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Solid-state NMR on Larger Biomolecules

By: Marc Baldus, ISOTEC® Stable Isotopes: Products for Solid State NMR, 2010, 2–4

Marc Baldus
Bijvoet Center for Biomolecular Research
Utrecht University,
Padualaan 8, 3584 CH Utrecht
The Netherlands

Introduction

In the last years, remarkable progress has been made to probe molecular structure of biological systems using Magic Angle Spinning solid-state NMR (ssNMR). Prominent examples relate to research areas that have remained challenging to classical structural biology methods such as membrane proteins1,2 and protein fibrils (see, e.g., Ref.3,4,5). In addition, ssNMR continues to contribute to a structural understanding of basic biological processes including enzyme catalysis or photosynthesis and is capable of studying far more complicated heterogeneous biomolecular systems such as bacterial cell walls6 or inclusion bodies7,8. Clearly, these advancements would have been impossible without methodological and instrumental progress in the field of ssNMR and the pioneering work of Griffin, Opella, Cross, Torchia and others in the field of biomolecular ssNMR. Yet, a decade ago, it was still unclear whether one would be able to obtain sequential assignments of larger proteins, not to mention the determination of their 3D structures from ssNMR data. Since then, ssNMR progress has been substantial and improvements in the field of solutionstate NMR continue to cross fertilize and speed up developments in solid-state NMR. Finally, the revolutionary developments in biochemistry and molecular biology in combination with isotope-labelling, and in more general sense, the ability to design biomolecular sample preparations for ssNMR studies has played a critical role. With further increasing molecular size, for example relating to proteins comprising several hundred amino acids, new challenges and opportunities lay ahead of us.

Biomolecular (Supra)structure & Dynamics

Isotope-labelling plays a critical role in establishing structural constraints using CC, CHHC or related correlation methods in a biomolecular context. Such experiments have thus far been crucial to determine molecular structures of larger peptides and proteins from MAS ssNMR data (for reviews, see e.g. Ref.9,10). Usually, uniform (13C,15N) isotope labeling is employed to perform an initial spectroscopic characterization of the biomolecule of interest. In polypeptides, a simple comparison of the 2D (13C,13C) cross peak pattern can be sufficient to assess structural homogeneity and short-range order. In the next stage, 15N spectra and, in particular, (15N,13C) 2D data further report on molecular order and 1H bonding. In such correlation experiments, polarization transfer can either involve through-space and through-bond interactions. The choice which polarization transfer scheme is most suitable may depend on experimental parameters such as available MAS rate, sample conditions (for example proteoliposomes vs. microcrystals) and intrinsic molecular properties such as mobility and polymorphism.

Using uniformly labeled samples, near-complete resonance assignments of several proteins encompassing about 100 amino-acids have been reported. In larger systems, three and potentially higher-dimensional correlation experiments that have already been described in the literature (see, e.g., Ref.11,12) are needed. Moreover, alternative isotope-labelling strategies play a prominent role to reduce spectral crowding in larger systems. For a long time, (see e.g. Ref.13) “forward” labeling where isotopelabeled amino acids are added to the growth medium have been used. Although such methods often do not totally remove spectral ambiguity, they strongly reduce spectroscopic overlap. “Pair-wise” amino acid labeling may be sufficient to isolate ssNMR signals of a specific residue. Recent applications of such strategies for example relate to larger membrane proteins14,15. In addition, block labeling16,17 as well as reverse18 labeling strategies have successfully been used in ssNMR. In these experiments, a dedicated set of amino-acid precursors or amino acids is used during expression. The combination of such measures was, for example, employed in the case of microcrystalline proteins19, amyloid4 and membrane proteins20,21. With increasing molecular size another option can be segmental labeling, in which only a fraction of the protein is studied and data are compared to larger constructs. Such “divide-and-conquer” strategies were for example employed to reassembled proteins22 and multi-domain membrane proteins23.

In general, intermolecular interactions play a prominent role in the solid state24 and structural studies in microcrystalline proteins or amyloid fibrils have employed dedicated labeling patterns that separate polarization transfer dynamics due to intra – or intermolecular transfer24 and the quenching thereof25. Indeed, mixing molecular species in different labeling patterns furthermore offers a route to probe intermolecular contacts in ssNMR4,26. In membranes, additional interactions involving the lipid-protein interface or surrounding water can be used to infer molecular orientation and global structure (see, e.g., Ref.27,28) and, at the same time, reduce spectral congestion.

Spectral simplification furthermore can be obtained using mobility filters 29 that separate signals sets of mobile and rigid protein components. Similar to the solution state, an additional reduction in spectral complexity may be obtained using paramagnetic quenchers and 1H/2H exchange experiments. In addition to the study of molecular motion, protein deuteration has been demonstrated to significantly enhance the possibilities to include proton evolution and detection dimensions in MAS-based solidstate NMR experiments. Such approaches have been useful to establish structural constraints of solid-phase proteins30,31,32 or to characterize protein-water interactions using multi-dimensional ssNMR methods33. With increasing levels of deuteration, impressive improvements in 1H line width have been reported34. Yet, protein deuteration often reduces protein expression levels, influences ssNMR resonance frequencies and CP efficiencies and compromises the possibility to probe structurally relevant protonproton distance constraints. As a result, ssNMR applications to complex biomolecules have thus far been limited. In the future, the combination of fractionally deuterated biomolecules, ultrahigh speed MAS and the use of dedicated multiple-pulse schemes may provide a compromise between enhanced 1H resolution and structural information.

Integrated approaches

Clearly, ssNMR provides a rich source of structural and dynamical information, even if molecules become larger and additional studies are necessary to streamline the determination of molecular structure and dynamics by ssNMR methods. At the same time, advances in other research areas such as theoretical chemistry and molecular modeling are taking place. These developments along with the increasing utility of other biophysical techniques strongly suggest that future biomolecular applications of ssNMR will profit from applying hybrid concepts to solve a challenging problem in structural biology or material science.

Already, the ability to predict the ssNMR shift from first principles or using hybrid strategies has changed the ways in which (isotropic and anisotropic) chemical-shift information is used. In proteins, the increasingly accurate correlation between ssNMR chemical shift and structure35 can be used to assess secondary structure or estimate structural changes. Other integrated approaches may combine NMR and molecular dynamics or modelling. For example, combining ssNMR, solution-state NMR and in silico modeling, we recently characterized structural and functional aspects of a 400 aa protein complex in membranes23. In these experiments, the judicious choice of the amino-acid labeling pattern was crucial to provide sufficient spectral resolution. It seems likely that such studies, together with the application of three – or even higher-dimensional ssNMR correlation experiments (see, e.g., 11,12) will improve the prospects to study large biomolecules under functionally relevant conditions.

Outlook

Post-genomic research efforts, high-throughput methodology and advances in areas such as mass spectrometry or electron microscopy have revealed that biological functioning is controlled by biomolecular interaction networks, often in a heterogeneous and dense molecular environment. For example, the cellular response to outside stimuli such as light or nutrients or the process of protein aggregation in the context of Alzheimer’s or Parkinson’s disease are taking place in a more complex and dense cellular environment than previously envisioned. To understand these fundamental processes at atomic resolution and restore them in a pharmacological context, structural biology tools are needed that can be applied in a complex molecular environment. SsNMR clearly has made progress to address such systems on the molecular level. At the same time, ssNMR can probe a large dynamic range, giving insight into molecular processes that take place from the time frame of nanoseconds to seconds.

With increasing molecular complexity, both spectroscopic sensitivity and resolution are of critical importance. Recently, exciting concepts that aim at enhancing ssNMR sensitivity have been described. These range from combining paramagnetic doping and ultra-fast Magic Angle Spinning (MAS)36 to the widespread application of Dynamic Nuclear Polarization (DNP)37. Such techniques will spark the development of additional sample preparation routes. For example, the combination of isotope and paramagnetic labeling, the introduction of non-natural amino acids or the tailored use of polarization agents will provide new possibilities to study biomolecules of increasing complexity.

At the same time, advancements in ssNMR methodology and instruments are likely to push the current boundary conditions of biomolecular ssNMR. Proteoliposomal complexes, cellular extracts, whole-cell preparations or tissue samples are just a few of the potential areas that ssNMR may be able to tackle in the future. Clearly, the prospects for ssNMR as a biomolecular tool to bridge the gap between traditional structural biology and cell biology are exciting and, without doubt, state-of-the-art sample preparation methods will be of vital relevance to realize such goals in the future.

Materials

     

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