This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Ionizable residues make up 25% of the residues in proteins. The in situ energetics of ionization determines what functional roles residues can play. Acid or base catalysts need pKas near physiological pH to be good proton donors or acceptors. Proton transfers need connecting residues where protonated and deprotonated states are thermally accessible. Clusters of residues of similar pKas can form internal buffers so protons can move as reactions progress. MCCE provides a way to consistently calculate and compare pKas in different proteins. The requested computer time will be used to calculate pKas for 500 disparate proteins. These will be analyzed to determine how proteins interact with charges. The results will be added to a searchable database of 35,000 calculated pKas (www.sci.ccny.cuny.edu/~mcce).
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