title: Comparative analysis of inner cavities and ligand migration in non-symbiotic AHb1 and AHb2.
abstract: This study reports a comparative analysis of the topological properties of inner cavities and the intrinsic dynamics of non-symbiotic hemoglobins AHb1 and AHb2 from Arabidopsis thaliana. The two proteins belong to the 3/3 globin fold and have a sequence identity of about 60%. However, it is widely assumed that they have distinct physiological roles. In order to investigate the structure-function relationships in these proteins, we have examined the bis-histidyl and ligand-bound hexacoordinated states by atomistic simulations using in silico structural models. The results allow us to identify two main pathways to the distal cavity in the bis-histidyl hexacoordinated proteins. Nevertheless, a larger accessibility to small gaseous molecules is found in AHb2. This effect can be attributed to three factors: the mutation Leu35(AHb1)→Phe32(AHb2), the enhanced flexibility of helix B, and the more favorable energetic profile for ligand migration to the distal cavity. The net effect of these factors would be to facilitate the access of ligands, thus compensating the preference for the fully hexacoordination of AHb2, in contrast to the equilibrium between hexa- and pentacoordinated species in AHb1. On the other hand, binding of the exogenous ligand introduces distinct structural changes in the two proteins. A well-defined tunnel is formed in AHb1, which might be relevant to accomplish the proposed NO detoxification reaction. In contrast, no similar tunnel is found in AHb2, which can be ascribed to the reduced flexibility of helix E imposed by the larger number of salt bridges compared to AHb1. This feature would thus support the storage and transport functions proposed for AHb2. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
authors.affiliation: Dipartimento di Scienze degli Alimenti, Università degli Studi di Parma, Parma, Italy. francesca.spyrakis@unipr.it
authors.forename: Francesca
authors.initials: F
authors.lastname: Spyrakis
authors.forename: Fátima
authors.initials: F
authors.lastname: Lucas
authors.forename: Axel
authors.initials: A
authors.lastname: Bidon-Chanal
authors.forename: Cristiano
authors.initials: C
authors.lastname: Viappiani
authors.forename: Victor
authors.initials: V
authors.lastname: Guallar
authors.forename: F Javier
authors.initials: FJ
authors.lastname: Luque
mesh_terms: D017360:Arabidopsis / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000378:metabolism*; D006418:Heme / Q000378:metabolism*; D006454:Hemoglobins / Q000737:chemistry / Q000378:metabolism*; D006639:Histidine / Q000378:metabolism; D007700:Kinetics; D008958:Models, Molecular; D009569:Nitric Oxide / Q000378:metabolism*; D010100:Oxygen / Q000378:metabolism*; D011485:Protein Binding; D011487:Protein Conformation
chemical_list: C470347:AHB1 protein, Arabidopsis; C109042:AHB2 protein, Arabidopsis; D029681:Arabidopsis Proteins; D006454:Hemoglobins; D009569:Nitric Oxide; D006418:Heme; D006639:Histidine; D010100:Oxygen
keywords: ANM; ED; K(d); Ligand migration; MD; Molecular simulations; Non-symbiotic hemoglobins; PELE; Protein Energy Landscape Exploration; Protein flexibility; RMDF; RMSD; Structure–function relationships; anisotropic network model; dissociation constant; essential dynamics; molecular dynamics; root-mean square deviation; root-mean square fluctuation