Structural Modeling and Membrane Interaction of Viral Proteins

To compare differences in the structure of WT UL37 and UL37 C819S, we generated tertiary structural models using AlphaFold2 (Google Colaboratory). UL37 WT and UL37 C819S were aligned using PyMol to determine the root mean standard deviation value (RMSD). To determine structural changes and differences in membrane interaction of the gK/UL20 complex, we predicted protein–protein complex formation using AlphaFold2- multimer (Google Colaboratory). The amino acid sequences of human alphaherpesvirus-1 glycoprotein K (gK) (Accession Number AFH41179.1) and UL20 (Accession Number QFQ61390.1) were retrieved from GenBank and used as input, alongside the gKΔ31–68/UL20Δ4–22 amino acid sequences. The predicted models were inserted into a bilipid membrane using MemProtMD. Briefly, MEMEMBED was used to orient the protein relative to a lipid membrane. A box of 80 Å in size (z-axis) was generated to contain the protein. The protein was contained in the box, and the x and y axes were determined by providing a distance of 30 Å from the protein. Dipalmitoylphosphatidylcholine (DPPC) lipid models were used to insert the protein into a bilipid membrane. The bilipid membrane was built with the following using the MARTINI 2.1 forcefield: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG), cardiolipin (CL) and glucosyl-lipopolysaccharide (UDP1). The coarse-grained molecular dynamics (CGMD) simulation was completed at 60 ns. At the end of the simulation, a snapshot was taken to convert the coarse-grained resolution to atomistic resolution using CG2AT-align.