Characterization of the Native Disulfide Isomers of the Novel χ-Conotoxin PnID: Implications for Further Increasing Conotoxin Diversity.

χ-Conotoxins are known for their ability to selectively inhibit norepinephrine transporters, an ability that makes them potential leads for treating various neurological disorders, including neuropathic pain. PnID, a peptide isolated from the venom of Conus pennaceus, shares high sequence homology with previously characterized χ-conotoxins. Whereas previously reported χ-conotoxins seem to only have a single native disulfide bonding pattern, PnID has three native isomers due to the formation of different disulfide bond patterns during its maturation in the venom duct. In this study, the disulfide connectivity and three-dimensional structure of these disulfide isomers were explored using regioselective synthesis, chromatographic coelution, and solution-state nuclear magnetic resonance spectroscopy. Of the native isomers, only the isomer with a ribbon disulfide configuration showed pharmacological activity similar to other χ-conotoxins. This isomer inhibited the rat norepinephrine transporter (IC50 = 10 ± 2 µM) and has the most structural similarity to previously characterized χ-conotoxins. In contrast, the globular isoform of PnID showed more than ten times less activity against this transporter and the beaded isoform did not display any measurable biological activity. This study is the first report of the pharmacological and structural characterization of an χ-conotoxin from a species other than Conus marmoreus and is the first report of the existence of natively-formed conotoxin isomers.

Multivalency, autoinhibition, and protein disorder in the regulation of interactions of dynein intermediate chain with dynactin and the nuclear distribution protein.

As the only major retrograde transporter along microtubules, cytoplasmic dynein plays crucial roles in the intracellular transport of organelles and other cargoes. Central to the function of this motor protein complex is dynein intermediate chain (IC), which binds the three dimeric dynein light chains at multivalent sites, and dynactin p150Glued and nuclear distribution protein (NudE) at overlapping sites of its intrinsically disordered N-terminal domain. The disorder in IC has hindered cryo-electron microscopy and X-ray crystallography studies of its structure and interactions. Here we use a suite of biophysical methods to reveal how multivalent binding of the three light chains regulates IC interactions with p150Glued and NudE. Using IC from Chaetomium thermophilum, a tractable species to interrogate IC interactions, we identify a significant reduction in binding affinity of IC to p150Glued and a loss of binding to NudE for constructs containing the entire N-terminal domain as well as for full-length constructs when compared to the tight binding observed with short IC constructs. We attribute this difference to autoinhibition caused by long-range intramolecular interactions between the N-terminal single α-helix of IC, the common site for p150Glued, and NudE binding, and residues closer to the end of the N-terminal domain. Reconstitution of IC subcomplexes demonstrates that autoinhibition is differentially regulated by light chains binding, underscoring their importance both in assembly and organization of IC, and in selection between multiple binding partners at the same site.

Motor proteins are the freight trains of the cell, transporting large molecular cargo from one location to another using an array of 'roads' known as microtubules. These hollow tubes are oriented, with one extremity (the plus-end) growing faster than the other (the minus-end). While over 40 different motor proteins travel towards the plus-end of microtubules, just one is responsible for moving cargo in the opposite direction. This protein, called dynein, performs a wide range of functions which must be carefully regulated, often through changes in the shape and interactions of various dynein segments. The intermediate chain is one of the essential subunits that form dynein, and it acts as a binding site for a range of molecular actors. In particular, it connects the three other dynein subunits (known as the light chains) to the dynein heavy chain containing the motor domain. It also binds to two non-dynein proteins: NudE, which helps to organise microtubules, and the p150^Glued region of dynactin, a protein required for dynein activity. Despite their distinct roles, p150^Glued and NudE attach to the same region of the intermediate chain, a highly flexible 'unstructured' segment which is difficult to study. How the binding of p150^Glued and NudE is regulated has therefore remained unsolved. In response, Jara et al. decided to investigate how the three dynein light chains may help to control interactions between the intermediate chain and non-dynein proteins. They used more stable versions of dynein, NudE and dynactin (from a fungus that grows at high temperatures) to produce the various subcomplexes formed by the intermediate chain, the three dynein light chains, and parts of p150^Glued and NudE. A suite of biophysical techniques was applied to study these structures, as they are challenging to capture using traditional approaches. This revealed that the unstructured region of the intermediate chain can fold back on itself, bringing together its two extremities; such folding blocks the p150^Glued and NudE binding site. This obstruction is cleared when the light chains bind to the intermediate chain, demonstrating how these three subunits can regulate dynein activity. In humans, mutations in dynein are associated with a range of serious neurological and muscular diseases. The work by Jara et al. brings new insight into the way this protein works; more importantly, it describes how to combine several biophysical techniques to study non-structured proteins, offering a blueprint that is likely to be relevant for a wide range of scientists.

Structural characterization of the self-association domain of swallow.

Swallow, a 62 kDa multidomain protein, is required for the proper localization of several mRNAs involved in the development of Drosophila oocytes. The dimerization of Swallow depends on a 71-residue self-association domain in the center of the protein sequence, and is significantly stabilized by a binding interaction with dynein light chain (LC8). Here, we detail the use of solution-state nuclear magnetic resonance spectroscopy to characterize the structure of this self-association domain, thereby establishing that this domain forms a parallel coiled-coil and providing insight into how the stability of the dimerization interaction is regulated.

Interplay of Disorder and Sequence Specificity in the Formation of Stable Dynein-Dynactin Complexes.

Cytoplasmic dynein is a eukaryotic motor protein complex that, along with its regulatory protein dynactin, is essential to the transport of organelles within cells. The interaction of dynein with dynactin is regulated by binding between the intermediate chain (IC) subunit of dynein and the p150Glued subunit of dynactin. Even though in the rat versions of these proteins this interaction primarily involves the single α-helix region at the N-terminus of the IC, in Drosophila and yeast ICs the removal of a nascent helix (H2) downstream of the single α-helix considerably diminishes IC-p150Glued complex stability. We find that for ICs from various species, there is a correlation between disorder in H2 and its contribution to binding affinity, and that sequence variations in H2 that do not change the level of disorder show similar binding behavior. Analysis of the structure and interactions of the IC from Chaetomium thermophilum demonstrates that the H2 region of C. thermophilum IC has a low helical propensity and establishes that H2 binds directly to the coiled-coil 1B (CC1B) domain of p150Glued, thus explaining why H2 is necessary for tight binding. Isothermal titration calorimetry, circular dichroism, and NMR studies of smaller CC1B constructs localize the region of CC1B most essential for a tight interaction with IC. These results suggest that it is the level of disorder in H2 of IC along with its charge, rather than sequence specificity, that underlie its importance in initiating tight IC-p150Glued complex formation. We speculate that the nascent H2 helix may provide conformational flexibility to initiate binding, whereas those species that have a fully folded H2 have co-opted an alternative mechanism for promoting p150Glued binding.

Characterization of Three Venom Peptides from the Spitting Spider Scytodes thoracica.

We present the solution-state NMR structures and preliminary functional characterizations of three venom peptides identified from the spitting spider Scytodes thoracica. Despite little sequence identity to other venom peptides, structural characterization reveals that these peptides contain an inhibitor cystine knot motif common to many venom peptides. These are the first structures for any peptide or protein from spiders of the Scytodidae family. Many venom peptides target neuronal ion channels or receptors. However, we have not been able to determine the target of these Scytodes peptides so we can only state with certainty the channels and receptors that they do not target.

Solution structures of two homologous venom peptides from Sicarius dolichocephalus.

We present solution-state NMR structures for two putative venom peptides from Sicarius dolichocephalus. These peptides were identified from cDNA libraries created from venom gland mRNA and then recombinantly expressed. They are the first structures from any species of Sicarius spiders, and the first peptide structures for any haplogyne spiders. These peptides are homologous to one another, and while they have at most only 20% sequence identity with known venom peptides their structures follow the inhibitor cystine knot motif that has been found in a broad range of venom peptides.

Broadband excitation pulses for high-field solid-state nuclear magnetic resonance spectroscopy.

In nuclear magnetic resonance spectroscopy, experimental limits due to the radiofrequency transmitter and/or coil means that conventional radiofrequency pulses ("hard pulses") are sometimes not sufficiently powerful to excite magnetization uniformly over a desired range of frequencies. Effects due to nonuniform excitation are most frequently encountered at high magnetic fields for nuclei with a large range of chemical shifts. Using optimal control theory, we have designed broadband excitation pulses that are suitable for solid-state samples under magic-angle-spinning conditions. These pulses are easy to implement, robust to spinning frequency variations, and radiofrequency inhomogeneities, and only four times as long as a corresponding hard pulse. The utility of these pulses for uniformly exciting (13) C nuclei is demonstrated on a 900 MHz (21.1 T) spectrometer.

The effect of biradical concentration on the performance of DNP-MAS-NMR.

With the technique of dynamic nuclear polarization (DNP) signal intensity in solid-state MAS-NMR experiments can be enhanced by 2-3 orders of magnitude. DNP relies on the transfer of electron spin polarization from unpaired electrons to nuclear spins. For this reason, stable organic biradicals such as TOTAPOL are commonly added to samples used in DNP experiments. We investigated the effects of biradical concentration on the relaxation, enhancement, and intensity of NMR signals, employing a series of samples with various TOTAPOL concentrations and uniformly (13)C, (15)N labeled proline. A considerable decrease of the NMR relaxation times (T(1), T(2)(∗), and T(1)(ρ)) is observed with increasing amounts of biradical due to paramagnetic relaxation enhancement (PRE). For nuclei in close proximity to the radical, decreasing T(1)(ρ) reduces cross-polarization efficiency and decreases in T(2)(∗) broaden the signal. Additionally, paramagnetic shifts of (1)H signals can cause further line broadening by impairing decoupling. On average, the combination of these paramagnetic effects (PE; relaxation enhancement, paramagnetic shifts) quenches NMR-signals from nuclei closer than 10Å to the biradical centers. On the other hand, shorter T(1) times allow the repetition rate of the experiment to be increased, which can partially compensate for intensity loss. Therefore, it is desirable to optimize the radical concentration to prevent additional line broadening and to maximize the signal-to-noise observed per unit time for the signals of interest.

A comparison of NCO and NCA transfer methods for biological solid-state NMR spectroscopy.

Three different techniques (adiabatic passage Hartman-Hahn cross-polarization, optimal control designed pulses, and EXPORT) are compared for transferring (15)N magnetization to (13)C in solid-state NMR experiments under magic-angle-spinning conditions. We demonstrate that, in comparison to adiabatic passage Hartman-Hahn cross-polarization, optimal control transfer pulses achieve similar or better transfer efficiencies for uniformly-(13)C,(15)N labeled samples and are generally superior for samples with non-uniform labeling schemes (such as 1,3- and 2-(13)C glycerol labeling). In addition, the optimal control pulses typically use substantially lower average RF field strengths and are more robust with respect to experimental variation and RF inhomogeneity. Consequently, they are better suited for demanding samples.

Solution structure of the U2 snRNP protein Rds3p reveals a knotted zinc-finger motif.

Rds3p, a component of the U2 snRNP subcomplex SF3b, is essential for pre-mRNA splicing and is extremely well conserved in all eukaryotic species. We report here the solution structure of Rds3p, which reveals an unusual knotted fold unrelated to previously known knotted proteins. Rds3p has a triangular shape with a GATA-like zinc finger at each vertex. Pairs of cysteines contributing to each finger are arranged nonsequentially in a permuted arrangement reminiscent of domain-swapping but which here involves segments of subdomains within a single chain. We suggest that the structure arose through a process of segment swapping after gene duplication. The fingers are connected through beta-strands and loops, forming an overall topology strongly resembling a "triquetra knot." The conservation and surface properties of Rds3p suggest that it functions as a platform for protein assembly within the multiprotein SF3b complex of U2 snRNP. The recombinant protein used for structure determination is biologically active, as it restores splicing activity in a yeast splicing extract depleted of native Rds3p.

QQ-HSQC: a quick, quantitative heteronuclear correlation experiment for NMR spectroscopy.

Quantitative heteronuclear single quantum coherence (Q-HSQC) is a variant of the HSQC experiment that provides quantitative peak areas. This is accomplished by combining signals acquired using four different INEPT delays. Consequently, the experiment requires four times as many scans as the HSQC experiment to achieve the same resolution in the indirect dimension. We have removed this drawback by modifying the Q-HSQC experiment so that signals corresponding to different INEPT delays are acquired simultaneously from different parts of the sample. This new experiment, which we call Quick, Quantitative HSQC (QQ-HSQC), has the quantitative properties of the Q-HSQC experiment but only requires as many scans as a conventional HSQC experiment.

Qualitative and quantitative measurements of hydrogen bond mediated scalar couplings in acyclic 1,3-diols.

[Structure: see text] OH...OH hydrogen bond mediated scalar couplings have been observed in acyclic syn- and anti-1,3-diols using a 2D 1H COSYLR NMR experiment and quantified with an uncertainty of +/-0.02 Hz with a selective-excitation spin-echo NMR experiment. A theoretical investigation confirmed the importance of the hydrogen bond in mediating the spin-spin coupling in these systems.

Quantification of phosphocholine and glycerophosphocholine with 31P edited 1H NMR spectroscopy.

Choline and the related compounds phosphocholine (PC) and glycerophosphocholine (GPC) are considered to be important metabolites in oncology. Past studies have demonstrated correlations linking the relative ratios and concentrations of these metabolites with the development and progression of cancer. Currently, in vivo and tissue ex vivo magnetic resonance spectroscopy methods have mostly centered on measuring the total concentration of these metabolites and have difficulty in differentiating between them. Here, a new scheme that uses (31)P edited (1)H spectroscopy to quantify the concentrations of choline, PC and GPC in biological samples is reported and its applicability is demonstrated using samples of human brain tumor extracts. This method is particularly well-suited for analytical situations where the PC and GPC resonances are not sufficiently resolved and/or are obscured by other metabolites. Consequently, this scheme has the potential to be used for the analysis of choline compounds in ex vivo tissue samples.

Solid-phase synthesis and 1H and 13C high-resolution magic angle spinning NMR of 13C-labeled resin-bound saccharides.

We show how high-resolution magic angle-spinning NMR spectroscopy can be used to characterize 13C-labeled saccharides that have been prepared using solid-phase synthesis techniques while they are still bound to a solid-support resin. With the use of 13C-labeled glucose as the starting material, we have successfully synthesized mono-, di- and trisaccharides with uniform 13C labeling of the saccharide rings. Using these materials, we have been able to assign the 13C and 1H spectra and to characterize various impurities on the resin beads.

Single-scan longitudinal relaxation measurements in high-resolution NMR spectroscopy.

Several single-scan experiments for the measurement of the longitudinal relaxation time (T1) are proposed. These experiments result in fast and accurate determinations of the relaxation rate, are relatively robust to pulse imperfections, and preserve information about the chemical shift. The method used in these experiments is to first encode the T1 values as a spatial variation of the magnetization and then to read out this variation either by applying a weak gradient during acquisition or by sequentially observing different slices of the sample. As a result, it is possible to reduce the time necessary to determine the T1 values by one or two orders of magnitude. This time saving comes at the expense of the signal-to-noise level of the resulting spectrum and some chemical shift resolution.

Processing DOSY spectra using the regularized resolvent transform.

A new method for processing diffusion ordered spectroscopy (DOSY) data is presented. This method, the regularized resolvent transform (iRRT-the i denoting the adaptation of the method to evaluate the inverse Laplace transform), is better than conventional processing techniques for generating 2D DOSY spectra using data that has poor chemical shift resolution. From the same data, it is possible to use the iRRT to generate 1D subspectra corresponding to different components of the sample mixture; these subspectra compare favorably to 1D spectra of the pure substances. Both the 2D spectra and the 1D subspectra offer a vast improvement over results generated using a conventional processing technique (non-linear least-squares fitting). Consequently, we present the iRRT as a stable and reliable tool for solving the inverse Laplace transform problem present in experiments such as DOSY.

Temperature accuracy and temperature gradients in solution-state NMR spectrometers.

In solution-state NMR spectrometers, there is a systematic deviation between the temperature of the sample and the temperature reported by the spectrometer. In addition, temperature gradients are often present in the sample. The size of both the temperature deviations and the temperature gradients depends on several factors, including the temperature, the flow rate of the heating/cooling gas, and the amount of radiofrequency heating.

Solution-state dynamic nuclear polarization at high magnetic field.

The goal of dynamic nuclear polarization (DNP) is to enhance NMR signals by transferring electron spin polarization to the nuclei. Although mechanisms such as the solid effect and thermal mixing can be used for DNP in the solid state, currently, the only practical mechanism in solutions is the Overhauser effect (OE), which usually arises due to dipolar relaxation between electrons and the nuclei. At magnetic fields greater than approximately 1 T, dipolar relaxation does not result in a useful enhancement and therefore the conventional wisdom is that DNP should not work in solutions at high magnetic fields. However, scalar relaxation due to time-dependent scalar couplings has a different magnetic field dependence and can lead to substantial OE enhancements. At room temperature and at a magnetic field of 5 T (211 MHz for protons, 140 GHz for electrons), we have observed that scalar relaxation between electrons and nuclei results in NMR signal enhancements of 180, 42, -36, and 8, for 31P, 13C, 15N, and 19F, respectively.