Modeling of the human rhinovirus C capsid suggests a novel topography with insights on receptor preference and immunogenicity

Abstract

Features of human rhinovirus (RV)-C virions that allow them to use novel cell receptors and evade immune responses are unknown. Unlike the RV-A+B, these isolates cannot be propagated in typical culture systems or grown for structure studies. Comparative sequencing, I-TASSER, MODELLER, ROBETTA, and refined alignment techniques led to a structural approximation for C15 virions, based on the extensive, resolved RV-A+B datasets. The model predicts that all RV-C VP1 proteins are shorter by 21 residues relative to the RV-A, and 35 residues relative to the RV-B, effectively shaving the RV 5-fold plateau from the particle. There are major alterations in VP1 neutralizing epitopes and the structural determinants for ICAM-1 and LDLR receptors. The VP2 and VP3 elements are similar among all RV, but the loss of sequence "words" contributing Nim1ab has increased the apparent selective pressure among the RV-C to fix mutations elsewhere in the VP1, creating a possible compensatory epitope.

Keywords: Capsid structure; I-Tasser; Immunogenicity; Model; Receptor binding; Rhinovirus; Rhinovirus C.

Figure 1. RV capsid arrangement

(A) Particles have 60 crystallographic subunits with VP1 (blue), VP2 (green) and VP3 (red) and VP4 (internal) proteins arranged in icosahedral symmetry. (B) A canyon-like depression circles each 5-fold axis from which a hydrophobic drug-binding pocket extends into the interior of each VP1. (C) Subunit ribbon diagram of A16 shows protein contributions to the north and south walls of the canyon. A biological assembly protomer would include this VP1, a VP2+4 precursor (VP0), and the VP3 from the adjacent (clockwise) crystallographic subunit. Figure modeled after Hadfield et al 1995 (40).

Figure 2. Structure comparison

Ribbon diagrams for A16 (gray) and C15 (blue, green, yellow, red; models) are labeled with features, using the nomenclature of Rossmann et al 1985 (29). The structures were formatted, oriented and rendered in MacPyMOL (35).

Figure 3. Core structure elements

The VP1-3 sequences for A16, B14 and C15 are illustrated to scale showing the color-coded locations of α and β segments using the nomenclature of Rossmann et al 1985 (29). The A16 and B14 elements are according to determined structures. The C15 elements are inferred by analogy in sequence alignments. B14 loops encoding neutralization escape mutations (Nim) are highlighted as are key, relative C15 deletions in VP1 (e.g. Δ13).

Figure 4. Surface topography

(A) Protomer PDB files for A14, B14 and C15 (model) were extrapolated to full icosahedral capsids using UCSF Chimera (38). The color scale illustrates the particle radius, spanning 130 Å (blue) to 165 Å (orange). (B) In parallel, radially depth-cued “roadmaps” show the surface topographies for respective crystallographic subunits as calculated by RIVEM (39). The applied color scale is the same as A. (C). Cross sections of the particles in A, through equivalent 5-fold axes, compare the protein depths of the canyon region and 5-fold plateau. The structures were aligned, displayed and rendered using UCSF Chimera (38).

Figure 5. Surface character

(A,C,E) Roadmap (39) surface depictions for A16, B14 and C15 are color-coded by amino acid types. The color bins includ, acidic (Asp, Glu), polar (Asn, Gln, Ser and Thr), neutral (Ala, Cys, Ile, Gly, Leu, Met, Phe, Pro, Trp, Tyr and Val) and basic (Arg, His and Lys) residues. (B,D,F) Similar roadmaps depict species surface residue conservation. Capsid alignment positions were queried for conservation (% amino acid identity) relative to each species’ consensus sequence. The observed identity, encoded in continuous grayscale (black = 100% conserved, white = 0% conserved), is superimposed on the A16, B14 and C15 residue positions.

Figure 6. Immunogenic sites

(A) A B14 (4rhv) biological protomer highlights residues mapped with escape mutations to a panel of neutralizing monoclonal antibodies, as defined by Sherry et al 1986 (28). (B) The neutralizing immunogenic sites (Nims) cluster on the virion surface (intense colored residues) as part of continuous surface loops (strong outlines). The Nim2 and Nim3 epitopes are partially discontinuous with contributions from VP1 (blue) and non-adjacent segments of VP2 (green) and VP3 (red). These loops define the sequence fragments queried for Nim conservation in Table 3. (C,D,E) A16, B14 and C15 particles were rendered as in Fig 4 except that color was assigned by protein type (as in B) and a semi-transparent sphere was added, masking the topography below a cutoff of 155 Å. The remaining brightly colored features mark residues above this height, and for B14, include all mapped Nim escape mutation sites.