skip to main content


Title: CO Bonding in Hexa- and Pentacoordinate Carboxy-Neuroglobin - A QM/MM and Local Vibrational Mode Study
We present a comprehensive investigation on the different role of CO in carboxy- neuroglobin i) as ligand of the heme group in the active site forming a bond with the heme iron and ii) dissociated from the heme group but still trapped inside the active site, focusing on two specific orientations, one with CO perpendicular to the plane defined by the distal histidine of the enzyme (form A) and one with CO located parallel to that plane (form B). Our study includes wild type carboxy-neuroglobin and nine known protein mutations. Considering that the distal histidine interacting with the heme group can adapt two different tautomeric forms and the two possible orientations of the dissociated CO, a total of 36 protein systems were analyzed in this study. Fully optimized geometries and vibrational frequencies were calculated at the QM/MM level, followed by the local mode analysis, to decode CO bond properties. The intrinsic bond strengths derived from the local mode analysis, complemented with NBO and QTAIM data, reveal that the strength of the CO bond, in the hexacoordinate (where CO is a ligand of the heme group) and pentacoordinate (where CO is dissociated from the heme group) scenarios, is dominated by through bond and through space charge transfer between CO and Fe, fine-tuned by electrostatic and dispersion interactions with the side chain amino acids in the distal heme pocket. Suggestions are made as to advise on how protein modifications can influence the molecular properties of the coordinated or dissociated CO, which could serve the fine-tuning of existing and the design of new neuroglobin models with specific FeC and CO bond strengths.  more » « less
Award ID(s):
2102461
NSF-PAR ID:
10342535
Author(s) / Creator(s):
Date Published:
Journal Name:
Journal of computational chemistry
ISSN:
0192-8651
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Hydrogen bonds (HB)s are the most abundant motifs in biological systems. They play a key role in determining protein–ligand binding affinity and selectivity. We designed two pharmaceutically beneficial HB databases, database A including ca. 12,000 protein–ligand complexes with ca. 22,000 HBs and their geometries, and database B including ca. 400 protein–ligand complexes with ca. 2200 HBs, their geometries, and bond strengths determined via our local vibrational mode analysis. We identified seven major HB patterns, which can be utilized as a de novo QSAR model to predict the binding affinity for a specific protein–ligand complex. Glycine was reported as the most abundant amino acid residue in both donor and acceptor profiles, and N–H⋯O was the most frequent HB type found in database A. HBs were preferred to be in the linear range, and linear HBs were identified as the strongest. HBs with HB angles in the range of 100–110°, typically forming intramolecular five-membered ring structures, showed good hydrophobic properties and membrane permeability. Utilizing database B, we found a generalized Badger’s relationship for more than 2200 protein–ligand HBs. In addition, the strength and occurrence maps between each amino acid residue and ligand functional groups open an attractive possibility for a novel drug-design approach and for determining drug selectivity and affinity, and they can also serve as an important tool for the hit-to-lead process. 
    more » « less
  2. Bernd Reif (Ed.)
    It has long been known that the alteration of protein side chains that occlude or expose the heme cofactor to water can greatly affect the stability of the oxyferrous heme state. Here, we demonstrate that the rate of dynamically driven water penetration into the core of an artificial oxygen transport protein also correlates with oxyferrous state lifetime by reducing global dynamics, without altering the structure of the active site, via the simple linking of the two monomers in a homodimeric artificial oxygen transport protein using a glycine-rich loop. The tethering of these two helices does not significantly affect the active site structure, pentacoordinate heme-binding affinity, reduction potential, or gaseous ligand affinity. It does, however, significantly reduce the hydration of the protein core, as demonstrated by resonance Raman spectroscopy, backbone amide hydrogen exchange, and pKa shifts in buried histidine side chains. This further destabilizes the charge-buried entatic state and nearly triples the oxyferrous state lifetime. These data are the first direct evidence that dynamically driven water penetration is a rate-limiting step in the oxidation of these complexes. It furthermore demonstrates that structural rigidity that limits water penetration is a critical design feature in metalloenzyme construction and provides an explanation for both the failures and successes of earlier attempts to create oxygen-binding proteins. 
    more » « less
  3. In this work, we investigated bonding features of 15 ruthenium(II) nitrile complexes of the type [Ru(tpy)(L)-(CH 3 CN)] n+ , containing the tridentate tpy ligand (tpy = 2,2′:6′,2″-terpyridine) and various bidentate ancillary ligands L; 12 compounds originally synthesized by Loftus et al. [J. Phys. Chem. C 123, 10291–10299 (2019)] and three new complexes. We utilized local vibrational force constants derived from the local mode theory as a quantitative measure of bond strength complemented with the topological analysis of the electron density and the natural bond orbital analysis. Loftus et al. suggested that nitrile dissociation occurs after light induced singlet–triplet transition of the original complexes and they used as a measure of nitrile release efficiency quantum yields for ligand exchange in water. They observed larger quantum yields for complexes with smaller singlet–triplet energy gaps. The major goal of this work was to assess how the Ru–NC and Ru–L bond strengths in these 15 compounds relate to and explain the experimental data of Loftus et al., particularly focusing on the question whether there is a direct correlation between Ru–NC bond strength and measured quantum yield. Our study provides the interesting result that the compounds with the highest quantum yields also have the strongest Ru–NC bonds suggesting that breaking the Ru–NC bond is not the driving force for the delivery process rather than the change of the metal framework as revealed by first results of a unified reaction valley approach investigation of the mechanism. Compounds with the highest quantum yield show larger electronic structure changes upon singlet–triplet excitation, i.e., larger changes in bond strength, covalency, and difference between the singlet and triplet HOMOs, with exception of the compound 12. In summary, this work provides new insights into the interplay of local properties and experimental quantum yields forming in synergy a useful tool for fine tuning of existing and future design of new nitrile releasing ruthenium compounds. We hope that this work will bring theoretical and experimental studies closer together and serves as an incubator for future collaboration between computational chemists and their experimental colleagues. 
    more » « less
  4. Abstract

    Ergothioneine (ESH) and ovothiol A (OSHA) are two natural thiol‐histidine derivatives. ESH has been implicated as a longevity vitamin and OSHA inhibits the proliferation of hepatocarcinoma. The key biosynthetic step of ESH and OSHA in the aerobic pathways is the O2‐dependent C−S bond formation catalyzed by non‐heme iron enzymes (e.g., OvoA in ovothiol biosynthesis), but due to the lack of identification of key reactive intermediate the mechanism of this novel reaction is unresolved. In this study, we report the identification and characterization of a kinetically competentS=1 iron(IV) intermediate supported by a four‐histidine ligand environment (three from the protein residues and one from the substrate) in enabling C−S bond formation in OvoA fromMethyloversatilis thermotoleran, which represents the first experimentally observed intermediate spin iron(IV) species in non‐heme iron enzymes. Results reported in this study thus set the stage to further dissect the mechanism of enzymatic oxidative C−S bond formation in the OSHA biosynthesis pathway. They also afford new opportunities to study the structure‐function relationship of high‐valent iron intermediates supported by a histidine rich ligand environment.

     
    more » « less
  5. Abstract

    Ergothioneine (ESH) and ovothiol A (OSHA) are two natural thiol‐histidine derivatives. ESH has been implicated as a longevity vitamin and OSHA inhibits the proliferation of hepatocarcinoma. The key biosynthetic step of ESH and OSHA in the aerobic pathways is the O2‐dependent C−S bond formation catalyzed by non‐heme iron enzymes (e.g., OvoA in ovothiol biosynthesis), but due to the lack of identification of key reactive intermediate the mechanism of this novel reaction is unresolved. In this study, we report the identification and characterization of a kinetically competentS=1 iron(IV) intermediate supported by a four‐histidine ligand environment (three from the protein residues and one from the substrate) in enabling C−S bond formation in OvoA fromMethyloversatilis thermotoleran, which represents the first experimentally observed intermediate spin iron(IV) species in non‐heme iron enzymes. Results reported in this study thus set the stage to further dissect the mechanism of enzymatic oxidative C−S bond formation in the OSHA biosynthesis pathway. They also afford new opportunities to study the structure‐function relationship of high‐valent iron intermediates supported by a histidine rich ligand environment.

     
    more » « less