MPKaDB: A pK_adatabase for exploring pH dependence in membrane proteins

Area of Science:

• Computational biology
• Structural biology
• Biophysics

Background:

• Membrane protein functions are often regulated by pH.
• Experimental determination of pH dependence is time-consuming and costly.

Purpose of the Study:

• To introduce MPKaDB, a comprehensive database for membrane protein pKa values.
• To enable rapid prediction of residue protonation states at specific pH values.
• To facilitate pH-coupled electrostatic characterization of membrane proteins.

Main Methods:

• Development of MPKaDB, a pKa database for membrane proteins.
• Implementation of a user-friendly search engine for protein retrieval.
• Calculation of residue-specific pKa values, isoelectric points (pI), and active site analysis.

Main Results:

• MPKaDB provides instant decoding of ionizable residue protonation states.
• The database offers pKa values, pI (cytoplasmic and extra-cytoplasmic), and active site screenings.
• Case studies demonstrate the application of MPKaDB in exploring pH-dependent protein function.

Conclusions:

• MPKaDB significantly accelerates the study of pH-dependent membrane protein behavior.
• The database serves as a valuable resource for understanding membrane protein structure-function relationships.
• MPKaDB aids in the efficient characterization of membrane proteins.