Analysis of the dimerization interface was performed using the Protein Interaction Calculator, with solvent-accessible surface areas calculated using Naccess.
Yeast eEF1A-eEF1Bα interacting amino acid residues and eEF1A domain-domain contacts (Figure 1) were identified using the Protein Interactions Calculator (PIC) [53].
Aromatic interactions and cation-pi interactions were predicted using the Protein Interaction Calculator (PIC) [12] and CaPTURE programs [13], respectively, for BSX (PDB id – 2FGL), BHX (Bacillus halodurans xylanase, PDB id – 2UWF) and BFX (Bacillus firmus xylanase).
To elucidate the mechanism of thermostability, the intramolecular interactions relative to the three amino acid residues were analyzed using the Protein Interactions Calculator (PIC) server (Indian Institute of Science, Bangalore, India; http://pic.mbu.iisc.ernet.in) [ 26].
We have shown that the flanking basic region forms two α-helices and interacts with H4 of the PWI domain via a hydrogen bond and hydrophobic and ionic interactions (details below), which were analysed using the Protein Interactions Calculator (http://pic.mbu.iisc.ernet.in/job.html).in/job.html
In an attempt to identify these factors contributing to the variation of thermostabilities in CGTases, the number of ionic interactions and disulfide bonds was examined for five CGTases and Novamyl with known 3D structure, using the Protein Interactions Calculator (PIC) programme (Tina et al. 2007).
Charges of CP and CP-chimera were calculated using Protein Calculator v3.3, (C. Putnam, The Scripps Research Institute, USA) at pH 7.4 and 4.8, corresponding to buffer conditions reflecting the CCMV CP disassembly and CCMV VLP reassembly steps as described above.
Using the RBS Calculator, a protein coding sequence's translation rate may be rationally controlled across a 100,000+ fold range.
The extinction coefficient for each protein was calculated using the biopolymer calculator (http://paris.chem.yale.edu/cgi-bin/extinct.pl) which was used with its absorbance at 280 nm to determine the protein concentrations.
