Boltzmann statistics rotational-echo double-resonance analysis

On the use of NMR distance measurements for assessing surface site homogeneity

The past few decades have seen tremendous growth in the area of single-site heterogeneous catalysis, which aims to combine the best aspects of homogeneous and heterogeneous catalysis, namely molecular-level site control and ease of separation/recycling. Despite this, we still do not have a means of assessing site homogeneity and whether the produced catalyst is indeed a "single-site". Recent developments have enabled the use of NMR-based distance measurements to determine the conformations and configurations of surface sites, leading to the question whether such measurements can be used to distinguish materials containing either single or multiple surface sites with otherwise indistinguishable NMR properties. We describe a Monte Carlo-based multi-structure search algorithm and its application to the determination of multi-site structures from supported metal complexes. The sensitivity of REDOR data to the existence of multiple sites is assessed using synthetic data and prior literature examples are revisited to determine whether the single-site approximation was indeed appropriate. We lastly apply this new methodology to differentiate the configurations of zirconocene complexes grafted onto alumina supports that were thermally treated at different temperatures.

Ultrafast Magic Angle Spinning Solid-State NMR Spectroscopy: Advances in Methodology and Applications

Solid-state NMR spectroscopy is one of the most commonly used techniques to study the atomic-resolution structure and dynamics of various chemical, biological, material, and pharmaceutical systems spanning multiple forms, including crystalline, liquid crystalline, fibrous, and amorphous states. Despite the unique advantages of solid-state NMR spectroscopy, its poor spectral resolution and sensitivity have severely limited the scope of this technique. Fortunately, the recent developments in probe technology that mechanically rotate the sample fast (100 kHz and above) to obtain "solution-like" NMR spectra of solids with higher resolution and sensitivity have opened numerous avenues for the development of novel NMR techniques and their applications to study a plethora of solids including globular and membrane-associated proteins, self-assembled protein aggregates such as amyloid fibers, RNA, viral assemblies, polymorphic pharmaceuticals, metal-organic framework, bone materials, and inorganic materials. While the ultrafast-MAS continues to be developed, the minute sample quantity and radio frequency requirements, shorter recycle delays enabling fast data acquisition, the feasibility of employing proton detection, enhancement in proton spectral resolution and polarization transfer efficiency, and high sensitivity per unit sample are some of the remarkable benefits of the ultrafast-MAS technology as demonstrated by the reported studies in the literature. Although the very low sample volume and very high RF power could be limitations for some of the systems, the advantages have spurred solid-state NMR investigation into increasingly complex biological and material systems. As ultrafast-MAS NMR techniques are increasingly used in multidisciplinary research areas, further development of instrumentation, probes, and advanced methods are pursued in parallel to overcome the limitations and challenges for widespread applications. This review article is focused on providing timely comprehensive coverage of the major developments on instrumentation, theory, techniques, applications, limitations, and future scope of ultrafast-MAS technology.

Amphotericin B assembles into seven-molecule ion channels: An NMR and molecular dynamics study

Amphotericin B, an antifungal drug with a long history of use, forms fungicidal ion-permeable channels across cell membranes. Using solid-state nuclear magnetic resonance spectroscopy and molecular dynamics simulations, we experimentally elucidated the three-dimensional structure of the molecular assemblies formed by this drug in membranes in the presence of the fungal sterol ergosterol. A stable assembly consisting of seven drug molecules was observed to form an ion conductive channel. The structure is somewhat similar to the upper half of the barrel-stave model proposed in the 1970s but substantially different in the number of molecules and in their arrangement. The present structure explains many previous findings, including structure-activity relationships of the drug, which will be useful for improving drug efficacy and reducing adverse effects.

Transient RNA Interactions Leave a Covalent Imprint on a Viral Capsid Protein

The hepatitis B virus (HBV) is the leading cause of persistent liver infections. Its DNA-based genome is synthesized through reverse transcription of an RNA template inside the assembled capsid shell. In addition to the structured assembly domain, the capsid protein harbors a C-terminal extension that mediates both the enclosure of RNA during capsid assembly and the nuclear entry of the capsid during infection. The arginine-rich motifs within this extension, though common to many viruses, have largely escaped atomic-scale investigation. Here, we leverage solution and solid-state nuclear magnetic resonance spectroscopy at ambient and cryogenic temperatures, under dynamic nuclear polarization signal enhancement, to investigate the organization of the genome within the capsid. Transient interactions with phosphate groups of the RNA backbone confine the arginine-rich motifs to the interior capsid space. While no secondary structure is induced in the C-terminal extension, interactions with RNA counteract the formation of a disulfide bond, which covalently tethers this peptide arm onto the inner capsid surface. Electrostatic and covalent contributions thus compete in the spatial regulation of capsid architecture. This disulfide switch represents a coupling mechanism between the structured assembly domain of the capsid and the enclosed nucleic acids. In particular, it enables the redox-dependent regulation of the exposure of the C-terminal extension on the capsid surface, which is required for nuclear uptake of the capsid. Phylogenetic analysis of capsid proteins from hepadnaviruses points toward a function of this switch in the persistence of HBV infections.

In-cell DNP NMR reveals multiple targeting effect of antimicrobial peptide

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DNP NMR allowed simultaneous monitoring of lipids, proteins and nucleic acids of E. coli cells.

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The bacterial stress response against an antimicrobial peptide was measured in situ.

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The antimicrobial peptide maculatin 1.1 significantly compacted nucleic acids in bacteria.

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Maculatin 1.1 prevented salt bridges forming between membrane lipids.

Dynamic nuclear polarization NMR spectroscopy was used to investigate the effect of the antimicrobial peptide (AMP) maculatin 1.1 on E. coli cells. The enhanced ¹⁵N NMR signals from nucleic acids, proteins and lipids identified a number of unanticipated physiological responses to peptide stress, revealing that membrane-active AMPs can have a multi-target impact on E. coli cells. DNP-enhanced ¹⁵N-observed ³¹P-dephased REDOR NMR allowed monitoring how Mac1 induced DNA condensation and prevented intermolecular salt bridges between the main E. coli lipid phosphatidylethanolamine (PE) molecules. The latter was supported by similar results obtained using E. coli PE lipid systems. Overall, the ability to monitor the action of antimicrobial peptides in situ will provide greater insight into their mode of action.

In-cell Solid-State NMR Studies of Antimicrobial Peptides

Antimicrobial peptides (AMPs) have attracted attention as alternatives to classic antibiotics due to their expected limited pressure on bacterial resistance mechanisms. Yet, their modes of action, in particular in vivo, remain to be elucidated. In situ atomistic-scale details of complex biomolecular assemblies is a challenging requirement for deciphering the complex modes of action of AMPs. The large diversity of molecules that modulate complex interactions limits the resolution achievable using imaging methodology. Herein, the latest advances in in-cell solid-state NMR (ssNMR) are discussed, which demonstrate the power of this non-invasive technique to provide atomic details of molecular structure and dynamics. Practical requirements for investigations of intact bacteria are discussed. An overview of recent in situ NMR investigations of the architecture and metabolism of bacteria and the effect of AMPs on various bacterial structures is presented. In-cell ssNMR revealed that the studied AMPs have a disruptive action on the molecular packing of bacterial membranes and DNA. Despite the limited number of studies, in-cell ssNMR is emerging as a powerful technique to monitor in situ the interplay between bacteria and AMPs.

Toxic Amyloid Tape: A Novel Mixed Antiparallel/Parallel β-Sheet Structure Formed by Amyloid β-Protein on GM1 Clusters

The abnormal aggregation of amyloid β-protein (Aβ) is considered central in the pathogenesis of Alzheimer's disease. We focused on membrane-mediated amyloidogenesis and found that amyloid fibrils formed on monosialoganglioside GM1 clusters were more toxic than those formed in aqueous solution. In this study, we investigated the structure of the toxic fibrils by Aβ-(1-40) in detail in comparison with less-toxic fibrils formed in aqueous solution. The less-toxic fibrils contain in-resister parallel β-sheets, whereas the structure of the toxic fibrils is unknown. Atomic force microscopy revealed that the toxic fibrils had a flat, tape-like morphology composed of a single β-sheet layer. Isotope-edited infrared spectroscopy indicated that almost the entire sequence of Aβ is included in the β-sheet. Chemical cross-linking experiments using Cys-substituted Aβs suggested that the fibrils mainly contained both in-resister parallel and two-residue-shifted antiparallel β-sheet structures. Solid-state NMR experiments also supported this conclusion. Thus, the toxic fibrils were found to possess a novel unique structure.

Probing Ionic Liquid Electrolyte Structure via the Glassy State by Dynamic Nuclear Polarization NMR Spectroscopy

Dynamic nuclear polarization (DNP)-enhanced solid-state NMR spectroscopy has been used to study an ionic liquid salt solution (N-methyl-N-propyl-pyrrolidinium bis(fluorosulfonyl)imide, C₃mpyrFSI, containing 1.0 m lithium bis(fluorosulfonyl)imide, ⁶LiFSI) in its glassy state at a temperature of 92 K. The incorporation of a biradical to enable DNP signal enhancement allowed the proximities of the lithium to the individual carbon sites on the pyrrolidinium cation to be probed using a ¹³C-⁶Li REDOR pulse sequence. Distributions in Li-C distances were extracted and converted into a 3D map of the locations of the Li⁺ relative to the C₃mpyr that shows remarkably good agreement with a liquid-phase molecular dynamics simulation.

Dynamic membrane interactions of antibacterial and antifungal biomolecules, and amyloid peptides, revealed by solid-state NMR spectroscopy

A variety of biomolecules acting on the cell membrane folds into a biologically active structure in the membrane environment. It is, therefore, important to determine the structures and dynamics of such biomolecules in a membrane environment. While several biophysical techniques are used to obtain low-resolution information, solid-state NMR spectroscopy is one of the most powerful means for determining the structure and dynamics of membrane bound biomolecules such as antibacterial biomolecules and amyloidogenic proteins; unlike X-ray crystallography and solution NMR spectroscopy, applications of solid-state NMR spectroscopy are not limited by non-crystalline, non-soluble nature or molecular size of membrane-associated biomolecules. This review article focuses on the applications of solid-state NMR techniques to study a few selected antibacterial and amyloid peptides. Solid-state NMR studies revealing the membrane inserted bent α-helical structure associated with the hemolytic activity of bee venom melittin and the chemical shift oscillation analysis used to determine the transmembrane structure (with α-helix and 310-helix in the N- and C-termini, respectively) of antibiotic peptide alamethicin are discussed in detail. Oligomerization of an amyloidogenic islet amyloid polypeptide (IAPP, or also known as amylin) resulting from its aggregation in a membrane environment, molecular interactions of the antifungal natural product amphotericin B with ergosterol in lipid bilayers, and the mechanism of lipid raft formation by sphingomyelin studied using solid state NMR methods are also discussed in this review article. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.

Antimicrobial Peptide Structures: From Model Membranes to Live Cells

The rise in antibiotic resistance has led to a renewed interest in antimicrobial peptides (AMPs) that target membranes. The mode of action of AMPs involves the disruption of the lipid bilayer and leads to growth inhibition and death of the bacteria. However, details at the molecular level of how these peptides kill bacteria and the reasons for the observed differences in selectivity remain unclear. Structural information is crucial for defining the molecular mechanism by which these peptides recognize, self-assemble and interact with a particular lipid membrane. Solid-state NMR is a non-invasive technique that allows the study of the structural details of lipid-peptide and peptide-peptide interactions. Following on from studies of antibiotic and lytic peptides, gramicidin A and melittin, respectively, we investigated maculatin 1.1, an AMP from the skin of Australian tree frogs that acts against Gram-positive bacteria. By using perdeuterated phospholipids and specifically labelled peptides, ² H, ³¹ P and {³¹ P}¹⁵ N REDOR solid-state NMR experiments have been used to localize, maculatin 1.1 in neutral and anionic model membranes. However, the structure, location and activity depend on the composition of the model membrane and current advances in solid-state NMR spectroscopy now allow structure determination of AMPs in live bacteria.

Amyloid scaffolds as alternative chlorosomes

Living systems contain remarkable functional capability built within sophisticated self-organizing frameworks. Defining the assembly codes that coordinate these systems could greatly extend nanobiotechnology. To that end, we have highlighted the self-assembling architecture of the chlorosome antenna arrays and report the emulation and extension of their features for the development of cell-compatible photoredox materials. We specifically review work on amyloid peptide scaffolds able to (1) organize light-harvesting chromophores, (2) break peptide bilayer symmetry for directional energy and electron transfer, and (3) incorporate redox active metal ions at high density for energy storage.

REDOR solid-state NMR as a probe of the membrane locations of membrane-associated peptides and proteins

Rotational-echo double-resonance (REDOR) solid-state NMR is applied to probe the membrane locations of specific residues of membrane proteins. Couplings are measured between protein (13)CO nuclei and membrane lipid or cholesterol (2)H and (31)P nuclei. Specific (13)CO labeling is used to enable unambiguous assignment and (2)H labeling covers a small region of the lipid or cholesterol molecule. The (13)CO-(31)P and (13)CO-(2)H REDOR respectively probe proximity to the membrane headgroup region and proximity to specific insertion depths within the membrane hydrocarbon core. One strength of the REDOR approach is use of chemically-native proteins and membrane components. The conventional REDOR pulse sequence with 100 kHz (2)H π pulses is robust with respect to the (2)H quadrupolar anisotropy. The (2)H T1's are comparable to the longer dephasing times (τ's) and this leads to exponential rather than sigmoidal REDOR buildups. The (13)CO-(2)H buildups are well-fitted to A×(1-e(-γτ)) where A and γ are fitting parameters that are correlated as the fraction of molecules (A) with effective (13)CO-(2)H coupling d=3γ/2. The REDOR approach is applied to probe the membrane locations of the "fusion peptide" regions of the HIV gp41 and influenza virus hemagglutinin proteins which both catalyze joining of the viral and host cell membranes during initial infection of the cell. The HIV fusion peptide forms an intermolecular antiparallel β sheet and the REDOR data support major deeply-inserted and minor shallowly-inserted molecular populations. A significant fraction of the influenza fusion peptide molecules form a tight hairpin with antiparallel N- and C-α helices and the REDOR data support a single peptide population with a deeply-inserted N-helix. The shared feature of deep insertion of the β and α fusion peptide structures may be relevant for fusion catalysis via the resultant local perturbation of the membrane bilayer. Future applications of the REDOR approach may include samples that contain cell membrane extracts and use of lower temperatures and dynamic nuclear polarization to reduce data acquisition times.

Progression of NMR studies of membrane-active peptides from lipid bilayers to live cells

Understanding the structure of membrane-active peptides faces many challenges associated with the development of appropriate model membrane systems as the peptide structure depends strongly on the lipid environment. This perspective provides a brief overview of the approach taken to study antimicrobial and amyloid peptides in phospholipid bilayers using oriented bilayers and magic angle spinning techniques. In particular, Boltzmann statistics REDOR and maximum entropy analysis of spinning side bands are used to analyse systems where multiple states of peptide or lipid molecules may co-exist. We propose that in future, rather than model membranes, structural studies in whole cells are feasible.

Solid-state NMR structure characterization of a 13CO-Labeled Ir(I) complex with a P,N-donor ligand including ultrafast MAS methods

The structural characterization of a (13)CO-labeled Ir(I) complex bearing an P,N-donor ligand (1-[2-(diphenylphosphino)ethyl]pyrazole), [Ir(PyP)((13)CO)Cl] is demonstrated using a series of tailored solid-state NMR techniques based on ultrafast (60 kHz) Magic Angle Spinning (MAS), which facilitates correlations with narrow proton line-widths. Our 1D (1)H MAS and 2D (13)C and (31)P CP-MAS NMR spectra provided structural information similar to that obtained using NMR spectroscopy in solution. We employed high-resolution 2D solid-state correlation spectroscopy ((1)H-(13)C HETCOR, (1)H-(31)P correlation) to characterize the networks of dipolar couplings between protons and carbon/phosphorus. (1)H-(1)H SQ-SQ correlation spectra showed the dipolar contacts between all protons in a similar fashion to its solution counterpart, NOESY. The use of the (1)H single quantum/double quantum experiments made it possible to observe the dipolar-coupling contacts between immediately adjacent protons. Additionally, internuclear (13)CO-(31)P distance measurements were performed using REDOR. The combination of all of these techniques made it possible to obtain comprehensive structural information on the molecule [Ir(PyP)((13)CO)Cl] in the solid state, which is in excellent agreement with the single crystal X-ray structure of the complex, and demonstrates the enormous value of ultrafast MAS NMR techniques for a broad range of future applications.

Context dependence of protein misfolding and structural strains in neurodegenerative diseases

Vast arrays of structural forms are accessible to simple amyloid peptides and environmental conditions can direct assembly into single phases. These insights are now being applied to the aggregation of the Aβ peptide of Alzheimer's disease and the identification of causative phases. We extend use of the imaging agent Pittsburgh compound B to discriminate among Aβ phases and begin to define conditions of relevance to the disease state. Also, we specifically highlight the development of methods for defining the structures of these more complex phases.

Phase networks of cross-β peptide assemblies

Recent evidence suggests that simple peptides can access diverse amphiphilic phases, and that these structures underlie the robust and widely distributed assemblies implicated in nearly 40 protein misfolding diseases. Here we exploit a minimal nucleating core of the Aβ peptide of Alzheimer's disease to map its morphologically accessible phases that include stable intermolecular molten particles, fibers, twisted and helical ribbons, and nanotubes. Analyses with both fluorescence lifetime imaging microscopy (FLIM) and transmission electron microscopy provide evidence for liquid-liquid phase separations, similar to the coexisting dilute and dense protein-rich liquid phases so critical for the liquid-solid transition in protein crystallization. We show that the observed particles are critical for transitions to the more ordered cross-β peptide phases, which are prevalent in all amyloid assemblies, and identify specific conditions that arrest assembly at the phase boundaries. We have identified a size dependence of the particles in order to transition to the para-crystalline phase and a width of the cross-β assemblies that defines the transition between twisted fibers and helically coiled ribbons. These experimental results reveal an interconnected network of increasing molecularly ordered cross-β transitions, greatly extending the initial computational models for cross-β assemblies.

Disentanglement of heterogeneous dynamics in mixed lipid systems

Static phosphorous NMR has been a powerful technique for the study of model supramolecular phospholipid structures. Application to natural lipid bilayers with complex compositions, however, has been severely limited by the difficulty in deconvoluting overlapping broad lineshapes. We demonstrate a solution to this problem, using a global fit to a few slow magic-angle spinning spectra, in combination with an adaptation of Boltzmann statistics maximum entropy. The method provides a model-free means to characterize a heterogeneous mix of lipid dynamics via a distribution of (31)P chemical shift anisotropies. It is used here to identify clear changes in membrane dynamics of a phosphatidylethanolamine and phosphatidylglycerol mixture, mimicking an Escherichia coli membrane upon addition of just 2% of the antimicrobial peptide maculatin 1.1. This illustration opens the prospect for investigation of arbitrarily complex natural lipid systems, important in many areas of biophysical chemistry and biomedicine.

Membrane interactions of antimicrobial peptides from Australian frogs

The membrane interactions of four antimicrobial peptides, aurein 1.2, citropin 1.1, maculatin 1.1 and caerin 1.1, isolated from Australian tree frogs, are reviewed. All four peptides are amphipathic alpha-helices with a net positive charge and range in length from 13 to 25 residues. Despite several similar sequence characteristics, these peptides compromise the integrity of model membrane bilayers via different mechanisms; the shorter peptides exhibit a surface interaction mechanism while the longer peptides may form pores in membranes.

Metal effects on the membrane interactions of amyloid-beta peptides

A beta (1-42) peptide, found as aggregated species in Alzheimer's disease brain, is linked to the onset of dementia. We detail results of 31P and 2H solid-state NMR studies of model membranes with A beta peptides and the effect of metal ions (Cu2+ and Zn2+), which are found concentrated in amyloid plaques. The effects on the lipid bilayer and the peptide structure are different for membrane incorporated or associated peptides. Copper ions alone destabilise the lipid bilayer and induce formation of smaller vesicles, but not when A beta(1-42) is associated with the bilayer membrane. A beta (25-35), a fragment from the C-terminal end of A beta(1-42), which lacks the metal coordinating sites found in the full length peptide, is neurotoxic to cortical cortex cell cultures. Addition of metal ions has little effect on membrane bilayers with A beta (25-35) peptides. 31P magic angle spinning NMR data show that A beta (1-42) and A beta (1-42)-Cu2+ complexes interact at the surface of anionic phospholipid membranes. Incorporated peptides, however, appear to disrupt the membrane more severely than associated peptides. Solid-state 13C NMR was used to compare structural changes of A beta (1-42) to those of A beta (25-35) in model membrane systems of anionic phospholipids and cholesterol. The A beta peptides appeared to have an increase in beta-strand structure at the C-terminus when added to phospholipid liposomes. The inclusion of Cu2+ also influenced the observed chemical shift of residues from the C-terminal half, providing structural clues for the lipid-associated A beta/metal complex. The results point to the complex pathway(s) for toxicity of the full-length peptide.