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Structure and Bonding
Series Editor:
D.M.P. Mingos, Oxford, United Kingdom
Editorial Board:
F.A. Armstrong, Oxford, United Kingdom
X. Duan, Beijing, China
L.H. Gade, Heidelberg, Germany
K.R. Poeppelmeier, Evanston, IL, USA
G. Parkin, NewYork, USA
M. Takano, Kyoto, Japan
For further volumes:
http://www.springer.com/series/430
Aims and Scope
The series Structure and Bonding publishes critical reviews on topics of research
concerned with chemical structure and bonding. The scope of the series spans the
entire Periodic Table and addresses structure and bonding issues associated with all of
the elements. It also focuses attention on new and developing areas of modern
structural and theoretical chemistry such as nanostructures, molecular electronics,
designed molecular solids, surfaces, metal clusters and supramolecular structures.
Physical and spectroscopic techniques used to determine, examine and model structures fall within the purview of Structure and Bonding to the extent that the focus is on
the scientific results obtained and not on specialist information concerning the
techniques themselves. Issues associated with the development of bonding models
and generalizations that illuminate the reactivity pathways and rates of chemical
processes are also relevant
The individual volumes in the series are thematic. The goal of each volume is to give
the reader, whether at a university or in industry, a comprehensive overview of an area
where new insights are emerging that are of interest to a larger scientific audience.
Thus each review within the volume critically surveys one aspect of that topic and
places it within the context of the volume as a whole. The most significant developments of the last 5 to 10 years should be presented using selected examples to illustrate
the principles discussed. A description of the physical basis of the experimental
techniques that have been used to provide the primary data may also be appropriate,
if it has not been covered in detail elsewhere. The coverage need not be exhaustive in
data, but should rather be conceptual, concentrating on the new principles being
developed that will allow the reader, who is not a specialist in the area covered, to
understand the data presented. Discussion of possible future research directions in the
area is welcomed.
Review articles for the individual volumes are invited by the volume editors.
In references Structure and Bonding is abbreviated Struct Bond and is cited as a
journal.
Christiane R. Timmel Jeffrey R. Harmer
Editors
Structural Information from
Spin-Labels and Intrinsic
Paramagnetic Centres in
the Biosciences
With contributions by
P.P. Borbat A.M. Bowen J.H. Freed D. Goldfarb
J.R. Harmer G. Jeschke J.P. Klare O. Schiemann
S.A. Shelke S.Th. Sigurdsson H.-J. Steinhoff
C.E. Tait C.R. Timmel R. Ward
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Editors
Christiane R. Timmel
Inorganic Chemistry Laboratory
University of Oxford
Oxford
United Kingdom
Jeffrey R. Harmer
Inorganic Chemistry Laboratory
University of Oxford
Oxford
United Kingdom
Centre for Advanced Imaging
University of Queensland
St Lucia
Australia
ISSN 0081-5993
ISSN 1616-8550 (electronic)
ISBN 978-3-642-39124-8
ISBN 978-3-642-39125-5 (eBook)
DOI 10.1007/978-3-642-39125-5
Springer Heidelberg New York Dordrecht London
Library of Congress Control Number: 2014933680
# Springer-Verlag Berlin Heidelberg 2014
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Preface
Contemporary science is ever more reliant on elucidating the structure and function
of matter’s molecular building blocks, be it in medical or materials research. Much
of today’s scientific progress hence depends crucially on the ability to measure
molecular structure and mechanism with ever-increasing sensitivity and accuracy,
with regard to both spatial and temporal resolutions. Electron paramagnetic resonance (EPR) with its wide armoury of powerful techniques has long been established as a versatile and powerful tool in the study of both structure and dynamics of
molecular systems. Thanks to the development of site-directed mutagenesis methodologies, the availability of suitable spin labels and the simultaneous technological and methodological developments, the applicability of the technique
particularly for the study of biological molecules and their assemblies seems
virtually boundless.
Many of the recent advances and applications of EPR spectroscopy relate to the
determination of structural constraints on the nanometre scale obtained from
systems containing paramagnetic centres, such as cofactors, metals, metal clusters
or indeed spin labels. Continuous wave (CW) and pulse EPR techniques exploit the
dipolar coupling between these paramagnetic centres in order to determine their
inter-spin distance(s). Double electron–electron resonance (DEER) or synonymously pulsed electron double resonance (PELDOR) is the EPR technique most
widely applied to the determination of distance constraints between paramagnetic
centres in frozen solutions or powders. Double quantum coherence (DQC) EPR
yields at least the same distance information as well as having several other virtues,
but is not as widespread due to the higher power requirements that are not provided
by most pulse spectrometers.
Over recent years the desire to study ever more complex (mainly biological)
systems has prompted the further development of both the spectroscopic techniques
(including novel or modified pulse sequences) and sophisticated data analysis and
interpretation methods. The design and synthesis of new spin labels has been driven
by ambitious goals such as the study of protein structure and dynamics in cells. At
the same time, the need for higher sensitivity such as what has been achieved at
v
vi
Preface
Ku-band has led to an increased interest in even higher frequency PELDOR at
Q- and W-band.
This volume of Structure and Bonding is devoted to a review of the state-of-theart EPR techniques in the determination of structure and dynamics of biological
systems with a particular focus on inter-spin distance measurements, some 13 years
after the excellent review of the same subject by L. J. Berliner, S. S. Eaton and G. R.
Eaton (Distance Measurements in Biological Systems by EPR, Vol. 19, 2000,
Kluwer Academic/Plenum Publishers, New York).
Borbat and Freed commence the series with an extensive review of the theoretical concepts of DQC EPR and DEER in the chapter “Pulse Dipolar Electron Spin
Resonance: Distance Measurements”. Technical aspects and sensitivity considerations are discussed in detail, as well as a new 5-pulse DEER sequence enabling
higher sensitivity and longer-range distance measurements. They show that these
three complementary techniques, which they implemented at Ku-band, offer outstanding versatility and very high sensitivity.
Jeschke discusses the data analysis and interpretation of experimental PELDOR
data in the chapter “Interpretation of Dipolar EPR Data in Terms of Protein
Structure”. Strategies for extracting information from the PELDOR trace
(i.e. mean inter-spin distance, distance distribution, number of spins and local
concentration) are described as well as the measurement conditions required for
optimal data collection and analysis. Furthermore, methods to infer backbone–
backbone distances from label–label distances are reviewed.
The methods for spin labelling of proteins and nucleic acids are examined in the
chapter “Site-Directed Nitroxide Spin Labeling of Biopolymers” by Shelke and
Sigurdsson. The three approaches, i.e. site-directed Nitroxide Spin Labeling, spin
labelling through biopolymer synthesis and non-covalent labelling, are described in
detail for proteins and nucleic acids. The authors also provide a comprehensive
overview of available spin labels and their characteristics.
Goldfarb reviews the existing methods of distance determination on systems
with paramagnetic metal-based spin labels, with a particular emphasis on Gd3+ in
the chapter “Metal-Based Spin Labeling for Distance Determination”. The advantages and limitations of metal-based spin labels over nitroxide spin labels are
presented, and a new approach to spin labelling based on high-spin metal ions
such as Mn2+ and Gd3+ is introduced. It is shown that the use of Gd3+ spin labels in
high-field measurements may lead to a much increased sensitivity as demonstrated
for a series of model systems.
Klare and Steinhoff focus on the use of CW EPR and pulse EPR methods to
obtain information on spin label side chain mobility, solvent accessibility, environment polarity and inter-spin distances with particular emphasis on membranebound proteins in the chapter “Structural Information from Spin-Labelled Membrane-Bound Proteins”. The theoretical background and techniques for determination of these properties are reviewed, and examples showing the use of these
techniques for the determination of structure and dynamics of membrane proteins
are given.
Preface
vii
Ward and Schiemann explore the recent developments and applications in the
study of oligonucleotides by CW and pulse dipolar EPR in the chapter “Structural
Information from Oligonucleotides”. Studies on model DNA and RNA systems
aimed at establishing the range, accuracy and robustness of distance determination
using PELDOR on these systems are presented, as well as the use of PELDOR to
identify structure elements and determine conformational changes.
Bowen at al. describe the practical and theoretical aspects of orientationselective PELDOR in the chapter “Orientation-Selective DEER Using Rigid Spin
Labels, Cofactors, Metals, and Clusters”. Experimental approaches to orientationselective PELDOR at different frequencies, methods for the calculation of
orientation-selective PELDOR traces and the interpretation of experimental data
in terms of both distance and orientation of pairs of spin labels are discussed in
detail. The chapter concludes with a report on recent applications employing
nitroxide spin-labelled and metal containing systems.
Oxford, United Kingdom
Christiane R. Timmel
Jeffrey R. Harmer
ThiS is a FM Blank Page
Contents
Pulse Dipolar Electron Spin Resonance: Distance Measurements . . . . . . . . . 1
Peter P. Borbat and Jack H. Freed
Interpretation of Dipolar EPR Data in Terms of Protein Structure . . . . . . 83
Gunnar Jeschke
Site-Directed Nitroxide Spin Labeling of Biopolymers . . . . . . . . . . . . . . . . . . . 121
Sandip A. Shelke and Snorri Th. Sigurdsson
Metal-Based Spin Labeling for Distance Determination . . . . . . . . . . . . . . . . . . 163
Daniella Goldfarb
Structural Information from Spin-Labelled Membrane-Bound
Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205
Johann P. Klare and Heinz-Ju¨rgen Steinhoff
Structural Information from Oligonucleotides . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249
Richard Ward and Olav Schiemann
Orientation-Selective DEER Using Rigid Spin Labels, Cofactors,
Metals, and Clusters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 283
Alice M. Bowen, Claudia E. Tait, Christiane R. Timmel,
and Jeffrey R. Harmer
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 329
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