Original Paper

European Biophysics Journal

, Volume 41, Issue 5, pp 449-460

First online:

Ionizable side chains at catalytic active sites of enzymes

  • David Jimenez-MoralesAffiliated withDepartment of Bioengineering, University of Illinois at Chicago
  • , Jie LiangAffiliated withDepartment of Bioengineering, University of Illinois at Chicago
  • , Bob EisenbergAffiliated withDepartment of Bioengineering, University of Illinois at ChicagoDepartment of Molecular Biophysics and Physiology, Rush University Email author 

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Catalytic active sites of enzymes of known structure can be well defined by a modern program of computational geometry. The CASTp program was used to define and measure the volume of the catalytic active sites of 573 enzymes in the Catalytic Site Atlas database. The active sites are identified as catalytic because the amino acids they contain are known to participate in the chemical reaction catalyzed by the enzyme. Acid and base side chains are reliable markers of catalytic active sites. The catalytic active sites have 4 acid and 5 base side chains, in an average volume of 1,072 Å3. The number density of acid side chains is 8.3 M (in chemical units); the number density of basic side chains is 10.6 M. The catalytic active site of these enzymes is an unusual electrostatic and steric environment in which side chains and reactants are crowded together in a mixture more like an ionic liquid than an ideal infinitely dilute solution. The electrostatics and crowding of reactants and side chains seems likely to be important for catalytic function. In three types of analogous ion channels, simulation of crowded charges accounts for the main properties of selectivity measured in a wide range of solutions and concentrations. It seems wise to use mathematics designed to study interacting complex fluids when making models of the catalytic active sites of enzymes.


Computational geometry Active site Charge density