Solid State NMR Spectroscopy for Biopolymers: Principles and Applications

465 Pages·2006·12.99 MB·English

by  Hazime Saitô

SOLIDSTATE NMRSPECTROSCOPY FOR BIOPOLYMERS
Solid State NMR Spectroscopy
for Biopolymers
Principles and Applications
Hazime Saitoˆ
Himeji Institute ofTechnology,Himeji, Japan
and Hiroshima University, Hiroshima, Japan
Isao Ando
Tokyo Instituteof Technology, Tokyo, Japan
Akira Naito
Yokohama National University, Yokohama,Japan
AC.I.P.CataloguerecordforthisbookisavailablefromtheLibraryofCongress.
ISBN-101-4020-4302-3(HB)
ISBN-13978-1-4020-4302-4(HB)
ISBN-101-4020-4303-1(e-book)
ISBN-13978-1-4020-4303-1(e-book)
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TABLE OF CONTENTS
Preface ix
Acknowledgements xi
1 Introduction 1
2 Solid State NMR Approach 7
2.1. CP-MAS and DD-MAS NMR 7
2.2. Quadrupolar Nuclei 19
3 Brief Outline of NMR Parameters 31
3.1. Chemical Shift 31
3.2. Relaxation Parameters 42
3.3. Dynamics-Dependent Suppression of Peaks 51
4 Multinuclear Approaches 59
4.1. 31P NMR 59
4.2. 2H NMR 68
4.3. 17O NMR 80
5 Experimental Strategies 89
5.1. Isotope Enrichment (Labeling) 89
5.2. Assignment of Peaks 97
5.3. Ultra-High Field and Ultra-High Speed
MAS NMR 113
6 NMR Constraints for Determination of Secondary Structure 127
6.1. Orientational Constraint 127
6.2. Interatomic Distances 149
6.3. Torsion Angles 173
6.4. Conformation-Dependent Chemical Shifts 181
vi Table of Contents
7 Dynamics 201
7.1. Fast Motions with Motional Frequency>106 Hz 204
7.2. Intermediate or Slow Motions with Frequencies
Between 106 and 103 Hz 206
7.3. Very Slow Motions with Frequency<103 Hz 213
8 Hydrogen-Bonded Systems 219
8.1. Hydrogen Bond Shifts 220
8.2. 2H Quadrupolar Coupling Constant 236
9 Fibrous Proteins 241
9.1. Collagen Fibrils 241
9.2. Elastin 246
9.3. Cereal Proteins 252
9.4. Silk Fibroin 254
9.5. Keratins 267
9.6. Bacteriophage Coat Proteins 276
10 Polysaccharides 289
10.1. Distinction of Polymorphs 290
10.2. Network Structure, Dynamics, and Gelation Mechanism 302
11 Polypeptides as New Materials 313
11.1. Liquid-Crystalline Polypeptides 313
11.2. Blend System 325
12 Globular Proteins 337
12.1. (Almost) Complete Assignment of 13C NMR
Spectra of Globular Proteins 337
12.2. 3D Structure: a-Spectrin SH3 Domain 339
12.3. Ligand-Binding to Globular Protein 342
13 Membrane Proteins I: Dynamic Picture 347
13.1. Bacteriorhodopsin 348
13.2. Phoborhodopsin and Its Cognate Transducer 362
13.3. Diacylglycerol Kinase 366
14 Membrane Proteins II: 3D Structure 373
14.1. 3D Structure of Mechanically Oriented
Membrane Proteins 373
14.2. Secondary Structure Based on Distance Constraints 384
15 Biologically Active Membrane-Associated Peptides 405
15.1. Channel-Forming Peptides 405
15.2. Antimicrobial Peptides 415
Table of Contents vii
15.3. Opioid Peptides 420
15.4. Fusion Peptides 424
15.5. Membrane Model System 425
16 Amyloid and Related Biomolecules 431
16.1. Amyloid b-Peptide (Ab) 431
16.2. Calcitonin 435
Glossary 443
Index 447
PREFACE
‘‘Biopolymers’’ are polymeric materials of biological origin, including
globular,membrane,andfibrousproteins,polypeptides,nucleicacids,poly-
saccharides, lipids, etc. and their assembly, although preference to respect-
ivesubjectsmaybedifferentamongreaderswhoaremoreinterestedintheir
biological significance or industrial and/or medical applications. Neverthe-
less,characterizingorrevealingtheirsecondarystructureanddynamicsmay
be an equally very important and useful issue for both kinds of readers.
Special interest in revealing the 3D structure of globular proteins, nucleic
acids,andpeptideswasarousedinrelationtothecurrentlyactiveStructural
Biology. X-ray crystallography and multidimensional solution NMR spec-
troscopy have proved to be the standard and indispensable means for this
purpose. There remain, however, several limitations to this end, if one
intends to expand its scope further. This is because these approaches are
not always straightforward to characterize fibrous or membrane proteins
owing to extreme difficulty in crystallization in the former, and insufficient
spectralresolutionduetosparingsolubilityorincreasedeffectivemolecular
mass in the presence of surrounding lipid bilayers in the latter.
It is a natural consequence to expect solid state NMR as an alternative
means for this purpose, because major developments in the past 30 years
witnessed remarkable progress of this technique. The expected NMR line
widths available from achieved high-resolution solid state NMR can be
manipulated experimentally and are not any more influenced by motional
fluctuationofproteinsunderconsiderationasawhole,incontrasttosolution
NMR. Accordingly, detailed structural information such as mutual orienta-
tion of molecules, interatomic distances, torsion angles, etc. is available
fromNMRparameterscontainedinsolidstateNMR,althoughmostofthem
are lost due to time-averaging in solution NMR.
This book is intended to give a comprehensive account as to how poly-
morphic, secondary, and dynamic structures of a variety of the above-
mentioned biopolymers are revealed by (high-resolution) solid state NMR.
ix
x Preface
In particular, a special emphasis is made toward the following two aspects:
historical or chronological consequences of a variety of applications and
dynamic aspect of the biopolymers. It is unfortunate that the latter aspect
seems to be sacrificed in recent years in exchange for better structural
information available from spectra taken either at lower temperature or
hydrationlevelfarfrombiologicalsignificance.Indeed,revealingdynamics
aspectofbiopolymersisreallyanexcellentandunrivaledmeansasrevealed
by solid state NMR study, as compared with other spectroscopic or diffrac-
tion methods. In this connection, it is emphasized that special attention to
recording spectra by the most simple DD-MAS (one-pulse excitation with
high-powerdecoupling)NMRistheunrivaledandonlymeanstobeableto
record signals from such a flexible but structured portion of a variety of
biopolymersystems,evenifanumberofcomplicatedpulsetechniqueshave
been developed to obtain more detailed information. Readers may realize
thatveryvaluablestructuralinformationisstillavailablefromsuchasimple
NMR technique. Indeed, we must bear in our mind Simplex Sigillum Veri
(the truth is reflected in simplicity), as known since old times.
Thisbookconsistsofthetwoparts:principlesandapplications.Inthefirst
part,abriefaccountofbasicprinciples,NMRparameters,experimentalstrat-
egies,anddynamicsavailablefromsolidstateNMRspectroscopyismade.Inthe
second part, on the other hand, illustrative examples of these techniques to
varioussubjectssuchashydrogen-bondedsystems,fibrousproteins,polysac-
charides, polypeptides as new materials, globular and membrane proteins,
membrane-associatedpeptideswithbiologicalfunctions,andamyloidandre-
latedbiomolecules,aregiven.Theorganizationofthisbookisthusliketextile
fabricswovenfromthewarpsofbiopolymersandtheweftofsolidstateNMR.
Thereferencesinthisbookareofcoursebynomeanstointendtoprovidea
complete compilation of related subjects. For this purpose, please consult
references cited in a variety of review articles or books. Many of the data
from our contributions are collaborative works with our colleagues and stu-
dentsatNationalCancerCenterResearchInstitute,HimejiInstituteofTech-
nology (currently University of Hyogo), Tokyo Institute of Technology,
Yokohama National University, Gunma University, Tokyo University of
Agriculture and Technology, especially with Professor A. Shoji, Professor
T.Asakura,andProfessorS.Tuzi,towhomtheauthorsaredeeplyindebted.
WearealsogratefultoDr.S.Kuroki,Dr.K. Nishimura,Dr.S.Yamaguchi,
Dr. M. Tanio, and Mr. I. Kawamura for their help in preparation of this
manuscript.
August 2005 Hazime Saitoˆ
Isao Ando
Akira Naito
ACKNOWLEDGEMENTS
We are indebted to the following authors and publishers for permission to
reproduce figures.
A. Abragam: Fig. 2.11
T. Asakura: Fig. 9.6
A. Bax: Fig. 6.28
M. F. Brown: Fig. 14.6
E. E. Burnell: Fig. 4.8
T. A. Cross: Figs. 6.3, 6.4, 6.8, 14.2, 14.9
J. H. Davis: Fig. 4.16
T. Erata: Fig. 10.7
L. Emsley: Fig. 5.9
R. R. Ernst: Figs. 5.7
B. C. Gerstein: Fig. 2.13
A. M. Gil: Fig. 9.3
R. G. Griffin: Fig. 12.2
R. E. W. Hancock: Fig. 15.6
J. Herzfeld: Fig. 14.7
M. Hong: Fig. 5.1
L. W. Jelinski: Fig. 9.8
K. K. Kumashiro: Fig. 9.2
M. H. Levitt: Figs. 6.25, 6.26
J. R. Lyerla, Jr.: Fig. 3.4
G. E. Maciel: Fig. 3.7
R. H. Marchessault: Fig. 10.3
B. H. Meier: Figs. 5.8, 5.12, 6.21, 9.7, 12.1
E. Oldfield: Figs. 4.10, 4.13, 7.3
S. J. Opella: Figs. 4.4, 4.15, 6.1, 6.5, 6.6, 6.7, 14.1, 14.3, 14.4
H. Oschkinat: Fig. 5.11
M. Pruski: Fig. 2.15
xi