Technical Highlight - June 2010
Short description: Use this software suite to design protein constructs and codon engineered genes for structural proteomics.
Worldwide structural genomics projects have produced plenty of three-dimensional structural biology data, but it's not the only useful information produced. The scale of the data from Protein Structure Initiative (PSI) and the other consortia means that it should be possible to draw conclusions that link two-dimensional gene sequence information to three-dimensional protein structure. Extracting this information in a way that would help design protein and nucleic acid constructs is a bioinformatics challenge – and the software and database Gene Composer can help.
The redundancy in the genetic code results in, on average, a single amino acid being able to be encoded three different codons, and so for a protein of 100 amino acids, there are 3100 different coding sequences. Changes in nucleotide sequence affect which DNA sequence elements are present and can alter messenger RNA structure. These factors in turn alter mRNA stability, and thus expression. In addition, it is well known that some species prefer certain codons, an important consideration for heterologous expression experiments.
PSI ATCG3D, with additional funding support from National Center for Research Resources, created Gene Composer to help design protein constructs and codon engineered nucleic acid sequences to better match the codon usage of expression hosts which may improve protein expression, purification and potentially crystallization. The software can also help design and order complete genes or overlapping oligonucleotides for PCR-based gene assembly.
D. Lorimer, A. Raymond, J. Walchli, M. Mixon, E. Wallace, A. Barrow, R. Grice, A. Burgin, L. Stewart Gene Composer: Database software for protein construct design, codon engineering, and gene synthesis.
BMC Biotechnol 9, 36 (2009). doi:10.1186/1472-6750-9-36
A. Raymond, S. Lovell, D. Lorimer, J. Walchli, M. Mixon, E. Wallace, K. Thompkins, K. Archer, A. Burgin, L. Stewart Combined protein construct and synthetic gene engineering for heterologous protein expression and crystallization using Gene Composer.
BMC Biotechnol 9, 37 (2009). doi:10.1186/1472-6750-9-37