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MPKaDB: A pKadatabase for exploring pH dependence in membrane proteins.

Jiahao He1, Yansheng Chen2, Jinxi Wu1

  • 1College of Computer Engineering, Jimei University, Xiamen 361021, China.

Journal of Molecular Biology
|March 4, 2026
PubMed
Summary

MPKaDB is a new database that quickly predicts the protonation states of membrane proteins. This tool helps researchers understand how pH affects protein function, saving time and resources.

Keywords:
active-site residueisoelectric pointpositive-inside ruleproton carrier

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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.