New approaches to structure determination by NMR spectroscopy

Synthesis of 13C-methyl-labeled amino acids and their incorporation into proteins in mammalian cells

Isotopic labeling of methyl-substituted proteinogenic amino acids with 13C has transformed applications of solution-based NMR spectroscopy and allowed the study of much larger and more complex proteins than previously possible with 15N labeling. Procedures are well-established for producing methyl-labeled proteins expressed in bacteria, with efficient incorporation of 13C-methyl labeled metabolic precursors to enable the isotopic labeling of Ile, Val, and Leu methyl groups. Recently, similar methodology has been applied to enable 13C-methyl labeling of Ile, Val, and Leu in yeast, extending the approach to proteins that do not readily fold when produced in bacteria. Mammalian or insect cells are nonetheless preferable for production of many human proteins, yet 13C-methyl labeling using similar metabolic precursors is not feasible as these cells lack the requisite biosynthetic machinery. Herein, we report versatile and high-yielding synthetic routes to 13C methyl-labeled amino acids based on palladium-catalyzed C(sp3)-H functionalization. We demonstrate the efficient incorporation of two of the synthesized amino acids, 13C-γ2-Ile and 13C-γ1,γ2-Val, into human receptor extracellular domains with multiple disulfides using suspension-cultured HEK293 cells. Production costs are reasonable, even at moderate expression levels of 2-3 mg purified protein per liter of medium, and the method can be extended to label other methyl groups, such as 13C-δ1-Ile and 13C-δ1,δ2-Leu. In summary, we demonstrate the cost-effective production of methyl-labeled proteins in mammalian cells by incorporation of 13C methyl-labeled amino acids generated de novo by a versatile synthetic route.

Shielding cone behavior in the spherical aromatic He@C606-: origin of the record for the most shielded encapsulated 3He nucleus and comparison to He@C706

The textbook concept of shielding cone is one of the characteristic properties for planar aromatic species, which explains the nuclear shielding of neighbor molecules located above and below the molecular plane. Here, we explore its resemblance in spherical aromatic fullerenes, where particularly for C₆₀^6-, it explains the record for the highest shielding observed via ³He-NMR for the endohedral ³He@C₆₀^6- species. Our results compare the behavior for He@C₆₀ and He@C₆₀^6- denoting relevant changes in their magnetic response behavior, where an induced shielding cone was observed for the latter with its long-range shielding character. In contrast to planar aromatics which give rise to a shielding cone property only for a perpendicularly oriented field, it was found that the shielding cone in spherical aromatic fullerenes occurs to any orientation. Thus, the orientation dependence behavior of the shielding cone is accounted, unraveling a characteristic shielding cone pattern in He@C₆₀^6- which further rationalizes its record on the most shielded He nucleus, upon rotation or tumbling from the aromatic ring about the applied field. For the C₇₀ case, the opposite situation has been characterized via ³He-NMR experiments, which is explained in terms of the deshielding/shielding region inside the C₇₀ cage. Graphical abstract.

Planar ten-membered 10-π-electron aromatic (CH)5(XH)5 {X = Ge, Sn} systems

Being monocyclic planar, benzene retains 6π Hückel aromatic backbone. However, for larger analogues, the repulsion between vicinal C-H bonds makes them nonplanar, as for [10]-annulene. Thus, on this basis, a planar 10-π-aromatic C₁₀H₁₀ is unreachable. A detailed structural comparison among the C₃H₃⁺, C₄H₄²⁺, C₅H₅^-, C₆H₆, C₇H₇⁺, C₈H₈²⁺, C₉H₉^-, and C₁₀H₁₀ systems supports that the repulsion between vicinal C-H bonds is the primary reason for the loss of planarity, despite the favorable aromatic electron count. In this respect, here we have discussed ten-membered monocyclic planar 10-π-aromatic, (CH)₅(XH)₅ {X = Si, Ge, Sn} systems, modeled by using DFT. From NBO analysis and the overall magnetic behavior it is shown that (CH)₅(GeH)₅, (CH)₅(SnH)₅ molecules are promising planar 10-π-aromatic system. Thus, such species represent plausible Hückel aromatic rings retaining a ten-membered backbone as discussed here, which may lead to the characterization of novel species expanding the chemistry of larger aromatic rings. We believe that the present study may open new avenues in the formation of 10-π-aromatic species. Graphical abstract Molecular modeling in quest of a planar 10-membered 10-π-electron aromatic system.

NMR methods for studying protein-protein interactions involved in translation initiation

Translation in the cell is carried out by complex molecular machinery involving a dynamic network of protein-protein and protein-RNA interactions. Along the multiple steps of the translation pathway, individual interactions are constantly formed, remodeled, and broken, which presents special challenges when studying this sophisticated system. NMR is a still actively developing technology that has recently been used to solve the structures of several translation factors. However, NMR also has a number of other unique capabilities, of which the broader scientific community may not always be aware. In particular, when studying macromolecular interactions, NMR can be used for a wide range of tasks from testing unambiguously whether two molecules interact to solving the structure of the complex. NMR can also provide insights into the dynamics of the molecules, their folding/unfolding, as well as the effects of interactions with binding partners on these processes. In this chapter, we have tried to summarize, in a popular format, the various types of information about macromolecular interactions that can be obtained with NMR. Special attention is given to areas where the use of NMR provides unique information that is difficult to obtain with other approaches. Our intent was to help the general scientific audience become more familiar with the power of NMR, the current status of the technological limitations of individual NMR methods, as well as the numerous applications, in particular for studying protein-protein interactions in translation.

Production in two-liter beverage bottles of proteins for NMR structure determination labeled with either 15N- or 13C-15N

The use of 2-L polyethylene terephthalate beverage bottles as a bacterial culture vessel has been recently introduced as an enabling technology for high-throughput structural biology [Sanville Millard, C. et al., 2003. Protein Express. Purif. 29, 311-320]. In the article following this one [Stols et al., this issue, pp. 95-102], this approach was elaborated for selenomethionine labeling used for multiwavelength anomalous dispersion phasing in the X-ray crystallographic determinations of protein structure. Herein, we report an effective and reproducible schedule for uniform 15N- and 13C-labeling of recombinant proteins in 2-L beverage bottles for structural determination by NMR spectroscopy. As an example, three target proteins selected from Arabidopsis thaliana were expressed in Escherichia coli Rosetta (DE3)/pLysS from a T7-based expression vector, purified, and characterized by electrospray ionization mass spectrometry and NMR analysis by 1H-15N heteronuclear single quantum correlation spectroscopy. The results show that expressions in the unlabeled medium provide a suitable control for estimation of the level of production of the labeled protein. Mass spectral characterizations show that the purified proteins contained a level of isotopic incorporation equivalent to the isotopically labeled materials initially present in the growth medium, while NMR analysis of the [U-15N]-labeled proteins provided a convenient method to assess the solution state properties of the target protein prior to production of a more costly double-labeled sample.

Modeling of the structural features of integral-membrane proteins reverse-environment prediction of integral membrane protein structure (REPIMPS)

The Profiles-3D application, an inverse-folding methodology appropriate for water-soluble proteins, has been modified to allow the determination of structural properties of integral-membrane proteins (IMPs) and for testing the validity of solved and model structures of IMPs. The modification, known as reverse-environment prediction of integral membrane protein structure (REPIMPS), takes into account the fact that exposed areas of side chains for many residues in IMPs are in contact with lipid and not the aqueous phase. This (1) allows lipid-exposed residues to be classified into the correct physicochemical environment class, (2) significantly improves compatibility scores for IMPs whose structures have been solved, and (3) reduces the possibility of rejecting a three-dimensional structure for an IMP because the presence of lipid was not included. Validation tests of REPIMPS showed that it (1) can locate the transmembrane domain of IMPs with single transmembrane helices more frequently than a range of other methodologies, (2) can rotationally orient transmembrane helices with respect to the lipid environment and surrounding helices in IMPs with multiple transmembrane helices, and (3) has the potential to accurately locate transmembrane domains in IMPs with multiple transmembrane helices. We conclude that correcting for the presence of the lipid environment surrounding the transmembrane segments of IMPs is an essential step for reasonable modeling and verification of the three-dimensional structures of these proteins.

Introduction to NMR of proteins

This unit aims to overview the application of NMR spectroscopy to proteins. It is not intended to provide an exhaustive "how to" guide, but rather to give a flavor of both well-established and emerging NMR techniques used in the elucidation of protein structure. It starts with a brief introduction to the basic principles of NMR and the information provided by this technique, and goes on to discuss the instrumentation involved, spectral assignment methods for small and large proteins, and the utility of other spin active nuclei (e.g., (13)C and (15)N) to aid assignment of the latter.

Protein engineering by expressed protein ligation

By allowing the controlled assembly of synthetic peptides and recombinant polypeptides, expressed protein ligation permits unnatural amino acids, biochemical probes, and biophysical probes to be specifically incorporated into semisynthetic proteins. A powerful feature of the method is its modularity; once the reactive recombinant pieces are in hand and the optimal ligation conditions have been developed, it is possible to quickly generate an array of semisynthetic analogs by simply attaching different synthetic peptide cassettes--in most cases the synthetic peptides will be small and easy to make. From a practical perspective, the rate-determining step in the process is usually not the ligation step (it is based on a simple and efficient chemical reaction), but rather the generation of the reactive polypeptide building blocks. In particular, optimizing the yields of recombinant polypeptide building blocks can require some initial effort. However, it should be noted that the initial investment in time required to optimize the production of the recombinant fragment is offset by the ease and speed with which one can produce the material thereafter. In the example described in this chapter, the yield of soluble intein fusion protein was slightly better using the GyrA intein than for the VMA intein, although in both cases significant amounts of fusion protein were present in the cell pellet. Studies are currently underway to identify optimal refolding conditions for GyrA fusion proteins solubilized from inclusion bodies.

Applications of NMR in drug discovery

In the half-century since its discovery, nuclear magnetic resonance (NMR) has become the single most powerful form of spectroscopy in both chemistry and structural biology. The dramatic technical advances over the past 10-15 years, which continue apace, have markedly increased the range of applications for NMR in the study of protein-ligand interactions. These form the basis for its most exciting uses in the drug discovery process, which range from the simple identification of whether a compound (or a component of a mixture) binds to a given protein, through to the determination of the full three-dimensional structure of the complex, with all the information this yields for structure-based drug design.

Molecular symmetry as an aid to geometry determination in ligand protein complexes

Dipole-dipole couplings between pairs of spin 12 nuclei, which can be measured from NMR spectra in field-ordered media, offer useful constraints on the orientation of various fragments in molecular systems. However, the orientation of fragments relative to a molecule fixed reference frame is often key to complete structure determination. Here, we demonstrate that the symmetry properties of molecular complexes can aid in the definition of a reference frame. It is shown that a threefold rotational symmetry axis dictates the direction and symmetry of the experimentally determined order tensor for alpha-methyl-mannose in fast exchange among the three symmetry-related binding sites of mannose binding protein. This approach facilitates studies of the geometry of the ligand in the protein-ligand complex and also may provide a novel route to structure determination of a homomultimeric protein.

NMR spectroscopy of large molecules and multimolecular assemblies in solution

New strategies and technical advances in NMR spectroscopy and biochemical methods for isotope labeling have enabled solution NMR studies of biomacromolecular systems of 100 kDa and larger. Recent progress has been made, in particular, with techniques for sequential resonance assignments, novel approaches for the direct observation of hydrogen bonds in nucleic acids and proteins, and segmental isotope labeling.

Peptide ligation and its application to protein engineering

The ability to assemble a target protein from a series of peptide fragments, either synthetic or biosynthetic in origin, enables the covalent structure of a protein to be modified in an unprecedented fashion. The present technologies available for performing such peptide ligations are discussed, with an emphasis on how these methodologies have been utilized in protein engineering to investigate biological processes.