DFT Analysis of Axial and Equatorial Effects on Heme−CO Vibrational Modes:  Applications to CooA and H−NOX Heme Sensor Proteins

Abstract

Determinants of the Fe-CO and C-O stretching frequencies in (imidazole) heme-CO adducts have been investigated via Density Functional Theory (DFT) analysis, in connection with puzzling characteristics of the heme sensor protein CooA, and of the H-NOX (Heme-Nitric Oxide and/or OXygen binding) family of proteins, including soluble guanylate cyclase (sGC). The computations show that two mechanisms of Fe-histidine bond weakening have opposite effects on the νFeC/νCO pattern. Mechanical tension is expected to raise νFeC with little change in νCO, while weakening of H-bond donation from the imidazole ligand has the opposite effect. Data on CooA indicate imidazole H-bond weakening associated with heme displacement, as part of the activation mechanism. The computations also reveal that protein-induced distortion of the porphyrin ring, a prominent structural feature of the H-NOX protein TtTar4H (Thermoanaerobacter tengcongensis Tar4 protein), has surprisingly little effect on νFeC or νCO. However, another structural feature, strong H-bonding to the propionates, is suggested to account for the weakened backbonding that is evident in sGC. TtTar4H-CO itself has an elevated νFeC, which is successfully modeled as a compression effect, resulting from steric crowding in the distal pocket. νFeC/νCO data, in conjunction with modeling, can provide valuable insight into mechanisms for heme-protein modulation.

Heme Reactivity is Uncoupled from Quaternary Structure in Gel-Encapsulated Hemoglobin: A Resonance Raman Spectroscopic Study

“…These bands are known to be sensitive to alterations in the Fe-His bond, in various heme proteins. 67 Thus the evolution in protein structure does not affect the structure of the CO-heme, but does affect the photoproduct deoxy-heme following CO dissociation.…”

Chemical reactivity of Synechococcus sp. PCC 7002 and Synechocystis sp. PCC 6803 hemoglobins: covalent heme attachment and bishistidine coordination

“…The electron density of the heme group can also be modulated by the interactions of the propionates with the protein [52–54]. In Synechocystis 6803 rGlbN [55, 56] and presumably in Synechococcus 7002 rGlbN as well, the 6-propionate is exposed to solvent, whereas the 7-propionate is engaged in electrostatic interactions and hydrogen bonds.…”

Experimental Documentation of the Structural Consequences of Hydrogen‐Bonding Interactions to the Proximal Cysteine of a Cytochrome P450

“…These directly correlated shifts of the ν(Fe-C) and ν(C-O) modes, both to higher frequency, are indicative of a diminished σ-donation of the trans-axial proximal thiolate ligand resulting from the newly introduced H-bonding histidine residue, such behavior being in agreement with predictions made from several high-level computational studies. [14,15,33] It is noted that earlier computational work, supported with modest experimental data for models, has previously been used to argue this point for the isoelectronic ferric NO adducts. [34] Furthermore, the behavior seen here for the vibrational modes of the Fe-C-O fragment is satisfyingly consistent with data reported for CO adducts of NOS.…”

“…[23] Thus, the plots shown at the bottom of Figure 3 present data acquired for CO adducts of mammalian NOS (stars), the CO adducts of WT CYP2B4 under various conditions (open squares) and the two points obtained here for the F429H mutant of CYP2B4 (solid squares); additional data reported for bacterial NOS proteins, as well as the isoelectronic Fe(III)NO adducts of cytochromes P450 and model compounds, are given in Figure S3 of Supporting Information. The inverse correlations of the ν(Fe-C) and ν(C-O) modes are generally accepted to reliably reflect variations in polarity of the distal heme pocket, [33,35] with displacements from one another along the vertical direction being the result of differences in the strength of the proximal ligand. Thus, the displacement of the NOS line from the CYP2B4 line arises because the Fe-S bonds of the NOSs are weakened by the presence of an H-bond from a conserved tryptophan residue in the proximal pocket; i.e., their ν(Fe-S) stretching frequencies generally occur near 338 cm −1 , [36] approximately 12-14 cm −1 lower than for cytochromes P450.…”