title: Kinetics and computational studies of ligand migration in nitrophorin 7 and its Δ1-3 mutant.
abstract: Nitrophorins (NPs) are nitric oxide (NO)-carrying heme proteins found in the saliva of the blood-sucking insect Rhodnius prolixus. Though NP7 exhibits a large sequence resemblance with other NPs, two major differential features are the ability to interact with negatively charged cell surfaces and the presence of a specific N-terminus composed of three extra residues (Leu1-Pro2-Gly3). The aim of this study is to examine the influence of the N-terminus on the ligand binding, and the topological features of inner cavities in closed and open states of NP7, which can be associated to the protein structure at low and high pH, respectively. Laser flash photolysis measurements of the CO rebinding kinetics to NP7 and its variant NP7(Δ1-3), which lacks the three extra residues at the N-terminus, exhibit a similar pattern and support the existence of a common kinetic mechanism for ligand migration and binding. This is supported by the existence of a common topology of inner cavities, which consists of two docking sites in the heme pocket and a secondary site at the back of the protein. The ligand exchange between these cavities is facilitated by an additional site, which can be transiently occupied by the ligand in NP7, although it is absent in NP4. These features provide a basis to explain the enhanced internal gas hosting capacity found experimentally in NP7 and the absence of ligand rebinding from secondary sites in NP4. The current data allow us to speculate that the processes of docking to cell surfaces and NO release may be interconnected in NP7, thereby efficiently releasing NO into a target cell. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
authors.affiliation: Departament de Fisicoquímica and Institut de Biomedicina, Universitat de Barcelona, Spain.
authors.forename: Ana
authors.initials: A
authors.lastname: Oliveira
authors.forename: Alessandro
authors.initials: A
authors.lastname: Allegri
authors.forename: Axel
authors.initials: A
authors.lastname: Bidon-Chanal
authors.forename: Markus
authors.initials: M
authors.lastname: Knipp
authors.forename: Adrian E
authors.initials: AE
authors.lastname: Roitberg
authors.forename: Stefania
authors.initials: S
authors.lastname: Abbruzzetti
authors.forename: Cristiano
authors.initials: C
authors.lastname: Viappiani
authors.forename: F Javier
authors.initials: FJ
authors.lastname: Luque
mesh_terms: D000818:Animals; D002248:Carbon Monoxide / Q000378:metabolism*; D018360:Crystallography, X-Ray; D006420:Hemeproteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D007700:Kinetics; D054834:Lipocalins / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009154:Mutation / Q000235:genetics*; D009569:Nitric Oxide / Q000378:metabolism*; D010782:Photolysis; D011487:Protein Conformation; D012239:Rhodnius / Q000378:metabolism*; D012471:Salivary Proteins and Peptides / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: D006420:Hemeproteins; D054834:Lipocalins; D012471:Salivary Proteins and Peptides; C090560:nitrophorin; D009569:Nitric Oxide; D002248:Carbon Monoxide
keywords: Ligand migration; MD; Molecular dynamics; NP; Nitric oxide; Nitrophorin 7; PS; RMSD; Reaction kinetics; l-α-phosphatidyl-l-serine; molecular dynamics; nitrophorin; root-mean square deviation