title: pH-dependent mechanism of nitric oxide release in nitrophorins 2 and 4.
abstract: Nitrophorins are NO carrier proteins that transport and release NO through a pH-dependent conformational change. They bind NO tightly in a low pH environment and release it in a higher pH environment. Experimental evidence shows that the increase in the NO dissociation equilibrium constant, K(d), is due mainly to an increase in the NO release rate. Structural and kinetic data strongly suggest that NPs control NO escape by modulating its migration from the active site to the solvent through a pH-dependent conformational change. NP2 and NP4 are two representative proteins of the family displaying a 39% overall sequence identity, and interestingly, NP2 releases NO slower than NP4. The proposal that NPs' NO release relies mainly on the NO escape rate makes NPs a very peculiar case among typical heme proteins. The connection between the pH-dependent conformational change and ligand release mechanism is not fully understood and the structural basis for the pH induced structural transition and the different NO release patterns in NPs are unresolved, yet interesting issues. In this work, we have used state of the art molecular dynamics simulations to study the NO escape process in NP2 and NP4 in both the low and high pH states. Our results show that both NPs modulate NO release by switching between a "closed" conformation in a low pH environment and an "open" conformation at higher pH. In both proteins, the change is caused by the differential protonation of a common residue Asp30 in NP4 and Asp29 in NP2, and the NO escape route is conserved. Finally, our results show that, in NP2, the conformational change to the "open" conformation is smaller than that for NP4 which results in a higher barrier for NO release.
authors.affiliation: Department of Chemistry, University of Florida, Gainesville, Florida 32611-8435, USA.
authors.forename: Jason M
authors.initials: JM
authors.lastname: Swails
authors.forename: Yilin
authors.initials: Y
authors.lastname: Meng
authors.forename: F Ann
authors.initials: FA
authors.lastname: Walker
authors.forename: Marcelo A
authors.initials: MA
authors.lastname: Marti
authors.forename: Dario A
authors.initials: DA
authors.lastname: Estrin
authors.forename: Adrian E
authors.initials: AE
authors.lastname: Roitberg
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D006420:Hemeproteins / Q000737:chemistry* / Q000378:metabolism; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009569:Nitric Oxide / Q000032:analysis* / Q000378:metabolism; D011487:Protein Conformation; D012471:Salivary Proteins and Peptides / Q000737:chemistry* / Q000378:metabolism; D017386:Sequence Homology, Amino Acid
chemical_list: D000596:Amino Acids; D006420:Hemeproteins; D012471:Salivary Proteins and Peptides; C090560:nitrophorin; D009569:Nitric Oxide