Cofactor proton binding

The oxidation/reduction of redox cofactors in biological systems is often coupled to proton binding/release either at the cofactor itself or at local amino acid residues, which provides the basic mechanochem-ical part of a proton pump such as that foimd in cytochrome c oxidase (95). Despite a thermodynamic cycle that provides that coupling of protonation of amino acids to the reduction process will result in a 60 mV/pH decrease unit in the reduction potential per proton boimd between the pAa values in the Fe(III) and Fe(II) states, the essential pumping of protons in the respiratory complexes has yet to be localized within their three-dimensional structures. 

Fig. 2. Creation of the receptor description file (RDF) for use with FlexX. Protein Structure Specify the correct PDB structure. Active-Site File The FlexX binding pocket can be defined as the amino acid residues within 7 A from a reference structure (e.g., a ligand structure translated to the protein active site midpoint as determined by PASS see Subheading 3.3.2.). Customize RDF File enables specification of metals, cofactors, protonation states, and torsions of residues (see Fig. 3).

The behaviour of the mutant enzymes where, for example, histidine-152 has been changed to alanine is compared with that of wild type enzymes.60 The 31P NMR chemical shift values and signal width for H152A mutant enzyme have shown the presence of two conformers open and closed forms of the enzyme that interconvert slowly on the NMR time scale. The tightness of the binding of the cofactor to the protein surface and its protonation state have been also discussed for intermediate Schiff bases in different steps of the catalytic cycle (Table 1). 

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