A heme pocket aromatic quadrupole modulates gas binding to cytochrome c′-β: Implications for NO sensors

Adams, Hannah R.; Svistunenko, Dimitri A.; Wilson, Michael T.; Fujii, Sotaro; Strange, R.W.; Hardy, Zoe A.; Vazquez, Priscilla A.; Dabritz, Tyler; Streblow, Gabriel J.; Andrew, Colin R.; Hough, Michael A.

doi:10.1016/j.jbc.2023.104742

Cited by 4 publications

(3 citation statements)

References 57 publications

(89 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A study of from Methylococcus capsulatus , which contains an analogous capping Phe residue (Phe32), suggested that a quadrupolar interaction between Phe32 and NO results in a modest destabilization of the Fe–NO bond. 18 While we do not observe that effect in cyt P460, there may be other factors influencing Fe–NO bonding. The increase in K d could be the result of either an increase in the off-rate or a decrease in the on-rate ( eqn (1) ).…”

Section: Resultscontrasting

confidence: 65%

Outer coordination sphere influences on cofactor maturation and substrate oxidation by cytochrome P460

et al. 2023

View full text Add to dashboard Cite

show abstract

Section: Resultscontrasting

confidence: 65%

Outer coordination sphere influences on cofactor maturation and substrate oxidation by cytochrome P460

et al. 2023

View full text Add to dashboard Cite

show abstract

“…Furthermore, cyt c′ shows a mixture of penta- and hexa-coordinate NO bound species as observed by a split Soret peak 395/415 nm. 40 As a weak band is consistently present in NO binding and NiR experiments at ∼420–430 nm, it is likely that a small fraction of NO-bound Adgb-GD remains as a hexa-coordinated species.…”

Section: Resultsmentioning

confidence: 93%

The circularly permuted globin domain of androglobin exhibits atypical heme stabilization and nitric oxide interaction

Reeder,

Deganutti,

Ukeri

et al. 2024

Chem. Sci.

Self Cite

View full text Add to dashboard Cite

show abstract

“…Various novel and important reports of weak interactions continue to emerge. For example, phosphorothioate DNA backbone (e.g., sulfur replacement of one phosphate oxygen atom) facilitates the interaction of even non‐DNA binding proteins with DNA through the weak interactions of the sulfur anion with alkyl groups of Lys/Arg residues (Hyjek‐Skladanowska et al, 2023), electronic polarization facilitates the interaction of the chloride anion with aliphatic protons in chloride‐pumping rhodopsin (Phan et al, 2023), or aromatic quadrupole in heme pockets modulates gas (e.g., NO, CO) binding (Adams et al, 2023). As the appreciation of weak interactions (of anions) in proteins continues to grow, we utilized AQcalc to generate an analysis of AQ (and CP, SB, and HBAQ) interactions in a variety of protein structures.…”

Section: Discussionmentioning

confidence: 99%

AQcalc: A web server that identifies weak molecular interactions in protein structures

Afshinpour,

Smith,

Chakravarty

2023

Protein Science

View full text Add to dashboard Cite

Weak molecular interactions play an important role in protein structure and function. Computational tools that identify weak molecular interactions are, therefore, valuable for the study of proteins. Here, we present AQcalc, a web server (https://aqcalcbiocomputing.com/) that can be used to identify anion–quadrupole (AQ) interactions, which are weak interactions involving aromatic residue (Trp, Tyr, and Phe) ring edges and anions (Asp, Glu, and phosphate ion) both within proteins and at their interfaces (protein‐protein, protein‐nucleic acids, and protein‐lipid bilayer). AQcalc identifies AQ interactions as well as clusters involving AQ, cation–π, and salt bridges, among others. Utilizing AQcalc we analyzed weak interactions in protein models, even in the absence of experimental structures, to understand the contributions of weak interactions to deleterious structural changes, including those associated with oncogenic and germline disease variants. We identified several deleterious variants with disrupted AQ interactions (comparable in frequency to cation–π disruptions). Amyloid fibrils utilize AQ to bury anions at frequencies that far exceed those observed for globular proteins. AQ interactions were detected three and five times more frequently than the hydrogen‐bonded AQ (HBAQ) in fibril structures and protein‐lipid bilayer interfaces, respectively. By contrast, AQ and HBAQ interactions were detected with similar frequencies in globular proteins. Collectively, these findings suggest AQcalc will be effective in facilitating fine structural analysis. As other web utilities designed to identify protein residue interaction networks do not report AQ interactions, wide use of AQcalc will enrich our understanding of residue interaction networks and facilitate hypothesis testing by identifying and experimentally characterizing these comparably weak but important interactions.This article is protected by copyright. All rights reserved.

show abstract

A heme pocket aromatic quadrupole modulates gas binding to cytochrome c′-β: Implications for NO sensors

Cited by 4 publications

References 57 publications

Outer coordination sphere influences on cofactor maturation and substrate oxidation by cytochrome P460

Outer coordination sphere influences on cofactor maturation and substrate oxidation by cytochrome P460

The circularly permuted globin domain of androglobin exhibits atypical heme stabilization and nitric oxide interaction

AQcalc: A web server that identifies weak molecular interactions in protein structures

Contact Info

Product

Resources

About