Computational protocol: Herpes Simplex Virus 1 UL37 Protein Tyrosine Residues Conserved among All Alphaherpesviruses Are Required for Interactions with Glycoprotein K, Cytoplasmic Virion Envelopment, and Infectious Virus Production

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Protocol publication

[…] Template-based modeling of the first 570 amino acids of the HSV-1 UL37 protein was conducted by homology modeling with Clustal Omega () and Modeler (). The X-ray crystal structure of PRV UL37 (PDB code 4K70) () was used as the modeling template. The amino acid sequence of the HSV-1 UL37 protein (NCBI RefSeq accession no. YP_009137112.1) was used for a multiple-sequence alignment (MSA) between 20 different strains of alphaherpesviruses, including HSV-2 and PRV. The MSA was constructed with the Clustal Omega sequence profile alignment () server provided by the Max Planck Institute (http://toolkit.tuebingen.mpg.de/clustalw/). The default options with the modification of 5× HMM were used to run Clustal Omega. After removal of the first 29 residues, the remaining 541 amino acids from the sequence were used to build the homology model with Modeler version 9.15. The HSV-1 UL37 protein model was visualized using molecular visualization package PyMol (PyMOL Molecular Graphics System, version 1.2r3pre; Schrödinger, LLC.). An alignment of HSV-2 UL37 (YP_009137112.1; AKC59563.1) with the beta-herpesvirus HCMV UL37 (Merlin; YP_081505.1) and the gamma-herpesvirus EBV (YP_001129450.1) was performed using the same parameters and software described above for the alphaherpesvirus UL37 proteins. […]

Pipeline specifications

Software tools Clustal Omega, Clustal W, PyMOL, merlin
Application Small-angle scattering
Organisms Human alphaherpesvirus 1, Human betaherpesvirus 5
Chemicals Alanine, Tyrosine