This article is part of the supplement: Selected articles from The 8th Annual Biotechnology and Bioinformatics Symposium (BIOT-2011)

Open Access Research

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

Catherine H Schein123*, David M Bowen12, Jessica A Lewis4, Kyung Choi12, Aniko Paul5, Gerbrand J van der Heden van Noort6, Wenzhe Lu2 and Dmitri V Filippov6

Author Affiliations

1 Institute for Translational Sciences, Computational Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Texas 77555–0857, USA

2 Departments of Biochemistry and Molecular Biology, University of Texas Medical Branch, Texas 77555–0857, USA

3 Microbiology and Immunology, University of Texas Medical Branch, Texas 77555–0857, USA

4 Department of Pathology, University of Texas Medical Branch, Galveston, Texas 77555–0857, USA

5 Dept. of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11790, USA

6 Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands

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BMC Bioinformatics 2012, 13(Suppl 13):S9  doi:10.1186/1471-2105-13-S13-S9

Published: 24 August 2012



Analysis 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.


The 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.


PCP-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.


The 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.