The Role of Protein Electrostatics in Facilitating the Catalysis of DEAD-box Proteins

Protein electrostatic states have been demonstrated to play crucial roles in catalysis, ligand binding, protein stability, and in the modulation of allosteric effects. Electrostatic states are demonstrated to appear conserved among DEAD-box motifs and evidence is presented that the structural changes that occur to DEAD box proteins upon ligand binding alter the DEAD-box motif electrostatics in a way the facilitates the catalytic role of the DEAD-box glutatmate.Comment: Published in the Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology (BIOCOMP 2008). Pages 708-71

Interrelationship Between Protein Electrostatics and Evolution in HCV and HIV Replicative Proteins

Protein electrostatics have been demonstrated to play a vital role in protein functionality, with many functionally important amino acid residues exhibiting an electrostatic state that is altered from that of a normal amino acid residue. Residues with altered electrostatic states can be identified by the presence of a pKa value that is perturbed by 2 or more pK units, and such residues have been demonstrated to play critical roles in catalysis, ligand binding, and protein stability. Within the HCV helicase and polymerase, as well as the HIV reverse transcriptase, highly conserved regions were demonstrated to possess a greater number and magnitude of perturbations than lesser conserved regions, suggesting that there is an interrelationship present between protein electrostatics and evolution.Comment: Published in the Proceedings of the 2007 International Conference on Bioinformatics and Computational Biology (BIOCOMP 2007). Pages 91-9

ESPSim: A JAVA Application for Calculating Electrostatic Potential Map Similarity Scores

ESPSim is an open source JAVA program that enables the comparisons of protein electrostatic potential maps via the computation of an electrostatic similarity measure. This program has been utilized to demonstrate a high degree of electrostatic similarity among the potential maps of lysozyme proteins, suggesting that protein electrostatic states are conserved within lysozyme proteins. ESPSim is freely available under the AGPL License from http://www.bioinformatics.org/project/?group_id=830Comment: Published in the Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology (BIOCOMP 2008). Pages 735-73