High-frequency pulsed ESR: probing conformational changes of biological molecules and controlling decoherence of electron spin-based qubits

An electron spin in solid-state systems has been an interesting tool in various fields. In structural biology, unpaired electron spins are eyes to probe to structural changes of a biological molecule and to measure the distance of two sites in the molecule. In quantum physics, an electron spin is proposed as a quantum bit (qubit) in which one can store and manipulate quantum information. Use of a single spin in diamond has recently been proposed for a magnetic sensor that enables to detect an individual electron or nuclear spin. A technique to manipulate and to detect electron spins is pulsed electron spin resonance (ESR) spectroscopy. In particular, high-frequency pulsed ESR spectroscopy is an emerging technique which has many advantages to access a new regime of physics.

“Filming” proteins in action

Observing the dynamical structure of proteins in liquid water is the key to understanding their function in living organisms. However, the dynamics of protein motion and conformal changes are extremely challenging to observe due to the small size, with the functional bending dynamics occurring at very high speeds. ESR spectroscopy is an emerging technique for the study of structure changes and dynamics of biomolecules. Compared with NMR which is widely used to determine structures of biomolecules in solution, ESR has advantages in sensitivity of absolute number of spins, spatial resolution for spin-spin distance measurements and time resolution of dynamical structure change [1]. Since many biomolecules don’t have unpaired spins, ESR studies in biomolecules often involve with a site-directed spin labeling (SDSL) technique [2]. In general, SDSL is placed by introducing an ESR-active nitroxide side chain at selected locations in proteins. The most common procedure for the introduction is through site-directed mutagenesis to introduce a reactive cysteine (SH in Fig. 1) followed by modifying the cysteine with a sulfhydryl-selective nitroxide reagent (Spin label I) to produce spin-labeled side chain (R1).

Fig.1. Reaction to generate spin-labeled side-chains on proteins [2].

Currently we are particularly interested to investigate conformational changes in proteorhodopsin (PR) which is a recently discovered photoactive protein in marine bacterioplanktons. PR belongs to a large class of membrane proteins, the heptahelical trans-membrane (7TM) proteins, that make up 40% of all drug targets. Static and dynamic structure of PR is still unknown, but PR is known to function as a light-driven proton pump like its sister 7TM protein, Bacteriorhodopsin (BR) which also undergoes a conformal transformation in response to light as shown in Fig. 2.

_______________ H⁺ ↓ ______________

_________________________________

H⁺ ↓

Fig.2. Conformational change of bacteriorhodopsin [3].

The conformational change is trigger by the isomerization of the retinal from the all-trans conformation to the 13-cis conformation with absorption of 568 nm light. Concurrently a proton is transferred from the Schiff base and then is released from extracellular side of the membrane within hundreds of microseconds. This brings the BR formation to M-intermediate state which shows the absorption peak at 410nm. Subsequently the Schiff base is indirectly reprotonated from the cytoplasmic side of the membrane. Then the retinal reisomerizes to the all-trans conformation within tens of milliseconds. These conformational changes have been probed by combining information taken by various techniques.

Our goal is to probe conformational changes of PR using high-frequency pulsed ESR and SDSL. Our developing ESR spectrometer is designed with nanosecond time resolution so that one can take snapshots of PR structure. Therefore, by controlling the timing of ESR detection, one can take snapshots at different timings. Then, by assembling these snapshots, one could film a “movie” of the PR protein structure.

Quenching Spin Decoherence

Overcoming spin decoherence is critical to spintronics and spin-based quantum information processing devices. For spins in the solid state, a coupling to a fluctuating spin bath is a major source of the decoherence. Our interest is to investigate sources of the spin decoherence in solid state-based spin systems and find methods to control and overcome the decoherence. We recently investigated nitrogen-vacancy (NV) center impurities on diamond and single-molecule magnets using 240 GHz pulsed EPR spectrometer.

One approach to reduce spin bath fluctuations is to bring the spin bath into a well-known quantum state that exhibits little or no fluctuations. A prime example is the case of a fully polarized spin bath. In the case of diamond, spin decoherence of the NV center is mainly dominated by a fluctuations of surrounding nitrogen (N) spins as shown in Fig. 3 (left). Therefore, by polarizing these N spins, the spin decoherence of NV centers can be suppressed (Fig. 3 (right)). We recently demonstrated that our ESR setup can polarize N spins completely with 8.5 Tesla and 2 Kelvin and this quenches the spin decoherence of NV centers [4].

Fig 3. Nitrogen-Vacancy (NV) center and Nitrogen (N) spin bath. N spins polarizes completely at 8.5 T and 2 K while N spin fluctuates rapidly at 300 K.

A single crystal of high-spin single-molecule magnets (SMMs) is an attractive testbed for quantum science and technologies because their magnetic properties can be easily tuned with highly flexible chemical synthesis of SMMs. High-spin SMMs are potentially suitable for applications of dense quantum memory and computing devices. Because SMM clusters are identical and interact weakly, the ensemble properties of single crystals of SMMs reflect the properties of a single cluster. However decoherence mechanism of high-spin SMM crystals has been poorly understood due to their strong spin decoherence. Using 240 GHz pulsed EPR, We have recently demonstrated coherent manipulation of a single-crystal of S=10 Fe8 single-molecule magnets (Fig. 4) for the first time.

Fig. 4. Schematic diagram of Fe8 molecule (Fe: Green, O: Red, N: Blue, C: Gray and H: White). The Fe8 molecule consists of eight Fe(III) (S = 5/2) ions which couple to each other to form an S = 10 ground state.

Through temperature dependence of spin relaxation times (T₁ and T₂), we identified the main decoherence source and found that spin decoherence is significantly suppressed with high magnetic fields and low temperature to extend spin decoherence time T₂ close to 1 microsecond [6]. We are currently investigating other source of decoherence in Fe8 SMM to further extend T₂.

Developing the world’s 1st FEL-based pulsed EPR spectrometer

At present, most high-power pulsed ESR spectrometers operate near 9.5 GHz (X-band) with kW-level peak power and 100 ns time resolution. However there many spin system which have shorter spin relaxation times T₁ and T₂. For example, spin relaxation times for SDSL of biological molecules in aqueous solution are typically less than 100 ns at room temperature. Thus, conventional pulsed ESR measurements of proteins are performed on frozen samples. A way to improve time resolution is to employ higher frequency of ESR. Thus, an imminent need in the development of next generation pulsed ESR is for higher magnetic field and frequency operation. At present, there exist instruments which operate at 95 GHz with time resolution shorter than 100 ns [6]. Beyond 100 GHz, the bottleneck for higher frequency pulsed ESR spectroscopy is a lack of high-power and narrow bandwidth source.

A Free-Electron Laser-based pulsed ESR operating in the sub-mm (THz) spectral region will have much better time resolution than these relaxation times and enable the investigation of biomolecules structure with ultrafast temporal resolution, like taking a snapshot of the molecule. The Sherwin group is pioneering the development of a high-frequency, high-power pulsed ESR instrument (Fig. 5) using the UCSB free-electron lasers (FEL) as the sub-mm wave (Terahertz) source [7]. The UCSB FEL's lase continuously from 120 GHz to 4.7 THz and offer high peak power ~kW, a important requirement for pulsed operation.

Fig 5. 240 GHz FEL-pulsed ESR spectrometer

Though normally a multimode source, extremely narrow linewidth 240GHz radiation was achieved recently using the technique of injection-locking as shown in Fig. 6, a key benchmark for the new pulsed ESR spectrometer [7].

Fig. 6. (a) Normal multimode operation, Δf=1 GHz. (b) Single-frequency operation of the FEL, Δf<500 kHz [7] (Left). A picture of injection-locking system (Right).

To create two ns pulses from quasi-cw FEL radiation, we are building a pulse slicer optimized at 240 GHz based on a photo-activated Si switch technique [8, 9].

Fig. 7. 240 GHz pulse slicer

We also built variable beam splitters and a diffraction compensating delay line for multiple pulse experiments [10]. The operating frequency of 240 GHz is too high for conventional microwave transmission techniques (e.g. coaxial cables and waveguides). In the 240 GHz ESR spectrometer custom quasi-optical components are used to the guide the beam. The system also employs a high homogeneity (<10 ppm/cm²) 9 Tesla superconducting magnet with an 88 mm bore (Oxford Instruments) and a home-built 240 GHz superheterodyne detection system. Currently the FEL-based pulsed EPR system is designed for >1kW input pulse power and sub-ns time resolution and is under development.

Flip that lab

We flipped an empty lab (storage room) to the ESR lab within a reasonable budget!

Before (Jan. 2006)