Probing the exposure of tyrosine and tryptophan residues in partially folded proteins and folding intermediates by CIDNP pulse-labeling

LC-Photo-CIDNP hyperpolarization of biomolecules bearing a quasi-isolated spin pair: Magnetic-Field dependence via a rapid-shuttling device

Liquid-state low-concentration photochemically induced dynamic nuclear polarization (LC-photo-CIDNP) is an emerging technology tailored to enhance the sensitivity of NMR spectroscopy via LED- or laser-mediated optical irradiation. LC-photo-CIDNP is particularly useful to detect solvent-exposed aromatic residues (Trp, Tyr), either in isolation or within polypeptides and proteins. This study investigates the magnetic-field dependence of the LC-photo-CIDNP of Trp-α-13C-β,β,2,4,5,6,7-d7, a Trp isotopolog bearing a quasi-isolated 1Hα-13Cαspin pair (QISP). We employed a new rapid-shuttling side-illumination field-cycling device that enables ultra-fast (90-120 ms) vertical movements of NMR samples within the bore of a superconducting magnet. Thus, LC-photo-CIDNP hyperpolarization occurs at low field, while hyperpolarized signals are detected at high field (700 MHz). Resonance lineshapes were excellent, and the effect of several fields (1.18-7.08 T range) on hyperpolarization efficiency could be readily explored. Remarkably, unprecedented LC-photo-CIDNP enhancements ε ≅ 1,200 were obtained at 50 MHz (1.18 T), suggesting exciting avenues to hypersensitive LED-enhanced NMR in liquids at low field.

Spin Hyperpolarization in Modern Magnetic Resonance

Magnetic resonance techniques are successfully utilized in a broad range of scientific disciplines and in various practical applications, with medical magnetic resonance imaging being the most widely known example. Currently, both fundamental and applied magnetic resonance are enjoying a major boost owing to the rapidly developing field of spin hyperpolarization. Hyperpolarization techniques are able to enhance signal intensities in magnetic resonance by several orders of magnitude, and thus to largely overcome its major disadvantage of relatively low sensitivity. This provides new impetus for existing applications of magnetic resonance and opens the gates to exciting new possibilities. In this review, we provide a unified picture of the many methods and techniques that fall under the umbrella term "hyperpolarization" but are currently seldom perceived as integral parts of the same field. Specifically, before delving into the individual techniques, we provide a detailed analysis of the underlying principles of spin hyperpolarization. We attempt to uncover and classify the origins of hyperpolarization, to establish its sources and the specific mechanisms that enable the flow of polarization from a source to the target spins. We then give a more detailed analysis of individual hyperpolarization techniques: the mechanisms by which they work, fundamental and technical requirements, characteristic applications, unresolved issues, and possible future directions. We are seeing a continuous growth of activity in the field of spin hyperpolarization, and we expect the field to flourish as new and improved hyperpolarization techniques are implemented. Some key areas for development are in prolonging polarization lifetimes, making hyperpolarization techniques more generally applicable to chemical/biological systems, reducing the technical and equipment requirements, and creating more efficient excitation and detection schemes. We hope this review will facilitate the sharing of knowledge between subfields within the broad topic of hyperpolarization, to help overcome existing challenges in magnetic resonance and enable novel applications.

The anatomy of unfolding of Yfh1 is revealed by site-specific fold stability analysis measured by 2D NMR spectroscopy

Most techniques allow detection of protein unfolding either by following the behaviour of single reporters or as an averaged all-or-none process. We recently added 2D NMR spectroscopy to the well-established techniques able to obtain information on the process of unfolding using resonances of residues in the hydrophobic core of a protein. Here, we questioned whether an analysis of the individual stability curves from each resonance could provide additional site-specific information. We used the Yfh1 protein that has the unique feature to undergo both cold and heat denaturation at temperatures above water freezing at low ionic strength. We show that stability curves inconsistent with the average NMR curve from hydrophobic core residues mainly comprise exposed outliers that do nevertheless provide precious information. By monitoring both cold and heat denaturation of individual residues we gain knowledge on the process of cold denaturation and convincingly demonstrate that the two unfolding processes are intrinsically different.

Pushing nuclear magnetic resonance sensitivity limits with microfluidics and photo-chemically induced dynamic nuclear polarization

Among the methods to enhance the sensitivity of nuclear magnetic resonance (NMR) spectroscopy, small-diameter NMR coils (microcoils) are promising tools to tackle the study of mass-limited samples. Alternatively, hyperpolarization schemes based on dynamic nuclear polarization techniques provide strong signal enhancements of the NMR target samples. Here we present a method to effortlessly perform photo-chemically induced dynamic nuclear polarization in microcoil setups to boost NMR signal detection down to sub-picomole detection limits in a 9.4T system (400 MHz ¹H Larmor frequency). This setup is unaffected by current major drawbacks such as the use of high-power light sources to attempt uniform irradiation of the sample, and accumulation of degraded photosensitizer in the detection region. The latter is overcome with flow conditions, which in turn open avenues for complex applications requiring rapid and efficient mixing that are not easily achievable on an NMR tube without resorting to complex hardware.

Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique with an inherently low sensitivity. Here, the authors present a combination of microcoils with photo-chemically induced dynamic nuclear polarization to boost NMR sensitivity down to sub-picomole detection limits.

Importance of polarization transfer in reaction products for interpreting and analyzing CIDNP at low magnetic fields

The magnetic field dependence of Chemically Induced Dynamic Nuclear Polarization (CIDNP) was studied for the amino acids N-acetyl histidine, N-acetyl tryptophan and N-acetyl tyrosine. It is demonstrated that at low field CIDNP is strongly affected by polarization redistribution in the diamagnetic molecules. Such a polarization transfer is of coherent nature and is due to spin coherences formed together with non-equilibrium population of the spin states. These coherences clearly manifest themselves in an oscillatory time dependence of polarization. Polarization transfer effects are most pronounced at nuclear spin Level Anti-Crossings (LACs), which also result in sharp features in the CIDNP field dependence. Thus, polarization transfer is an important factor, which has to be taken into account in order to interpret low-field CIDNP data on both qualitative and quantitative level. Possible applications of polarization transfer phenomena are also discussed in the paper. In particular, the role of LACs in spin order transfer is highlighted: LACs provide a new tool for precise manipulation of spin hyperpolarization and NMR enhancement of selected target spins.

Probing the non-native H helix translocation in apomyoglobin folding intermediates

Apomyoglobin folds via sequential helical intermediates that are formed by rapid collapse of the A, B, G, and H helix regions. An equilibrium molten globule with a similar structure is formed near pH 4. Previous studies suggested that the folding intermediates are kinetically trapped states in which folding is impeded by non-native packing of the G and H helices. Fluorescence spectra of mutant proteins in which cysteine residues were introduced at several positions in the G and H helices show differential quenching of W14 fluorescence, providing direct evidence of translocation of the H helix relative to helices A and G in both the kinetic and equilibrium intermediates. Förster resonance energy transfer measurements show that a 5-({2-[(acetyl)amino]ethyl}amino)naphthalene-1-sulfonic acid acceptor coupled to K140C (helix H) is closer to Trp14 (helix A) in the equilibrium molten globule than in the native state, by a distance that is consistent with sliding of the H helix in an N-terminal direction by approximately one helical turn. Formation of an S108C–L135C disulfide prevents H helix translocation in the equilibrium molten globule by locking the G and H helices into their native register. By enforcing nativelike packing of the A, G, and H helices, the disulfide resolves local energetic frustration and facilitates transient docking of the E helix region onto the hydrophobic core but has only a small effect on the refolding rate. The apomyoglobin folding landscape is highly rugged, with several energetic bottlenecks that frustrate folding; relief of any one of the major identified bottlenecks is insufficient to speed progression to the transition state.

Photo-CIDNP NMR spectroscopy of amino acids and proteins

Photo-chemically induced dynamic nuclear polarization (CIDNP) is a nuclear magnetic resonance (NMR) phenomenon which, among other things, is exploited to extract information on biomolecular structure via probing solvent-accessibilities of tryptophan (Trp), tyrosine (Tyr), and histidine (His) amino acid side chains both in polypeptides and proteins in solution. The effect, normally triggered by a (laser) light-induced photochemical reaction in situ, yields both positive and/or negative signal enhancements in the resulting NMR spectra which reflect the solvent exposure of these residues both in equilibrium and during structural transformations in "real time". As such, the method can offer - qualitatively and, to a certain extent, quantitatively - residue-specific structural and kinetic information on both the native and, in particular, the non-native states of proteins which, often, is not readily available from more routine NMR techniques. In this review, basic experimental procedures of the photo-CIDNP technique as applied to amino acids and proteins are discussed, recent improvements to the method highlighted, and future perspectives presented. First, the basic principles of the phenomenon based on the theory of the radical pair mechanism (RPM) are outlined. Second, a description of standard photo-CIDNP applications is given and it is shown how the effect can be exploited to extract residue-specific structural information on the conformational space sampled by unfolded or partially folded proteins on their "path" to the natively folded form. Last, recent methodological advances in the field are highlighted, modern applications of photo-CIDNP in the context of biological NMR evaluated, and an outlook into future perspectives of the method is given.

First principles study of photostability within hydrogen-bonded amino acids

The photochemistry and photophysics of a two-glycine minimal model is studied at the CASPT2//CASSCF level of theory. Different photoinduced processes are discussed, on the basis of the calculated minimum energy paths and the characterization of the electronic state crossings. Two main processes could provide UV-photostability to the hydrogen-bonded peptide system: (i) forward-backward photoinduced electron/proton transfer involving the H in the hydrogen bond, (ii) singlet-singlet energy transfer between two amino acids, providing ultrafast population of the low-energy n,π* state.

Identification of the peroxidase-generated intermolecular dityrosine cross-link in bovine α-lactalbumin

The peroxidase-mediated oxidation of calcium-depleted bovine α-lactalbumin generates a mixture of covalently bound protein oligomers with interesting foaming properties. Here, we isolated the initially formed covalent α-lactalbumin dimer and studied its mode of cross-linking. Liquid chromatography-Fourier transform mass spectrometry (LC-FTMS) of proteolytic digests revealed the unambiguous identification of a peroxidase-catalyzed covalent link between Tyr18 and Tyr50. This shows that, although the radical reaction is often regarded as a random reaction, the initial product formation is specific. Protein structural modeling indicates that the conjugation reaction between these tyrosines is sterically favored and involves initial noncovalent protein complex formation through charge compensation, facilitating intermolecular cross-linking. The identification of the Tyr18-Tyr50 cross-link supports the view that the peroxidase-mediated oxidation of apo α-lactalbumin is a sequential process, involving the formation of linear trimers and higher order oligomers.

Refolding of ribonuclease A monitored by real-time photo-CIDNP NMR spectroscopy

Photo-CIDNP NMR spectroscopy is a powerful method for investigating the solvent accessibility of histidine, tyrosine and tryptophan residues in a protein. When coupled to real-time NMR, this technique allows changes in the environments of these residues to be used as a probe of protein folding. In this paper we describe experiments performed to monitor the refolding of ribonuclease A following dilution from a high concentration of chemical denaturant. These experiments provide a good example of the utility of this technique which provides information that is difficult to obtain by other biophysical methods. Real-time photo-CIDNP measurements yield residue-specific kinetic data pertaining to the folding reaction, interpreted in terms of current knowledge of the folding of bovine pancreatic ribonuclease A.

Utilisation of an eta(3)-allyl hydride complex, formed by UV irradiation, as a controlled source of 16-electron (eta(5)-C(5)Me(5))Rh(CH(2)[double bond, length as m-dash]CHMe)

Low temperature UV irradiation of solutions of (eta(5)-C(5)Me(5))Rh(CH(2)[double bond, length as m-dash]CHMe)(2) yields (eta(5)-C(5)Me(5))Rh(eta(3)-CH(2)CHCH(2))(H), which provides controlled access to the 16-electron fragment (eta(5)-C(5)Me(5))Rh(CH(2)[double bond, length as m-dash]CHMe).

Protein binding onto surfactant-based synthetic vesicles

Synthetic vesicles were prepared by mixing anionic and cationic surfactants, aqueous sodium dodecylsulfate with didodecyltrimethylammonium or cetyltrimethylammonium bromide. The overall surfactant content and the (anionic/cationic) mole ratios allow one to obtain negatively charged vesicles. In the phase diagram, the vesicular region is located between a solution phase, a lamellar liquid crystalline dispersion, and a precipitate area. Characterization of the vesicles was performed by electrophoretic mobility, NMR, TEM, and DLS and we determined their uni-lamellar character, size, stability, and charge density. Negatively charged vesicular dispersions, made of sodium dodecylsulfate/didodecyltrimethylammonium bromide or sodium dodecylsulfate/cetyltrimethylammonium bromide, were mixed with lysozyme, to form lipoplexes. Depending on the protein/vesicle charge ratio, binding, surface saturation, and lipoplexes flocculation, or precipitation, occurs. The free protein in excess remains in solution, after binding saturation. The systems were investigated by thermodynamic (surface tension and solution calorimetry), DLS, CD, TEM, 1H NMR, transport properties, electrophoretic mobility, and dielectric relaxation. The latter two methods give information on the vesicle charge neutralization by adsorbed protein. Binding is concomitant to modifications in the double layer thickness of vesicles and in the surface charge density of the resulting lipoplexes. This is also confirmed by developing the electrophoretic mobility results in terms of a Langmuir-like adsorption isotherm. Charges in excess with respect to the amount required to neutralize the vesicle surface promote lipoplexes clustering and/or flocculation. Protein-vesicle interactions were observed by DLS, indicating changes in particle size (and in their distribution functions) upon addition of LYSO. According to CD, the bound protein retains its native conformation, at least in the SDS/CTAB vesicular system. In fact, changes in the alpha-helix and beta-sheet conformations are moderate, if any. Calorimetric methods indicate that the maximum heat effect for LYSO binding occurs at charge neutralization. They also indicate that enthalpic are by far the dominant contributions to the system stability. Accordingly, energy effects associated with charge neutralization and double-layer contributions are much higher than counterion exchange and dehydration terms.

Some Properties of Lysozyme−Lithium Perfluorononanoate Complexes

Mixtures containing lysozyme, LYSO, and a fully fluorinated surfactant, lithium perfluorononanoate, LiPFN, were investigated in a wide range of concentrations and mole ratios. To ensure consistency to the data, a comparison was made, when possible, with the more conventional SDS as surfactant. Molecular solutions, precipitates, and micellar phases have been observed. The region of existence for each phase depends on the LiPFN/LYSO mole ratios, r, and was determined by different experimental methods. Optical absorbance, CD, 19F NMR, viscosity, electrical conductivity, and dielectric relaxation methods were used. Some methods give information on the protein conformation, others on the state of the surfactant or on the collective system properties, respectively. Addition of LiPFN gives rise to a solution, a poly phase dispersion (at low surfactant to protein ratios) and to a micelle-mediated redissolution of the precipitates. Concomitant to the above macroscopic properties, peculiar effects in the state of LYSO are observed. Low amounts of surfactant reduce significantly the amount of alpha-helix in favor of the beta-sheet conformation of the protein. The former is almost completely regained once micelle-assisted redissolution of the complex occurs. The tertiary structure of the protein, conversely, is lost at low surfactant content and never recovered. Such evidence suggests the occurrence of a molten globule conformation for LYSO in micellar media.

1D Radical Motion in Protein Pocket: Proton-Coupled Electron Transfer in Human Serum Albumin

Photoinduced, proton-coupled electron transfer (ET) between 9,10-anthraquinone-2,6-disulfonate (ADQS) and an amino acid residue of tryptophan in human serum albumin (HSA) was observed using time-resolved electron paramagnetic resonance (TREPR). The ET reaction reduces the protein binding affinity of the ligand. TREPR chemically induced dynamic electron polarization (CIDEP) spectra establish that photoinduced ET takes place from the tryptophan residue (W214) to the excited triplet state of AQDS2- while bound in subdomain IIA, a protein cleft of HSA. The TREPR CIDEP signals also reveal that the anion radical of the ligand escapes toward the bulk water region by a one-dimensional translation diffusion process within the protein's pocket area. This pilot study of HSA demonstrates how TREPR CIDEP can provide significant means to investigate dynamic characteristics of protein-surface reactions.

Photo-CIDNP NMR spectroscopy of a heme-containing protein

There are relatively few examples of the application of photo-CIDNP NMR spectroscopy to chromophore-containing proteins. The most likely reason for this is that simultaneous absorption of light by the photosensitiser molecule and the protein chromophore reduces the effectiveness of the photochemical reaction that produces the observed nuclear polarisation. We present details of experiments performed on the air-oxidised form of a small cytochrome, from the thermophilic bacterium Hydrogenobacter thermophilus, using both the wild-type protein and apo and holo forms of a double alanine b-type mutant. We show that, along with the apo state, it is possible to generate CIDNP in the air-oxidised form of the b-type mutant, but not in the corresponding c-type cytochrome. This finding is supported by control experiments using horse-heart cytochrome c.

Multiple subsets of side-chain packing in partially folded states of alpha-lactalbumins

Photochemically induced dynamic nuclear polarization NMR pulse-labeling techniques have been used to obtain detailed information about side-chain surface accessibilities in the partially folded (molten globule) states of bovine and human alpha-lactalbumin prepared under a variety of well defined conditions. Pulse labeling involves generating nuclear polarization in the partially folded state, rapidly refolding the protein within the NMR sample tube, then detecting the polarization in the well dispersed native-state spectrum. Differences in the solvent accessibility of specific side chains in the various molten globule states indicate that the hydrophobic clusters involved in stabilizing the alpha-lactalbumin fold can be formed from interactions between a variety of different hydrophobic residues in both native and non-native environments. The multiple subsets of hydrophobic clusters are likely to result from the existence of distinct but closely related local minima on the free-energy landscape of the protein and show that the fold and topology of a given protein may be formed from degenerate groups of side chains.

Chemically amplified 19F-1H nuclear Overhauser effects

Chemically induced dynamic nuclear polarisation (CIDNP) is explored as a source of nuclear hyperpolarisation in heteronuclear Overhauser effect experiments. A photochemical reaction proceeding through a radical pair intermediate is used to enhance (19)F nuclear magnetisation in 3-fluorotyrosine by more than an order of magnitude with a corresponding increase in the amplitudes of (19)F-(1)H cross-relaxation and cross-correlation effects. The reactions employed are cyclic and leave the sample chemically unchanged. The potential for enhancing the sensitivity of heteronuclear NOEs in (19)F-labelled proteins is discussed.