Mutagenesis-guided modeling of the Lynx1–α7 nicotinic acetylcholine receptor complex: An iterative feedback-driven approach

This repository contains supplementary molecular dynamics (MD) simulation trajectories and comprehensive interaction analysis tables for the publication: Mutagenesis-guided modeling of the Lynx1–α7 nicotinic acetylcholine receptor complex: An iterative feedback-driven approachMaxim M. Zaigraev, Eugene A. Zhivov, Timofey R. Chelyadinskii, Mikhail A. Shulepko, Dmitrii S. Kulbatskii, Hong Qing, Quan Zhenzhen, Mikhail P. Kirpichnikov, Zakhar O. Shenkarev, Anton O. Chugunov, Ekaterina N. Lyukmanova.International Journal of Biological Macromolecules, 2026, 154624. DOI: 10.1016/j.ijbiomac.2026.154624 1. Supplementary MD Trajectories (Supplementary MD Trajectories.zip) Molecular dynamics trajectories of the membrane-embedded complex of human α7 nicotinic acetylcholine receptor (α7-nAChR; UniProt: P36544) with five GPI-anchored Lynx1 molecules (UniProt: P0DP58) are provided in this archive. Three independent 500 ns simulations were performed, each containing five symmetry-related Lynx1-binding sites (15 binding-site trajectories in total). The archive contains three folders: replica-1, replica-2, and replica-3. Each folder includes: 500ns-fit-skip5.xtc — processed MD trajectory (5,001 frames, 100 ps frame interval, spanning 0–500 ns); 500ns-fit.gro — reference coordinate structure (159,559 atoms); VIEW.pml — PyMOL visualization script with predefined selections, color schemes, and representation settings. (To visualize, launch PyMOL within the corresponding replica folder and run @VIEW.pml). Trajectory processing & fitting: The trajectories were fitted using the backbone atoms of α7-nAChR, excluding the flexible intracellular loop L (residues 344–430 in UniProt precursor numbering, corresponding to residues 322–408 in mature-sequence numbering) from the fitting selection. Loop L itself is retained in the deposited structures and trajectories. The deposited trajectories were subsampled by retaining every fifth frame, resulting in a frame interval of 100 ps (0.1 ns). Water molecules and Na⁺ and Cl⁻ ions were removed during post-processing to reduce file size; the receptor pentamer, five Lynx1 proteins, GPI anchors, canonical receptor N-glycans (Man3GlcNAc2 at Asn24, Asn68, Asn111 mature / Asn46, Asn90, Asn133 UniProt), membrane lipids (DOPC, DOPE, palmitoylsphingomyelin [PSM], and cholesterol), and five structural Ca²⁺ ions were retained. The simulations were performed in explicit solvent. Residue numbering in structure files: In the deposited .gro coordinate files (and VIEW.pml), protein residues follow UniProt precursor numbering (residues 23–502 for α7-nAChR and residues 21–91 for Lynx1). The supplementary tables contain the results of the original analyses reported in the article and were not recalculated from the subsampled trajectories deposited here. 2. Supplementary Tables (Supplementary Tables.zip) This archive contains both the manuscript's supplementary summary tables (Tables S4–S7) and the individual per-site, per-replica contact lifetime tables for all 15 binding-site trajectories. All tables are provided in Excel format (.xlsx) in two parallel residue-numbering schemes: _Mature: mature protein sequences used throughout the article text (excluding the 22-residue signal peptide of α7-nAChR and the 20-residue signal peptide of Lynx1); _Uniprot: full-length UniProt precursor sequences (P36544 for α7-nAChR, P0DP58 for Lynx1). GPI-anchor components retain their force-field residue identifiers. A. Summary Supplementary Tables (Tables S4–S7) Table S4 — Pairwise Lynx1–α7-nAChR contacts (Table_S4_Lynx1-A7_pairwise_*):Relative contact lifetimes between Lynx1 residues or GPI-anchor components and receptor residues, distinguishing the principal (+) and complementary (−) faces of each binding site, averaged across all 15 site trajectories. Worksheets report: Strong contacts: hydrogen bonds, ionic contacts, cation–π interactions, and aromatic stacking. Strong + PHOB-C: strong contacts combined with carbon-based hydrophobic contacts (5.0 Å cutoff). Table S5 — Per-residue contact summaries (Table_S5_Lynx1-A7_per-residue_*):Cumulative contact lifetimes for individual residues or GPI-anchor components, with contributions from individual contact types. Contains six worksheets: Lynx1 Strong contacts & Lynx1 Strong + PHOB-C A7 (+) Strong contacts & A7 (+) Strong + PHOB-C A7 (−) Strong contacts & A7 (−) Strong + PHOB-C Table S6 — Lynx1–membrane interactions (Table_S6_Lynx1-lipids_*):Contact lifetimes with membrane lipids (DOPC, DOPE, PSM, cholesterol), lipid-selectivity estimates, and structural region contributions. Worksheets include: Strong contacts Strong + PHOB-C MHP hydrophobic (identified using the molecular hydrophobicity potential approach) Lipid selectivity (contact fractions, membrane mole fractions, and enrichment ratios) Structural regions: strong-contact lifetimes summed over Lynx1 loops I–III, heads I–III, and the GPI anchor, including its glycan components. Table S7 — MM/PBSA computational alanine scanning (Table_S7_MMPBSA_*):Results of membrane-aware MM/PBSA calculations (memopt = 1) applied to site-specific α7-dimer–Lynx1 subsystems. Energy values are in kcal/mol; positive ΔΔG values indicate predicted destabilization of the complex. Worksheets include: ΔΔG summary: mean ΔΔG, s.d., and s.e.m. across all 15 site–replica combinations. Per-site ΔΔG: mutant and wild-type ΔG and ΔΔG values for each individual site and replica. Raw ΔG: underlying wild-type and mutant ΔG estimates, s.d., s.e.m., and the number of analyzed frames (1,001). B. Per-Site & Per-Replica Contact Lifetime Tables (Folders) Detailed interaction tables for each of the 15 individual binding-site trajectories (3 replicas × 5 sites: replica-1-site-1.xlsx to replica-3-site-5.xlsx): Per-site_channel_contacts_Mature/ & Per-site_channel_contacts_Uniprot/: Pairwise contact lifetimes between Lynx1 and α7-nAChR for each specific binding site. Each workbook contains six interaction-type worksheets: Ionic, H-bonds, Stacking, Cation-π, MHP, and Hydrophobic-C (columns: Lynx1 resn/resi, A7 resn/resi, A7 chain, A7 face, relative lifetime). Per-site_lipid_contacts_Mature/ & Per-site_lipid_contacts_Uniprot/: Lynx1 contact lifetimes with individual membrane lipid species (DOPC, DOPE, PSM, cholesterol [CHL1]) and total lipid contact lifetime for each specific binding site. Worksheets: Ionic, H-bonds, Cation-π, MHP, and Hydrophobic-C. In the per-site lipid tables, the “time” columns contain dimensionless cumulative contact lifetimes summed over individual molecules of each lipid species; “Total time” sums the four lipid-species columns. These values may exceed 1.0. Definitions: Relative contact lifetime denotes the fraction of analyzed trajectory frames in which a contact was present (range: 0.0 to 1.0). Cumulative lifetime sums contributions over multiple contact types and/or interaction partners and therefore may exceed 1.0.