Computational protocol: Structure Function Investigation of Vsp Serotypes of the Spirochete Borrelia hermsii

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Protocol publication

[…] Computer homology models were prepared for Vsps corresponding to several Vsp serotypes from B. hermsii HS1 and B. turicatae Oz1 strains. For this, five known crystallographic source structures were used, including three different B. burgdorferi OspC variants (B31, N40, HB19) , and B. turicatae Vsp1 in two different crystal forms , . The Protein Databank ids for these structures are 1yjg and 2ga0 for BtVsp1, 1g5z for Bb N40 OspC, 1f1m for Bb HB19 OspC, and 1ggq for Bb B31 OspC. All five structures are defined to near-atomic resolution (1.8–2.7 Å) and all have reasonable model statistics and geometry (Rfree 21.5–27.5%, r.m.s. bonds 0.004–0.022 Å, no Ramachandran plot outliers). The initial step in the homology modeling process was careful preparation of a multiple sequence alignment of each Vsp target with the crystal structures, guided by inspection of the superimposed models using molecular graphics. Within variable loops, gaps and/or insertions were positioned to maximize similarity of residue substitutions. For example, introduction of staggered gaps into the alignment between BtVsp1 and BtVsp2 better conserves hydrophobic burial properties of a variable loop between helices 2 and 3. The multiple sequence alignments and single-subunit structural models were the inputs to automated homology modeling using the program Modeller and/or to the Swiss Model server . Full Vsp dimers were then generated from single subunit coordinate sets by application of two-fold symmetry; this procedure is simpler than generating full dimer homology models. All model dimers were inspected for problem areas (Ramachandran outliers, high energy areas, poor geometry areas, clashes at the dimer interface). Problems were corrected either by revision of the multiple sequence alignment, or by manual adjustments of the model, guided by the crystal structures. Model coordinates were subsequently optimized with respect to standard geometry and constrained to obey perfect two-fold symmetry using Refmac without X-ray restraints . The homology models lacked only the N-terminal and C-terminal residues that are not present in the crystal structures. Pairwise alignment scores of Vsp dome region sequences were obtained using ClustalW (Version 7.6.0.87). All known Vsp proteins from B. hermsii HS1 and B. turicatae Oz1 Vsp's were included in this analysis (). […]

Pipeline specifications

Software tools MODELLER, SWISS-MODEL, Clustal W
Application Protein structure analysis
Organisms Mus musculus, Borrelia hermsii, Borrelia turicatae
Diseases Arthritis, Borrelia Infections, Infection, Relapsing Fever, X-Linked Combined Immunodeficiency Diseases