Structural Elucidation of Bisulfite Adducts to Pseudouridine That Result in Deletion Signatures during Reverse Transcription of RNA.

The recent report of RBS-Seq to map simultaneously the epitranscriptomic modifications N1-methyladenosine, 5-methylcytosine, and pseudouridine (Ψ) via bisulfite treatment of RNA provides a key advance to locate these important modifications. The locations of Ψ were found by a deletion signature generated during cDNA synthesis after bisulfite treatment for which the chemical details of the reaction are poorly understood. In the present work, the bisulfite reaction with Ψ was explored to identify six isomers of bisulfite adducted to Ψ. We found four of these adducts involved the heterocyclic ring, similar to the reaction with other pyrimidines. The remaining two adducts were bonded to the 1' carbon, which resulted in opening of the ribose ring. The utilization of complementary 1D- and 2D-NMR, Raman, and electronic circular dichroism spectroscopies led to the assignment of the two ribose adducts being the constitutional isomers of an S- and an O-adduct of bisulfite to the ribose, and these are the final products after heating. A mechanistic proposal is provided to rationalize chemically the formation and stereochemistries of all six isomeric bisulfite adducts to Ψ; conversion of intermediate adducts to the two final products is proposed to involve E2, SN2', and [2,3]-sigmatropic shift reactions. Lastly, a synthetic RNA template with Ψ at a known location was treated with bisulfite, leading to a deletion signature after reverse transcription, supporting the RBS-Seq report. This classical bisulfite reaction used for epigenomic and epitranscriptomic sequencing diverges from the C nucleoside Ψ to form stable bisulfite end products that yield signatures for next-generation sequencing.

Measuring and Modeling Highly Accurate 15 N Chemical Shift Tensors in a Peptide.

NMR studies measuring chemical shift tensors are increasingly being employed to assign structure in difficult-to-crystallize solids. For small organic molecules, such studies usually focus on 13 C sites, but proteins and peptides are more commonly described using 15 N amide sites. An important and often neglected consideration when measuring shift tensors is the evaluation of their accuracy against benchmark standards, where available. Here we measure 15 N tensors in the dipeptide glycylglycine at natural abundance using the slow-spinning FIREMAT method with SPINAL-64 decoupling. The accuracy of these 15 N tensors is evaluated by comparing to benchmark single crystal NMR 15 N measurements and found to be statistically indistinguishable. These FIREMAT experimental results are further used to evaluate the accuracy of theoretical predictions of tensors from four different density functional theory (DFT) methods that include lattice effects. The best theoretical approach provides a root mean square (rms) difference of ±3.9 ppm and is obtained from a fragment-based method and the PBE0 density functional.

Intrinsic domain and loop dynamics commensurate with catalytic turnover in an induced-fit enzyme.

Arginine kinase catalyzes reversible phosphoryl transfer between ATP and arginine, buffering cellular ATP concentrations. Structures of substrate-free and -bound enzyme have highlighted a range of conformational changes thought to occur during the catalytic cycle. Here, NMR is used to characterize the intrinsic backbone dynamics over multiple timescales. Relaxation dispersion indicates rigid-body motion of the N-terminal domain and flexible dynamics in the I182-G209 loop, both at millisecond rates commensurate with k(cat), implying that either might be rate limiting upon catalysis. Lipari-Szabo analysis indicates backbone flexibility on the nanosecond timescale in the V308-V322 loop, while the rest of the enzyme is more rigid in this timescale. Thus, intrinsic dynamics are most prominent in regions that have been independently implicated in conformational changes. Substrate-free enzyme may sample an ensemble of different conformations, of which a subset is selected upon substrate binding, with critical active site residues appropriately configured for binding and catalysis.

Reverse micelle encapsulation as a model for intracellular crowding.

Reverse micelles are discrete nanoscale particles composed of a water core surrounded by surfactant. The amount of water within the core of reverse micelles can be easily manipulated to directly affect the size of the reverse micelle particle. The water loading capacity of reverse micelles varies with temperature, and water can be shed if reverse micelles are exposed to low temperatures. The use of water shedding from the reverse micelle provides precise and comprehensive control over the amount of water available to solvate host molecules. Proteins encapsulated within reverse micelles can be studied to determine the effects of confinement and excluded volume. The data presented here provide an important bridge between commonly employed dilute in vitro studies and studies of the effects of a crowded environment, as found in vivo. Ubiquitin was encapsulated within bis(2-ethylhexyl) sodium sulfosuccinate AOT reverse micelles under various degrees of confinement and was compared with an analogously reconstituted sample of ubiquitin in the commonly used molecular crowding agent bovine serum albumin. The effects of encapsulation were monitored using chemical shift perturbation analysis of the amide (1)H and (15)N resonances. The results also reconcile alternative interpretations of protein cold denaturation within reverse micelles.

Stabilization of RNA oligomers through reverse micelle encapsulation.

The cellular milieu is rich in diversity of both simple and complex molecules and is also quite crowded. By contrast, typical sample concentrations employed for in vitro investigation of biophysics and structural biology make use of purified macromolecules in simple buffer systems at concentrations that range from micromolar to millimolar. Although this formulation has proven to be compatible with a wide range of biological and structural studies, it is quite different from the relatively crowded conditions typically found within cells. The importance of these crowding effects for proteins has been recognized for some time, but the equivalent analysis is underexplored in nucleic acids. Encapsulation with surfactant-based reverse micelles has emerged as an effective biophysical tool, allowing study of the influence of ionic strength, pH, hydration, and crowding on biologically active macromolecules over a wide range of conditions. We have encapsulated an oligonucleotide model of TAR RNA from HIV and the 5' stem loop oligonucleotide of the U4 snRNA. Observation of imino (1)H resonances is an established method for evaluating the stability of nucleic acid oligonucleotides, implying the presence of stacked, hydrogen bonded base pairs. Inspection of (1)H NMR spectra of the RNA molecules reveals that the intensity of several of the imino resonances increases upon encapsulation. Additional resonances not observed in spectra of the oligonucleotides free in solution support the suggestion that the molecules have gained stability. These results indicate that RNA oligonucleotides may acquire significant stability in the presence of cellular levels of crowding.

Use of reverse micelles in membrane protein structural biology.

Membrane protein structural biology is a rapidly developing field with fundamental importance for elucidating key biological and biophysical processes including signal transduction, intercellular communication, and cellular transport. In addition to the intrinsic interest in this area of research, structural studies of membrane proteins have direct significance on the development of therapeutics that impact human health in diverse and important ways. In this article we demonstrate the potential of investigating the structure of membrane proteins using the reverse micelle forming surfactant dioctyl sulfosuccinate (AOT) in application to the prototypical model ion channel gramicidin A. Reverse micelles are surfactant based nanoparticles which have been employed to investigate fundamental physical properties of biomolecules. The results of this solution NMR based study indicate that the AOT reverse micelle system is capable of refolding and stabilizing relatively high concentrations of the native conformation of gramicidin A. Importantly, pulsed-field-gradient NMR diffusion and NOESY experiments reveal stable gramicidin A homodimer interactions that bridge reverse micelle particles. The spectroscopic benefit of reverse micelle-membrane protein solubilization is also explored, and significant enhancement over commonly used micelle based mimetic systems is demonstrated. These results establish the effectiveness of reverse micelle based studies of membrane proteins, and illustrate that membrane proteins solubilized by reverse micelles are compatible with high resolution solution NMR techniques.

Assignment of 1H, 13C, and 15N resonances of the RNA binding protein Snu13p from Saccharomyces cerevisiae.

Snu13p is a highly conserved RNA binding protein from Saccharomyces cerevisiae required for both eukaryotic pre-mRNA splicing and pre-rRNA processing. The 1H, 13C, and 15N assignments were determined from multidimensional, multinuclear NMR experiments conducted at 25 degrees C.

Functional implications for a prototypical K-turn binding protein from structural and dynamical studies of 15.5K.

The kink-turn (K-turn) motif is recognized and bound by a family of proteins that act as nucleation factors for ribonucleoparticle assembly. The binding of various proteins to a conserved RNA structural motif known as the K-turn has been shown to be an important component of regulation in the ribosome, in the spliceosome, and in RNA modification. 15.5K is a prototypical example of a K-turn binding protein, which has been shown to bind the 5'-U4 stem-loop of the spliceosome and the box C/D motif. We describe the solution NMR structure of free 15.5K, as well as studies of conformational flexibility from 15N NMR relaxation and H/D exchange experiments. The protein appears well-structured aside from conformational fluctuation in alpha3. Flexibility in fast time scale motions and the observation of limited intermediate and slow motions further characterize the free protein and may suggest local contributions to recognition and binding.

Temperature dependence of fast dynamics in proteins.

The temperature dependence of the internal dynamics of recombinant human ubiquitin has been measured using solution NMR relaxation techniques. Nitrogen-15 relaxation has been employed to obtain a measure of the amplitude of subnanosecond motion at amide N-H sites in the protein. Deuterium relaxation has been used to obtain a measure of the amplitude of motion of methyl-groups in amino-acid side chains. Data was obtained between 5 and 55 degrees C. The majority of amide N-H and methyl groups show a roughly linear (R(2)>0.75) temperature dependence of the associated Lipari-Szabo model-free squared generalized-order parameter (O(2)) describing the amplitude of motion. Interestingly, for those sites showing a linear response, the temperature dependence of the backbone is distinct from that of the methyl-bearing side chains with the former being characterized by a significantly larger Lambda-value, where Lambda is defined as d ln(1 - O)/d lnT. These results are comparable to the sole previous such study of the temperature dependence of protein motion obtained for a calmodulin-peptide complex. This suggests that the distinction between the main chain and methyl-bearing side chains may be general. Insight into the temperature dependence is gathered from a simple two-state step potential model.

Fast local backbone dynamics of encapsulated ubiquitin.

Backbone dynamics of ubiquitin confined within AOT reverse micelles have been evaluated based on analysis of 15N NMR relaxation data. Results indicate that upon encapsulation the protein experiences a slight overall increase in the value of the order parameter, S2, indicating a restriction in the average amplitude of fast local N-H bond vector motion. The largest increases in S2 upon encapsulation were concentrated in the region of beta-sheet 2 and, additionally, at the transitions of secondary structure motifs and loop regions. In addition, statistical analysis of the residue average ratio of the 15N longitudinal and transverse NMR relaxation time constants indicates that chemical exchange contributions to relaxation are consistent with previous aqueous studies. Earlier studies have demonstrated that native protein structure can be maintained in the encapsulated state. These results presented here establish that the dynamical behavior of encapsulated ubiquitin is likewise nativelike and adds important new observations regarding the enhancement of protein stability under confinement.

Dynamics of low temperature induced water shedding from AOT reverse micelles.

The effects of low temperature and ionic strength on water encapsulated within reverse micelles were investigated by solution NMR. Reverse micelles composed of AOT and pentane and solutions with varying concentrations of NaCl were studied at temperatures ranging from 20 degrees C to -30 degrees C. One-dimensional (1)H solution NMR spectroscopy was used to monitor the quantity and structure of encapsulated water. At low temperatures, e.g., -30 degrees C, reverse micelles lose water at rates that are dependent on the ionic strength of the aqueous nanopool. The final water loading (w0 = [water]/[surfactant]) of the reverse micelles is likewise dependent on the ionic strength of the aqueous phase. Remarkably, water resonance(s) at temperatures between -20 degrees C and -30 degrees C displayed fine structure indicating the presence of multiple transient water populations. Results of this study demonstrate that reverse micelles are an excellent vehicle for studies of confined water across a broad range of conditions, including the temperature range that provides access to the supercooled state.

Low-temperature studies of encapsulated proteins.

Water-soluble proteins encapsulated within reverse micelles may be studied under a variety of conditions, including low temperature and a wide range of buffer conditions. Direct high-resolution detection of information relating to protein folding intermediates and pathways can be monitored by low-temperature solution NMR. Ubiquitin encapsulated within AOT reverse micelles was studied using multidimensional multinuclear solution NMR to determine the relationship between protein structure, temperature, and ionic strength. Ubiquitin resonances were monitored by 15N HSQC NMR experiments at varying temperatures and salt concentrations. Our results indicate that the structure of the encapsulated protein at low temperature experiences perturbation arising from two major influences, which are reverse micelle-protein interactions and low-temperature effects (e.g., cold denaturation). These two effects are impossible to distinguish under conditions of low ionic strength. Elevated concentrations of nondenaturing salt solutions defeat the effects of reverse micelle-protein interactions and reveal low-temperature protein unfolding. High ionic strength shielding stabilizes the reverse micelle at low temperatures, which reduces the electrostatic interaction between the protein and reverse micelle surfaces, allowing the phenomenon of cold denaturation to be explored.

A PFG NMR experiment for translational diffusion measurements in low-viscosity solvents containing multiple resonances.

Pulsed gradient simulated-echo (PGSE) NMR diffusion measurements provide a facile and accurate means for determining the self-diffusion coefficients for molecules over a wide range of sizes and conditions. The measurement of diffusion in solvents of low intrinsic viscosity is particularly challenging, due to the persistent presence of convection. Although convection can occur in most solvent systems at elevated temperatures, in lower viscosity solvents (e.g., short chain alkanes), convection may manifest itself even at ambient laboratory temperatures. In most circumstances, solvent suppression will also be required, and for solvents that have multiple resonances, effective suppression can likewise represent a substantial challenge. In this article, we report an NMR experiment that combines a double-stimulated echo PFG approach with a WET-based solvent suppression scheme that effectively and simultaneously address the issues of dynamic range and the deleterious effects of convection. The experiment described will be of general benefit to studies aimed at the characterization of diffusion of single molecules directly dissolved in low-viscosity solvents, and should also be of substantial utility in studies of supramolecular assemblies such as reverse-micelles dissolved in apolar solvents.

Preparation, characterization, and NMR spectroscopy of encapsulated proteins dissolved in low viscosity fluids.

Encapsulating a protein in a reverse micelle and dissolving it in a low-viscosity solvent can lower the rotational correlation time of a protein and thereby provides a novel strategy for studying proteins in a variety of contexts. The preparation of the sample is a key element in this approach and is guided by a number of competing parameters. Here we examine the applicability of several strategies for the preparation and characterization of encapsulated proteins dissolved in low viscosity fluids that are suitable for high performance NMR spectroscopy. Ubiquitin is used as a model system to explore various issues such as the homogeneity of the encapsulation, characterization of the hydrodynamic performance of reverse micelles containing protein molecules, and the effective pH of the water environment of the reverse micelle.

Influence of induced fit in the interaction of Bacillus subtilis trp RNA-binding attenuator protein and its RNA antiterminator target oligomer.

In the presence of excess tryptophan, tryptophan-activated TRAP (trp RNA-binding attenuator protein) binds to a specific target in the trp-leader transcript, which induces the formation of a transcription terminator and transcription halts in the leader region. In the absence of tryptophan, TRAP does not bind RNA, an antiterminator forms, and the operon is expressed. Although the ternary complex involving TRAP (Bacillus stearothermophilus), tryptophan, and the RNA target has recently been crystallized, efforts to obtain structural data for the apo-form of TRAP (in any species) have not been successful. We have used multidimensional/multinuclear nuclear magnetic resonance (NMR) spectroscopy to probe the structure-function relationship in the TRAP-activated system, and have obtained high-resolution multidimensional/multinuclear NMR spectra of TRAP in all three of its functional states: tryptophan-free or apo-TRAP, tryptophan-activated TRAP, and tryptophan-activated TRAP-RNA ternary complex. Chemical shift perturbation analysis of the NMR data clarifies the interpretation of results obtained from previous crystal studies. Results presented herein demonstrate that tryptophan binding induces an essential structural change in TRAP that supports high-affinity binding of the RNA target oligonucleotide.

A simple and effective NMR cell for studies of encapsulated proteins dissolved in low viscosity solvents.

Application of triple-resonance and isotope-edited-NOE methods to the study of increasingly larger macromolecules and their complexes remains a central goal of solution NMR spectroscopy. The slow reorientational motion of larger molecules leads to rapid transverse relaxation and results in losses in both resolution and sensitivity of multidimensional-multinuclear solution NMR experiments. A recently described technique employs a physical approach to increase the tumbling rate of macromolecules in an attempt to preserve access to the full range of structural restraints available to studies of smaller systems. This technique involves encapsulation of a hydrated protein in a surfactant shell which is subsequently solubilized in a low viscosity solvent. A simple, efficient and cost effective NMR cell that accommodates the moderate liquefaction pressures required in the encapsulation method is described. Application of the method to the 56 kD triose phosphate isomerase homodimer is demonstrated.

Dissection of the pathway of molecular recognition by calmodulin.

Amide hydrogen exchange has been used to examine the structural dynamics and energetics of the interaction of a peptide corresponding to the calmodulin-binding domain of smooth muscle myosin light chain kinase (smMLCKp) with calcium-saturated calmodulin. Heteronuclear NMR (15)N-(1)H correlation spectroscopy was used to quantify amide proton exchange rates of the uniformly (15)N-labeled domain bound to calmodulin. A key feature of a proposed model for molecular recognition by calmodulin [Ehrhardt et al. (1995) Biochemistry 34, 2731-2738] is tested by examination of the dependence of amide hydrogen exchange on applied hydrostatic pressure. Hydrogen exchange rates and corresponding protection factors (1/K(op)) for individual amide protons of the bound smMLCKp domain span 5 orders of magnitude at ambient pressure. Individual protection factors decrease significantly in a linear fashion with increasing hydrostatic pressure. A common pressure dependence is revealed by a constant large negative volume change across the residues comprising the core of the bound helical domain. The pattern of protection factors and their response to hydrostatic pressure is consistent with a structural reorganization that results in the concerted disruption of ion pairs between calmodulin and the bound domain. These observations reinforce a model for the molecular recognition pathway where formation of the initial encounter complex is followed by helix-coil transitions in the bound state and subsequent concerted formation of the extensive ion pair network defining the intermolecular contact surface between CaM and the target domain in the final, compact complex structure.