inserts a lipid

Identifying and quantifying membrane interactions of the protein human cis-prenyltransferase

Prenyl chains come in multiple sizes, fulfilling unique and essential functions across all domains of life. Prenyl chains are synthesized by prenyltransferase proteins. Despite their structural similarity, prenyltransferases exhibit substantial functional diversity to create lipophilic products of varying lengths. Human cis-prenyltransferase (h-cisPT) is a tetrameric enzyme responsible for the synthesis of long prenyl chains, consisting of 20-prenyl-unit products that are essential to specific posttranslational modifications such as N-glycosylation upon downstream processing. These long products are hypothesized to transfer from h-cisPT to the ER membrane, but the mechanism of this transfer is not known. We use molecular dynamics simulations to identify a consistent membrane binding pose for h-cisPT. By quantifying protein-membrane contacts, we identify the aromatic amino acid residues in the conserved catalytic domain as critical to membrane binding. Determining relative protein-membrane binding free energies through free energy perturbation highlights the importance of these residues for membrane association, as mutations lower membrane affinity by as much as 27 kcal/mol. These results are validated using FRET to demonstrate decreased catalytic activity and membrane binding in response to mutation. Together, our results suggest a possible mechanism for prenyl substrate transfer, where key aromatic residues facilitate h-cisPT binding to the ER membrane in an orientation that holds the substrate-containing active site near the membrane surface. Molecular dynamics simulations of the mutant exhibiting lower FRET show greater orientational variability relative to wild type. This evidence for a specific orientation of h-cisPT provides a structural basis for isoprenoid association to the membrane during synthesis and prior to its release.

Plant protein-lipid interfaces studied by molecular dynamics simulations

The delineation of protein-lipid interfaces is essential for understanding the mechanisms of various membrane-associated processes crucial to plant development and growth, including signalling, trafficking, and membrane transport. Due to their highly dynamic nature, the precise characterization of lipid-protein interactions by experimental techniques is challenging. Molecular dynamics simulations provide a powerful computational alternative with a spatial-temporal resolution allowing the atomistic-level description. In this review, we aim to introduce plant scientists to molecular dynamics simulations. We describe different steps of performing molecular dynamics simulations and provide a broad survey of molecular dynamics studies investigating plant protein-lipid interfaces. Our aim is also to illustrate that combining molecular dynamics simulations with artificial intelligence-based protein structure determination opens up unprecedented possibilities for future investigations of dynamic plant protein-lipid interfaces.

More than meets the eye: knowns and unknowns of the trafficking of small secreted proteins in Arabidopsis

Small proteins represent a significant portion of the cargo transported through plant secretory pathways, playing crucial roles in developmental processes, fertilization, and responses to environmental stresses. Despite the importance of small secreted proteins, substantial knowledge gaps persist regarding the regulatory mechanisms governing their trafficking along the secretory pathway, and their ultimate localization or destination. To address these gaps, we conducted a comprehensive literature review, focusing particularly on trafficking and localization of Arabidopsis small secreted proteins with potential biochemical and/or signaling roles in the extracellular space, typically those within the size range of 101-200 amino acids. Our investigation reveals that while at least six members of the 21 mentioned families have a confirmed extracellular localization, eight exhibit intracellular localization, including cytoplasmic, nuclear, and chloroplastic locations, despite the presence of N-terminal signal peptides. Further investigation into the trafficking and secretion mechanisms of small protein cargo could not only deepen our understanding of plant cell biology and physiology but also provide a foundation for genetic manipulation strategies leading to more efficient plant cultivation.