Triple-resonance Nuclear Magnetic Resonance Research Articles

Robust automated backbone triple resonance NMR assignments of proteins using Bayesian-based simulated annealing

Assignment of resonances of nuclear magnetic resonance (NMR) spectra to specific atoms within a protein remains a labor-intensive and challenging task. Automation of the assignment process often remains a bottleneck in the exploitation of solution NMR spectroscopy for the study of protein structure-dynamics-function relationships. We present an approach to the assignment of backbone triple resonance spectra of proteins. A Bayesian statistical analysis of predicted and observed chemical shifts is used in conjunction with inter-spin connectivities provided by triple resonance spectroscopy to calculate a pseudo-energy potential that drives a simulated annealing search for the most optimal set of resonance assignments. Termed Bayesian Assisted Assignments by Simulated Annealing (BARASA), a C++ program implementation is tested against systems ranging in size to over 450 amino acids including examples of intrinsically disordered proteins. BARASA is fast, robust, accommodates incomplete and incorrect information, and outperforms current algorithms – especially in cases of sparse data and is sufficiently fast to allow for real-time evaluation during data acquisition.

Expression of 2H, 13C, 15N-labeled NIST-Fab fragment in the methylotrophic yeast Komagataella phaffii for nuclear magnetic resonance studies

Labeling of proteins with deuterium is an essential tool in overcoming size limitations in the application of nuclear magnetic resonance (NMR) spectroscopy to proteins larger than 30 kilodaltons (kDa). A non-originator antigen-binding fragment (Fab) of NIST RM 8671 NISTmAb, so called yNIST-Fab, is a ~ 50 kDa protein, with 5 native disulfide linkages, that can be expressed in properly folded form in methylotrophic Komagataella phaffii (formerly Pichia pastoris). Further, the K. phaffii host can support the production of perdeuterated yNIST-Fab which is necessary to obtain well-resolved TROSY-based tripleresonance NMR spectra for chemical shift assignment of the peptide backbone resonances. Here, we examined growth conditions and effects of media composition to maximize biomass generation and expression yield of the 2H, 13C, 15N-enriched NIST-Fab fragment. Triple-labeled yNIST-Fab with ~93% deuteration reduced the 1HN, 15N and 13C-linewidths in the NMR spectra, allowing sequential NMR assignment of backbone resonance a key step toward sequence-specific structural and dynamic studies of Fab fragments and intact antibodies.

Mechanism of Competitive Inhibition and Destabilization of Acidothermus cellulolyticus Endoglucanase 1 by Ionic Liquids.

The ability of ionic liquids (ILs) to solubilize cellulose has sparked interest in their use for enzymatic biomass processing. However, this potential is yet to be realized, primarily because ILs inactivate requisite cellulases by mechanisms that are yet to be identified. We used a combination of enzymology, circular dichroism (CD), nuclear magnetic resonance (NMR), and molecular dynamics (MD) methods to investigate the molecular basis for the inactivation of the endocellulase 1 (E1) from Acidothermus cellulolyticus by the imidazolium IL 1-butyl-3-methylimidazolium chloride ([BMIM][Cl]). Enzymatic studies revealed that [BMIM][Cl] inactivates E1 in a biphasic manner that involves rapid, reversible inhibition, followed by slow, irreversible deactivation. Backbone NMR signals of the 40.5 kDa E1 were assigned by triple resonance NMR methods, enabling monitoring of residue-specific perturbations. 1H-15N NMR titration experiments revealed that [BMIM][Cl] binds reversibly to the E1 active site, indicating that reversible deactivation is due to competitive inhibition of substrate binding. Prolonged incubation with [BMIM][Cl] led to substantial global changes in the 1H-15N heteronuclear single quantum coherence NMR and CD spectra of E1 indicative of protein denaturation. Notably, weak interactions between [BMIM][Cl] and residues at the termini of several helices were also observed, which, together with MD simulations, suggest that E1 denaturation is promoted by [BMIM][Cl]-induced destabilization of helix capping structures. In addition to identifying determinants of E1 inactivation, our findings establish a molecular framework for engineering cellulases with improved IL compatibility.

From Nanodiscs to Isotropic Bicelles: A Procedure for Solution Nuclear Magnetic Resonance Studies of Detergent-Sensitive Integral Membrane Proteins

Nanodiscs and isotropic bicelles are promising membrane mimetics in the field of solution nuclear magnetic resonance (NMR) spectroscopy of integral membrane proteins (IMPs). Despite varied challenges to solution NMR studies of IMPs, we attribute the paucity of solution NMR structures in these environments to the inability of diverse IMPs to withstand detergent treatment during standard nanodisc and bicelle preparations. Here, we present a strategy that creates small isotropic bicelles from IMPs co-translationally embedded in large nanodiscs using cell-free expression. Our results demonstrate appreciable gains in NMR spectral quality while preserving lipid-IMP contacts. We validate the approach on the detergent-sensitive LspA, which finally allowed us to perform high-quality triple-resonance NMR experiments for structural studies. Our strategy of producing bicelles from nanodiscs comprehensively avoids detergent during expression and preparation and is suitable for solution NMR spectroscopy of lipid-IMP complexes.

(13)C/(15)N-Enriched l-Dopa as a Triple-Resonance NMR Probe to Monitor Neurotransmitter Dopamine in the Brain and Liver Extracts of Mice.

In an attempt to monitor μm‐level trace constituents, we applied here 1H‐{13C‐15N} triple‐resonance nuclear magnetic resonance (NMR) to 13C/15N‐enriched l‐Dopa as the inevitable precursor of the neurotransmitter dopamine in the brain. The perfect selectivity (to render endogenous components silent) and μm‐level sensitivity (700 MHz spectrometer equipped with a cryogenic probe) of triple‐resonance allowed the unambiguous and quantitative metabolic and pharmacokinetic analyses of administered l‐Dopa/dopamine in the brain and liver of mice. The level of dopamine generated in the brain (within the range 7–76 μm, which covers the typical stimulated level of ∼30 μm) could be clearly monitored ex vivo, but was slightly short of the detection limit of a 7 T MR machine for small animals. This work suggests that μm‐level trace constituents are potential targets of ex vivo monitoring as long as they contain N atom(s) and their appropriate 13C/15N‐enrichment is synthetically accessible.

Rapid Proton-Detected NMR Assignment for Proteins with Fast Magic Angle Spinning

Using a set of six 1H-detected triple-resonance NMR experiments, we establish a method for sequence-specific backbone resonance assignment of magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectra of 5–30 kDa proteins. The approach relies on perdeuteration, amide 2H/1H exchange, high magnetic fields, and high-spinning frequencies (ωr/2π ≥ 60 kHz) and yields high-quality NMR data, enabling the use of automated analysis. The method is validated with five examples of proteins in different condensed states, including two microcrystalline proteins, a sedimented virus capsid, and two membrane-embedded systems. In comparison to contemporary 13C/15N-based methods, this approach facilitates and accelerates the MAS NMR assignment process, shortening the spectral acquisition times and enabling the use of unsupervised state-of-the-art computational data analysis protocols originally developed for solution NMR.

Expression, Purification, Characterization, and Solution Nuclear Magnetic Resonance Study of Highly Deuterated Yeast Cytochrome c Peroxidase with Enhanced Solubility

Here we present the preparation, biophysical characterization, and nuclear magnetic resonance (NMR) spectroscopy study of yeast cytochrome c peroxidase (CcP) constructs with enhanced solubility. Using a high-yield Escherichia coli expression system, we routinely produced uniformly labeled [(2)H,(13)C,(15)N]CcP samples with high levels of deuterium incorporation (96-99%) and good yields (30-60 mg of pure protein from 1 L of bacterial culture). In addition to simplifying the purification procedure, introduction of a His tag at either protein terminus dramatically increases its solubility, allowing preparation of concentrated, stable CcP samples required for multidimensional NMR spectroscopy. Using a range of biophysical techniques and X-ray crystallography, we demonstrate that the engineered His tags neither perturb the structure of the enzyme nor alter the heme environment or its reactivity toward known ligands. The His-tagged CcP constructs remain catalytically active yet exhibit differences in the interaction with cytochrome c, the physiological binding partner, most likely because of steric occlusion of the high-affinity binding site by the C-terminal His tag. We show that protein perdeuteration greatly increases the quality of the double- and triple-resonance NMR spectra, allowing nearly complete backbone resonance assignments and subsequent study of the CcP by heteronuclear NMR spectroscopy.

A set of triple-resonance nuclear magnetic resonance experiments for structural characterization of organophosphorus compounds in mixture samples

The 1H, 13C correlation NMR spectroscopy utilizes JCH couplings in molecules, and provides important structural information from small organic molecules in the form of carbon chemical shifts and carbon-proton connectivities. The full potential of the 1H, 13C correlation NMR spectroscopy has not been realized in the Chemical Weapons Convention (CWC) related verification analyses due to the sample matrix, which usually contains a high amount of non-related compounds obscuring the correlations of the relevant compounds. Here, the results of the application of 1H, 13C, 31P triple-resonance NMR spectroscopy in characterization of OP compounds related to the CWC are presented. With a set of two-dimensional triple-resonance experiments the JHP, JCH and JPC couplings are utilized to map the connectivities of the atoms in OP compounds and to extract the carbon chemical shift information. With the use of the proposed pulse sequences the correlations from the OP compounds can be recorded without significant artifacts from the non-OP compound impurities in the sample. Further selectivity of the observed correlations is achieved with the application of phosphorus band-selective pulse in the pulse sequences to assist the analysis of multiple OP compounds in mixture samples. The use of the triple-resonance experiments in the analysis of a complex sample is shown with a test mixture containing typical scheduled OP compounds, including the characteristic degradation products of nerve agents sarin, soman, and VX. The viability of the approach in verification analysis is demonstrated in the analysis of the 30th OPCW Proficiency Test sample.

Molecular Mechanism of Action of β-Hairpin Antimicrobial Peptide Arenicin: Oligomeric Structure in Dodecylphosphocholine Micelles and Pore Formation in Planar Lipid Bilayers

The membrane-active, cationic, β-hairpin peptide, arenicin, isolated from marine polychaeta Arenicola marina exhibits a broad spectrum of antimicrobial activity. The peptide in aqueous solution adopts the significantly twisted β-hairpin conformation without pronounced amphipathicity. To assess the mechanism of arenicin action, the spatial structure and backbone dynamics of the peptide in membrane-mimicking media and its pore-forming activity in planar lipid bilayers were studied. The spatial structure of the asymmetric arenicin dimer stabilized by parallel association of N-terminal strands of two β-hairpins was determined using triple-resonance nuclear magnetic resonance (NMR) spectroscopy in dodecylphosphocholine (DPC) micelles. Interaction of arenicin with micelles and its oligomerization significantly decreased the right-handed twist of the β-hairpin, increased its amphipathicity, and led to stabilization of the peptide backbone on a picosecond to nanosecond time scale. Relaxation enhancement induced by water-soluble (Mn(2+)) and lipid-soluble (16-doxylstearate) paramagnetic probes pointed to the dimer transmembrane arrangement. Qualitative NMR and circular dichroism study of arenicin-2 in mixed DPC/1,2-dioleoyl-sn-glycero-3-phosphoglycerol bicelles, sodium dodecyl sulfate micelles, and lipid vesicles confirmed that a similar dimeric assembly of the peptide was retained in membrane-mimicking systems containing negatively charged lipids and detergents. Arenicin-induced conductance was dependent on the lipid composition of the membrane. Arenicin low-conductivity pores were detected in the phosphatidylethanolamine-containing lipid mixture, whereas the high-conductivity pores were observed in an exclusively anionic lipid system. The measured conductivity levels agreed with the model in which arenicin antimicrobial activity was mediated by the formation of toroidal pores assembled of two, three, or four β-structural peptide dimers and lipid molecules. The structural transitions involved in arenicin membrane-disruptive action are discussed.

Expression, purification, detergent screening and solution NMR backbone assignment of the human potassium channel accessory subunit MiRP1

MiRP1 (MinK related protein 1) is a membrane protein in the KCNE family. It can associate with and modulate various voltage gated potassium channels. Mutations in human MiRP1 have been found to cause many congenital and acquired long QT syndromes, which are potentially life-threatening cardiac arrhythmias. Here, human MiRP1 was over-expressed in Escherichia coli, purified and eluted into different detergents. Two dimensional 1H–15N correlated solution nuclear magnetic resonance (NMR) spectra of the human MiRP1 in four different detergent micelles indicated that high resolution solution NMR spectrum can be obtained for human MiRP1 in detergent lyso-myristoylphosphatidylglycerol (LMPG). Circular dichroism (CD) spectroscopy of human MiRP1 indicated a high content of alpha-helical secondary structure in LMPG. Backbone assignments of most MiRP1 residues were achieved through a series of triple resonance NMR experiments. Secondary structure analysis based on backbone chemical shifts showed several stretches of alpha-helices along the primary sequence of MiRP1 in LMPG.

Segmental isotopic labeling of multi-domain and fusion proteins by protein trans-splicing in vivo and in vitro

Segmental isotopic labeling is a powerful labeling technique for reducing nuclear magnetic resonance (NMR) signal overlap, which is associated with larger proteins by incorporating stable isotopes into only one region of a protein for NMR detections. Segmental isotopic labeling can not only reduce complexities of NMR spectra but also retain possibilities to carry out sequential resonance assignments by triple-resonance NMR experiments. We described in vivo (i.e., in Escherichia coli) and in vitro protocols for segmental isotopic labeling of multi-domain and fusion proteins via protein trans-splicing (PTS) using split DnaE intein without any refolding steps or alpha-thioester modification. The advantage of PTS approach is that it can be carried out in vivo by time-delayed dual-expression system with two controllable promoters. A segmentally isotope-labeled protein can be expressed in Escherichia coli within 1 d once required vectors are constructed. The total preparation time of a segmentally labeled sample can be as short as 7-13 d depending on the protocol used.

Microgram-scale protein structure determination by NMR

Using conventional triple-resonance nuclear magnetic resonance (NMR) experiments with a 1 mm triple-resonance microcoil NMR probe, we determined near complete resonance assignments and three-dimensional (3D) structure of the 68-residue Methanosarcina mazei TRAM protein using only 72 mug (6 microl, 1.4 mM) of protein. This first example of a complete solution NMR structure determined using microgram quantities of protein demonstrates the utility of microcoil-probe NMR technologies for protein samples that can be produced in only limited quantities.

Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution.

The physical basis of protein structure, dynamics and function has been intensely studied for several decades. Indeed since the new millennium there has been a tremendous expansion in the number of unique topological folds that have been characterized at high resolution by crystallographic and nuclear magnetic resonance (NMR) based methods. In the midst of this rush towards a grand scale structural genomics effort, a quieter effort dedicated to the experimental characterization of protein conformational heterogeneity has also emerged. The influence of atomic scale structure on molecular recognition and catalysis by proteins is often the focus of attention while the role of dynamics is largely unknown and frequently ignored. Nevertheless, it has long been recognized that proteins are indeed dynamic systems. Early insights into the time scale and character of protein internal motion largely employed local optical probes, unresolved hydrogen exchange, and one dimensional NMR techniques that, though limited, revealed a startling complexity and richness in the internal motion of proteins.1–5 These initial views contributed significantly to the development of current treatments of protein dynamics and thermodynamics.6 The connection to biological function rather than just biological form is more recent. Internal protein dynamics can potentially affect protein function through a variety of mechanisms, some of which are tautological or obvious in nature while others are subtle and remain to be fully explored and appreciated. There are now several examples of protein-protein and protein-ligand interactions that illustrate that dynamics may be fundamentally linked to function in several ways. Nuclear magnetic resonance (NMR) spectroscopy is very much at the center of current efforts to illuminate the nature of protein dynamics and their role in biological function. Here we will focus on the use of solution NMR methods to provide fast subnanosecond dynamics of protein side chains. The interested reader is referred to separate reviews in this issue by Goehlert and Stone,7 Tolman8 and Palmer and Massi9 discussing dynamics of the polypeptide backbone. The emerging success of NMR spectroscopy in the arena of protein dynamics rests on four general areas of development over the past two decades. First and perhaps foremost, triple resonance NMR spectroscopy now provides an efficient and robust set of tools for the comprehensive resonance assignment of proteins of significant size.10,11 These methods, in turn, derive much of their power from companion isotopic enrichment strategies,12,13 which have been subsequently refined to allow for isotopic labeling patterns that are optimized for NMR relaxation studies (vide infra). Two-dimensional sampling of relaxation has allowed for comprehensive studies to be efficiently undertaken, albeit with great instrumental cost.14–16 A variety of technical issues such as the effects of macromolecular tumbling and the influence of competing relaxation mechanisms have also been largely resolved (vide infra). These advances have positioned solution NMR spectroscopy to efficiently and comprehensively characterize the fast internal dynamics of proteins of significant size. This review seeks to provide a compact but reasonably complete description of the theoretical and technical foundation for solution NMR relaxation methods that are currently being brought to bear on fast sub-nanosecond protein side chain dynamics and to present a summary of current findings and their possible significance. A survey of basic observations about side chain dynamics derived from NMR-relaxation studies is presented along with several analyses meant to dispel commonly held but apparently inaccurate correlations between dynamics, structure and function. How dynamics can enter into fundamental thermodynamic and kinetic aspects of protein function is also reviewed and illustrated with intriguing results from several systems that point to a promising future for this area of inquiry.

Peptides and the development of double‐ and triple‐resonance solid‐state NMR of aligned samples*

Peptides have been instrumental in the development of solid-state nuclear magnetic resonance (NMR) spectroscopy, and their roles in the development of solid-state NMR of aligned samples is reviewed. In particular, the roles of synthetic peptides in the development of triple-resonance methods are described. Recent developments of pulse sequences and NMR probes for triple-resonance NMR of aligned samples are presented.

Resonance assignment of13C−15N-labeled snake neurotoxin II fromNaja oxiana

Neurotoxin II fromNaja oxiana venom is a short-chain snake curaremimetic neurotoxin containing four disulfide bonds. We obtained13C-15N-labeled neurotoxin II to study its internal dynamics and surface properties with atomic resolution. The recombinant protein has the native spatial structure and is biologically active. The nearly complete assignment of1H,13C and15N resonances for neurotoxin II was obtained by heteronuclear triple-resonance nuclear magnetic resonance spectroscopy. Analysis of the secondary chemical shifts of the1Hα,13Cα,13Cβ and13CO nuclei reveal their strong correlation with the protein secondary structure.

RNAPack: An Integrated NMR Approach to RNA Structure Determination

Over the last decade, a vast number of useful nuclear magnetic resonance (NMR) experiments have been developed and successfully employed to determine the structure and dynamics of RNA oligonucleotides. Despite this progress, high-resolution RNA structure determination by NMR spectroscopy still remains a lengthy process and requires programming and extensive calibrations to perform NMR experiments successfully. To accelerate RNA structure determination by NMR spectroscopy, we have designed and programmed a package of RNA NMR experiments, called RNAPack. The user-friendly package contains a set of semiautomated single, double, and triple resonance NMR experiments, which are fully optimized for high-resolution RNA solution structure determination on Varian NMR spectrometers. RNAPack provides an autocalibration feature that allows rapid calibration of all NMR experiments in a single step and thereby speeds up the NMR data collection and eliminates user errors. In our laboratory, we have successfully employed this technology to solve RNA solution structures of domains of the internal ribosome entry site of the genomic hepatitis C viral RNA in less than 3 months. RNAPack therefore makes NMR spectroscopy an attractive and rapid structural tool and allows integration of atomic resolution structural information into biochemical studies of large RNA systems.

1H,13C and15N resonance assignment for barnase

The nearly complete assignment of1H,13C and15N resonances for bacterial ribonuclease barnase produced byBacillus amyloliquefaciens was obtained by standard methods of heteronuclear triple-resonance nuclear magnetic resonance spectroscopy. Analysis of the secondary chemical shifts of the backbone1Hα,13Cα and13CO nuclei reveal their strong correlation with the protein secondary structure.

Use of deuterium labeling in NMR: overcoming a sizeable problem

In summary, the use of deuteration in combination with uniformly 13C- and 15N-labeling dramatically improves the quality of NMR spectra of larger proteins. These improvements allow the backbone and side-chain signals of larger proteins to be assigned and aids in the acquisition and analysis of NOE data. Using these methods, three-dimensional structures of proteins up to 30kDa have been determined [[[20]xStructure and ligand recognition of the phosphotyrosine binding domain of Shc. Zhou, M.-M...., and Fesik, S.W. Nature. 1995; 378: 584–592Crossref | PubMedSee all References, [31]xX-ray and NMR structure of human Bcl-xL, an inhibitor of programmed cell death. Muchmore, S.W...., and Fesik, S.W. Nature. 1996; 381: 335–341Crossref | PubMedSee all References, [32]xStructure of Bcl-xL–Bak peptide complex reveals how regulators of apoptosis interact. Sattler, M...., and Fesik, S.W. Science. 1996; : in pressSee all References] SWF, unpublished data]. Further developments of NMR methods and variation of labeling techniques promise to push the molecular weight limit even further.

Three-dimensional Structure of the Human Immunodeficiency Virus Type 1 Matrix Protein

The HIV-1 matrix protein forms an icosahedral shell associated with the inner membrane of the mature virus. Genetic analyses have indicated that the protein performs important functions throughout the viral life-cycle, including anchoring the transmembrane envelope protein on the surface of the virus, assisting in viral penetration, transporting the proviral integration complex across the nuclear envelope, and localizing the assembling virion to the cell membrane. We now report the three-dimensional structure of recombinant HIV-1 matrix protein, determined at high resolution by nuclear magnetic resonance (NMR) methods. The HIV-1 matrix protein is the first retroviral matrix protein to be characterized structurally and only the fourth HIV-1 protein of known structure. NMR signal assignments required recently developed triple-resonance ( 1H, 13C, 15N) NMR methodologies because signals for 91% of 132 assigned H a protons and 74% of the 129 assignable backbone amide protons resonate within chemical shift ranges of 0.8 p.p.m. and 1 p.p.m., respectively; A total of 636 nuclear Overhauser effect-derived distance restraints were employed for distance geometry-based structure calculations, affording an average of 13.0 NMR-derived distance restraints per residue for the experimentally constrained amino acids. An ensemble of 25 refined distance geometry structures with penalties (sum of the squares of the distance violations) of 0.32 Å 2 or less and individual distance violations under 0.06 Å was generated; best-fit superposition of ordered backbone heavy atoms relative to mean atom positions afforded root-mean-square deviations of 0.50 (±0.08) Å. The folded HIV-1 matrix protein structure is composed of five α-helices, a short 3 10 helical stretch, and a three-strand mixed β-sheet. Helices I to III and the 3 10 helix pack about a central helix (IV) to form a compact globular domain that is capped by the β-sheet. The C-terminal helix (helix V) projects away from the β-sheet to expose carboxyl-terminal residues essential for early steps in the HIV-1 infectious cycle. Basic residues implicated in membrane binding and nuclear localization functions cluster about an extruded cationic loop that connects β-strands 1 and 2. The structure suggests that both membrane binding and nuclear localization may be mediated by complex tertiary structures rather than simple linear determinants.

Applications of triple resonance NMR techniques to the study of polymer structure and reactivity

AbstractThe utility of isotopic labeling combined with triple resonance nuclear magnetic resonance (NMR) techniques for polymer structure and reactivity investigations will be demonstrated. One dimensional (1D) and two dimensional (2D) 1H/19F/13C triple resonance NMR experiments have been used to study the structure of fluoropolymers; and 1H/2H/13C triple resonance techniques have been used to study the reactivity of poly[(styrene‐alt‐(methyl methacrylate)] and the structure of deuterated polybutadiene. These methods provide a unique ability to selectively detect resonances of structural features that are present in minute amounts in polymers, without interference from the much larger signals of the rest of the polymer.