A molecular model for the major conformational substates in heme proteins

Abstract

4. The holoazurin Trp 'Lb absorption band red shifts ca. 1 nm compared to apoazurin, while the 'Bb transition red shifts ca. 2 nm. The hydrophobicity of the Trp environment appears little changed between Cu(I) azurin, Cu(II) azurin, and apoazurin as evidenced by the narrowness of the Trp 'Lb 0-0 bands and from the Raman band shape for the Trp 1354-cm'1 band. The Trp 0-0 'Li, absorption spectral shifts most likely derive from subtle environmental changes, possibly alterations at sites somewhat distant from the Trp ring, such as alterations in electrostatic interaction from the Cu site.5. The absorption difference spectra (oxidized minus reduced as well as holoazurin minus apoazurin) show large changes in the 200-300-nm spectral region which presumably derive from alterations in sulfur and imidazole -* Cu(II) charge-transfer transitions. Numerous charge-transfer transitions can occur since the Cu is ligated to two histidines, one cysteine, and one methionine; simple Cu(II)-(imidazole)4 complexes show increased absorbances throughout the 200-300-nm spectral region (Figure 6).We thus conclude that facile energy transfer between the Trp and the Cu-ligand complex is responsible for the fluorescence quenching in Trp. Presumably this quenching occurs between the Trp 'Laib states and a Cu-ligand charge-transfer state. In addition, the Trp absorption spectral shifts between the Cu(I) azurin, Cu(II) azurin, and apoazurin suggest intimate coupling between the electronic transitions of the Cu-ligand complex and those of Trp. It is possible that strong excitonic interactions are present.

Application of molecular dynamics and free energy perturbation methods to metalloporphyrin‐ligand systems ii: Co and dioxygen binding to myoglobin

“…These estimates are qualitative, but suggest that the contributions made by the distal histidine toward the free energy difference between the CO and O2 ligands are about 90% due to polar effects (electrostatic energy) and about 10% due to steric effects (van der Waals energy). This estimate, which suggests that the interaction between the bound ligands and the distal histidine is largely an electrostatic interaction, is consistent with the molecular model of Oldfield et al (1991). These workers presented a model of the major conformational substates of the COligated forms of several Hbs, Mbs, and peroxidases solely in terms of an electrical perturbation of the bound CO.…”

Neuroglobin dynamics observed with ultrafast 2D-IR vibrational echo spectroscopy

“…1). Experiments, theory, and molecular dynamics simulations have shown that both the local and global coupling between protein structure and the CO vibrational transition frequency is mainly through the electric field along the CO bond (19,20,24,29,30,(35)(36)(37). The protein residues range from charged, to polar, to nonpolar.…”

Heme Environmental Structure of CooA Is Modulated by the Target DNA Binding

“…The CϭO stretching frequency, (CϭO), appeared at 1969 cm Ϫ1 for natural abundance CO and at 1927 cm Ϫ1 for 13 CO. There is a well-known inverse correlation between the frequencies of the Fe-CO and CϭO stretching modes (15,(31)(32), which can be used to estimate the strength of the proximal ligand. The frequencies measured for CooA-CO lie on the line composed by heme proteins with neutral histidine as a proximal ligand (correlation plot not shown).…”