Neutron Scattering in Biology - Fitter Gutberlet and Katsaras
.pdfbiological and medical physics, biomedical engineering
biological and medical physics, biomedical engineering
The fields of biological and medical physics and biomedical engineering are broad, multidisciplinary and dynamic. They lie at the crossroads of frontier research in physics, biology, chemistry, and medicine. The Biological and Medical Physics, Biomedical Engineering Series is intended to be comprehensive, covering a broad range of topics important to the study of the physical, chemical and biological sciences. Its goal is to provide scientists and engineers with textbooks, monographs, and reference works to address the growing need for information.
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Editor-in-Chief:
Elias Greenbaum, Oak Ridge National Laboratory,
Oak Ridge, Tennessee, USA
Editorial Board:
Masuo Aizawa, Department of Bioengineering,
Tokyo Institute of Technology, Yokohama, Japan
Olaf S. Andersen, Department of Physiology,
Biophysics & Molecular Medicine,
Cornell University, New York, USA
Robert H. Austin, Department of Physics, Princeton University, Princeton, New Jersey, USA
James Barber, Department of Biochemistry,
Imperial College of Science, Technology
and Medicine, London, England
Howard C. Berg, Department of Molecular
and Cellular Biology, Harvard University,
Cambridge, Massachusetts, USA
Victor Bloomf ield, Department of Biochemistry, University of Minnesota, St. Paul, Minnesota, USA
Robert Callender, Department of Biochemistry,
Albert Einstein College of Medicine,
Bronx, New York, USA
Britton Chance, Department of Biochemistry/
Biophysics, University of Pennsylvania,
Philadelphia, Pennsylvania, USA
Steven Chu, Department of Physics,
Stanford University, Stanford, California, USA
Louis J. DeFelice, Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA
Johann Deisenhofer, Howard Hughes Medical
Institute, The University of Texas, Dallas,
Texas, USA
George Feher, Department of Physics,
University of California, San Diego, La Jolla,
California, USA
Hans Frauenfelder, CNLS, MS B258,
Los Alamos National Laboratory, Los Alamos,
New Mexico, USA
Ivar Giaever, Rensselaer Polytechnic Institute,
Troy, New York, USA
Sol M. Gruner, Department of Physics, Princeton University, Princeton, New Jersey, USA
Judith Herzfeld, Department of Chemistry,
Brandeis University, Waltham, Massachusetts, USA
Mark S. Humayun, Doheny Eye Institute,
Los Angeles, California, USA
Pierre Joliot, Institute de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, France
Lajos Keszthelyi, Institute of Biophysics, Hungarian Academy of Sciences, Szeged, Hungary
Robert S. Knox, Department of Physics
and Astronomy, University of Rochester, Rochester,
New York, USA
Aaron Lewis, Department of Applied Physics,
Hebrew University, Jerusalem, Israel
Stuart M. Lindsay, Department of Physics
and Astronomy, Arizona State University,
Tempe, Arizona, USA
David Mauzerall, Rockefeller University,
New York, New York, USA
Eugenie V. Mielczarek, Department of Physics
and Astronomy, George Mason University, Fairfax,
Virginia, USA
Markolf Niemz, Klinikum Mannheim,
Mannheim, Germany
V. Adrian Parsegian, Physical Science Laboratory,
National Institutes of Health, Bethesda,
Maryland, USA
Linda S. Powers, NCDMF: Electrical Engineering, Utah State University, Logan, Utah, USA
Earl W. Prohofsky, Department of Physics, Purdue University, West Lafayette, Indiana, USA
Andrew Rubin, Department of Biophysics, Moscow
State University, Moscow, Russia
Michael Seibert, National Renewable Energy
Laboratory, Golden, Colorado, USA
David Thomas, Department of Biochemistry,
University of Minnesota Medical School,
Minneapolis, Minnesota, USA
Samuel J. Williamson, Department of Physics, New York University, New York, New York, USA
J. Fitter T. Gutberlet J. Katsaras
Neutron Scattering
in Biology
Techniques and Applications
With 240 Figures
123
Dr. Jorg¨ Fitter |
Dr. John Katsaras |
|
Forschungszentrum Julich¨ GmbH |
National Research Council |
|
Abt. IBI-2 |
|
Chalk River |
52425 Julich,¨ |
Germany |
K0J 1J0 Ontario, Canada |
e-mail: j.fitter@fz-juelich.de |
e-mail: john.katsaras@nrc.gc.ca |
Dr. Thomas Gutberlet
Laboratory of Neutron Scattering Paul Scherrer Institut
5232 Villigen, Switzerland e-mail: thomas.gutberlet@psi.ch
Library of Congress Control Number: 2005934097
ISSN 1618-7210
ISBN-10 3-540-29108-3 Springer Berlin Heidelberg New York
ISBN-13 978-3-540-29108-4 Springer Berlin Heidelberg New York
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Preface
“Certainly no subject or field is making more progress on so many fronts at the present moment, than biology, and if we were to name the most powerful assumption of all, which leads one on and on in an attempt to understand life, it is that all things are made of atoms, and that everything that living things do can be understood in terms of the jigglings and wigglings of atoms.”
Richard P. Feynmann, from “Six easy pieces” (1963)
In 1932, James Chadwick discovered the neutron, but initially the only sources of neutrons were from the radioactive decay of unstable nuclei. It was not until 1942 when Enrico Fermi constructed the first nuclear reactor in the squash courts beneath the University of Chicago’s Stagg Field, that a controlled and sustained nuclear chain reaction was achieved. After World War II, nuclear reactors became available for civilian research, and in 1945 Ernest Wollan set up a double-crystal di ractometer at ORNL’s Graphite Reactor. This marks the beginning of neutron scattering.
Neutrons produced by present reactorand accelerator-based sources, typically have wavelengths in the order of ˚Angstroms, and hence are wellsuited for probing the structures and motions of molecules. For biological materials rich in hydrogen, the large di erence in scattering cross-sections between hydrogen and deuterium provides the possibility of contrast variation, a powerful method achieved by selective deuteration for emphasizing, or not, the scattering from a particular portion of a molecule or molecular assembly. Using a variety of scattering methods, the structures and dynamics of biological systems can be determined.
The present compilation aims to provide the reader with some of the important applications of neutron scattering in structural biology, biophysics, and systems relevant to biology.
The location of hydrogen atoms in biomolecules such as, proteins, is – despite the high brilliance and power of third generation synchrotron
VI Preface
sources – not readily available by X-ray crystallography or related physical techniques. In the case of hydrogens attached to electronegative atoms (e.g., O and N), even high resolution X-ray structures (resolution <1 ˚A) cannot unequivocally locate these H atoms. On the other hand, these atoms can e ectively be located using high resolution crystallographic neutron di raction methods. Radiation damage leading to changes in metal oxidation state and subsequent loss of hydrogens can also pose a problem with X-rays, but not so with neutrons. When good quality, large (>1 mm3) single crystals cannot be obtained, low resolution neutron di raction o ers an alternative technique in determining the hydrated structure of macromolecules and their various hydrogen-bonding patterns.
Small-angle neutron scattering (SANS) is probably the technique most often applied to biological materials as it can probe the size, shape and conformation of macromolecules and macromolecular complexes in aqueous solution on a length scale from ten to several thousand ˚Angstroms. The ability to scatter from materials in solution allows for biologically relevant conditions to be mimicked, and also permits for the study of samples that are either di cult or impossible to crystallize. In recent years, SANS has greatly benefited from the production of “cold neutrons” that have wavelengths 10–20 times larger than “thermal neutrons”, allowing SANS to examine complex materials, such as living cells.
Over the past decade, neutron reflectometry has increasingly become an important technique for the characterization of biological and biomimetic thin films attached to a solid support, in contact with water. Advancements in sample environments, instrumentation, and data analysis now make it possible to obtain high resolution information about the composition of these materials along the axis perpendicular to the plane of the membrane or substrate. Most recently, a newly developed phase-sensitive neutron reflectometry technique also allows direct inversion of the reflectometry data to obtain unique compositional depth profiles of the films in question.
Studies exploring the relationship between the function and the dynamics of biological systems are still in their nascent stages. Incoherent neutron scattering (INS) techniques such as, elastic (EINS), quasielastic (QINS), and inelastic (IINS) neutron scattering, along with molecular dynamics (MD) simulations o er the real possibility of investigating the dynamics associated with a molecule’s biological function(s). Using the large incoherent scattering crosssection intrinsic to naturally abundant hydrogen atoms, various INS type measurements can be carried out. These results, in conjunction with MD simulations, o er a glimpse of for example, a protein’s internal structure on the picosecond time scale. Moreover, the current developments of intense pulsed neutron sources promise, in the near future, to accelerate our understanding of the relationship between a molecule’s dynamics and its function.
The study of materials under di cult environmental conditions (such as high magnetic fields, high pressures, shear, and 100% relative humidity) is by no means straight forward and requires specialized equipment. In many
Preface VII
cases, these experiments are better accommodated by the fact that neutrons interact weakly, thus nondestructively, with many commonly used materials (e.g., aluminum and its alloys) that are readily available and suitable for the construction of sample environments. The conditions created by these specialized environments provide us with a more detailed physical understanding of biologically relevant materials.
The present volume begins with a general introduction into the generation and properties of neutrons and is followed by a series of papers describing the various elastic and inelastic neutron scattering techniques used to study biological and biologically relevant systems. The reader is introduced to the basic principles of neutron crystallography, low resolution neutron di raction, neutron small-angle scattering, neutron reflectometry, inelastic and quasielastic neutron scattering, and neutron spin echo spectroscopy. Papers describing sample environments and preparatory techniques, in addition to molecular dynamics simulations used to evaluate the neutron data, are also included. Finally, there are a series of papers describing recent neutron research that has elucidated the structure and dynamics of soluble proteins, membrane embedded proteins, and of complex biological aggregates.
The editors wish to express their great appreciation to all of the contributors whose diligence, e orts, and timeliness made this compilation possible.
J¨ulich |
J¨org Fitter |
Villigen |
Thomas Gutberlet |
Chalk River |
John Katsaras |
Spring 2005 |
|
Contents
1 Neutron Scattering for Biology |
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T.A. Harroun, G.D. Wignall, J. Katsaras . . . . . . . . . . . . . . . . . . . . . . . . . . . |
1 |
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1.1 |
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . |
1 |
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1.2 |
Production of Neutrons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . |
2 |
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1.3 |
Elements of Neutron Scattering Theory . . . . . . . . . . . . . . . . . . . . . . . |
5 |
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1.3.1 |
Properties of Neutrons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . |
5 |
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1.3.2 Energy and Momentum Transfer . . . . . . . . . . . . . . . . . . . . . . . |
5 |
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1.3.3 |
Di raction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . |
6 |
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1.3.4 Scattering Length and Cross-Section . . . . . . . . . . . . . . . . . . . . |
7 |
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1.3.5 Coherent and Incoherent Cross-Sections . . . . . . . . . . . . . . . . . |
8 |
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1.4 |
Neutron Di raction and Contrast . . . . . . . . . . . . . . . . . . . . . . . . . . . . . |
10 |
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1.4.1 |
Contrast and Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . |
11 |
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1.4.2 |
Contrast and Dynamics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . |
13 |
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1.4.3 |
Contrast and Biology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . |
13 |
1.5 |
Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . |
16 |
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References . . |
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . |
17 |
Part I Elastic Techniques
2 Single Crystal Neutron Di raction
and Protein Crystallography
C.C. Wilson, D.A. Myles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
2.2Single Crystal Neutron Di ractometers:
Basic Principles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 2.2.1 Development of Single Crystal Neutron Di ractometers . . . 25
2.2.2Achievements of Neutron Macromolecular
Crystallography at Reactor Sources . . . . . . . . . . . . . . . . . . . . . 25 2.2.3 Developments at Spallation Sources . . . . . . . . . . . . . . . . . . . . 28
XContents
2.2.4Forward Look for Instrumentation
for Neutron Macromolecular Crystallography . . . . . . . . . . . . 29 2.2.5 Improvements in Sources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 2.3 Information from Neutron Crystallography . . . . . . . . . . . . . . . . . . . . 32 2.3.1 Neutron Crystallography of Molecular Materials . . . . . . . . . 32 2.3.2 Neutron Crystallography in Structural Biology . . . . . . . . . . . 33
2.3.3Sample and Data Requirements
for Single Crystal Neutron Di raction . . . . . . . . . . . . . . . . . . 34
2.4Brief Review of the Use of Neutron Di raction
in the Study of Biological Structures . . . . . . . . . . . . . . . . . . . . . . . . . . 35 2.4.1 Location of Hydrogen Atoms . . . . . . . . . . . . . . . . . . . . . . . . . . 36 2.4.2 Solvent Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 2.4.3 Hydrogen Exchange . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39 2.4.4 Low Resolution Studies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39 2.4.5 Other Biologically Relevant Molecules . . . . . . . . . . . . . . . . . . 39
2.5 Recent Developments and Future Prospects . . . . . . . . . . . . . . . . . . . . 41 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
3 Neutron Protein Crystallography:
Hydrogen and Hydration in Proteins
N. Niimura . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
3.2 Complementarity of Neutrons and X-rays . . . . . . . . . . . . . . . . . . . . . . 44
3.2.1 Refinement of Hydrogen Positions . . . . . . . . . . . . . . . . . . . . . . 44
3.2.2Hydrogen Atoms Which Cannot be Predicted
Stereochemically . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45 3.3 Hydrogen Bonding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50 3.3.1 Weak and Strong Hydrogen Bonding . . . . . . . . . . . . . . . . . . . 50 3.3.2 Bifurcated Hydrogen Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
3.4 H/D Exchange . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52 3.5 Hydration in Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 3.5.1 Experimental Observation of Hydration Molecules . . . . . . . . 55 3.5.2 Classification of Hydration . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 3.5.3 Dynamic Behavior of Hydration . . . . . . . . . . . . . . . . . . . . . . . . 58
3.6 Crystallization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59 3.7 Conclusions and Future Prospects . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
4 Neutron Protein Crystallography: Technical Aspects and Some Case Studies at Current Capabilities and Beyond
M. Blakeley, A.J.K. Gilboa, J. Habash, J.R. Helliwell, D. Myles,
J. Raftery . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63 4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63 4.2 Data Collection Perspectives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64