ArticleJournal of the American Chemical Society2010
Ultrafast dynamics of diatomic ligand binding to nitrophorin 4.
Article in Journal of the American Chemical Society, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 42 citations in OpenAlex.
- Unusually FastInternational journal of molecular sciences · 2021Article
- Electrostatic Tuning of the Ligand Binding Mechanism by Glu27 in Nitrophorin 7.Scientific reports · 2018Article
- Ultrafast CO Kinetics in Heme Proteins: Adiabatic Ligand Binding and Heavy Atom Tunneling.Journal of the American Chemical Society · 2017Article
- Structure and Activation of Soluble Guanylyl Cyclase, the Nitric Oxide Sensor.Antioxidants & redox signaling · 2017Review
- Motion of proximal histidine and structural allosteric transition in soluble guanylate cyclase.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Dimerization of nitrophorin 4 at low pH and comparison to the K1A mutant of nitrophorin 1.Biochemistry · 2015Article
- NMR studies of the dynamics of high-spin nitrophorins: comparative studies of NP4 and NP2 at close to physiological pH.Biochemistry · 2015Article
- Structure and dynamics of the membrane attaching nitric oxide transporter nitrophorin 7.F1000Research · 2015Article
- NMR investigations of nitrophorin 2 belt side chain effects on heme orientation and seating of native N-terminus NP2 and NP2(D1A).Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2014Article
- Investigations of heme distortion, low-frequency vibrational excitations, and electron transfer in cytochrome c.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- YC-1 binding to the β subunit of soluble guanylyl cyclase overcomes allosteric inhibition by the α subunit.Biochemistry · 2014Article
- pH-dependent picosecond structural dynamics in the distal pocket of nitrophorin 4 investigated by 2D IR spectroscopy.The journal of physical chemistry. B · 2013Article
- NMR studies of the dynamics of nitrophorin 2 bound to nitric oxide.Biochemistry · 2013Article
- Effect of DNA binding on geminate CO recombination kinetics in CO-sensing transcription factor CooA.The Journal of biological chemistry · 2012Article
- pH-Dependent conformational changes in proteins and their effect on experimental pK(a)s: the case of Nitrophorin 4.PLoS computational biology · 2012Article
- Following ligand migration pathways from picoseconds to milliseconds in type II truncated hemoglobin from Thermobifida fusca.PloS one · 2012Article
- Electronic properties of the highly ruffled heme bound to the heme degrading enzyme IsdI.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
Nitrophorin 4 (NP4) is a heme protein that stores and delivers nitric oxide (NO) through pH-sensitive conformational change. This protein uses the ferric state of a highly ruffled heme to bind NO tightly at low pH and release it at high pH. In this work, the rebinding kinetics of NO and CO to NP4 are investigated as a function of iron oxidation state and the acidity of the environment. The geminate recombination process of NO to ferrous NP4 at both pH 5 and pH 7 is dominated by a single approximately 7 ps kinetic phase that we attribute to the rebinding of NO directly from the distal pocket. The lack of pH dependence explains in part why NP4 cannot use the ferrous state to fulfill its function. The kinetic response of ferric NP4NO shows two distinct phases. The relative geminate amplitude of the slower phase increases dramatically as the pH is raised from 5 to 8. We assign the fast phase of NO rebinding to a conformation of the ferric protein with a closed hydrophobic pocket. The slow phase is assigned to the protein in an open conformation with a more hydrophilic heme pocket environment. Analysis of the ultrafast kinetics finds the equilibrium off-rate of NO to be proportional to the open state population as well as the pH-dependent amplitude of escape from the open pocket. When both factors are considered, the off-rate increases by more than an order of magnitude as the pH changes from 5 to 8. The recombination of CO to ferrous NP4 is observed to have a large nonexponential geminate amplitude with rebinding time scales of approximately 10(-11)-10(-9) s at pH 5 and approximately 10(-10)-10(-8) s at pH 7. The nonexponential CO rebinding kinetics at both pH 5 and pH 7 are accounted for using a simple model that has proven effective for understanding CO binding in a variety of other heme systems (Ye, X.; et al. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 14682).
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