Solid-state NMR Approach Research Articles

Solid-state NMR compositional analysis of sputum from people with cystic fibrosis

People with the genetic disease cystic fibrosis (CF) often have chronic airway infections and produce airway secretions called sputum. A better understanding of sputum composition is desired in order to track changes in response to CF therapeutics and to improve laboratory models for the study of CF airway infections. The glycosylated protein mucin is a primary component. Along with extracellular DNA, mucin gives rise to the high viscoelasticity of sputum, which inhibits airway clearance and is thought to promote chronic airway infections in people with CF. Past studies of sputum composition identified additional biomolecular components of sputum including other proteins, both glycosylated and not glycosylated, free amino acids, and lipids. Typically, studies of sputum, as well as other complex biological materials, have focused on soluble or isolated components. Solid-state NMR is not limited to the study of soluble components. Instead, it can provide molecular-level information about insoluble biological samples. Additionally, solid-state NMR can provide information about sample composition without requiring any processing of the sample, eliminating the possibility of misestimating certain components due to insolubility or potential sample loss in isolation steps. In this study, we used both 13C and 31P CPMAS to investigate the total composition of sputum samples obtained from six people with CF. We compared these spectra to those of commercially available mucin, DNA, and phospholipid samples. Lastly, we performed complementary biochemical analyses to identify specific proteins present in the sputum samples. Overall, our findings provide insight into the composition of unprocessed sputum samples from people with CF, which can be used as a benchmark for future investigations of CF and infections in the airways of people with CF. Further, this study provides opportunities to expand the solid-state NMR approach to include dynamic nuclear polarization (DNP) to obtain high-resolution information of sputum and similar biological samples that are not feasible to isotopically enrich.

A comprehensive solid-state NMR and theoretical modeling study to reveal the structural evolution of layered yttrium hydroxide upon calcination

Layered rare earth hydroxides (LREHs) are a new family of ion-exchangeable layered metal hydroxides, which have extensive applications in various fields due to the unique properties of rare earth cations in the layered structure and the anion exchange capacity. The transformation of layered metal hydroxides to new layered phases that can be restored through the memory effect is critical for their chemistry and applications. However, the structure details of these new phases such as the coordination environments of rare earth cations/counterions and their evolution as a function of calcination temperature remain unclear to date. Herein, a comprehensive 89Y/35Cl solid-state NMR (ssNMR) and theoretical modeling approach was used to reveal the structural evolution of a representative LREH, namely LYH-Cl, upon calcination. We first identified partial decomposition products of Y3O(OH)5Cl2 and Y(OH)3 during the dehydration stage, then uncovered the preferential removal of hydroxide ions on yttrium sites coordinated with chlorine during the dehydroxylation stage, and finally determined the preferential removal of chlorine exposed to the surface of layers during the dechlorination stage. The coordination environments of Y3+ and Cl− undergo significant changes upon calcination, revealed by ssNMR experiments. These findings thus help us to overcome the obstacles impeding the rational design and synthesis of LREH-based functional materials via memory effect, underscoring the vast potential of ssNMR in deepening the understanding of layered metal hydroxides and related materials.

Solid-state NMR spectroscopic analysis for structure determination of a zinc-bound catalytic amyloid fibril.

Zinc ions are commonly involved in enzyme catalysis and protein structure stabilization, but their coordination geometry of zinc-protein complex is rarely determined. Here, in this chapter, we introduce a systematic solid-state NMR approach to determine the oligomeric assembly and Zn2+ coordination geometry of a de novo designed amyloid fibrils that catalyze zinc dependent ester hydrolysis. NMR chemical shifts and intermolecular contacts confirm that the peptide forms parallel-in-register β-sheets, with the two forms of Zn2+ bound histidines in each peptide. The amphiphilic parallel β-sheets assemble into stacked bilayers that are stabilized by hydrophobic side chains between β-sheets. The conformations of the histidine side chains, determined by 13C-15N distance measurements, reveal how histidines protrude from the β-sheet. 1H-15N correlation spectra show that the single-Zn2+ coordinated histidine associated with dynamic water. The resulting structure provides insight into how metal ions contribute to stabilizing the protein structure and driving its catalytic reactivity.

Rapid Determination of the Topology of Oligomeric α-Helical Membrane Proteins by Water- and Lipid-Edited Methyl NMR.

Single-span oligomeric α-helical transmembrane proteins are common in virus ion channels, which are targets of antiviral drugs. Knowledge about the high-resolution structures of these oligomeric α-helical bundles is so far scarce. Structure determination of these membrane proteins by solid-state NMR traditionally requires resolving and assigning protein chemical shifts and measuring many interhelical distances, which are time-consuming. To accelerate experimental structure determination, here we introduce a simple solid-state NMR approach that uses magnetization transfer from water and lipid protons to the protein. By detecting the water- and lipid-transferred intensities of the high-sensitivity methyl 13C signals of Leu, Val, and Ile residues, which are highly enriched in these membrane proteins, we can derive models of the topology of these homo-oligomeric helical bundles. The topology is specified by the positions of amino acid residues in heptad repeats and the orientations of residues relative to the channel pore, lipids, and the helical interface. We demonstrate this water- and lipid-edited methyl NMR approach on the envelope (E) protein of SARS-CoV-2, the causative agent of the COVID-19 pandemic. We show that water-edited and lipid-edited 2D 13C-13C correlation spectra can be measured with sufficient sensitivity. Even without resolving multiple residues of the same type in the NMR spectra, we can obtain the helical bundle topology. We apply these experiments to the structurally unknown E proteins of the MERS coronavirus and the human coronavirus NL63. The resulting structural topologies show interesting differences in the positions of the aromatic residues in these three E proteins, suggesting that these viroporins may have different mechanisms of activation and ion conduction.

A high-field cellular DNP-supported solid-state NMR approach to study proteins with sub-cellular specificity.

Studying the structural aspects of proteins within sub-cellular compartments is of growing interest. Dynamic nuclear polarization supported solid-state NMR (DNP-ssNMR) is uniquely suited to provide such information, but critically lacks the desired sensitivity and resolution. Here we utilize SNAPol-1, a novel biradical, to conduct DNP-ssNMR at high-magnetic fields (800 MHz/527 GHz) inside HeLa cells and isolated cell nuclei electroporated with [13C,15N] labeled ubiquitin. We report that SNAPol-1 passively diffuses and homogenously distributes within whole cells and cell nuclei providing ubiquitin spectra of high sensitivity and remarkably improved spectral resolution. For cell nuclei, physical enrichment facilitates a further 4-fold decrease in measurement time and provides an exclusive structural view of the nuclear ubiquitin pool. Taken together, these advancements enable atomic interrogation of protein conformational plasticity at atomic resolution and with sub-cellular specificity.

(Invited) Elucidating the Structure and Function of the Electrode-Electrolyte Interface By New Solid State NMR Approaches

The development of high-energy, long-lasting energy storage systems based on rechargeable batteries relies on our ability to control charge storage and degradation processes in the bulk of the electrode materials and at the electrode-electrolyte interface. NMR spectroscopy is exceptionally suited to follow the electrochemical and chemical processes in the bulk of the electrodes and electrolyte, providing atomic scale structural insight into the charge storage mechanisms and ion transport properties. However, interfacial properties, such as the processes governing charge transport between the electrode and the electrolyte, are much harder to study. These processes typically involve thin, heterogeneous and disordered layers that are formed chemically/electrochemically in the battery cell or artificially through coating the electrode material. While NMR is in principle an excellent approach for probing disordered phases, its low sensitivity presents an enormous challenge in the detection of interfacial processes.In this talk I will describe recent approaches to overcome the sensitivity limitation by the use of Dynamic Nuclear Polarization (DNP). In DNP, the large electron spin polarization is used to boost the sensitivity of NMR spectroscopy by orders of magnitude. I will show how we can use this approach to detect the solid-electrolyte interphase (SEI), electrode coatings as well as the electrode’s bulk, with unprecedented sensitivity. Furthermore, I will present new approaches to probe ion transport properties of various interfaces. These allow us to get insight into the functional role of interfaces, which along with the chemical and structural insight, can provide design rules for beneficial interfaces, an essential aspect for developing long-lasting energy storage systems.

Imaging active site chemistry and protonation states: NMR crystallography of the tryptophan synthase α-aminoacrylate intermediate

NMR-assisted crystallography-the integrated application of solid-state NMR, X-ray crystallography, and first-principles computational chemistry-holds significant promise for mechanistic enzymology: by providing atomic-resolution characterization of stable intermediates in enzyme active sites, including hydrogen atom locations and tautomeric equilibria, NMR crystallography offers insight into both structure and chemical dynamics. Here, this integrated approach is used to characterize the tryptophan synthase α-aminoacrylate intermediate, a defining species for pyridoxal-5'-phosphate-dependent enzymes that catalyze β-elimination and replacement reactions. For this intermediate, NMR-assisted crystallography is able to identify the protonation states of the ionizable sites on the cofactor, substrate, and catalytic side chains as well as the location and orientation of crystallographic waters within the active site. Most notable is the water molecule immediately adjacent to the substrate β-carbon, which serves as a hydrogen bond donor to the ε-amino group of the acid-base catalytic residue βLys87. From this analysis, a detailed three-dimensional picture of structure and reactivity emerges, highlighting the fate of the L-serine hydroxyl leaving group and the reaction pathway back to the preceding transition state. Reaction of the α-aminoacrylate intermediate with benzimidazole, an isostere of the natural substrate indole, shows benzimidazole bound in the active site and poised for, but unable to initiate, the subsequent bond formation step. When modeled into the benzimidazole position, indole is positioned with C3 in contact with the α-aminoacrylate Cβ and aligned for nucleophilic attack. Here, the chemically detailed, three-dimensional structure from NMR-assisted crystallography is key to understanding why benzimidazole does not react, while indole does.

Resolving Atomic‐Scale Interactions in Nonfullerene Acceptor Organic Solar Cells with Solid‐State NMR Spectroscopy, Crystallographic Modelling, and Molecular Dynamics Simulations

Fused-ring core nonfullerene acceptors (NFAs), designated "Y-series," have enabled high-performance organic solar cells (OSCs) achieving over 18% power conversion efficiency (PCE). Since the introduction of these NFAs, much effort has been expended to understand the reasons for their exceptional performance. While several studies have identified key optoelectronic properties that govern high PCEs, little is known about the molecular level origins of large variations in performance, spanning from 5% to 18% PCE, for example, in the case of PM6:Y6 OSCs. Here, a combined solid-state NMR, crystallography, and molecular modeling approach to elucidate the atomic-scale interactions in Y6 crystals, thin films, and PM6:Y6 bulk heterojunction (BHJ) blends is introduced. It is shown that the Y6 morphologies in BHJ blends are not governed by the morphology in neat films or single crystals. Notably, PM6:Y6 blends processed from different solvents self-assemble into different structures and morphologies, whereby the relative orientations of the sidechains and end groups of the Y6 molecules to their fused-ring cores play a crucial role in determining the resulting morphology and overall performance of the solar cells. The molecular-level understanding of BHJs enabled by this approach will guide the engineering of next-generation NFAs for stable and efficient OSCs.

Evidence for amylose inclusion complexes with multiple acyl chain lipids using solid-state NMR and theoretical approaches

Amylose is known to form inclusion complexes in the presence of hydrophobic guests. Among lipids, only single-chain fatty acids have been reported as possible guests with the surrounding amylose in a well-defined V-helix conformation. Using experimental 13C solid-state NMR, we studied the formation of inclusion complexes between amylose and a variety of multiple-chains lipids of increasing complexity. Molecular dynamics simulations and calculations of 13C isotropic chemical shifts using the Density Functional Theory approach were performed to support the interpretation of experimental spectra. We provide unambiguous evidences that amylose forms inclusion complexes with lipids bearing multiple acyl chains. Amylose conformations around these lipids are characterized by {ϕ,ψ} anomeric bond dihedral angles near {115°,105°}. In the 13C NMR spectra, this translates into C1 and C4 chemical shifts of 102.5 ppm and 81.1 ppm, regardless of the helical conformation of the amylose surrounding the acyl chains.

A novel multinuclear solid-state NMR approach for the characterization of kidney stones.

The spectroscopic study of pathological calcifications (including kidney stones) is extremely rich and helps to improve the understanding of the physical and chemical processes associated with their formation. While Fourier transform infrared (FTIR) imaging and optical/electron microscopies are routine techniques in hospitals, there has been a dearth of solid-state NMR studies introduced into this area of medical research, probably due to the scarcity of this analytical technique in hospital facilities. This work introduces effective multinuclear and multidimensional solid-state NMR methodologies to study the complex chemical and structural properties characterizing kidney stone composition. As a basis for comparison, three hydrates (, 2 and 3) of calcium oxalate are examined along with nine representative kidney stones. The multinuclear magic angle spinning (MAS) NMR approach adopted investigates the , , and nuclei, with the and MAS NMR data able to be readily deconvoluted into the constituent elements associated with the different oxalates and organics present. For the first time, the full interpretation of highly resolved NMR spectra is presented for the three hydrates, based on the structure and local dynamics. The corresponding MAS NMR data indicates the presence of low-level inorganic phosphate species; however, the complexity of these data make the precise identification of the phases difficult to assign. This work provides physicians, urologists and nephrologists with additional avenues of spectroscopic investigation to interrogate this complex medical dilemma that requires real, multitechnique approaches to generate effective outcomes.

Surface Fingerprinting of Faceted Metal Oxides and Porous Zeolite Catalysts by Probe-Assisted Solid-State NMR Approaches.

Acid catalysis in heterogeneous systems such as metal oxides and porous zeolites has been widely involved in various catalytic processes for chemical and petrochemical industries. In acid-catalyzed reactions, the performance (e.g., activity and selectivity) is closely associated with the acidic features of the catalysts, viz., type (Lewis vs Brønsted acidity), distribution (external vs internal surface), strength (strong vs weak), concentration (amount), and spatial interactions of acidic sites. The characterization of local structure and acidic properties of these active sites has important implications for understanding the reaction mechanism and the practical catalytic applications of acidic catalysts. Among diverse acidity characterization approaches, the solid-state nuclear magnetic resonance (SSNMR) technique with suitable probe molecules has been recognized as a reliable and versatile tool. Such a probe-assisted SSNMR approach could provide qualitative (type, distribution, and spatial interactions) and quantitative (strength and concentration) information on each acidic site. This Account aims to integrate our recent important findings in determining the structures and acidic characteristics of some typical metal oxide and zeolite catalysts by using the probe-assisted SSNMR technique, as well as clarifying the continuously evolving process of each discrete acidic site under hydrothermal or chemical treatments even at the molecular level with multiscale theoretical simulations.More specifically, we will describe herein the development and applications of the probe-assisted SSNMR methods, such as trimethylphosphine (TMP) and acetonitrile-d3 (CD3CN) in conjunction with advanced two-dimensional (2D) homo- and heteronuclear correlation spectroscopy, for characterizing the structures and properties of acidic sites in varied solid catalysts. Moreover, relevant information regarding the surface fingerprinting of various facets on crystalline metal oxide nanoparticles and active centers inside porous zeolites, the mapping of relevant spatial interactions, and the verification of structure-activity correlation were investigated as well. Relevant discussions are mainly based on the recent NMR experiments of our collaborating research groups, including (i) determining the acidic characterization with probe-assisted SSNMR approaches, (ii) mapping various active centers (or crystalline facets), and (iii) revealing their influence on catalytic performance of solid acid catalyst systems. It is anticipated that this information may provide more in-depth insights toward our fundamental understanding of solid acid catalysis.

Solid-State NMR Spectroscopy for Studying Microtubules and Microtubule-Associated Proteins.

In this chapter, we describe the preparatory and spectroscopic procedures forconducting solid-state NMR experiments on microtubules (MTs) obtained from human cells and their complexes with microtubule-associated proteins (MAPs). Next to labeling and functional assembly of MTs and MT-MAP complexes, we discuss solid-state NMR approaches, including fast MAS and hyperpolarization methods that can be used to examine these systems. Such studies can provide novel insight into the dynamic properties of MTs and MT-MAP complexes.

Solid-state NMR approaches to investigate large enzymes in complex with substrates and inhibitors.

Enzyme catalysis is omnipresent in the cell. The mechanisms by which highly evolved protein folds enable rapid and specific chemical transformation of substrates belong to the marvels of structural biology. Targeting of enzymes with inhibitors has immediate application in drug discovery, from chemotherapeutics over antibiotics to antivirals. NMR spectroscopy combines multiple assets for the investigation of enzyme function. The non-invasive technique can probe enzyme structure and dynamics and map interactions with substrates, cofactors and inhibitors at the atomic level. With experiments performed at close to native conditions, catalytic transformations can be monitored in real time, giving access to kinetic parameters. The power of NMR in the solid state, in contrast with solution, lies in the absence of fundamental size limitations, which is crucial for enzymes that are either membrane-embedded or assemble into large soluble complexes exceeding hundreds of kilodaltons in molecular weight. Here we review recent progress in solid-state NMR methodology, which has taken big leaps in the past years due to steady improvements in hardware design, notably magic angle spinning, and connect it to parallel biochemical advances that enable isotope labelling of increasingly complex enzymes. We first discuss general concepts and requirements of the method and then highlight the state-of-the-art in sample preparation, structure determination, dynamics and interaction studies. We focus on examples where solid-state NMR has been instrumental in elucidating enzyme mechanism, alone or in integrative studies.

Improved Understanding of Atomic Ordering in Y4SixAl2–xO9–xNx Materials Using a Combined Solid-State NMR and Computational Approach

Ceramics based around silicon aluminum oxynitrides are of both fundamental structural chemistry and technological interest. Certain oxynitride crystal structures allow very significant compositional variation through extensive Si/N exchange for Al/O, which implies a degree of atomic ordering. In this study, solid-state 29Si MAS NMR and variable field 1D and 2D 27Al MAS NMR measurements are combined with density functional theory calculations of both the structural and NMR interaction parameters for various points across the Y4Si2O7N2-Y4Al2O9 compositional range. This series provides numerous possibilities for significant variation of atomic ordering in the local ditetrahedral (Si,Al)2O7-xNx units. The two slightly structurally inequivalent aluminum sites in Y4Al2O9 are unambiguously assigned to the observed resonances. Computational findings on Y4Si2O7N2 demonstrate that the single observed 29Si NMR resonance covers a range of local inequivalent silicon environments. For the first time, the MAS NMR and neutron diffraction data from the Y4SiAlO8N structure have been directly reconciled, thus establishing aspects of atomic order and disorder that characterize this system. This comparison suggests that, although the diffraction data indicates long-range structural order supporting a highly crystalline character, the short-range information afforded by the solid-state NMR measurements indicates significant atomic disorder throughout the (Si,Al)2O7-xNx units.

Site-specific resolution of anionic residues in proteins using solid-state NMR spectroscopy.

NMR spectroscopy is commonly used to infer site-specific acid dissociation constants (pKa) since the chemical shift is sensitive to the protonation state. Methods that probe atoms nearest to the functional groups involved in acid/base chemistry are the most sensitive for determining the protonation state. In this work, we describe a magic-angle-spinning (MAS) solid-state NMR approach to measure chemical shifts on the side chain of the anionic residues aspartate and glutamate. This method involves a combination of double quantum spectroscopy in the indirect dimension and REDOR dephasing to provide a sensitive and resolved view of these amino acid residues that are commonly involved in enzyme catalysis and membrane protein transport. To demonstrate the applicability of the approach, we carried out measurements using a microcrystalline soluble protein (ubiquitin) and a membrane protein embedded in lipid bilayers (EmrE). Overall, the resolution available from the double quantum dimension and confidence in identification of aspartate and glutamate residues from the REDOR filter make this method the most convenient for characterizing protonation states and deriving pKa values using MAS solid-state NMR.

Isolated zirconium centres captured from aqueous solution: the structure of zirconium mandelate revealed from NMR crystallography.

Zirconium tetramandelate (2-hydroxy-2-phenylacetate) has been used for selective gravimetric analysis of zirconium for over 70 years. Herein its crystal structure is reported from synchrotron powder X-ray diffraction and 13C solid-state NMR. The complex is a rare example of isolated zirconium cations, rather than the clusters prevalent in aqueous solutions.

Measuring multiple 17O-13C J-couplings in naphthalaldehydic acid: a combined solid state NMR and density functional theory approach.

A combined multinuclear solid state NMR and gauge included projected augmented wave, density functional theory (GIPAW DFT) computational approach is evaluated to determine the four heteronuclear 1J(13C,17O) couplings in solid 17O enriched naphthalaldehydic acid. Direct multi-field 17O magic angle spinning (MAS), triple quantum MAS (3QMAS) and double rotation (DOR) experiments are initially utilised to evaluate the accuracy of the DFT approximations used in the calculation of the isotropic chemical shifts (δiso), quadrupole coupling constants (CQ) and asymmetry (ηQ) parameters. These combined approaches give δiso values of 313, 200 and 66 ppm for the carbonyl (C[double bond, length as m-dash]O), ether (-O-) and hydroxyl (-OH) environments, respectively, with the corresponding measured quadrupole products (PQ) being 8.2, 9.0 and 10.6 MHz. The geometry optimised DFT structure derived using the CASTEP code gives firm agreement with the shifts observed for the ether (δiso = 223, PQ = 9.4 MHz) and hydroxyl (δiso = 62, PQ = 10.5 MHz) environments but the unoptimised experimental XRD structure has better agreement for the carbonyl group (δiso = 320, PQ = 8.3 MHz). The determined δiso and ηQ values are shown to be consistent with bond lengths closer to 1.222 Å (experimental length) rather than the geometry optimised length of 1.238 Å. The geometry optimised DFT 1J(13C,17O) coupling to the hydroxyl is calculated as 20 Hz and the couplings to the ether were calculated to be 37 (O-C[double bond, length as m-dash]O) and 32 (O-C-OH) Hz. The scalar coupling parameters for the unoptimised experimental carbonyl group predict a 1J(13C,17O) value of 28 Hz, whilst optimisation gives a value of 27 Hz. These calculated 1J(13C,17O) couplings, together with estimations of the probability of each O environment being isotopically labelled (determined by electrospray ionisation mass spectrometry) and the measured refocussable transverse dephasing (T2') behaviour, are combined to simulate the experimental decay behaviour. Good agreement between the measured and calculated decay behaviour is observed.

N-Hydroxysuccinimide-activated esters as a functionalization agent for amino cellulose: synthesis and solid-state NMR characterization

We propose a mild and versatile synthesis protocol based on N-hydroxysuccinimide-activated esters for the introduction of new functionalities to cellulose, using as starting point established protocols for the tosylation of cellulose and its subsequent reaction with a diamine linker. As a proof of concept, we describe the functionalization of microcrystalline cellulose with a N-hydroxysuccinimide-activated ester of benzophenone, a photoreactive functional group. Irradiation of the final product with UV light yields a self-standing polymer film and is expected to result in cross-linking among cellulose chains. To monitor structural changes at the molecular level, each functionalization step is characterized by a multinuclear solid-state NMR approach. DNP-enhanced 15N CP MAS NMR experiments reveal the formation of the amide bond to the photoreactive linker and deliver further information about the binding situation of nitrogen-containing groups in these materials. The flexible synthesis protocol described here can be easily extended to a broad range of other functionalities of interest, both for the cellulose and macromolecular research.

How does the mood stabilizer lithium bind ATP, the energy currency of the cell: Insights from solid-state NMR

BackgroundLithium, in the form of a salt, is a mood stabilizer and a leading drug for the treatment of bipolar disorder. It has a very narrow therapeutic range and a variety of side effects. Lithium can replace magnesium and other cations in enzymes and small molecules, among them ATP, thereby affecting and inhibiting many biochemical pathways. The form of binding of lithium ions to ATP is not known. MethodsHere we extract the binding environment of lithium in solid ATP using a multi-nuclear multi-dimensional solid-state NMR approach. ResultsWe determine that the coordination sphere of lithium includes, at a distance of 3.0(±0.4) Å, three phosphates; the two phosphates closest to the ribose ring from one ATP molecule, and the middle phosphate from another ATP molecule. A water molecule most probably completes the fourth coordination. Despite the use of excess lithium in the preparations, sodium ions still remain bound to the sample, at distances of 4.3–5.5 Å from Li, and coordinate the first phosphate and two terminal phosphates. ConclusionsSolid-state NMR enables to unravel the exact coordination of lithium in ATP showing binding to three phosphates from two molecules, none of which are the terminal gamma phosphate. General significanceThe methods we use are applicable to study lithium bound to a variety of ATP-bound enzymes, or to other cellular targets of lithium, consequently suggesting a molecular basis for its mode of action.

Design Parameters of Tissue‐Engineering Scaffolds at the Atomic Scale

Stem‐cell behavior is regulated by the material properties of the surrounding extracellular matrix, which has important implications for the design of tissue‐engineering scaffolds. However, our understanding of the material properties of stem‐cell scaffolds is limited to nanoscopic‐to‐macroscopic length scales. Herein, a solid‐state NMR approach is presented that provides atomic‐scale information on complex stem‐cell substrates at near physiological conditions and at natural isotope abundance. Using self‐assembled peptidic scaffolds designed for nervous‐tissue regeneration, we show at atomic scale how scaffold‐assembly degree, mechanics, and homogeneity correlate with favorable stem cell behavior. Integration of solid‐state NMR data with molecular dynamics simulations reveals a highly ordered fibrillar structure as the most favorable stem‐cell scaffold. This could improve the design of tissue‐engineering scaffolds and other self‐assembled biomaterials.