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And Cryogenic Probe-Assisted NMR Enables Hypersensitive Analysis of Biomolecules at Submicromolar Concentration

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And Cryogenic Probe-Assisted NMR Enables Hypersensitive Analysis of Biomolecules at Submicromolar Concentration Laser- and cryogenic probe-assisted NMR enables hypersensitive analysis of biomolecules at submicromolar concentration Yusuke Okunoa,b, Miranda F. Mechaa, Hanming Yanga, Lingchao Zhua, Charles G. Frya, and Silvia Cavagneroa,1 aDepartment of Chemistry, University of Wisconsin–Madison, Madison, WI 53706; and bLaboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 Edited by Angela M. Gronenborn, University of Pittsburgh School of Medicine, Pittsburgh, PA, and approved May 6, 2019 (received for review December 3, 2018) Solution-state NMR typically requires 100 μM to 1 mM samples. and large sensitivity gains. The main recent advances, which led This limitation prevents applications to mass-limited and aggregation- to the emergence of photo-CIDNP as a nuclear hyperpolariza- prone target molecules. Photochemically induced dynamic nuclear po- tion technique in solution, are listed below. larization was adapted to data collection on low-concentration sam- First, 13C steady-state photo-CIDNP (22) proved to more ef- ples by radiofrequency gating, enabling rapid 1D NMR spectral fectively boost NMR signal-to-noise (S/N) than 1Hor15N ap- acquisition on aromatic amino acids and proteins bearing aromatic proaches. Second, fluorescein (Fig. 1B) was found to be a much residues at nanomolar concentration, i.e., a full order of magnitude more efficient photo-sensitizer than the traditionally employed below other hyperpolarization techniques in liquids. Both backbone flavin mononucleotide (FMN) at low sample concentration (24). 1 13 H -C and side-chain resonances were enhanced, enabling secondary Third, data collection in the presence of catalytic amounts of the and tertiary structure analysis of proteins with remarkable spectral oxygen-scavenging enzymes glucose oxidase (GO) and catalase 13 editing, via the C PREPRINT pulse sequence. Laser-enhanced 2D NMR (CAT) (25) enhanced S/N by largely mitigating quenching of the μ spectra of 5 M proteins at 600 MHz display 30-fold better S/N than photoexcited triple state of fluorescein (9, 26) (Fig. 1C). The conventional 2D data collected at 900 MHz. Sensitivity enhancements above three innovations led to the rapid detection of small BIOPHYSICS AND achieved with this technology, denoted as low-concentration photo- molecules in solution at low micromolar concentration (24). COMPUTATIONAL BIOLOGY CIDNP (LC-photo-CIDNP), depend only weakly on laser intensity, high- In this work, we show that photo-CIDNP hyperpolarization can lighting the opportunity of safer and more cost-effective hypersensi- be extended from free amino acids (Fig. 1 D and E) to folded and tive NMR applications employing low-power laser sources. unfolded proteins (Fig. 1F) and can be combined with cryogenic probe technology via the 13C PREPRINT sequence (Fig. 1G)and hyperpolarization | photo-CIDNP | NMR | proteins | amino acids low-power lasers to achieve large sensitivity gains. Rapid NMR data collection of small and large biomolecules in solution is now pos- MR is an atomic-resolution noninvasive method to probe sible within the nanomolar concentration regime. Nmolecular structure and dynamics. This technique is, how- This approach, which is tailored to dilute samples in solution, ever, inherently insensitive due to the unfavorable distribution of is denoted here as low-concentration photo-CIDNP (LC-photo- nuclear spin states at the near-ambient temperature used in most CIDNP). applications. Methods implemented over the years to overcome the low sensitivity of NMR in liquids include the use of high Significance applied magnetic fields, data acquisition in the time domain followed by Fourier transform, fast data collection schemes, and cryogenic probes (1–3). More recently, nuclear-spin hyperpolar- Despite its prominent role in structural biology, NMR spectros- ization including Overhauser dynamic nuclear polarization (4, 5), copy is hampered by extremely poor sensitivity. In this work, we optical pumping (6–9), parahydrogen-induced polarization (10, 11), develop a laser-assisted methodology, LC-photo-CIDNP, to en- signal amplification by reversible exchange (12), and dissolution hance NMR sensitivity for the detection of amino acids and pro- dynamic nuclear polarization (D-DNP) (13–17) have displayed teins in solution down to nanomolar concentration. Our method significant potential (3). is significant because it enables detection of nanomolar concen- Despite the above technological advances, typical liquid-state trations of aromatic amino acids (Trp and Tyr), either in their free NMR experiments employing hyperpolarization still require very state or within proteins, in only a few seconds. Hence, the LC- photo-CIDNP approach renders data collection thousands of times expensive instrumentation; harsh hyperpolarization conditions; faster than laser-free NMR experiments performed on higher- long polarization times; and last but not least, ≥50–100 μM field spectrometers. Further, LC-photo-CIDNP is readily applicable sample concentration. In addition, NMR data collection of di- to both 1D and 2D data collection mode. Rapid detection of lute biomolecules in physiologically relevant milieux is often proteins in solution at nanomolar concentration by NMR spec- unfeasible. While some of the above challenges may in principle troscopy is unprecedented. be overcome by concentrating NMR samples and employing probes accommodating small sample volumes, this process is Author contributions: Y.O., M.F.M., H.Y., and S.C. designed the research; Y.O., M.F.M., often unfeasible due to limited amounts of available material or to and H.Y. performed the experiments and analyzed the data; L.Z. and C.G.F. provided undesirable aggregation. In summary, there is a compelling need to technical assistance and comments on the paper; and Y.O., M.F.M., H.Y. and S.C. wrote further enhance the sensitivity of solution-state NMR spectroscopy. the paper. Photochemically induced dynamic nuclear polarization The authors declare no conflict of interest. (photo-CIDNP) is a spin-selective technique involving the tran- This article is a PNAS Direct Submission. sient generation of radical pairs (Fig. 1A). This methodology has Published under the PNAS license. been traditionally employed to gauge macromolecular solvent- 1To whom correspondence may be addressed. Email: [email protected]. exposure (18–20). More recently, photo-CIDNP has been com- This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. bined with heteronuclear correlation spectroscopy (21, 22) and 1073/pnas.1820573116/-/DCSupplemental. heavy atom-containing additives (23) to achieve spectral-editing www.pnas.org/cgi/doi/10.1073/pnas.1820573116 PNAS Latest Articles | 1of10 Downloaded by guest on September 28, 2021 Fig. 1. Basic aspects of hypersensitive NMR spectroscopy via low-concentration photochemically induced dynamic nuclear polarization (LC-photo-CIDNP).(A) Cartoon representation of photo-CIDNP radical pair mechanism. The symbol isc denotes inter-system crossing. (B) Structure of fluorescein, the photo-CIDNP dye. (C) Transient electronic absorption spectrum of fluorescein, illustrating the triplet–triplet absorption in the absence and presence of the GO-CAT oxygen- scavenging system. Black dashed lines denote single-exponential fits (see also SI Appendix, section 2.7). (D) Structure of tryptophan (Trp) and tyrosine (Tyr), two representative photo-CIDNP–active amino acids. (E) Dark (laser-off) and light (laser-on) 1H-detected 13C photo-CIDNP acquired with a room temperature probe (600 MHz) on 1 μMTrp.(F) Structure of the SH3 protein (56), highlighting its Trp and Tyr. (G) The 13C PREPRINT pulse sequence, which enables 1H- 13 detected C photo-CIDNP NMR of low-concentration samples (LC-photo-CIDNP) in the presence of a cryogenic probe. The parameter tL denotes the laser irradiation time (488 nm, Ar ion laser, 200 ms). The τ delay was set to 1/4 JCH (1.7 ms). T is the constant chemical shift evolution time in the indirect dimension, which was set to 13.3 and 26.7 ms for side-chain and Cα carbons, respectively. The parameter Δ denotes the perturbation-recovery delay (150 ms) that follows ϕ = − − ϕ = − ϕ = − − − − laser irradiation. The phase cycling was rec x, x, x, x; 1 y, y; 2 y, y, x, x, y, y, x, x. Results and Discussion NMR cryogenic probes for data collection in liquids enable LC-Photo-CIDNP in the Presence of a Cryogenic Probe: Challenges and increases in sensitivity by threefold to fourfold relative to room- Solutions. In this section, we use the term cryogenic probes to temperature probes (27–29) by supercooling the spectrometer denote solution-state NMR probes where the sample tempera- components used for detection, hence reducing the observed ture is not cryogenic. These probes ought not to be confused with noise induced by random currents (27–30). In cryogenic probes, solid-state NMR probes, which typically cool the sample and the temperature of receiver coil and preamplifier is independent coils but often not the preamplifier. of sample temperature. Hence, the latter can typically be set 2of10 | www.pnas.org/cgi/doi/10.1073/pnas.1820573116 Okuno et al. Downloaded by guest on September 28, 2021 within a wide range of values (ca. −40 to +120 °C). The ratio of The 1H-detected 13C LC-photo-CIDNP experiments focusing α the current induced by a signal to the current induced by noise on the 1H region were carried out with the 13C PREPRINT pulse (US/UN) can be expressed as (31) sequence on a 600-MHz spectrometer equipped with a cryogenic μ .pffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi probe. An excellent S/N was achieved on a 1- M Trp sample in only 16 s (Fig. 2A). Reference data acquired either on the same 600- S=N ∝ US=UN ∝ 1 TcRc + Ta½Rc + Rs + TsRs, [1] MHz spectrometer under dark (i.e., laser-off) conditions or with the pulse-field-gradient sensitivity-enhanced constant-time 1H,13C where Tc, Ta, and Ts are the temperatures of the coil, preampli- HSQC (1H,13C CT-SE-HSQC) pulse sequence (34) at 900 MHz, fier, and sample, respectively, and Rc and Rs are the resistance of yielded only noise (Fig.
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