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Network and atomistic simulations unveil the structural determinants of mutations linked to retinal diseases.

Mariani S, Dell'Orco D, Felline A, Raimondi F, Fanelli F - PLoS Comput. Biol. (2013)

Bottom Line: Mathematical modeling, in line with electrophysiological recordings, indicates reduction of phosphodiesterase 6 (PDE) recognition and activation as the main determinants of the pathological phenotype.Protein Structure Network analyses additionally suggest that the observed slight reduction of theRGS9-catalyzed GTPase activity of transducin depends on perturbed communication between RGS9 and GTP binding site.Analogous approaches are suitable to unveil the mechanism of information transfer in any signaling network either in physiological or pathological conditions.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.

ABSTRACT
A number of incurable retinal diseases causing vision impairments derive from alterations in visual phototransduction. Unraveling the structural determinants of even monogenic retinal diseases would require network-centered approaches combined with atomistic simulations. The transducin G38D mutant associated with the Nougaret Congenital Night Blindness (NCNB) was thoroughly investigated by both mathematical modeling of visual phototransduction and atomistic simulations on the major targets of the mutational effect. Mathematical modeling, in line with electrophysiological recordings, indicates reduction of phosphodiesterase 6 (PDE) recognition and activation as the main determinants of the pathological phenotype. Sub-microsecond molecular dynamics (MD) simulations coupled with Functional Mode Analysis improve the resolution of information, showing that such impairment is likely due to disruption of the PDEγ binding cavity in transducin. Protein Structure Network analyses additionally suggest that the observed slight reduction of theRGS9-catalyzed GTPase activity of transducin depends on perturbed communication between RGS9 and GTP binding site. These findings provide insights into the structural fundamentals of abnormal functioning of visual phototransduction caused by a missense mutation in one component of the signaling network. This combination of network-centered modeling with atomistic simulations represents a paradigm for future studies aimed at thoroughly deciphering the structural determinants of genetic retinal diseases. Analogous approaches are suitable to unveil the mechanism of information transfer in any signaling network either in physiological or pathological conditions.

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Network structure of the phototransduction model in a rod cell used in the present work.The different forms depict the molecular species involved in the cascade, whereas lines or arrows indicate reversible or irreversible reactions, respectively. Those reactions whose kinetic parameters were changed in this study are numbered and listed accordingly in Table 1. In this respect, red numbers indicate those reactions that were changed to properly model the NCNB pathological conditions. The molecules involved in these reactions, i.e. GαGTP, PDE, and RGS, are blue, green, and magenta, respectively. Filled red rectangles indicate the stoichiometric quantity of the specific molecule in the heteromeric complex, when higher than one. Yellow stars indicate the number of PDE-activated catalytic subunits. Hexagons indicate the molecular species that were used in atomistic simulations.
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pcbi-1003207-g001: Network structure of the phototransduction model in a rod cell used in the present work.The different forms depict the molecular species involved in the cascade, whereas lines or arrows indicate reversible or irreversible reactions, respectively. Those reactions whose kinetic parameters were changed in this study are numbered and listed accordingly in Table 1. In this respect, red numbers indicate those reactions that were changed to properly model the NCNB pathological conditions. The molecules involved in these reactions, i.e. GαGTP, PDE, and RGS, are blue, green, and magenta, respectively. Filled red rectangles indicate the stoichiometric quantity of the specific molecule in the heteromeric complex, when higher than one. Yellow stars indicate the number of PDE-activated catalytic subunits. Hexagons indicate the molecular species that were used in atomistic simulations.

Mentions: A number of incurable diseases in the visual system involve one or more components of the phototransduction signaling network (Figure 1). Visual phototransduction is the G protein-mediated process that generates a neuronal signal following light capture by visual pigments in photoreceptor cells (rods and cones). A unique feature of rod cells, the vertebrate photoreceptors dedicated to dim light vision, is the capability to transduce signals from even single photons due to an extremely efficient amplification not paralleled by other signal transduction pathways [1], [2]. The first event in scotopic vision is the absorption of a photon by rhodopsin (R), the cornerstone of family A of the seven-transmembrane G protein coupled receptors (GPCRs), which leads to the formation of the signaling active state (R*) [3], [4]. The latter, in turn, catalyzes the exchange of bound GDP for GTP on the αβγ heterotrimeric G protein transducin (Gt). The GTP-bound α subunit (GαGTP) dissociates from the βγ dimer thus stimulating the activation of phosphodiesterase 6 (PDE), a tetramer made of two nearly identical α and β catalytic subunits and two identical γ subunits [5]. The binding of GαGTP to the γ subunit of PDE (PDEγ) releases its inhibitory constraint on the catalytic subunits, thus leading to the hydrolysis of guanosine 3′,5′-cyclic monophosphate (cGMP), followed by a rapid closure of the cGMP-gated ionic channels in the outer membrane and a drop in the circulating current. The lowering in intracellular calcium concentration, associated with cell hyperpolarization ultimately signals the presence of light to the secondary neurons of retina. Signaling shutoff includes at least three calcium feedback mechanisms as well as the simultaneous deactivation of GαGTP and PDE. In this respect, the termination of PDE activation by GαGTP is achieved when the GTP-bound to Gα is hydrolyzed to GDP by the intrinsic GTPase activity of the protein. The latter process is significantly accelerated by a multiprotein complex containing the ninth member of the Regulators of G protein Signaling (RGS) family, hereafter indicated as RGS [6]. As a result of the GTPase Activating Protein (GAP) action of RGS, the GαGDP complex re-associates with the βγ dimer restoring the GαGDP-βγ heterotrimer (i.e. Gt).


Network and atomistic simulations unveil the structural determinants of mutations linked to retinal diseases.

Mariani S, Dell'Orco D, Felline A, Raimondi F, Fanelli F - PLoS Comput. Biol. (2013)

Network structure of the phototransduction model in a rod cell used in the present work.The different forms depict the molecular species involved in the cascade, whereas lines or arrows indicate reversible or irreversible reactions, respectively. Those reactions whose kinetic parameters were changed in this study are numbered and listed accordingly in Table 1. In this respect, red numbers indicate those reactions that were changed to properly model the NCNB pathological conditions. The molecules involved in these reactions, i.e. GαGTP, PDE, and RGS, are blue, green, and magenta, respectively. Filled red rectangles indicate the stoichiometric quantity of the specific molecule in the heteromeric complex, when higher than one. Yellow stars indicate the number of PDE-activated catalytic subunits. Hexagons indicate the molecular species that were used in atomistic simulations.
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Related In: Results  -  Collection

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pcbi-1003207-g001: Network structure of the phototransduction model in a rod cell used in the present work.The different forms depict the molecular species involved in the cascade, whereas lines or arrows indicate reversible or irreversible reactions, respectively. Those reactions whose kinetic parameters were changed in this study are numbered and listed accordingly in Table 1. In this respect, red numbers indicate those reactions that were changed to properly model the NCNB pathological conditions. The molecules involved in these reactions, i.e. GαGTP, PDE, and RGS, are blue, green, and magenta, respectively. Filled red rectangles indicate the stoichiometric quantity of the specific molecule in the heteromeric complex, when higher than one. Yellow stars indicate the number of PDE-activated catalytic subunits. Hexagons indicate the molecular species that were used in atomistic simulations.
Mentions: A number of incurable diseases in the visual system involve one or more components of the phototransduction signaling network (Figure 1). Visual phototransduction is the G protein-mediated process that generates a neuronal signal following light capture by visual pigments in photoreceptor cells (rods and cones). A unique feature of rod cells, the vertebrate photoreceptors dedicated to dim light vision, is the capability to transduce signals from even single photons due to an extremely efficient amplification not paralleled by other signal transduction pathways [1], [2]. The first event in scotopic vision is the absorption of a photon by rhodopsin (R), the cornerstone of family A of the seven-transmembrane G protein coupled receptors (GPCRs), which leads to the formation of the signaling active state (R*) [3], [4]. The latter, in turn, catalyzes the exchange of bound GDP for GTP on the αβγ heterotrimeric G protein transducin (Gt). The GTP-bound α subunit (GαGTP) dissociates from the βγ dimer thus stimulating the activation of phosphodiesterase 6 (PDE), a tetramer made of two nearly identical α and β catalytic subunits and two identical γ subunits [5]. The binding of GαGTP to the γ subunit of PDE (PDEγ) releases its inhibitory constraint on the catalytic subunits, thus leading to the hydrolysis of guanosine 3′,5′-cyclic monophosphate (cGMP), followed by a rapid closure of the cGMP-gated ionic channels in the outer membrane and a drop in the circulating current. The lowering in intracellular calcium concentration, associated with cell hyperpolarization ultimately signals the presence of light to the secondary neurons of retina. Signaling shutoff includes at least three calcium feedback mechanisms as well as the simultaneous deactivation of GαGTP and PDE. In this respect, the termination of PDE activation by GαGTP is achieved when the GTP-bound to Gα is hydrolyzed to GDP by the intrinsic GTPase activity of the protein. The latter process is significantly accelerated by a multiprotein complex containing the ninth member of the Regulators of G protein Signaling (RGS) family, hereafter indicated as RGS [6]. As a result of the GTPase Activating Protein (GAP) action of RGS, the GαGDP complex re-associates with the βγ dimer restoring the GαGDP-βγ heterotrimer (i.e. Gt).

Bottom Line: Mathematical modeling, in line with electrophysiological recordings, indicates reduction of phosphodiesterase 6 (PDE) recognition and activation as the main determinants of the pathological phenotype.Protein Structure Network analyses additionally suggest that the observed slight reduction of theRGS9-catalyzed GTPase activity of transducin depends on perturbed communication between RGS9 and GTP binding site.Analogous approaches are suitable to unveil the mechanism of information transfer in any signaling network either in physiological or pathological conditions.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.

ABSTRACT
A number of incurable retinal diseases causing vision impairments derive from alterations in visual phototransduction. Unraveling the structural determinants of even monogenic retinal diseases would require network-centered approaches combined with atomistic simulations. The transducin G38D mutant associated with the Nougaret Congenital Night Blindness (NCNB) was thoroughly investigated by both mathematical modeling of visual phototransduction and atomistic simulations on the major targets of the mutational effect. Mathematical modeling, in line with electrophysiological recordings, indicates reduction of phosphodiesterase 6 (PDE) recognition and activation as the main determinants of the pathological phenotype. Sub-microsecond molecular dynamics (MD) simulations coupled with Functional Mode Analysis improve the resolution of information, showing that such impairment is likely due to disruption of the PDEγ binding cavity in transducin. Protein Structure Network analyses additionally suggest that the observed slight reduction of theRGS9-catalyzed GTPase activity of transducin depends on perturbed communication between RGS9 and GTP binding site. These findings provide insights into the structural fundamentals of abnormal functioning of visual phototransduction caused by a missense mutation in one component of the signaling network. This combination of network-centered modeling with atomistic simulations represents a paradigm for future studies aimed at thoroughly deciphering the structural determinants of genetic retinal diseases. Analogous approaches are suitable to unveil the mechanism of information transfer in any signaling network either in physiological or pathological conditions.

Show MeSH
Related in: MedlinePlus