Examining weak protein-protein interactions in start codon recognition via NMR spectroscopy

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

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High-resolution solution NMR structure of rhNGF has been determined.

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Quinary interactions characterize ATP binding to rhNGF.

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SPR, ITC and STD-NMR reveal ATP binding to rhNGF with mM affinity.

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NMR and MD analysis pinpoint to the presence of two binding sites of ATP on rhNGF.

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Stoichiometry of ATP-Mg²⁺ or Zn²⁺-rhNGF mixtures affects K_D affinity to TrkA/p75^NTR.

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.

Detection of intermolecular transferred-NOE interactions in small and medium size protein complexes: RANTES complexed with a CCR5 N-terminal peptide

NMR is a powerful tool for studying structural details of protein/peptide complexes exhibiting weak to medium binding (K_D > 10 μm). However, it has been assumed that intermolecular nuclear Overhauser effect (NOE) interactions are difficult to observe in such complexes. We demonstrate that intermolecular NOEs can be revealed by combining the ¹³ C-edited/¹³ C-filtered experiment with the transferred NOE effect (TRNOE). Due to the TRNOE phenomenon, intermolecular NOE cross peaks are characterized by both the chemical shifts (CSs) of the protein protons and the average CSs of the peptide protons, which are dominated by the CSs of the protons of the free peptide. Previously, the TRNOE phenomenon was used almost exclusively to investigate the conformation of small ligands bound to large biomolecules. Here, we demonstrate that TRNOE can be extended to enable the study of intermolecular interactions in small- and medium-sized protein complexes. We used the ¹³ C-edited/¹³ C-filtered TRNOE experiment to study the interactions of the chemokine regulated upon activation, normal T cell, expressed and secreted (RANTES) with a 27-residue peptide, containing two sulfotyrosine residues, representing the N-terminal segment of the CCR5 receptor ((Nt-CCR5(1-27). The TRNOE phenomenon led to more than doubling of the signal-to-noise ratios (SNRs) for the intermolecular NOEs observed in the ¹³ C-edited/¹³ C-filtered experiment for the 11.5-kDa monomeric RANTES/Nt-CCR5(1-27) complex. An even better improvement in the SNR was achieved with dimeric Nt-CCR5(1-27)/RANTES (23 kDa), especially in comparison with the spectra measured with a 1 : 1 protein to peptide ratio. In principle, the isotope-edited/isotope-filtered TRNOE spectrum can discern all intermolecular interactions involving nonexchangeable protons in the complex.

Towards interpretation of intermolecular paramagnetic relaxation enhancement outside the fast exchange limit

In an exchanging system between major and minor species, the transverse paramagnetic relaxation enhancement rate observed on the resonances of the major species (Γ 2 (app) ) is dependent upon the exchange regime between the species. Quantitative analysis of PRE data in such systems typically assumes that the overall exchange rate k ex between the species is fast on the PRE time scale (k ex ≫ Γ2). Recently, we have characterized the kinetics of binding of the model protein ubiquitin to large (LUV) and small (SUV) unilamellar lipid-based nanoparticles or liposomes (Ceccon A, Tugarinov V, Bax A, Clore GM (2016). J Am Chem Soc 138:5789-5792). Building upon these results and taking advantage of a strong paramagnetic agent with an isotropic g-tensor, Gd(3+), we were able to measure intermolecular methyl carbon and proton PREs between paramagnetically-tagged liposomes and ubiquitin. In the limit of fast exchange (k ex ≫ Γ2) the ratio of the apparent proton to carbon methyl PREs, ((1)Hm-Γ 2 (app) )/((13)Cm-Γ 2 (app) ), is equal to the square of the ratio of the gyromagnetic ratios of the two nuclei, (γΗ/γC)(2). However, outside the fast exchange regime, under intermediate exchange conditions (e.g. when Γ2 is comparable in magnitude to k ex) the ((1)Hm-Γ 2 (app) )/((13)Cm-Γ 2 (app) ) ratio provides a reliable measure of the 'true' methyl PREs.

The molecular mechanism of nuclear transport revealed by atomic-scale measurements

Nuclear pore complexes (NPCs) form a selective filter that allows the rapid passage of transport factors (TFs) and their cargoes across the nuclear envelope, while blocking the passage of other macromolecules. Intrinsically disordered proteins (IDPs) containing phenylalanyl-glycyl (FG)-rich repeats line the pore and interact with TFs. However, the reason that transport can be both fast and specific remains undetermined, through lack of atomic-scale information on the behavior of FGs and their interaction with TFs. We used nuclear magnetic resonance spectroscopy to address these issues. We show that FG repeats are highly dynamic IDPs, stabilized by the cellular environment. Fast transport of TFs is supported because the rapid motion of FG motifs allows them to exchange on and off TFs extremely quickly through transient interactions. Because TFs uniquely carry multiple pockets for FG repeats, only they can form the many frequent interactions needed for specific passage between FG repeats to cross the NPC.

DOI:http://dx.doi.org/10.7554/eLife.10027.001

Eukaryotic cells have a nucleus that contains most of the organism's genetic material. Two layers of membrane form an envelope around the nucleus and protect its contents from the rest of the cell's interior. However, this protective barrier must also allow certain proteins and nucleic acids(collectively called ‘cargo’) to move in and out of the nucleus.

Cargo molecules can pass through channel-like structures called nuclear pore complexes, which are embedded in the nuclear envelope. However, transport across this barrier is highly selective. While small molecules can pass freely through nuclear pore complexes, larger cargo can only be transported when they are bound to so-called transport factors. The nuclear pore complex is a large structure made up of more than 30 different proteins called nucleoporins. Like all proteins, nucleoporins are built from amino acids. Many nucleoporins contain repeating units of two amino acids, namely phenylalanine (which is often referred to as ‘F’) and glycine (or ‘G’). These ‘FG nucleoporins’ are found on the inside of the nuclear pore complex and interact with transport factors to allow them to transit across the nuclear envelope.

Several models have been put forward to explain how FG nucleoporins block the passage of most molecules. But it was unclear from these models how these nucleoporins could do this while simultaneously allowing the selective and fast transport of nuclear transport receptors. There was also a major lack of experimental data that probed the behavior of FG nucleoporins in detail.

Hough, Dutta et al. have now used a technique called nuclear magnetic resonance spectroscopy (or NMR for short) to address this issue. NMR can be used to analyze the structure of proteins and how they interact with other molecules. This analysis revealed that FG nucleoporins never adopt an ordered three-dimensional shape, even briefly; instead they remain unfolded or disordered, moving constantly. Nevertheless, and unlike many other unfolded proteins, FG nucleoporins do not aggregate into clumps. This is because they are constantly changing and continuously interacting with other molecules present inside the cell, which prevents them from aggregating.

Hough, Dutta et al. also observed that the repeating units in the FG nucleoporins engaged briefly with a large number of sites or pockets present on the transport factors. These FG repeats can bind and then release the transport factors at unusually high speeds, which enables the transport factors to move quickly through the nuclear pore complex. This transit is specific because only transport factors have a high capacity for interacting with the FG repeats. These findings provide an explanation for how the nuclear pore complex achieves fast and selective transport. Further work is needed to see whether certain FG nucleoporins specifically interact with a particular type of transport factor, to provide preferred transport routes through the nuclear pore complex.

DOI:http://dx.doi.org/10.7554/eLife.10027.002