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Multifrequency and Multiresonance EPR Techniques Applied to Nitroxide Radicals and Nitroxide-Labeled Systems

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Multifrequency and Multiresonance EPR Techniques Applied to Nitroxide Radicals and Nitroxide-Labeled Systems Multifrequency and multiresonance EPR techniques applied to nitroxide radicals and nitroxide-labeled systems Inaugural dissertation for the attainment of the title of doctor in the Faculty of Mathematics and Natural Sciences at the Heinrich Heine University Düsseldorf presented by Anna Irena Nalepa from Dąbrowa Tarnowska (Poland) Düsseldorf, September 2015 i from the Max Planck Institute for Chemical Energy Conversion at the Heinrich Heine University Düsseldorf Published by permission of the Faculty of Mathematics and Natural Sciences at Heinrich Heine University Düsseldorf Supervisor: Prof. Wolfgang Lubitz Co-supervisor: Prof. Claus Seidel Date of the oral examination: 28/09/2015 ii Abstract Site-directed spin labeling (SDSL) of target proteins with nitroxide radicals in conjunction with electron paramagnetic resonance (EPR) spectroscopy is a powerful method for elucidation of macromolecular structure and conformational dynamics on the molecular level. Moreover, information on the microenvironment properties at the site of the spin label can be inferred from the analysis of the magnetic interaction parameters of the nitroxide. This thesis focuses on the development of high-field/high-frequency EPR methodology for detailed characterization of the local environment. Heterogeneity of this local environment results in distinct nitroxide radical populations. In order to gain insight into the nature of these populations and to correlate them with local environment properties this work is mostly focused on investigation of model systems. Since the spin probe employed in this work is structurally related to the most widely applied nitroxide in structural biology, the MTS ((1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl)methanethiosulfonate) spin label, the conclusions are valid for SDSL proteins. The following topics are addressed in this work: i. Comparison of W-band (94 GHz) cw and pulsed EPR techniques to probe distinct populations of a nitroxide spin probe is made. These populations are typically not completely resolved in W-band cw EPR spectra of protonated SDSL systems due to broad EPR lines. This enforces either the necessity of system perdeuteration to decrease the EPR linewidth or to perform cw EPR experiments at even higher magnetic fields/ higher microwave frequencies to increase the spectral resolution. In this work the applicability of a pulsed EPR technique, ELDOR-detected NMR (EDNMR) at a moderately high microwave frequency of 94 GHz, is tested. It is shown that W-band EDNMR is the best-suited EPR technique for the characterization of distinct nitroxide populations. Its advantages include: (i) superior sensitivity as compared to ENDOR (complementary pulsed EPR technique) and (ii) capability to obtain spectral information for protonated systems. These advantages are crucial for the future applications of the EDNMR technique to SDSL systems. ii. In most protic solvents, including water, several distinct nitroxide radical populations are resolved using W-band EDNMR. Their origin is addressed and it is unequivocally shown that they correspond to different hydrogen-bonding situations of the nitroxide. Moreover, comparison of several protic solvents leads to the conclusion that magnetic parameters of nitroxides are predominantly influenced by the H-bonding situation of the radical. The solvent polarity exerts a minor effect on the nitroxide magnetic parameters. This has to be taken into account for correct interpretation of polarity/proticity profiles obtained in SDSL proteins and in biological membranes. iii. The influence of the thermal history of the sample on nitroxide radical populations in frozen, aqueous solution is investigated. Using W-band EDNMR it is shown, that annealing of shock frozen samples above the glass transition temperature causes rearrangements of H-bonds between water and nitroxide. This is reflected as a change in the ratio of spin probe populations in which nitroxides are described with different magnetic interaction parameters. Therefore, reproducible sample freezing is required for reliable polarity/proticity profiles obtained at low temperature by X-band (9.4 GHz) cw EPR in biomacromolecules. iii iv. The applicability of the W-band EDNMR technique to determine the site-specific water content is shown. The studied paramagnetic probes included: (i) the nitroxide radical, (ii) the nitroxide radical attached to bacterial photosynthetic reaction center (bRC) from Rhodobacter sphaeroides R26 and (iii) ionic states of native cofactors in bRC. The admixture of the disaccharide trehalose allows for additional manipulation of the hydration level of the studied systems. The limitations for local water sensing using nitroxides or native paramagnetic centers 17 are specified both for D2O or H2 O exchange experiments. Importantly, it is demonstrated that 17 W-band EDNMR on nitroxides in conjunction with H2 O water exchange has the potential to provide quantitative information on the site-specific water content in macromolecules. iv Zusammenfassung Die ortsspezifische Spinmarkierung (site-directed spin labeling, SDSL) von Proteinen mit Nitroxidradikalen in Verbindung mit Elektronenspinresonanz (electron paramagnetic resonance, EPR)-Spektroskopie ist eine effiziente Methode zur Aufklärung der makromolekularen Struktur und Konformationsdynamik auf molekularer Ebene. Darüber hinaus können Informationen über Eigenschaften der Mikroumgebung am Ort des Spinlabels aus der Analyse der Parameter der magnetischen Wechselwirkungen des Nitroxids erhalten werden. Die vorliegende Arbeit beschäftgt sich mit der Entwicklung von Hochfeld-/Hochfrequenz-EPR-Methodologien zur detaillierten Charakterisierung der unmittelbaren Umgebung des Radikals. Im Falle einer Heterogenität dieser lokalen Umgebung liegen unterscheidbare Populationen der Nitroxidradikale vor. Um Einblick in die Natur dieser Populationen zu erhalten und diese mit Eigenschaften der lokalen Umgebung zu korrelieren, konzentriert sich diese Dissertation vor allem auf die Untersuchung von Modellsystemen. Da die in dieser Arbeit verwendete Spinsonde strukturell ähnlich zu dem in der Strukturbiologie am häufigsten verwendeten Nitroxid, dem Spinlabel MTS ((1-oxyl-2,2,5,5-tetramethylpyrroline-3- methyl)methanethiosulfonate), ist, sind die hier gezogenen Schlussfolgerungen auch für entsprechende SDSL-Proteine gültig. Folgende Themenbereiche werden in dieser Arbeit behandelt: i. W-Band (94 GHz) cw und gepulste EPR-Techniken zur Untersuchung unterschiedlicher Populationen einer Nitroxid-Spinsonde werden verglichen. In W-band cw EPR-Spektren protonierter SDSL-Systeme sind diese Populationen üblicherweise nicht komplett aufgelöst aufgrund der breiten EPR-Linien. Dies macht entweder die Perdeuterierung der Probe erforderlich, um die EPR-Linienbreite zu verringern, oder cw EPR-Experimente bei noch höheren Magnetfeldern und Mikrowellenfrequenzen durchzuführen, um die spektrale Auflösung zu erhöhen. In der vorliegenden Arbeit wird eine gepulste EPR-Technik, ELDOR- detektierte NMR (EDNMR) bei einer mittelhohen Mikrowellenfrequenz von 94 GHz, auf ihre Anwendbarkeit hin untersucht. Es wird gezeigt, dass W-band EDNMR die am besten geeignete EPR-Technik zur Charakterisierung unterschiedlicher Nitroxidpopulationen ist. Zu den Vorteilen gehören: (i) ihre höhere Empfindlichkeit verglichen mit ENDOR (komplementäre gepulste EPR-Technik) und (ii) die Möglichkeit, Informationen über protonierte Systeme zu erhalten. Diese Vorteile sind entscheidend für die zukünftige Anwendung der EDNMR-Technik auf SDSL-Systeme. ii. In den meisten protischen Lösungsmitteln, einschließlich Wasser, können mehrere unterscheidbare Nitroxidradikalpopulationen mittels W-Band EDNMR aufgelöst werden. Bezogen auf ihren Ursprung wird eindeutig gezeigt, dass sie zwei unterschiedlichen Wasserstoffbrücken-Bindungssituationen des Nitroxids zuzuordnen sind. Außerdem führt der Vergleich mehrerer protischer Lösungsmittel zu dem Schluss, dass die magnetischen Parameter des Nitroxids hauptsächlich durch die H-Brücken-Bindungssituation des Radikals beeinflusst werden. Die Polarität des Lösemittels hat einen geringeren Einfluß auf seine magnetischen Parameter. Dies muss zur korrekten Interpretation von Polaritäts-/Protizitätsprofilen, berücksichtigt werden die in SDSL-Proteinen und biologischen Membranen erhalten wurden. iii. Der Einfluss der thermischen Vorgeschichte der Probe auf die Nitroxidradikalpopulationen in gefrorener wässriger Lösung wird untersucht. Mittels W-Band EDNMR wird gezeigt, dass das v Erwärmen schockgefrorener Proben über die Glasübergangstemperatur eine Neuausrichtung der H-Brücken zwischen Wasser und dem Nitroxid bewirkt. Diese zeigt sich als Veränderung des Verhältnisses der Spinsondenpopulationen, in der Nitroxide mit unterschiedlichen magnetischen Wechselwirkungsparametern beschrieben werden. Daher ist ein reproduzierbares Verfahren beim Einfrieren von Proben notwendig, um verlässliche Polaritäts- /Protizitätsprofile, die bei tiefen Temperaturen mittels X-band (9.4 GHz) cw EPR in Biomakromolekülen erhalten werden, zu erstellen. iv. Die Anwendbarkeit der W-band EDNMR-Technik zur Bestimmung des ortsspezifischen Wassergehalts wird gezeist. Die untersuchten paramagnetischen Sonden umfassen: (i) das Nitroxidradikal, (ii) das an das bakterielle photosynthetische Reaktionszentrum (bRC) von Rhodobacter sphaeroides R26 gebundene Nitroxidradikal und (iii) ionische Zustände nativer Kofaktoren in bRC. Hinzumischen des Disaccharids Trehalose ermöglicht eine zusätzliche Manipulation des Hydrationszustands der studierten
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