DOI: 10.5281/zenodo.18493444
title: Probable lipid phosphate phosphatase from wheat (Triticum aestivum) predicted structure via E8 lattice topological optimization

description: Protein target

This record contains the predicted 3D structure of a probable lipid phosphate phosphatase (LPP-like protein) from bread wheat (Triticum aestivum, UniProt A0A096MKF9, 346 amino acids), generated using the E8 Navigator — a symmetry-based, non-data-driven protein folding method.MAPLLALLALLQLGPASHCPNPGISVGTMRTGSSFDLGDKVSYRCSSTNLVLTGSVERECLSNGVWSGSEPICRQPYSYDFPEDVASALGTSFTHLLGATNPIQKRTENLGRKIQIQRSGHLNLYLLLDASQSVSEKDFNIFKESAFLMVDRIFSFEIKVSVAIITFASRPKIIMSVLNERSQNVMEVMDSLDSVCYKDHENATGTNTYEALNSVYLMMNNQMDRLGMETSAWQEIRHAIILLTDGKSNMGGSPKPAVDNIREILGISRNRNDYLDIYAIGVGKLDVDWKELNELGSKKDGERHAFILQDAKAVQQVFEHILDVSKLTDTICGVGNMSVNASDQERTPWQVTFKPKSKETCQGSLISDQWVLTAAHCFHDAQMEDRHLWRVIVGDPTSHHGKEFHVEEVLVAPGFNVHAKQSQGISEFYADDIALLKLSQRVKMSSHARPICLPCTVGANMALRRSPGSTCKDHETELLSQQKVPAHFVALNGNRMNINLRTGPERTSCIEAVSQNKGSFPGLTNVSEVVTDQFLCSGMEGDDSPCKGESGGAVFLERRYRFFQVGLVSWGLFDPCHGSSNKNLRRKPPHGVVPRDFHISLFRLQPWLRQHLDGVLDFLPL

Biological relevance

Lipid phosphate phosphatases (LPPs) are membrane-bound enzymes that dephosphorylate bioactive lipid phosphates such as phosphatidic acid, lysophosphatidic acid, and ceramide-1-phosphate. In plants, these enzymes play key roles in lipid signaling, membrane remodeling, stress responses (drought, salt, pathogen attack), root development, and seed oil content. As a major crop species, understanding wheat LPPs could contribute to improving stress tolerance and yield in agriculture.

Why this is a challenging folding problem

This wheat LPP is structurally difficult and largely unsolved:



Predicted 6 transmembrane helices with extracellular and cytoplasmic domains

No experimental high-resolution 3D structure exists for this protein or close plant orthologs (most solved LPP structures are from bacteria or mammals)

Transmembrane proteins with flexible loops and active-site regions often receive moderate-to-low confidence in AI predictions

Plant-specific sequence divergence makes homology modeling and MSA-based approaches less reliable


These features make it a strong test case for alternative folding methods on agriculturally relevant transmembrane enzymes.

Method: E8 Navigator

The structure was generated using the E8 Navigator, a topology-driven folding engine that projects the amino acid sequence onto the exceptional Lie group E8 lattice based on physicochemical properties. Folding is performed as symmetry-constrained optimization on the E8 manifold, guided by a holographic coherence metric (Ψ) and convergence to ultra-low error states — without multiple sequence alignments, neural networks, or patterns memorized from the PDB.

Results

The output PDB (A0A096MKF9_E8_prediction.pdb) converged with Ψ = 2.00 and very low final error(ERR: 0.00010668), producing a compact transmembrane helical bundle with extended loop regions and no major steric clashes. The model is consistent with expected LPP family topology (6 TM helices + catalytic domain).

Significance

Lipid phosphate phosphatases are important regulators in plant stress responses and lipid metabolism, yet plant orthologs remain structurally under-characterized. A coherent, clash-free prediction from a purely symmetry-based method offers an orthogonal perspective to current AI predictors and provides a useful model for functional studies or crop improvement research.

The prediction is shared openly for visualization, alignment against AlphaFold models, community evaluation, and comparison with other folding approaches.

Files included



A0A096MKF9_E8_prediction.pdb — full predicted structure