Cell-free synthesis and amino acid-selective stable isotope labeling of proteins for NMR analysis

Direct Observation of Membrane-Associated H-Ras in the Native Cellular Environment by In-Cell 19F-NMR Spectroscopy

Ras acts as a molecular switch to control intracellular signaling on the plasma membrane (PM). Elucidating how Ras associates with PM in the native cellular environment is crucial for understanding its control mechanism. Here, we used in-cell nuclear magnetic resonance (NMR) spectroscopy combined with site-specific ¹⁹F-labeling to explore the membrane-associated states of H-Ras in living cells. The site-specific incorporation of p-trifluoromethoxyphenylalanine (OCF₃Phe) at three different sites of H-Ras, i.e., Tyr32 in switch I, Tyr96 interacting with switch II, and Tyr157 on helix α5, allowed the characterization of their conformational states depending on the nucleotide-bound states and an oncogenic mutational state. Exogenously delivered ¹⁹F-labeled H-Ras protein containing a C-terminal hypervariable region was assimilated via endogenous membrane-trafficking, enabling proper association with the cell membrane compartments. Despite poor sensitivity of the in-cell NMR spectra of membrane-associated H-Ras, the Bayesian spectral deconvolution identified distinct signal components on three ¹⁹F-labeled sites, thus offering the conformational multiplicity of H-Ras on the PM. Our study may be helpful in elucidating the atomic-scale picture of membrane-associated proteins in living cells.

Specific isotopic labelling and reverse labelling for protein NMR spectroscopy: using metabolic precursors in sample preparation

The study of protein structure, dynamics and function by NMR spectroscopy commonly requires samples that have been enriched ('labelled') with the stable isotopes 13C and/or 15N. The standard approach is to uniformly label a protein with one or both of these nuclei such that all C and/or N sites are in principle 'NMR-visible'. NMR spectra of uniformly labelled proteins can be highly complicated and suffer from signal overlap. Moreover, as molecular size increases the linewidths of NMR signals broaden, which decreases sensitivity and causes further spectral congestion. Both effects can limit the type and quality of information available from NMR data. Problems associated with signal overlap and signal broadening can often be alleviated though the use of alternative, non-uniform isotopic labelling patterns. Specific isotopic labelling 'turns on' signals at selected sites while the rest of the protein is NMR-invisible. Conversely, specific isotopic unlabelling (also called 'reverse' labelling) 'turns off' selected signals while the rest of the protein remains NMR-visible. Both approaches can simplify NMR spectra, improve sensitivity, facilitate resonance assignment and permit a range of different NMR strategies when combined with other labelling tools and NMR experiments. Here, we review methods for producing proteins with enrichment of stable NMR-visible isotopes, with particular focus on residue-specific labelling and reverse labelling using Escherichia coli expression systems. We also explore how these approaches can aid NMR studies of proteins.

Segmental and site-specific isotope labelling strategies for structural analysis of posttranslationally modified proteins

Posttranslational modifications can alter protein structures, functions and locations, and are important cellular regulatory and signalling mechanisms. Spectroscopic techniques such as nuclear magnetic resonance, infrared and Raman spectroscopy, as well as small-angle scattering, can provide insights into the structural and dynamic effects of protein posttranslational modifications and their impact on interactions with binding partners. However, heterogeneity of modified proteins from natural sources and spectral complexity often hinder analyses, especially for large proteins and macromolecular assemblies. Selective labelling of proteins with stable isotopes can greatly simplify spectra, as one can focus on labelled residues or segments of interest. Employing chemical biology tools for modifying and isotopically labelling proteins with atomic precision provides access to unique protein samples for structural biology and spectroscopy. Here, we review site-specific and segmental isotope labelling methods that are employed in combination with chemical and enzymatic tools to access posttranslationally modified proteins. We discuss illustrative examples in which these methods have been used to facilitate spectroscopic studies of posttranslationally modified proteins, providing new insights into biology.

Robust Cell-Free Expression of Sub-Pathological and Pathological Huntingtin Exon-1 for NMR Studies. General Approaches for the Isotopic Labeling of Low-Complexity Proteins

The high-resolution structural study of huntingtin exon-1 (HttEx1) has long been hampered by its intrinsic properties. In addition to being prone to aggregate, HttEx1 contains low-complexity regions (LCRs) and is intrinsically disordered, ruling out several standard structural biology approaches. Here, we use a cell-free (CF) protein expression system to robustly and rapidly synthesize (sub-) pathological HttEx1. The open nature of the CF reaction allows the application of different isotopic labeling schemes, making HttEx1 amenable for nuclear magnetic resonance studies. While uniform and selective labeling facilitate the sequential assignment of HttEx1, combining CF expression with nonsense suppression allows the site-specific incorporation of a single labeled residue, making possible the detailed investigation of the LCRs. To optimize CF suppression yields, we analyze the expression and suppression kinetics, revealing that high concentrations of loaded suppressor tRNA have a negative impact on the final reaction yield. The optimized CF protein expression and suppression system is very versatile and well suited to produce challenging proteins with LCRs in order to enable the characterization of their structure and dynamics.

Amino-acid selective isotope labeling enables simultaneous overlapping signal decomposition and information extraction from NMR spectra

Signal overlapping is a major bottleneck for protein NMR analysis. We propose a new method, stable-isotope-assisted parameter extraction (SiPex), to resolve overlapping signals by a combination of amino-acid selective isotope labeling (AASIL) and tensor decomposition. The basic idea of Sipex is that overlapping signals can be decomposed with the help of intensity patterns derived from quantitative fractional AASIL, which also provides amino-acid information. In SiPex, spectra for protein characterization, such as ¹⁵N relaxation measurements, are assembled with those for amino-acid information to form a four-order tensor, where the intensity patterns from AASIL contribute to high decomposition performance even if the signals share similar chemical shift values or characterization profiles, such as relaxation curves. The loading vectors of each decomposed component, corresponding to an amide group, represent both the amino-acid and relaxation information. This information link provides an alternative protein analysis method that does not require "assignments" in a general sense; i.e., chemical shift determinations, since the amino-acid information for some of the residues allows unambiguous assignment according to the dual selective labeling. SiPex can also decompose signals in time-domain raw data without Fourier transform, even in non-uniformly sampled data without spectral reconstruction. These features of SiPex should expand biological NMR applications by overcoming their overlapping and assignment problems.

Cell-free expression of natively folded hydrophobins

Hydrophobins are a family of cysteine-rich proteins unique to filamentous fungi. The proteins are produced in a soluble form but self-assemble into organised amphipathic layers at hydrophilic:hydrophobic interfaces. These layers contribute to transitions between wet and dry environments, spore dispersal and attachment to surfaces for growth and infection. Hydrophobins are characterised by four disulphide bonds that are critical to their structure and function. Thus, obtaining correctly folded, soluble and functional hydrophobins directly from bacterial recombinant expression is challenging and in most cases, initial denaturation from inclusion bodies followed by oxidative refolding are required to obtain folded proteins. Here, we report the use of cell-free expression with E. coli cell lysate to directly obtain natively folded hydrophobins. All six of the hydrophobins tested could be expressed after optimisation of redox conditions. For some hydrophobins, the inclusion of the disulfide isomerase DsbC further enhanced expression levels. We are able to achieve a yield of up to 1 mg of natively folded hydrophobin per mL of reaction. This has allowed the confirmation of the correct folding of hydrophobins with the use of ¹⁵N-cysteine and ¹⁵N-¹H nuclear magnetic resonance experiments within 24 h of starting from plasmid stocks.

Methyl TROSY spectroscopy: A versatile NMR approach to study challenging biological systems

A major goal in structural biology is to unravel how molecular machines function in detail. To that end, solution-state NMR spectroscopy is ideally suited as it is able to study biological assemblies in a near natural environment. Based on methyl TROSY methods, it is now possible to record high-quality data on complexes that are far over 100 kDa in molecular weight. In this review, we discuss the theoretical background of methyl TROSY spectroscopy, the information that can be extracted from methyl TROSY spectra and approaches that can be used to assign methyl resonances in large complexes. In addition, we touch upon insights that have been obtained for a number of challenging biological systems, including the 20S proteasome, the RNA exosome, molecular chaperones and G-protein-coupled receptors. We anticipate that methyl TROSY methods will be increasingly important in modern structural biology approaches, where information regarding static structures is complemented with insights into conformational changes and dynamic intermolecular interactions.

Toward a genome scale sequence specific dynamic model of cell-free protein synthesis in Escherichia coli

In this study, we developed a dynamic mathematical model of E. coli cell-free protein synthesis (CFPS). Model parameters were estimated from a dataset consisting of glucose, organic acids, energy species, amino acids, and protein product, chloramphenicol acetyltransferase (CAT) measurements. The model was successfully trained to simulate these measurements, especially those of the central carbon metabolism. We then used the trained model to evaluate the performance, e.g., the yield and rates of protein production. CAT was produced with an energy efficiency of 12%, suggesting that the process could be further optimized. Reaction group knockouts showed that protein productivity was most sensitive to the oxidative phosphorylation and glycolysis/gluconeogenesis pathways. Amino acid biosynthesis was also important for productivity, while overflow metabolism and TCA cycle affected the overall system state. In addition, translation was more important to productivity than transcription. Finally, CAT production was robust to allosteric control, as were most of the predicted metabolite concentrations; the exceptions to this were the concentrations of succinate and malate, and to a lesser extent pyruvate and acetate, which varied from the measured values when allosteric control was removed. This study is the first to use kinetic modeling to predict dynamic protein production in a cell-free E. coli system, and could provide a foundation for genome scale, dynamic modeling of cell-free E. coli protein synthesis.

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Protein production is biphasic, powered initially by glucose and later by pyruvate.

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Protein is produced with an energy efficiency of only 12%.

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Protein productivity is most sensitive to oxidative phosphorylation and glycolysis.

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Protein production is robust to allosteric control.

Structure determination of supra-molecular assemblies by solid-state NMR: Practical considerations

In the cellular environment, biomolecules assemble in large complexes which can act as molecular machines. Determining the structure of intact assemblies can reveal conformations and inter-molecular interactions that are only present in the context of the full assembly. Solid-state NMR (ssNMR) spectroscopy is a technique suitable for the study of samples with high molecular weight that allows the atomic structure determination of such large protein assemblies under nearly physiological conditions. This review provides a practical guide for the first steps of studying biological supra-molecular assemblies using ssNMR. The production of isotope-labeled samples is achievable via several means, which include recombinant expression, cell-free protein synthesis, extraction of assemblies directly from cells, or even the study of assemblies in whole cells in situ. Specialized isotope labeling schemes greatly facilitate the assignment of chemical shifts and the collection of structural data. Advanced strategies such as mixed, diluted, or segmental subunit labeling offer the possibility to study inter-molecular interfaces. Detailed and practical considerations are presented with respect to first setting up magic-angle spinning (MAS) ssNMR experiments, including the selection of the ssNMR rotor, different methods to best transfer the sample and prepare the rotor, as well as common and robust procedures for the calibration of the instrument. Diagnostic spectra to evaluate the resolution and sensitivity of the sample are presented. Possible improvements that can reduce sample heterogeneity and improve the quality of ssNMR spectra are reviewed.

Sequence Specific Modeling of E. coli Cell-Free Protein Synthesis

Cell-free protein synthesis (CFPS) is a widely used research tool in systems and synthetic biology. However, if CFPS is to become a mainstream technology for applications such as point of care manufacturing, we must understand the performance limits and costs of these systems. Toward this question, we used sequence specific constraint based modeling to evaluate the performance of E. coli cell-free protein synthesis. A core E. coli metabolic network, describing glycolysis, the pentose phosphate pathway, energy metabolism, amino acid biosynthesis, and degradation was augmented with sequence specific descriptions of transcription and translation and effective models of promoter function. Model parameters were largely taken from literature; thus the constraint based approach coupled the transcription and translation of the protein product, and the regulation of gene expression, with the availability of metabolic resources using only a limited number of adjustable model parameters. We tested this approach by simulating the expression of two model proteins: chloramphenicol acetyltransferase and dual emission green fluorescent protein, for which we have data sets; we then expanded the simulations to a range of additional proteins. Protein expression simulations were consistent with measurements for a variety of cases. The constraint based simulations confirmed that oxidative phosphorylation was active in the CAT cell-free extract, as without it there was no feasible solution within the experimental constraints of the system. We then compared the metabolism of theoretically optimal and experimentally constrained CFPS reactions, and developed parameter free correlations which could be used to estimate productivity as a function of carbon number and promoter type. Lastly, global sensitivity analysis identified the key metabolic processes that controlled CFPS productivity and energy efficiency. In summary, sequence specific constraint based modeling of CFPS offered a novel means to a priori estimate the performance of a cell-free system, using only a limited number of adjustable parameters. While we modeled the production of a single protein in this study, the approach could easily be extended to multiprotein synthetic circuits, RNA circuits, or the cell-free production of small molecule products.

Protein labeling strategies for liquid-state NMR spectroscopy using cell-free synthesis

Preparation of a protein sample for liquid-state nuclear magnetic resonance (NMR) spectroscopy analysis requires optimization of many parameters. This review describes labeling strategies for obtaining assignments of protein resonances. Particular emphasis is placed on the advantages of cell-free protein production, which enables exclusive labeling of the protein of interest, thereby simplifying downstream processing steps and increasing the availability of different labeling strategies for a target protein. Furthermore, proteins can be synthesized in milligram yields, and the open nature of the cell-free system allows the addition of stabilizers, scrambling inhibitors or hydrophobic solubilization environments directly during the protein synthesis, which is especially beneficial for membrane proteins. Selective amino acid labeling of the protein of interest, the possibility of addressing scrambling issues and avoiding the need for labile amino acid precursors have been key factors in enabling the introduction of new assignment strategies based on different labeling schemes as well as on new pulse sequences. Combinatorial selective labeling methods have been developed to reduce the number of protein samples necessary to achieve a complete backbone assignment. Furthermore, selective labeling helps to decrease spectral overlap and overcome size limitations for solution NMR analysis of larger complexes, oligomers, intrinsically disordered proteins and membrane proteins.

A Simple and Rapid Method for Preparing a Cell-Free Bacterial Lysate for Protein Synthesis

Cell-free protein synthesis (CFPS) systems are important laboratory tools that are used for various synthetic biology applications. Here, we present a simple and inexpensive laboratory-scale method for preparing a CFPS system from E. coli. The procedure uses basic lab equipment, a minimal set of reagents, and requires less than one hour to process the bacterial cell mass into a functional S30-T7 extract. BL21(DE3) and MRE600 E. coli strains were used to prepare the S30-T7 extract. The CFPS system was used to produce a set of fluorescent and therapeutic proteins of different molecular weights (up to 66 kDa). This system was able to produce 40-150 μg-protein/ml, with variations depending on the plasmid type, expressed protein and E. coli strain. Interestingly, the BL21-based CFPS exhibited stability and increased activity at 40 and 45°C. To the best of our knowledge, this is the most rapid and affordable lab-scale protocol for preparing a cell-free protein synthesis system, with high thermal stability and efficacy in producing therapeutic proteins.

Protein synthesis directly from PCR: progress and applications of cell-free protein synthesis with linear DNA

A rapid, versatile method of protein expression and screening can greatly facilitate the future development of therapeutic biologics, proteomic drug targets and biocatalysts. An attractive candidate is cell-free protein synthesis (CFPS), a cell-lysate-based in vitro expression system, which can utilize linear DNA as expression templates, bypassing time-consuming cloning steps of plasmid-based methods. Traditionally, such linear DNA expression templates (LET) have been vulnerable to degradation by nucleases present in the cell lysate, leading to lower yields. This challenge has been significantly addressed in the recent past, propelling LET-based CFPS as a useful tool for studying, screening and engineering proteins in a high-throughput manner. Currently, LET-based CFPS has promise in fields such as functional proteomics, protein microarrays, and the optimization of complex biological systems.

Spectral editing at ultra-fast magic-angle-spinning in solid-state NMR: facilitating protein sequential signal assignment by HIGHLIGHT approach

This study demonstrates a novel spectral editing technique for protein solid-state NMR (SSNMR) to simplify the spectrum drastically and to reduce the ambiguity for protein main-chain signal assignments in fast magic-angle-spinning (MAS) conditions at a wide frequency range of 40-80 kHz. The approach termed HIGHLIGHT (Wang et al., in Chem Comm 51:15055-15058, 2015) combines the reverse (13)C, (15)N-isotope labeling strategy and selective signal quenching using the frequency-selective REDOR pulse sequence under fast MAS. The scheme allows one to selectively observe the signals of "highlighted" labeled amino-acid residues that precede or follow unlabeled residues through selectively quenching (13)CO or (15)N signals for a pair of consecutively labeled residues by recoupling (13)CO-(15)N dipolar couplings. Our numerical simulation results showed that the scheme yielded only ~15% loss of signals for the highlighted residues while quenching as much as ~90% of signals for non-highlighted residues. For lysine-reverse-labeled micro-crystalline GB1 protein, the 2D (15)N/(13)Cα correlation and 2D (13)Cα/(13)CO correlation SSNMR spectra by the HIGHLIGHT approach yielded signals only for six residues following and preceding the unlabeled lysine residues, respectively. The experimental dephasing curves agreed reasonably well with the corresponding simulation results for highlighted and quenched residues at spinning speeds of 40 and 60 kHz. The compatibility of the HIGHLIGHT approach with fast MAS allows for sensitivity enhancement by paramagnetic assisted data collection (PACC) and (1)H detection. We also discuss how the HIGHLIGHT approach facilitates signal assignments using (13)C-detected 3D SSNMR by demonstrating full sequential assignments of lysine-reverse-labeled micro-crystalline GB1 protein (~300 nmol), for which data collection required only 11 h. The HIGHLIGHT approach offers valuable means of signal assignments especially for larger proteins through reducing the number of resonance and clarifying multiple starting points in sequential assignment with enhanced sensitivity.

Cotranslational incorporation of non-standard amino acids using cell-free protein synthesis

Over the last years protein engineering using non-standard amino acids has gained increasing attention. As a result, improved methods are now available, enabling the efficient and directed cotranslational incorporation of various non-standard amino acids to equip proteins with desired characteristics. In this context, the utilization of cell-free protein synthesis is particularly useful due to the direct accessibility of the translational machinery and synthesized proteins without having to maintain a vital cellular host. We review prominent methods for the incorporation of non-standard amino acids into proteins using cell-free protein synthesis. Furthermore, a list of non-standard amino acids that have been successfully incorporated into proteins in cell-free systems together with selected applications is provided.

A simplified and robust protocol for immunoglobulin expression in Escherichia coli cell-free protein synthesis systems

Cell‐free protein synthesis (CFPS) systems allow for robust protein expression with easy manipulation of conditions to improve protein yield and folding. Recent technological developments have significantly increased the productivity and reduced the operating costs of CFPS systems, such that they can compete with conventional in vivo protein production platforms, while also offering new routes for the discovery and production of biotherapeutics. As cell‐free systems have evolved, productivity increases have commonly been obtained by addition of components to previously designed reaction mixtures without careful re‐examination of the essentiality of reagents from previous generations. Here we present a systematic sensitivity analysis of the components in a conventional Escherichia coli CFPS reaction mixture to evaluate their optimal concentrations for production of the immunoglobulin G trastuzumab. We identify eight changes to the system, which result in optimal expression of trastuzumab. We find that doubling the potassium glutamate concentration, while entirely eliminating pyruvate, coenzyme A, NAD, total tRNA, folinic acid, putrescine and ammonium glutamate, results in a highly productive cell‐free system with a 95% reduction in reagent costs (excluding cell‐extract, plasmid, and T7 RNA polymerase made in‐house). A larger panel of other proteins was also tested and all show equivalent or improved yields with our simplified system. Furthermore, we demonstrate that all of the reagents for CFPS can be combined in a single freeze‐thaw stable master mix to improve reliability and ease of use. These improvements are important for the application of the CFPS system in fields such as protein engineering, high‐throughput screening, and biotherapeutics. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:823–831, 2015

Quantitative proteomics in the field of microbiology

Quantitative proteomics has become an indispensable analytical tool for microbial research. Modern microbial proteomics covers a wide range of topics in basic and applied research from in vitro characterization of single organisms to unravel the physiological implications of stress/starvation to description of the proteome content of a cell at a given time. With the techniques available, ranging from classical gel-based procedures to modern MS-based quantitative techniques, including metabolic and chemical labeling, as well as label-free techniques, quantitative proteomics is today highly successful in sophisticated settings of high complexity such as host-pathogen interactions, mixed microbial communities, and microbial metaproteomics. In this review, we will focus on the vast range of techniques practically applied in current research with an introduction of the workflows used for quantitative comparisons, a description of the advantages/disadvantages of the various methods, reference to hallmark publications and presentation of applications in current microbial research.

Selective (15)N-labeling of the side-chain amide groups of asparagine and glutamine for applications in paramagnetic NMR spectroscopy

The side-chain amide groups of asparagine and glutamine play important roles in stabilizing the structural fold of proteins, participating in hydrogen-bonding networks and protein interactions. Selective (15)N-labeling of side-chain amides, however, can be a challenge due to enzyme-catalyzed exchange of amide groups during protein synthesis. In the present study, we developed an efficient way of selectively labeling the side chains of asparagine, or asparagine and glutamine residues with (15)NH2. Using the biosynthesis pathway of tryptophan, a protocol was also established for simultaneous selective (15)N-labeling of the side-chain NH groups of asparagine, glutamine, and tryptophan. In combination with site-specific tagging of the target protein with a lanthanide ion, we show that selective detection of (15)N-labeled side-chains of asparagine and glutamine allows determination of magnetic susceptibility anisotropy tensors based exclusively on pseudocontact shifts of amide side-chain protons.

NMR approaches for structural analysis of multidomain proteins and complexes in solution

NMR spectroscopy is a key method for studying the structure and dynamics of (large) multidomain proteins and complexes in solution. It plays a unique role in integrated structural biology approaches as especially information about conformational dynamics can be readily obtained at residue resolution. Here, we review NMR techniques for such studies focusing on state-of-the-art tools and practical aspects. An efficient approach for determining the quaternary structure of multidomain complexes starts from the structures of individual domains or subunits. The arrangement of the domains/subunits within the complex is then defined based on NMR measurements that provide information about the domain interfaces combined with (long-range) distance and orientational restraints. Aspects discussed include sample preparation, specific isotope labeling and spin labeling; determination of binding interfaces and domain/subunit arrangements from chemical shift perturbations (CSP), nuclear Overhauser effects (NOEs), isotope editing/filtering, cross-saturation, and differential line broadening; and based on paramagnetic relaxation enhancements (PRE) using covalent and soluble spin labels. Finally, the utility of complementary methods such as small-angle X-ray or neutron scattering (SAXS, SANS), electron paramagnetic resonance (EPR) or fluorescence spectroscopy techniques is discussed. The applications of NMR techniques are illustrated with studies of challenging (high molecular weight) protein complexes.

Multiple amino acid-excluded genetic codes for protein engineering using multiple sets of tRNA variants

A "simplified genetic code", with only 19 amino acids assigned to the sense codons, was recently developed. In this study, we describe novel simplified codes in which multiple amino acids are simultaneously excluded from the universal code. In the simplest code, tryptophan, cysteine, tyrosine, and asparagine codons are assigned to serine by using four kinds of tRNA (Ser) variants. The results revealed that various sets of amino acids can easily be excluded from the universal code, using our strategy for genetic code simplification. A simplified genetic code is useful as an engineering tool for the improvement of industrial enzymes and pharmaceuticals, and also provides new insights into the assessment of protein evolution. Simplified codes in which multiple amino acids are simultaneously excluded from the code can be more effective tools than codes excluding only one amino acid.

Isotope labeling methods for large systems

A major drawback of nuclear magnetic resonance (NMR) spectroscopy compared to other methods is that the technique has been limited to relatively small molecules. However, in the last two decades the size limit has been pushed upwards considerably and it is now possible to use NMR spectroscopy for structure calculations of proteins of molecular weights approaching 100 kDa and to probe dynamics for supramolecular complexes of molecular weights in excess of 500 kDa. Instrumental for this progress has been development in instrumentation and pulse sequence design but also improved isotopic labeling schemes that lead to increased sensitivity as well as improved spectral resolution and simplification. These are described and discussed in this chapter, focusing on labeling schemes for amide proton and methyl proton detected experiments. We also discuss labeling methods for other potentially useful positions in proteins.

Isotope labeling methods for relaxation measurements

Nuclear magnetic spin relaxation has emerged as a powerful technique for probing molecular dynamics. Not only is it possible to use it for determination of time constant(s) for molecular reorientation but it can also be used to characterize internal motions on time scales from picoseconds to seconds. Traditionally, uniformly (15)N labeled samples have been used for these experiments but it is clear that this limits the applications. For instance, sensitivity for large systems is dramatically increased if dynamics is probed at methyl groups and structural characterization of low-populated states requires measurements on (13)Cα, (13)Cβ or (13)CO or (1)Hα. Unfortunately, homonuclear scalar couplings may lead to artifacts in the latter types of experiments and selective isotopic labeling schemes that only label the desired position are necessary. Both selective and uniform labeling schemes for measurements of relaxation rates for a large number of positions in proteins are discussed in this chapter.

How to investigate interactions between membrane proteins and ligands by solid-state NMR

Solid-state NMR is an established method for biophysical studies of membrane proteins within the lipid bilayers and an emerging technique for structural biology in general. In particular magic angle sample spinning has been found to be very useful for the investigation of large membrane proteins and their interaction with small molecules within the lipid bilayer. Using a number of examples, we illustrate and discuss in this chapter, which information can be gained and which experimental parameters need to be considered when planning such experiments. We focus especially on the interaction of diffusive ligands with membrane proteins.

Utilization of lysine ¹³C-methylation NMR for protein-protein interaction studies

Chemical modification is an easy way for stable isotope labeling of non-labeled proteins. The reductive (13)C-methylation of the amino group of the lysine side-chain by (13)C-formaldehyde is a post-modification and is applicable to most proteins since this chemical modification specifically and quickly proceeds under mild conditions such as 4 °C, pH 6.8, overnight. (13)C-methylation has been used for NMR to study the interactions between the methylated proteins and various molecules, such as small ligands, nucleic acids and peptides. Here we applied lysine (13)C-methylation NMR to monitor protein-protein interactions. The affinity and the intermolecular interaction sites of methylated ubiquitin with three ubiquitin-interacting proteins were successfully determined using chemical-shift perturbation experiments via the (1)H-(13)C HSQC spectra of the (13)C-methylated-lysine methyl groups. The lysine (13)C-methylation NMR results also emphasized the importance of the usage of side-chain signals to monitor the intermolecular interaction sites, and was applicable to studying samples with concentrations in the low sub-micromolar range.

Solid-state NMR spectroscopy of proteins

Solid-state NMR spectroscopy proved to be a versatile tool for characterization of structure and dynamics of complex biochemical systems. In particular, magic angle spinning (MAS) solid-state NMR came to maturity for application towards structural elucidation of biological macromolecules. Current challenges in applying solid-state NMR as well as progress achieved recently will be discussed in the following chapter focusing on conceptual aspects important for structural elucidation of proteins.

Selective isotope labeling of recombinant proteins in Escherichia coli

Selective stable-isotope labeling is a useful technique to study structures of proteins, especially intrinsically disordered proteins, by nuclear magnetic resonance spectroscopy. Here, we describe a simple method for amino acid selective isotope labeling of recombinant proteins in E. coli. This method only requires addition of an excess of unlabeled amino acids and, if necessary, enzyme inhibitors to the culture medium. Its efficiency has been demonstrated even in labeling with glutamine or glutamate that is easily converted to other amino acid types by the metabolic pathways of E. coli.

Cell-free expression of disulfide-containing eukaryotic proteins for structural biology

We describe Escherichia coli based cell-free production of milligram quantities of eukaryotic proteins containing native disulfide bonds. Using a previously described expression system, we systematically investigated the influence of redox potential variation in the reaction mixture and the impact of adding disulfide bond catalysts on soluble protein production. It is then shown that the optimized reaction conditions for native disulfide bond formation can be combined with the use of N-terminal fusion constructs with the GB1 domain for increased expression yields. The resulting cell-free system is suitable for stable-isotope labeling and does not require chemical pretreatment of the cell extract to stabilize the redox potential. For the human doppel protein, the mouse doppel protein and mouse interleukin-22 we obtained 0.3-0.7 mg of purified native protein per milliliter of reaction mixture. Formation of disulfide bonds was validated using the Ellman assay, and native folding of the three proteins was monitored by NMR and CD spectroscopy.

1.12 Labeling Techniques

The current status of isotope-assisted multidimensional nuclear magnetic resonance (NMR) spectroscopy for protein structural studies is reviewed. After introducing various classic isotope labeling methods, some new emerging technologies, such as the stereo-array isotope labeling method, are described. The concomitant development of advanced stable isotope labeling strategies, NMR instrumentation, sophisticated NMR measurements, spectral analysis, and structural calculation algorithms is essential to overcome the current limitations restricting the use of protein NMR spectroscopy.

Cell-free protein production for NMR studies

The cell-free expression system using an Escherichia coli extract is a practical method for producing isotope-labeled proteins. The advantage of the cell-free system over cellular expression is that any isotope-labeled amino acid can be incorporated into the target protein with minimal scrambling, thus providing opportunities for advanced isotope labeling of proteins. We have modified the standard protocol for E. coli cell-free expression to cope with two problems specific to NMR sample preparation. First, endogenous amino acids present in the E. coli S30 extract lead to dilution of the added isotope. To minimize the content of the remaining amino acids, a gel filtration step is included in the preparation of the E. coli extract. Second, proteins produced by the cell-free system are not necessarily homogeneous due to incomplete processing of the N-terminal formyl-methionine residue, which complicates NMR spectra. Therefore, the protein of interest is engineered to contain a cleavable N-terminal histidine-tag, which generates a homogeneous protein after the digestion of the tag. Here, we describe the protocol for modified E. coli cell-free expression.

Suppression of isotope scrambling in cell-free protein synthesis by broadband inhibition of PLP enymes for selective 15N-labelling and production of perdeuterated proteins in H2O

Selectively isotope labelled protein samples can be prepared in vivo or in vitro from selectively labelled amino acids but, in many cases, metabolic conversions between different amino acids result in isotope scrambling. The best results are obtained by cell-free protein synthesis, where metabolic enzymes are generally less active, but isotope scrambling can never be suppressed completely. We show that reduction of E. coli S30 extracts with NaBH(4) presents a simple and inexpensive way to achieve cleaner selective isotope labelling in cell-free protein synthesis reactions. The purpose of the NaBH(4) is to inactivate all pyridoxal-phosphate (PLP) dependent enzymes by irreversible reduction of the Schiff bases formed between PLP and lysine side chains of the enzymes or amino groups of free amino acids. The reduced S30 extracts retain their activity of protein synthesis, can be stored as well as conventional S30 extracts and effectively suppress conversions between different amino acids. In addition, inactivation of PLP-dependent enzymes greatly stabilizes hydrogens bound to α-carbons against exchange with water, minimizing the loss of α-deuterons during cell-free production of proteins from perdeuterated amino acids in H(2)O solution. This allows the production of highly perdeuterated proteins that contain protons at all exchangeable positions, without having to back-exchange labile deuterons for protons as required for proteins that have been synthesized in D(2)O.

Contemporary methods in structure determination of membrane proteins by solution NMR

Integral membrane proteins are vital to life, being responsible for information and material exchange between a cell and its environment. Although high-resolution structural information is needed to understand how these functions are achieved, membrane proteins remain an under-represented subset of the protein structure databank. Solution NMR is increasingly demonstrating its ability to help address this knowledge shortfall, with the development of a diverse array of techniques to counter the challenges presented by membrane proteins. Here we document the advances that are helping to define solution NMR as an effective tool for membrane protein structure determination. Developments introduced over the last decade in the production of isotope-labeled samples, reconstitution of these samples into the growing selection of NMR-compatible membrane-mimetic systems, and the approaches used for the acquisition and application of structural restraints from these complexes are reviewed.

An economical method for producing stable-isotope labeled proteins by the E. coli cell-free system

Improvement of the cell-free protein synthesis system (CF) over the past decade have made it one of the most powerful protein production methods. The CF approach is especially useful for stable-isotope (SI) labeling of proteins for NMR analysis. However, it is less popular than expected, partly because the SI-labeled amino acids used for SI labeling by the CF are too expensive. In the present study, we developed a simple and inexpensive method for producing an SI-labeled protein using Escherichia coli cell extract-based CF. This method takes advantage of endogenous metabolic conversions to generate SI-labeled asparagine, glutamine, cysteine, and tryptophan, which are much more expensive than the other 16 kinds of SI-labeled amino acids, from inexpensive sources, such as SI-labeled algal amino acid mixture, SI-labeled indole, and sodium sulfide, during the CF reaction. As compared with the conventional method employing 20 kinds of SI-labeled amino acids, highly enriched uniform SI-labeling with similar labeling efficiency was achieved at a greatly reduced cost with the newly developed method. Therefore, our method solves the cost problem of the SI labeling of proteins using the CF.

Affinity-based, biophysical methods to detect and analyze ligand binding to recombinant proteins: matching high information content with high throughput

Affinity-based technologies have become impactful tools to detect, monitor and characterize molecular interactions using recombinant target proteins. This can aid the understanding of biological function by revealing mechanistic details, and even more importantly, enables the identification of new improved ligands that can modulate the biological activity of those targets in a desired fashion. The selection of the appropriate technology is a key step in that process, as each one of the currently available technologies offers a characteristic type of biophysical information about the ligand-binding event. Alongside the indisputable advantages of each of those technologies they naturally display diverse restrictions that are quite frequently related to the target system to be studied but also to the affinity, solubility and molecular size of the ligands. This paper discusses some of the theoretical and experimental aspects of the most common affinity-based methods, what type of information can be gained from each one of those approaches, and what requirements as well as limitations are expected from working with recombinant proteins on those platforms and how those can be optimally addressed.

Cell-free protein production system with the E. coli crude extract for determination of protein folds

Escherichia coli cell extract-based coupled transcription-translation cell-free system has been developed for large-scale production of protein samples for both X-ray crystallography (selenomethionine substitution) and NMR (stable-isotope labeling). For both cases, higher labeling/substitution efficiency can be achieved compared with the production using cell-based expression system. In addition, as the system is easily adapted to automated and/or high-throughput procedures, it is an especially suitable protein expression method for structural genomics and proteomics project. In this chapter, the procedure for large-scale protein production for structure determination using our E. coli cell-free system is presented.

SAIL – stereo-array isotope labeling

Optimal stereospecific and regiospecific labeling of proteins with stable isotopes enhances the nuclear magnetic resonance (NMR) method for the determination of the three-dimensional protein structures in solution. Stereo-array isotope labeling (SAIL) offers sharpened lines, spectral simplification without loss of information and the ability to rapidly collect and automatically evaluate the structural restraints required to solve a high-quality solution structure for proteins up to twice as large as before. This review gives an overview of stable isotope labeling methods for NMR spectroscopy with proteins and provides an in-depth treatment of the SAIL technology.

Stable-isotope dilution LC–MS for quantitative biomarker analysis

The ability to conduct validated analyses of biomarkers is critically important in order to establish the sensitivity and selectivity of the biomarker in identifying a particular disease. The use of stable-isotope dilution (SID) methodology in combination with LC–MS/MS provides the highest possible analytical specificity for quantitative determinations. This methodology is now widely used in the discovery and validation of putative exposure and disease biomarkers. This review will describe the application of SID LC–MS methodology for the analysis of small-molecule and protein biomarkers. It will also discuss potential future directions for the use of this methodology for rigorous biomarker analysis.

Cell-free expression and stable isotope labelling strategies for membrane proteins

Membrane proteins are highly underrepresented in the structural data-base and remain one of the most challenging targets for functional and structural elucidation. Their roles in transport and cellular communication, furthermore, often make over-expression toxic to their host, and their hydrophobicity and structural complexity make isolation and reconstitution a complicated task, especially in cases where proteins are targeted to inclusion bodies. The development of cell-free expression systems provides a very interesting alternative to cell-based systems, since it circumvents many problems such as toxicity or necessity for the transportation of the synthesized protein to the membrane, and constitutes the only system that allows for direct production of membrane proteins in membrane-mimetic environments which may be suitable for liquid state NMR measurements. The unique advantages of the cell-free expression system, including strong expression yields as well as the direct incorporation of almost any combination of amino acids with very little metabolic scrambling, has allowed for the development of a wide-array of isotope labelling techniques which facilitate structural investigations of proteins whose spectral congestion and broad line-widths may have earlier rendered them beyond the scope of NMR. Here we explore various labelling strategies in conjunction with cell-free developments, with a particular focus on alpha-helical transmembrane proteins which benefit most from such methods.

Synthesis of a hetero subunit RNA modification enzyme by the wheat germ cell-free translation system

Cell-free translation systems are a powerful tool for the production of many kinds of proteins. However, there are some barriers to improve the system in order to make it a more convenient approach. These include the fact that the production of proteins made up of hetero subunits is difficult. In this chapter, we describe the synthesis of yeast tRNA (m(7)G46) methyltransferase as a model protein. This enzyme catalyzes transfer of a methyl group from S-adenosyl-L-methionine to guanine at position 46 in tRNA and generates N(7)-methylguanine. Yeast tRNA (m(7)G46) methyltransferase is composed of two protein subunits, Trm8 and Trm82. To obtain the active Trm8-Trm82 complex, co-translation of both subunits is necessary. Preparation of mRNAs, in vitro synthesis and purification of the complex are explained in this chapter.