MM/PBSA analysis of molecular dynamics simulations of bovine β‐lactoglobulin: Free energy gradients in conformational transitions?

The pH-driven opening and clo- sure of -lactoglobulin EF loop, acting as a lid and closing the internal cavity of the protein, has been studied by molecular dynamics (MD) simulations and free energy calculations based on molecular mechanics/Poisson-Boltzmann (PB) solvent-acces- sible surface area (MM/PBSA) methodology. The forms above and below the transition pH differ presumably only in the protonation state of residue Glu89. MM/PBSA calculations are able to reproduce qualitatively the thermodynamics of the transition. The analysis of MD simulations using a combination of MM/PBSA methodology and the colony energy approach is able to highlight the driving forces implied in the transition. The analysis suggests that global rearrangements take place before the equilib- rium local conformation is reached. This conclusion may bear general relevance to conformational tran- sitions in all lipocalins and proteins in general.