Dissection of Nitric Oxide binding pathway in Nitrobindins reveals hidden structural details
Year: 2025
Authors: Iagatti A., Messias A., De Simone G., Sebastiani F., Patrizi B., Bocedi A., Estrin D., Ascenzi P., Foggi P., Coletta M.
Autors Affiliation: CNR, INO CNR Natl Inst Opt, Via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy; European Lab Nonlinear Spect LENS, Via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy; Univ Buenos Aires, Inst Quim Fis Mat Medio Ambiente & Energia INQUIMA, CONICET, Intendente Guiraldes 2160,C1428EGA, Buenos Aires, Argentina; Univ Roma Tre, Dept Sci, I-00146 Rome, Italy; Univ Firenze, Dept Chem Ugo Schiff DICUS, I-50019 Sesto Fiorentino, Italy; Univ Roma Tor Vergata, Dept Chem Sci & Technol, I-00133 Rome, Italy; Lincei Acad, I-00165 Rome, Italy; Univ Perugia, Dept Chem Biol & Biotechnol, I-06123 Perugia, Italy; IRCCS Fdn Bietti, Rome, Italy.
Abstract: Nitric Oxide (NO) rebinding after a very short laser pulse (<10-12 s) has been investigated in nitrobindins (Nbs) from plant Arabidopsis thaliana (At-Nb) and zebrafish Danio rerio (Dr-Nb). Nbs are ten-stranded anti-parallel all beta-barrel heme-proteins present along the evolutionary ladder, from bacteria to man. They display an open distal heme pocket, easily accessible to the bulk solvent, since the histidine residue, facing the distal side of the heme in most all-alpha-helical hemoproteins, is absent. Further, they display a proximal histidine residue as the fifth coordinating ligand to the heme-Fe atom, which is severely weakened, or even cleaved, upon NO binding; in particular, spectroscopic evidence shows that in NO-bound Dr-Nb(II) the proximal bond is absent, whereas in At-Nb(II) NO binding induces a structural stress. Noteworthy, NO geminate recombination is very fast in both Nb(II) proteins, being essentially completed within 3 x 10-11 s and involving >80 % of the photo-dissociated molecules. This behavior is drastically different from what observed in alpha-helical heme-proteins, such as myoglobin and hemoglobin, which show a multiphasic and slower geminate rebinding process. Thus, it suggests that the open heme pocket does not facilitate the outward diffusion of the photo-dissociated NO, but instead the lack of residues in the immediate proximity likely helps the ligand to keep an optimal space configuration for fast rebinding. The dissection of outward and inward ligand pathway steps allows a better comprehension of determinants for NO binding to heme-proteins, a crucial event for blood flow regulation in poorly vascularized tissues, like the eye’s retina.
Journal/Review: INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
Volume: 331 Pages from: 148406-1 to: 148406-13
More Information: A.I. gratefully acknowledges the National Recovery and Resilience Plan (NRRP) , Mission 4, Component 2, Investment 1.1, Call for tender No. 1409 published on 14.9.2022 by the Italian Ministry of University and Research (MUR) , funded by the European Union – NextGenerationEU (Project Title VISIO-CUP B53D23025290001-Grant Assign-ment Decree No. P2022ALSMP) . G.D.S. and P.A. gratefully acknowledge the support of Roma Tre University (Grant Dipartimenti di Eccellenza, Legge 232/2016, Articolo 1, Comma 314-337) . F.S. acknowledges the support of MUR-Italy (Progetto Dipartimenti di Eccellenza 2023-2027, CUP B97G22000740001-DICUS 2.0, allocated to the Department of Chemistry Ugo Schiff) . M.C. gratefully acknowledges the support of the Ministry of Health, Italy and of Fondazione Roma.KeyWords: Nitric oxide binding; Nitrobindins; Laser photolysis; Intra-molecular dynamics; Energetic barriers; Ultrafast spectroscopyDOI: 10.1016/j.ijbiomac.2025.148406
