Predicting Catalytic Proton Donors and Nucleophiles in Enzymes: How Adding Dynamics Helps Elucidate the...

Area of Science:

• Biochemistry
• Computational Biology
• Enzymology

Background:

• Understanding enzyme active site mechanisms is crucial for predicting enzyme function.
• Identifying proton donors and nucleophiles, key catalytic residues, remains a challenge.
• Structure-function relationships in enzymes are not fully understood.

Purpose of the Study:

• To investigate the determinants of pKa order in enzyme active sites.
• To compare the predictive power of different computational methods for pKa calculations.
• To elucidate the role of dynamics versus static structure in enzyme catalysis.

Main Methods:

• Calculated pKa values for catalytic dyads in five enzymes using three computational methods.
• Employed continuous constant pH molecular dynamics simulations.
• Analyzed hydrogen bonding and solvent exposure of catalytic residues.

Main Results:

• Constant pH molecular dynamics simulations accurately reproduced experimental pKa orders.
• Stabilization of the negative nucleophile is linked to increased hydrogen bonding and solvent exposure.
• Static structure-based calculations did not reveal the observed trends.

Conclusions:

• Enzyme dynamics play a critical role in determining the function of catalytic residues.
• Molecular dynamics simulations offer insights into structure-function relationships beyond static structures.
• Further studies with larger datasets are needed to generalize these findings.