Endogenous modulators of neurotrophin signaling: Landscape of the transient ATP-NGF interactions

Francesca Paoletti; Franci Merzel; Alberto Cassetta; Iza Ogris; Sonia Covaceuszach; Jože Grdadolnik; Doriano Lamba; Simona Golič Grdadolnik

doi:10.1016/j.csbj.2021.05.009

Endogenous modulators of neurotrophin signaling: Landscape of the transient ATP-NGF interactions

Comput Struct Biotechnol J. 2021 May 7:19:2938-2949. doi: 10.1016/j.csbj.2021.05.009. eCollection 2021.

Authors

Francesca Paoletti¹, Franci Merzel¹, Alberto Cassetta², Iza Ogris¹, Sonia Covaceuszach², Jože Grdadolnik¹, Doriano Lamba^{2

3}, Simona Golič Grdadolnik¹

Affiliations

¹ Laboratory for Molecular Structural Dynamics, Theory Department, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.
² Institute of Crystallography - C.N.R.- Trieste Outstation. Area Science Park - Basovizza, S.S.14 - Km. 163.5, I-34149 Trieste, Italy.
³ Interuniversity Consortium "Biostructures and Biosystems National Institute", Viale delle Medaglie d'Oro 305, I-00136 Roma, Italy.

Abstract

The Nerve Growth Factor (NGF) neurotrophin acts in the maintenance and growth of neuronal populations. Despite the detailed knowledge of NGF's role in neuron physiology, the structural and mechanistic determinants of NGF bioactivity modulated by essential endogenous ligands are still lacking. We present the results of an integrated structural and advanced computational approach to characterize the extracellular ATP-NGF interaction. We mapped by NMR the interacting surface and ATP orientation on NGF and revealed the functional role of this interaction in the binding to TrkA and p75^NTR receptors by SPR. The role of divalent ions was explored in conjunction with ATP. Our results pinpoint ATP as a likely transient molecular modulator of NGF signaling, in health and disease states.

Keywords: ARIA, Ambiguous Restraints for Iterative Assignment; ATP modulation; BDNF, Brain Derived Neurotrophic Factor; CARA, Computer Aided Resonance Assignment; CS-E, Chrondroitin Sulfate E; CSP, Chemical Shift Perturbation; DSF, Differential Scanning Fluorimetry; EI-MS, Electron Ionization Mass Spectrometry; Endogenous ligands; FGF2, Fibroblast Growth Factor 2; FT-IR, Fourier Transform Infrared Spectroscopy; HBD, Heparin Binding Domain; HSQC, Heteronuclear Single Quantum Coherence; ITC, Isothermal Titration Calorimetry; MALDI-TOF MS, Matrix Assisted Laser Desorption Ionization-Time Of Flight Mass Spectrometry; MD, Molecular Dynamics; MS, Mass Spectrometry; NGF interactions; NGF, Nerve Growth Factor; NMR, Nuclear Magnetic Resonance; NOE, Nuclear Overhouser Effect; NOESY, Nuclear Overhauser Effect Spectroscopy; NT, NeuroTrophin; Neurotrophins; P20, Polysorbate 20; PME, Particle Mesh Ewald; RMSD, Root Mean Square Deviation; SAR, Structure-Activity Relationship; SPR, Surface Plasmon Resonance; STD, Saturation-Transfer Difference; TrkA, Tyrosine Kinase Receptor A; TrkA, p75NTR receptors; p75NTR, p75 NeuroTrophin Receptor; proNGF, proNGF – NGF precursor; rh-proNGF, recombinant human proNGF – NGF precursor; rhNGF, recombinant human NGF; rmNGF, recombinant mouse NGF.