Physicochemical property consensus sequences for functional analysis, design of multivalent antigens and targeted antivirals

Abstract

BackgroundAnalysis of large sets of biological sequence data from related strains or organisms is complicated by superficial redundancy in the set, which may contain many members that are identical except at one or two positions. Thus a new method, based on deriving physicochemical property (PCP)-consensus sequences, was tested for its ability to generate reference sequences and distinguish functionally significant changes from background variability.MethodsThe PCP consensus program was used to automatically derive consensus sequences starting from sequence alignments of proteins from Flaviviruses (from the Flavitrack database) and human enteroviruses, using a five dimensional set of Eigenvectors that summarize over 200 different scalar values for the PCPs of the amino acids. A PCP-consensus protein of a Dengue virus envelope protein was produced recombinantly and tested for its ability to bind antibodies to strains using ELISA.ResultsPCP-consensus sequences of the flavivirus family could be used to classify them into five discrete groups and distinguish areas of the envelope proteins that correlate with host specificity and disease type. A multivalent Dengue virus antigen was designed and shown to bind antibodies against all four DENV types. A consensus enteroviral VPg protein had the same distinctive high pKa as wild type proteins and was recognized by two different polymerases.ConclusionsThe process for deriving PCP-consensus sequences for any group of aligned similar sequences, has been validated for sequences with up to 50% diversity. Ongoing projects have shown that the method identifies residues that significantly alter PCPs at a given position, and might thus cause changes in function or immunogenicity. Other potential applications include deriving target proteins for drug design and diagnostic kits.

Vaccination With a Single Consensus Envelope Protein Ectodomain Sequence Administered in a Heterologous Regimen Induces Tetravalent Immune Responses and Protection Against Dengue Viruses in Mice

“…Many studies have demonstrated that consensus predictions could outperform single sequence determination method in vaccine design (Mallios, 2003; Moutaftsi et al, 2006; Yan et al, 2007). Importantly, not only conserved regions but also variable sites could be incorporated in the consensus sequences, and such design does not seem to alter structural and functional properties of target protein on a given location (Schein et al, 2012).…”

Polyglutamine Repeats in Viruses

“…This means that they may be selectively excised during generation of subgenomic RNAs or resumption of active growth after latent periods. Thus, rational reference sequences of viruses should be based on those obtained from direct isolates of diseased tissue or consensus sequences covering many isolates [ 111 – 113 ].…”

Sequence specificity for uridylylation of the viral peptide linked to the genome (VPg) of enteroviruses

“…It is designed to be useful for sets with many sequences (such as viral isolates) that have a high superficial redundancy (i.e., nearly identical sequences that differ at only a few positions). The rationale and details of the method are described in detail elsewhere (Bowen et al, 2012; Danecek et al, 2010; Danecek and Schein, 2010; Schein et al, 2012). Here, the PCP-con program was used to determine a consensus of 31 of the most diverse EV VPg sequences (Figure 1).…”