Research

Methodological Developments:

• Inclusion of pH and electrostatic potential effects in molecular dynamics simulations.

• Inclusion of electrochemical gradients in membrane modeling.

• Protein Electrostatics.

• Prediction of pKa's and redox potentials:

  • Thermodynamics of Electron-Proton Coupling.
  • Tautomerism in pKa Calculations.
  • Prediction of pKa’s using Linear Response Approximation.
• Conformational analysis and characterization of energy landscapes.

Application to systems of biological and biomedical interest:

Present

• pH effects on ß-lactoglobulin.
• Electrochemical gradient effects on proton pumps (bacteriorhodopsin and cytochrome c oxidase).

Past

• pH-induced protein folding/misfolding (prion protein, surfactant protein C).
• Peptide and protein interactions with biological membranes and membrane like-systems (kyotorphin, surfactant protein C).
• Peptide dendrimers.
• Prediction of protein partition coefficients in two-phase systems.