Influence of Backbone Conformations of Human Carbonic Anhydrase II on Carbon Dioxide Hydration:  Hydration Pathways and Binding of Bicarbonate

Abstract

In this study, the hydration of carbon dioxide and the formation of bicarbonate in human carbonic anhydrase II have been examined. From semiempirical QM/MM molecular dynamics studies, dominant conformations of the protein backbone, possibly contributing to the catalytic activity, have been isolated and further examined by means of density functional QM/MM methods. In agreement with experimental observations, a binding site for cyanate, which acts as an inhibitor, has been located, whereas for carbon dioxide, depending on the conformation of the protein environment, either a different binding site or no binding site has been found. In the latter case, carbon dioxide diffuses barrierless to the zinc-bound oxygen, and then a weakly bound bicarbonate complex is formed. The formed complex is characterized by a long C-O bond to the zinc-bound hydroxide. The nature of the calculated stationary points was verified by determination of vibrational frequencies. Finally, the dissociation of the formed bicarbonate from zinc has been considered. Therefore, a water molecule was included in the QM zone of the QM/MM hybrid potential, and minimization yielded a pentacoordinated intermediate. From a potential energy scan, an activation energy of 6.2 kcal/mol for dissociation of bicarbonate from Zn has been found.

Comparison and Analysis of Zinc and Cobalt-Based Systems as Catalytic Entities for the Hydration of Carbon Dioxide

“…The CPCM activation barriers for product release from Zn 2+ overestimate the stabilization for the calculated barrier for bicarbonate dissociation in the macrocycles. Loferer et al, using QM/MM methods [81], calculated a barrier of 6.2 kcal/mole for bicarbonate dissociation in CAII, and from these calculations barriers of 3.19 ( N3 -Zn) and 4.68 kcal/mole ( N4 -Zn) were obtained. Interestingly, the activation barriers for product release are much higher for Ph -Zn (9.40 kcal/mole) and Ben -Zn (11.82 kcal/mole).…”

The Missing Link in COS Metabolism: A Model Study on the Reactivation of Carbonic Anhydrase from its Hydrosulfide Analogue

“…The role of other amino acid residues in the catalytic mechanism has been addressed in studies by Bottoni3a and Liedl 3b. They demonstrated that some of the residues, especially Glu106 and Thr199, are directly involved in some steps of CO 2 fixation.…”

Carbonic Anhydrase as a Model for Biophysical and Physical-Organic Studies of Proteins and Protein−Ligand Binding

“…Jain and coworkers examined the affinity of compounds of the form p-H 2 NSO 2 C 6 H 4 CONH-CH 2 C 6 H n F 5−n (55)(56)(57)(58), and the X-ray crystal structures of these ligands complexed with HCA II, to explore the nature of the interaction between the secondary phenyl ring of the ligand and Pro202 and Phe131 of CA II. 180,249,515,516,597,598 Using HCA II and a mutant of HCA II where Phe131 was mutated to Val, the investigators claimed to dissect the interactions between the secondary recognition element and wild-type HCA II into (i) dipole-induced dipole interactions between the fluorinated ring of SRE and Pro202, (ii) dipole-quadrupole interactions between the fluorinated ring of SRE and Phe131, and (iii) quadrupole-quadrupole interactions between the fluorinated ring of SRE and Phe131.…”