Solid-State NMR: Applications in biomembrane structure

PRELIMS.pdf
Preface
Foreword
Outline placeholder
Biomembranes: the Holy Grail
Editor biographies
Frances Separovic
Marc-Antoine Sani
List of contributors
CH001.pdf
Chapter 1 Solid-state NMR methods for studying membrane systems
Overview
1.1 Introduction
1.2 Using NMR as a reporter on membrane structure
1.3 Dynamics in biological membranes
1.4 Probing the surface charge of membranes with solid-state NMR
1.5 Lateral domain formation
1.6 Lipid/protein interactions
1.6.1 Insight into protein/lipid headgroup association by 31P CP MAS NMR
1.6.2 Studying annular lipids bound to integral membrane proteins
1.6.3 Studying non-annular lipids bound to integral membrane proteins
1.7 Membrane remodeling
1.8 Summary
Acknowledgements
References
CH002.pdf
Chapter 2 Characterization of lipid behaviour in model biomembranes using 2H solid-state NMR
Abstract
2.1 Introduction
2.2 The quadrupole interaction
2.3 The wideline 2H NMR spectra of chain-deuterated phospholipids in bilayers
2.4 The quadrupole echo
2.5 Characterizing phospholipid bilayer phases using wideline 2H NMR
2.6 Using spectral subtraction to identify boundaries of two-phase coexistence regions in bilayer temperature-composition phase diagrams
2.7 Beyond difference spectroscopy—defining liquid crystalline phase coexistence with 2H NMR
2.8 Summary
References
CH003.pdf
Chapter 3 Deuterium solid-state NMR of whole bacteria: sample preparation and effects of cell envelope manipulation
Overview
3.1 Structure and composition of bacterial cell envelopes
3.2 Sample preparation
3.3 Static 2H NMR of Gram(−) and Gram(+) bacteria
3.4 2H NMR of bacteria with cell envelope perturbation
3.5 What have we learned from 2H NMR of bacteria so far?
References
CH004.pdf
Chapter 4 Solid-state NMR study of microalgal membranes and cell walls
Abstract
4.1 Overview
4.2 Microalgal cell membrane composition and architecture
4.2.1 Microalgal cell wall and plasma membrane
4.2.2 Photosynthetic organelles (thylakoids and chloroplast)
4.2.3 lipid droplets and free fatty acids
4.3 Technical considerations
4.3.1 Observable nuclei for microalgal membranes studies
4.3.2 Solution and solid-state NMR
4.4 NMR of lipid extracts and model membranes
4.5 In vivo, in-cell and in situ NMR
4.5.1 1H-NMR based approaches
4.5.2 1D 13C solid-state NMR methods
4.5.3 2D-13C and 15N-NMR experiments
4.6 Conclusion and future prospects
Acknowledgements
References
CH005.pdf
Chapter 5 Determining the mechanism of action of host defense peptides: solid-state NMR approaches
Abstract
5.1 Introduction
5.2 Model membranes
5.3 Whole cells
5.4 Conclusions
References
CH006.pdf
Chapter 6 19F NMR of biomembranes
Abstract
6.1 Introduction
6.2 19F NMR
6.2.1 Advantages of 19F as NMR probe
6.2.2 Limitations of 19F NMR
6.2.3 19F NMR bridges the gap
6.2.4 Hardware requirements
6.2.5 Typical 19F NMR chemical shifts
6.3 Introducing 19F into biomembranes
6.3.1 19F-labels
6.3.2 Biosynthetic incorporation of 19F
6.3.3 Chemical introduction of 19F
6.4 Line narrowing techniques for 19F NMR of biomembranes
6.4.1 Multipulse solid-state 19F NMR
6.4.2 Oriented samples for solid-state 19F NMR
6.4.3 Magic angle spinning 19F NMR
6.4.4 Solution NMR of membrane proteins in membrane mimetics
6.5 Solid-state 19F NMR distance measurements in biomembranes
6.5.1 Distance measurements in oriented samples
6.5.2 Distance measurements under MAS
6.5.3 Multidimensional solid-state 19F NMR experiments
6.5.4 Ligands bound to membrane proteins
6.5.5 Intermolecular interactions of oligomeric membrane proteins and peptides
6.5.6 Distance measurements in solution
6.6 Solid-state 19F NMR orientation measurements in biomembranes
6.6.1 Orientation dependence in solid-state 19F NMR
6.6.2 Mobility and orientation
6.6.3 Molecular orientation in membranes from 19F NMR on oriented samples
6.6.4 Peptide re-alignment transitions in membranes revealed by solid-state 19F NMR
6.6.5 Peptide mobility in membranes
6.6.6 Orientation and mobility of lipids and small lipid-soluble molecules
6.7 Probing the environment
6.7.1 Conformational changes
6.7.2 Probing solvent environment
6.8 19F NMR in native membranes
6.9 Conclusions
Acknowledgements
References
CH007.pdf
Chapter 7 Structure, topology and dynamics of membrane-associated peptides by solid-state NMR
Summary
7.1 Introduction
7.2 Solid-state NMR spectroscopic approaches
7.3 The anisotropy of solid-state NMR interactions
7.4 Sample preparation
7.4.1 Peptides
7.4.2 Sample preparation: bicelles and supported lipid bilayer
7.5 Oriented solid-state NMR spectroscopy to study the conformation, topology and dynamics of peptides in membranes
7.6 Sample heterogeneity and orientational distributions
7.7 Membrane lipid composition
7.8 Taking peptide motions into consideration
7.9 Signal enhancement by DNP
Acknowledgement
References
CH008.pdf
Chapter 8 Solid-state NMR and dynamic nuclear polarization studies of molecular interactions in membranes
Abstract
8.1 Introduction
8.2 Membranes in the presence of small organic molecules
8.3 Membrane-active proteins and peptides
8.4 Transmembrane proteins
8.5 Membrane studies by NMR
8.6 Native membranes
8.7 Wideline and oriented membranes NMR
8.7.1 Deuterium NMR
8.7.2 Lipid phase analysis by 31P wideline NMR
8.7.3 High resolution NMR in oriented membranes – 15N PISEMA
8.8 High resolution sample spinning solid-state NMR
8.8.1 Membrane studies by 13C MAS NMR
8.8.2 Membrane interactions monitored by 31P MAS NMR
8.8.3 Correlation NMR spectroscopy in membranes
8.9 Dynamic nuclear polarization
8.10 Summary
Acknowledgements
References
CH009.pdf
Chapter 9 Mapping dynamics in membrane proteins with solid-state NMR: methods and examples
9.1 Introduction
9.2 NMR strategies to monitor dynamics
9.3 Monitoring dynamics with CP-based methods
9.3.1 WISE
9.3.2 CPPI
9.3.3 LG-CP
9.3.4 Dynamics in oriented NMR
9.4 Monitoring dynamics with heteronuclear DD recoupling-based methods
9.4.1 DIPSHIFT
9.4.2 REDOR
9.4.3 Symmetry-based schemes
9.5 Monitoring dynamics with CSA recoupling methods
9.5.1 2DCSA and SUPER
9.5.2 Symmetry-based schemes for CSA recoupling
9.6 Examples of studying dynamics in membrane proteins
9.6.1 Cross-polarisation based filtering
9.6.2 Rotational-echo based experiments
9.6.3 Protein structures using SLF experiments
9.7 Schemes for higher MAS and stronger couplings
9.7.1 REDOR-schemes with dipole–dipole coupling scaling
9.7.2 Equivalence of DIPSHIIT and REDOR pulse schemes
9.7.3 DIPSHIFT and REDOR at higher MAS frequencies
9.8 Conclusions
Acknowledgements
References
CH010.pdf
Chapter 10 Solid-state NMR studies of peripherally membrane-associated proteins: dealing with dynamics, disorder and dilute conditions
Abstract
10.1 Peripheral and conditional membrane proteins
10.1.1 What are peripheral membrane proteins?
10.1.2 Structural studies of peripheral membrane proteins.
10.2 Solid-state NMR studies of peripheral membrane proteins
10.3 Case studies of ssNMR on peripheral membrane proteins
10.3.1 Lipid-bound cytochrome c as a pro-apoptotic lipid peroxidase
10.3.2 Myelin basic protein
10.3.3 The Pleckstrin homology domain of PLC-δ1
10.4 Lessons learned
10.5 Conclusions
Acknowledgements
References
CH011.pdf
Chapter 11 Structural dynamics of G protein-coupled receptors in lipid membranes investigated by solid-state NMR spectroscopy
Overview/Abstract
11.1 Introduction
11.2 Preparative options for studying GPCRs by NMR spectroscopic tools
11.2.1 Construct optimization and expression systems
11.2.2 Isotopic labeling
11.2.3 Reconstitution into membranes and membrane mimetics
11.3 Methodological options for studying dynamics of GPCRs by solid-state NMR
11.3.1 Isotropic chemical shift changes
11.3.2 Influence of motions on anisotropic chemical shift interactions
11.3.3 Molecular order parameters
11.3.4 Relaxation rates
11.4 Examples
11.4.1 Chemokine receptor CXCR1
11.4.2 Neuropeptide Y receptor type 2
11.4.3 Growth hormone secretagogue receptor
11.5 Conclusions
Acknowledgement
References
CH012.pdf
Chapter 12 Hybridizing isotropic and anisotropic solid-state NMR restraints for membrane protein structure determination
Abstract
12.1 Oriented-sample solid-state NMR (OS-ssNMR) structure determination of membrane proteins
12.2 Chemical shift anisotropy
12.3 Dipolar coupling
12.4 Scaling of orientational restraints due to conformational and topological dynamics
12.5 Hybridization of isotropic and anisotropic restraints
12.6 Summary
Acknowledgments
References
CH013.pdf
Chapter 13 Beyond structure: understanding dynamics in membrane protein complexes
Overview
13.1 Introduction
13.2 Membrane protein dynamics
13.3 NMR studies of dynamics of specific membrane protein systems
13.3.1 Anabaena sensory rhodopsin
13.3.2 Outer membrane proteins
13.3.3 Bacterial transmembrane chemoreceptors
13.4 Conclusions
Acknowledgement
References
CH014.pdf
Chapter 14 Solid-state NMR methods for investigations of membrane protein structure and dynamics
Abstract
14.1 Introduction
14.2 Structure determination
14.2.1 Sample preparation
14.2.2 Dipolar recoupling techniques
14.2.3 Resonance assignments
14.2.4 NMR structural restraints
14.3 Proton detection in membrane proteins
14.4 Dynamics
14.4.1 Protein dynamics
14.4.2 NMR methods for studying protein dynamics
14.4.3 Opportunity for observing mobile regions in membrane proteins
14.5 Conclusions and perspective
Acknowledgements
References
CH015.pdf
Chapter 15 Proton-detected solid-state NMR and its applications to membrane proteins
Abstract
15.1 Introduction
15.2 Fast MAS and deuteration
15.3 Spectroscopic possibilities of proton-detected ssNMR
15.3.1 General trends in proton-detected ssNMR
15.3.2 Signal assignment in proton-detected ssNMR
15.3.3 H/D exchange and interactions with small molecules
15.3.4 Protein structure calculation in proton-detected ssNMR
15.3.5 Relaxation and elucidation of protein dynamics
15.4 Proton detection for membrane proteins
15.4.1 General considerations
15.4.2 Preparative issues
15.4.3 Example studies using ssNMR for membrane proteins
15.4.4 Perspectives
References