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A type of Lewis acid-base chemistry involves the formation of a complex ion (or a coordination complex) comprising a central atom, typically a transition metal cation, surrounded by ions or molecules called ligands. These ligands can be neutral molecules like H2O or NH3, or ions such as CN− or OH−. Often, the ligands act as Lewis bases, donating a pair of electrons to the central atom. These types of Lewis acid-base reactions are examples of a broad subdiscipline called coordination...
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In complexation reactions, metal cations are the electron pair acceptors, and the ligands are the electron pair donors. The stability of the metal complexes depends primarily on the complexing ability of the central metal ion and the nature of the ligands. Generally, the complexing ability of the metal ion depends on the size and charge of the ion. As the metal ion size increases, the stability of the metal complexes decreases, provided that the valency of the metal ion and the ligands remain...
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Metal ions can be separated from one another by complexation with organic ligands–the chelating agent– to form uncharged chelates. Here, the chelating agent must contain hydrophobic groups and behave as a weak acid, losing a proton to bind with the metal. Since most organic ligands used in this process are insoluble or undergo oxidation in the aqueous phase, the chelating agent is initially added to the organic phase and extracted into the aqueous phase. The metal-ligand complex is...
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Ladder diagrams are useful for evaluating equilibria involving metal-ligand complexes. The vertical scale of the ladder diagram represents the concentration of unreacted or free ligand, pL. The horizontal lines on the scale depict the log of stepwise formation constants for metal-ligand complexes and indicate the dominant species in all the regions.
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Carbonic Anhydrases: Different Active Sites, Same Metal Selectivity Rules.

Nikoleta Kircheva1, Silvia Angelova1,2, Todor Dudev3

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Carbonic anhydrases bind metals, but how they choose and protect them is unclear. This study reveals the physical principles governing metal competition in these vital enzymes.

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DFT calculationcarbonic anhydrasemetal competitionmetalloenzyme

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Area of Science:

  • Biochemistry
  • Bioinorganic Chemistry
  • Computational Chemistry

Background:

  • Carbonic anhydrases are essential metalloenzymes found across all domains of life, catalyzing CO2 hydration.
  • Despite a conserved catalytic mechanism, carbonic anhydrase families lack common ancestry and show diverse metal-binding site structures.
  • The principles governing metal affinity, selectivity, and protection in these sites remain poorly understood.

Purpose of the Study:

  • To investigate the physical principles behind metal affinity and selectivity in carbonic anhydrase active sites.
  • To understand how native metals are protected from displacement by competing metal ions.
  • To elucidate the thermodynamic factors influencing metal competition in various carbonic anhydrase metal-binding sites.

Main Methods:

  • Utilized density functional theory (DFT) calculations.
  • Employed polarizable continuum model (PCM) computations.
  • Studied the thermodynamic outcome of metal cation competition in diverse active site models.

Main Results:

  • Quantified the Gibbs energy changes associated with metal competition by varying metal type, active site structure, composition, and solvent exposure.
  • Identified key physical principles governing metal competition across different carbonic anhydrase families.
  • Demonstrated how active site properties dictate the selectivity and protection of the native metal ion.

Conclusions:

  • The study provides fundamental insights into the determinants of metal ion selection and retention in carbonic anhydrases.
  • Understanding these principles is crucial for enzyme function and potential biotechnological applications.
  • Computational methods effectively delineate the physical basis of metal competition in metalloenzymes.