Functional tuning of the catalytic residue pKa in a de novo designed esterase

• Published in: Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2017-09, Vol.85 (9), p.1656-1665
• Main Authors: Hiebler, Katharina, Lengyel, Zsófia, Castañeda, Carlos A., Makhlynets, Olga V.
• Format: Article
• Language: English
• Subjects: Acetic acid; Calcium; Calcium ions; Calcium-binding protein; Calmodulin; Catalysis; Computer applications; Efficiency; electrostatic potential; Electrostatic properties; Electrostatics; Empirical analysis; Enzymes; ester hydrolysis; Esterase; Histidine; Hydrophobicity; NMR; Nuclear magnetic resonance; p-Nitrophenylacetic acid; pH effects; pH rate profile; pKa of histidine; Proteins; Spectrometers
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.25321

ABSTRACT AlleyCatE is a de novo designed esterase that can be allosterically regulated by calcium ions. This artificial enzyme has been shown to hydrolyze p‐nitrophenyl acetate (pNPA) and 4‐nitrophenyl‐(2‐phenyl)‐propanoate (pNPP) with high catalytic efficiency. AlleyCatE was created by introducing a single‐histidine residue (His144) into a hydrophobic pocket of calmodulin. In this work, we explore the determinants of catalytic properties of AlleyCatE. We obtained the pKa value of the catalytic histidine using experimental measurements by NMR and pH rate profile and compared these values to those predicted from electrostatics pKa calculations (from both empirical and continuum electrostatics calculations). Surprisingly, the pKa value of the catalytic histidine inside the hydrophobic pocket of calmodulin is elevated as compared to the model compound pKa value of this residue in water. We determined that a short‐range favorable interaction with Glu127 contributes to the elevated pKa of His144. We have rationally modulated local electrostatic potential in AlleyCatE to decrease the pKa of its active nucleophile, His144, by 0.7 units. As a direct result of the decrease in the His144 pKa value, catalytic efficiency of the enzyme increased by 45% at pH 6. This work shows that a series of simple NMR experiments that can be performed using low field spectrometers, combined with straightforward computational analysis, provide rapid and accurate guidance to rationally improve catalytic efficiency of histidine‐promoted catalysis. Proteins 2017; 85:1656–1665. © 2017 Wiley Periodicals, Inc.