Michael K. Bowman
Department of Chemistry, The University of Alabama, Box 870336 Tuscaloosa, Alabama 35487-0336 USA
E-mail:mkbowman@ua.edu
The relaxation of electron spins can reveal important details about the physical structure, spatial organization and the energy levels of paramagnetic centers in solids.
The spin-lattice relaxation of centers with S>½ often involves thermally-activated transitions to excited spin states. The activation energy obtained from the temperature dependence of spin-lattice relaxation reveals the Zero-Field-Splitting or exchange interaction in the paramagnetic center. The dipolar interaction gives information about the physical distance between paramagnetic centers or their local concentration. When every center has relatively long spin relaxation times, microwave pulse can be used to manipulate the dipolar interaction in DEER, PELDOR and instantaneous diffusion measurements. Rapid spin relaxation of one kind of paramagnetic centers modulates the dipolar interaction and enhances spin relaxation of the other centers. Such relaxation enhancement allows probes of the three dimensional structure of proteins or can reveal the location of free radical intermediates. Examples from the high-spin heme in the nitric oxide synthase enzyme, the semiquinone intermediate in the cytochrome bc1
protein complex and from clusters of trityl radicals will be shown. Some key schemes and expressions are given for reference below.
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93
Membrane proteins study by nitroxide labeling combined with Continuous Wave EPR
Nikolay P. Isaev Introduction
Membrane proteins (MP) are coded by around 30% of all the genes in most genomes; approximately 60% of drug targets are located at the cell surface [Overington 2006]. Despite such importance, only 3’000 MP structures are available in Protein Data Bank (PDB) (totally 120’000 structures are stored there). Such misbalance between the biological relevance and the fraction in PDB originates from MP complexity. Membrane necessity for functioning makes convenient structural methods like X-ray crystallography and NMR difficult to use. Membranes with embedded proteins are difficult to crystallize and too heavy to rotate fast enough for high-resolution NMR. Despite fast methodology development [2015 Caffrey, 2013 Hagn], MP structure determination is still problematic, so all available methods that provide partial information are relevant and helpful.
This lecture will describe using of standard continuous wave (CW) electron paramagnetic resonance (EPR) X-band 9 GHz spectrometer for MP structure investigation, advantages and disadvantages of such approach, and suitable systems for study. The lecture will be divided in several parts: (1) protein site-directed spin-labeling by nitroxides, (2) nitroxide spectrum and CW EPR measurement, (3) room temperature nitroxide label motions and (4) quenching by water and membrane soluble quenchers, (5) cryogenic temperature (180 K) environment polarity study and (6) distance measurement between nitroxides (<2 nm). A good example of all methods application except (6) can be found in [Raba 2015].
Proteins spin-labeling
For EPR signal observation one requires an unpaired electron spin. For example, it can be located on metal ions in metalloproteins or paramagnetic organic molecules in the electron transfer chains related to photosynthesis or breath. In this case one can study closest environment of paramagnetic species in native environment, but remote parts of protein remain inaccessible. Also EPR silent proteins are invisible for EPR. To overcome these limitations and study all types of proteins one can chemically attach paramagnetic molecule to the chosen protein position. This procedure is called site- directed spin-labeling (SDSL) and in this chapter we will consider the most common way of its application.
SDSL became available after invention of site-directed mutagenesis in the late 70s and 80s (1993 Nobel prize), which allowed one to introduce any changes in DNA sequence of proteins. SDSL was first published by W. Hubbel and colleagues in 1989
[Altenbach 1989 and 1990]. Spin labels were developed and used for proteins labeling earlier [Lichtenstein 1972, Berliner 1976]. The most common way of spin-labeling is by disulphide bond formation with amino acid cystein (fig.1). The most common spin label is MTSSL, which is shown in fig. 1 (1-oxyl-2,2,5,5-tetramethylpyrroline-3- methyl)methanethiosulfonate, MW 264) [Berliner 1982]. This reaction occurs by itself in natural for proteins conditions, which facilitates its usability.
Figure 1. Site-directed spin-labeling
[Klare 2009]
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[Dunkel PhD]
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[Dunkel PhD]
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95
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Figure 3.a) Isotropic immobilized (powder) nitroxide spectrum (thick black line) and individual hf components (thin color/gray line). Values of the polar angle are indicated. b) Lock-in detection of an absorption line using magnetic field modulation (above) and resulting derivative spectrum (below). c) Derivative of the spectrum in fig. 3a.
Room temperature nitroxide motions
Nitroxide spectrum changes in the case of orientational motions. In the limit of fast motions, when all orientations in hf components will be averaged out, the spectrum will look like three narrow lines (fig. 4). In between fast motion and powder regimes we will observe diverse spectrum shapes caused by different degrees of hf components averaging by motion. In fig. 4 one can see that increasing rotational correlation time will lead to two universal spectrum changes: full spectrum broadening and central component broadening. In the course of this lecture we will not go further than those two spectrum details interpretation. If one would like to simulate whole spectrum I recommend MultiComponent program written by Christian Altenbach [Alt web], by which one can simulate nitroxide spectrum changes due to all possible molecular motions and their combinations.
Let’s consider different motional regimes of MTSSL attached to protein. Nitroxide has a long linker, so if it is bound to an unfolded loop of the protein, i.e., almost without external steric restrictions, its rotational motion will be almost like for free radical. In the protein depth spin label will be almost immobilized. If the label is in intermediate situation, for example, bound to the protein rigid surface, it will participate in the variety of motions with different correlation times depending on its closeness to the rigid surface.
Figure 4. a) Simulated spectra for isotropic rotation with different correlation times. b) Nitroxide spin label mobility map for water soluble protein.
[web.nmsu.edu]
a
[Scleidt 2007]
b
a b c
[McHaourab 1996]
96 The easy way to interpret nitroxide motions distribution is to analyze the fastest and the slowest parts. Central component width – the distance between positive and negative peaks in the derivative spectrum - is mostly determined by the fastest motions, because a twice as wide line will result in approx. 4 times less intense derivative, as is shown in fig. 5. Such nonlinear
behavior strongly emphasizes the fastest motion. The slowest motions can be characterized by spectrum second moment, or dispersion, which is calculated as the sum of normallized spectrum intensities multiplied by square of magnetic field deviation from spectrum center of mass. Wider spectrum parts, caused by the slowest motions, will contribute more to the second moment and thus it is more sensitive to the slowest motions.
In [McHaourab1996] it was first proposed to combine SDSL with two spectrum parameters analysis to determine the structure of soluble proteins. The reciprocal values of the central component width and spectrum second moment represent the tendency that larger value is faster motion. In fig. 4b one can see interpretation of these two parameters in terms of label environment.
In the case of membrane proteins interpretation remains the same for labels that are exposed to water or buried in protein, but dynamics of labels that have contact with membrane may be slowed down [Klare 2009 fig. 4], so in this case further analysis is required.
Room temperature nitroxide quenching by water and membrane soluble quenchers
Let’s consider the interplay between MW radiation and spin-lattice relaxation T1 on the example of two level system. Spin-lattice relaxation, which originates in thermal fluctuations, is a mechanism that moves two level system towards Boltzmann’s populations distribution P1/P2=exp(-ΔE/kT) from any initial state. In the case of X-band EPR the difference between levels is 0.4K in thermal units, what means that only every one out of 1500 electron spins is polarized by magnetic field.
MW generates both transitions between levels, and the probability of transition is proportional to the level population. It means that if only lower level is populated we’d see only MW absorption, if only higher level is populated we’d see only emission. If levels are equally populated we’d see no change in MW power, because emission will be equal to absorption, what means zero EPR signal. If we begin with all spins on lower level and T1 absence, we’d have absorption that populates higher level.
Difference in populations would be reduced and ultimately would become zero, what means no absorption and no EPR signal.
Figure 6. a) Saturation of MW absorbance (EPR signal) with increasing MW power. b) Scheme of experiment with O2 and Ni(EDDA) paramagnetic quenchers for MP. c) Insertion depth parameter Ф=ln(WO2/WNi) calculated from bacteriorhodopsin nitroxide labels exchange rate with O2 and Ni.
a b
c
Figure 5.Same integral intensity lines with two-fold difference in width (left) and their derivatives (right)
[Altenbach1994]
[Dunkel PhD]
[Dunkel PhD]
97
In thermally equilibrated system we’d have Bolzmann’s distribution, what means that every 1500th electron spin can absorb MW; other 1499 spins will equally absorb and emit MW. If the MW induces spin transitions slower than the reverse equilibration of T1, i.e., Bolzmann’s distribution is not affected, we’ll have constant absorption. If MW power is increased, we’ll have a growth of absorption rate until it becomes the same order of magnitude as T1 relaxation, which will result in saturation.
A further increase of MW power will lead to population equilibration and disappearance of MW absorption.
Paramagnetic quenchers, such as O2 or Ni(EDDA), can increase nitroxide T1 relaxation rate by exchange interaction, which will increase the power level of saturation, as is shown in fig. 6b.
By measuring saturation power P1/2 in the presence and absence of quenchers one can calculate nitroxide exchange rate W with O2 or Ni and then calculate the insertion depth parameter Ф=ln(WO2/WNi) that does not depend on viscosity, steric constraints imposed by the environment and EPR lineshape [Altenbach 1993]. The depth parameter can be also written in terms of quenchers chemical potentials Ф=-(μO2-μNi)/RT+const, so if the standard chemical potentials have a simple monotonic depth dependence, then Ф for two similar-sized reagents of different partition properties will be a useful measure of depth, which was shown experimentally (fig. 6c).
To measure saturation one should have a resonator with high intensity of MW magnetic field, what is unattainable in regular rectangular resonators. One has to use dielectric or loop-gap resonators like Bruker md and ms series or MolSpec loop-gap resonator [Mol web]. Also one has to get rid of oxygen in solution, which is usually done by using gas transparent TPX-capillaries [Mol web] (approx. price is 60$/piece), and blowing nitrogen gas into the resonator.
Cryogenic temperature environment polarity study
Nitroxide can form hydrogen bonds with solvent molecules, and this interaction shifts electron density along π-orbit of N-O bond (fig.7a). An electron density increase on nitrogen atom will increase hf tensor Azz value, which can be measured from the immobilized spectrum at <180 K as half distance between low-field maximum and high-field minimum, as is shown in fig. 7b. Such simple approach allows one to estimate the nitroxide environment polarity and make a conclusion about protein structure as is shown in fig. 7c. For more applications and experimental details see [Savitsky 2004 and Mobius 2005]. At higher temperatures nitroxide motion changes the spectrum shape, and only full spectrum simulation can provide Azz value with a lower accuracy.
Figure 7. a) Changes of electron density distribution on π-orbit of N-O bond by hydrogen bonding of water. b) Measurement of Azz in immobilized nitroxide spectrum at 180 K.
c) Experimental Azz values that were obtained for bacteriorhodopsin protein.
[Dunkel PhD]
a b
[Savitsky 2004]
[Dunkel PhD]
Cryogen One can between dipole-d another.
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99
Quadrupolar nuclei. NMR crystallography approach.
Olga B. Lapina
Boreskov Institute of Catalysis, pr. Lavrentieva 5, 630090 Novosibirsk, Russia Novosibirsk State University, Pirogova 2, 630090 Novosibirsk: Russia
E-mail: olga@catalysis.ru
The NMR crystallography is an emerging method for atomic-resolution structural analysis of different types of materials including well crystalline compounds, defect and amorphous systems. Unlike many diffraction techniques, solid-state NMR is not restricted to periodic boundary conditions and thus can be used to fully describe the structure of materials, including studies of local order and/or disorder. Recognizing these efforts, IUPAC has established a separate commission on NMR Crystallography and Related Methods at the Montreal General Assembly of the International Union of Crystallography in August 2014.
The NMR crystallography is based on the combination of the state of the art high-resolution solid-state NMR experiments with the state of the art DFT GIPAW computations allowing to determine structural and dynamic characteristics in a variety of systems.
Modern solid-state NMR spectroscopy has now in its inventory NMR spectrometers with magnetic field strength of up to 23.5 T (1H at 1 GHz), magic angle spinning (MAS) probes capable of spinning samples as fast as 100 kHz, as well as modern electronic components and devices which allow to realize complex acquisition programs with radio-frequency pulses of desirable characteristics. In order to analyze NMR spectra of quadrupolar nuclei, a number of software programs have been developed, allowing the researcher to extract parameters of chemical shift and nuclear quadrupole interaction tensors, as well as their mutual orientation.
There is no universal clear-cut roadmap for experimental determination of NMR parameters of quadrupolar nuclei, because in addition to the above mentioned tensor parameters their NMR spectra would depend on the nature of nuclei (the resonance frequency in the given magnetic field), spin relaxation dynamics, as well as on the different spin-spin interactions.
In this lecture I am going to give a short description of the modern solid state NMR of quadrupolar nuclei and on several examples demonstrate NMR crystallography approaches for oxide based systems.
Solid state NMR spectra of quadrupolar nuclei.
Within the strong magnetic field approximation, spin Hamiltonian describing the interactions of magnetic field with the quadrupolar nuclear spin (I > 1/2) has the form:
, (1)
where is the Hamiltonian describing the Zeeman interaction of nuclear spin I with magnetic field B0; and is the gyromagnetic ratio.