Neutron scattering in biology: techniques and applications
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Berlin [u.a.]
Springer
2006
|
| Schriftenreihe: | Biological and medical physics, biomedical engineering
|
| Schlagworte: | |
| Online-Zugang: | Inhaltstext Inhaltsverzeichnis |
| Beschreibung: | XXIV, 557 S. Ill., graph. Darst. 235 mm x 155 mm |
| ISBN: | 3540291083 9783540291084 |
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| 245 | 1 | 0 | |a Neutron scattering in biology |b techniques and applications |c Jörg Fitter ... (eds.) |
| 264 | 1 | |a Berlin [u.a.] |b Springer |c 2006 | |
| 300 | |a XXIV, 557 S. |b Ill., graph. Darst. |c 235 mm x 155 mm | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 490 | 0 | |a Biological and medical physics, biomedical engineering | |
| 650 | 7 | |a Biophysique |2 ram | |
| 650 | 4 | |a Neutrons - Diffusion | |
| 650 | 7 | |a Neutrons - Diffusion |2 ram | |
| 650 | 7 | |a Spectroscopie moléculaire |2 ram | |
| 650 | 4 | |a Neutron Diffraction |x methods | |
| 650 | 4 | |a Neutrons |x Scattering | |
| 650 | 0 | 7 | |a Biologie |0 (DE-588)4006851-1 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Neutronenstreuung |0 (DE-588)4041980-0 |2 gnd |9 rswk-swf |
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Datensatz im Suchindex
| _version_ | 1804135132629565440 |
|---|---|
| adam_text | CONTENTS
1 NEUTRON SCATTERING FOR BIOLOGY
T.A. HARROUN, G.D. WIGNALL, J. KATSARAS
...........................
1
1.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . 1
1.2 PRODUCTION OF NEUTRONS . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . 2
1.3 ELEMENTS OF NEUTRON SCATTERING THEORY . . . . . . . . . . . . . . .
. . . . . . . . 5
1.3.1 PROPERTIES OF NEUTRONS . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . 5
1.3.2 ENERGY AND MOMENTUM TRANSFER . . . . . . . . . . . . . . . . . . .
. . . . 5
1.3.3 DIFFRACTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . 6
1.3.4 SCATTERING LENGTH AND CROSS-SECTION . . . . . . . . . . . . . . .
. . . . . 7
1.3.5 COHERENT AND INCOHERENT CROSS-SECTIONS . . . . . . . . . . . . . .
. . . 8
1.4 NEUTRON DIFFRACTION AND CONTRAST . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 10
1.4.1 CONTRAST AND STRUCTURE . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 11
1.4.2 CONTRAST AND DYNAMICS . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 13
1.4.3 CONTRAST AND BIOLOGY . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . 13
1.5 CONCLUSIONS................................................ 16
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 17
PART I ELASTIC TECHNIQUES
2 SINGLE CRYSTAL NEUTRON DIFFRACTION
AND PROTEIN CRYSTALLOGRAPHY
C.C. WILSON, D.A. MYLES
.........................................
21
2.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . 21
2.2 SINGLE CRYSTAL NEUTRON DIFFRACTOMETERS:
BASICPRINCIPLES............................................ 22
2.2.1 DEVELOPMENT OF SINGLE CRYSTAL NEUTRON DIFFRACTOMETERS . . . 25
2.2.2 ACHIEVEMENTS OF NEUTRON MACROMOLECULAR
CRYSTALLOGRAPHY AT REACTOR SOURCES . . . . . . . . . . . . . . . . . . .
. . 25
2.2.3 DEVELOPMENTS AT SPALLATION SOURCES . . . . . . . . . . . . . . . .
. . . . 28
XC
O
N
T
E
N
T
S
2.2.4 FORWARD 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
2.3.3 SAMPLE AND DATA REQUIREMENTS
FOR SINGLE CRYSTAL NEUTRON DIFFRACTION . . . . . . . . . . . . . . . . .
. 34
2.4 BRIEF REVIEW OF THE USE OF NEUTRON DIFFRACTION
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
3.2.2 HYDROGEN ATOMS WHICH CANNOT BE PREDICTED
STEREOCHEMICALLY . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 45
3.3 HYDROGENBONDING ......................................... 50
3.3.1 WEAK AND STRONG HYDROGEN BONDING . . . . . . . . . . . . . . . . .
. . 50
3.3.2 BIFURCATED HYDROGEN BONDS . . . . . . . . . . . . . . . . . . . .
. . . . . . . 51
3.4 H/DEXCHANGE............................................. 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 CONCLUSIONSANDFUTUREPROSPECTS ............................ 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
CONTENTS XI
4.3 REALIZING A COMPLETE STRUCTURE:
THE COMPLEMENTARY ROLES OF X-RAY
AND NEUTRON PROTEIN CRYSTALLOGRAPHY . . . . . . . . . . . . . . . . . .
. . . . . . . 65
4.4 CRYO-NEUTRON PROTEIN CRYSTALLOGRAPHY . . . . . . . . . . . . . . . .
. . . . . . . . 66
4.5 CURRENT TECHNIQUE, SOURCE,
ANDAPPARATUSDEVELOPMENTS................................ 67
4.6 PLANSFORTHEESSANDNPX.................................. 69
4.7 CONCLUSIONSANDFUTUREPROSPECTS ............................ 69
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 72
5 DETERGENT BINDING IN MEMBRANE PROTEIN CRYSTALS
BY NEUTRON CRYSTALLOGRAPHY
P. TIMMINS
.....................................................
73
5.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . 73
5.2 ADVANTAGES OF NEUTRONS . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . 73
5.3 INSTRUMENTATION AND DATA REDUCTION . . . . . . . . . . . . . . . . .
. . . . . . . . 75
5.3.1 THE CRYSTALLOGRAPHIC PHASE PROBLEM . . . . . . . . . . . . . . . .
. . . 76
5.4 COMPARISON OF PROTEIN DETERGENT INTERACTIONS
IN SEVERAL MEMBRANE PROTEIN CRYSTALS . . . . . . . . . . . . . . . . . .
. . . . . . 78
5.4.1 REACTION CENTERS AND LIGHT HARVESTING COMPLEXES . . . . . . . 79
5.4.2 PORINS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . 80
5.5 CONCLUSIONS................................................ 82
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 82
6 HIGH-ANGLE NEUTRON FIBER DIFFRACTION
IN THE STUDY OF BIOLOGICAL SYSTEMS
V.T. FORSYTH, I.M. PARROT
.........................................
85
6.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . 85
6.2 FIBERS AND FIBER DIFFRACTION . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . 86
6.3 NEUTRON FIBER DIFFRACTION: GENERAL ISSUES . . . . . . . . . . . . .
. . . . . . . . . 87
6.4 FACILITIES FOR NEUTRON FIBER DIFFRACTION . . . . . . . . . . . . . .
. . . . . . . . . . 90
6.5 NUCLEICACIDS.............................................. 92
6.6 CELLULOSE .................................................. 98
6.7 CONCLUSIONSANDFUTUREPROSPECTS ............................100
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 103
7 NEUTRON SCATTERING FROM BIOMATERIALS
IN COMPLEX SAMPLE ENVIRONMENTS
J. KATSARAS, T.A. HARROUN, M.P. NIEH, M. CHAKRAPANI, M.J. WATSON,
V.A. RAGHUNATHAN
...............................................
107
7.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . 107
7.2 ALIGNMENT IN A MAGNETIC FIELD . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . 107
7.2.1 MAGNETIC ALIGNMENT OF LIPID BILAYERS . . . . . . . . . . . . . . .
. . . . 108
7.2.2 NEUTRON SCATTERING IN A MAGNETIC FIELD: OTHER EXAMPLES . . 111
7.3 HIGHPRESSURESTUDIES.......................................113
7.3.1 HYDROSTATIC PRESSURE AND ALIGNED LIPID BILAYERS . . . . . . . . .
114
XII CONTENTS
7.3.2 HIGH PRESSURE NEUTRON SCATTERING EXPERIMENTS:
OTHEREXAMPLES .....................................117
7.4 SHEAR FLOW INDUCED STRUCTURES
IN BIOLOGICALLY RELEVANT MATERIALS . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 118
7.4.1 SHEAR CELLS SUITABLE FOR NEUTRON SCATTERING . . . . . . . . . . .
. . . 118
7.4.2 SHEAR STUDIES OF BIOLOGICALLY RELEVANT SYSTEMS . . . . . . . . . .
. 119
7.5 COMPARISON OF A NEUTRON AND X-RAY SAMPLE ENVIRONMENT . . . . . . .
120
7.5.1 100% RELATIVE HUMIDITY SAMPLE CELLS . . . . . . . . . . . . . . .
. . . 120
7.6 CONCLUSIONS................................................121
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 122
8 SMALL-ANGLE NEUTRON SCATTERING
FROM BIOLOGICAL MOLECULES
J.K. KRUEGER, G.D. WIGNALL
.......................................
127
8.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . 127
8.1.1 WHY NEUTRON SCATTERING IS APPROPRIATE AND COMPARISON
WITH OTHER LOW-
Q
SCATTERING TECHNIQUES . . . . . . . . . . . . . . . . 127
8.1.2 COMPLEMENTARY ASPECTS OF LIGHT, SMALL-ANGLE NEUTRON
AND X-RAY SCATTERING FOR SOLUTION STUDIES . . . . . . . . . . . . . . .
130
8.2 ELEMENTS OF NEUTRON SCATTERING THEORY . . . . . . . . . . . . . . .
. . . . . . . . 131
8.2.1 COHERENT AND INCOHERENT CROSS-SECTIONS . . . . . . . . . . . . . .
. . . 131
8.2.2 SCATTERING LENGTH DENSITY . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 134
8.2.3 CONTRAST VARIATION . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 135
8.3 PRACTICAL ASPECTS OF SANS EXPERIMENTS AND DATA ANALYSIS . . . . . .
137
8.3.1 SANS INSTRUMENTATION . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 137
8.3.2 THE IMPORTANCE OF ABSOLUTE CALIBRATION
AND HAVING WELL-CHARACTERIZED SAMPLES . . . . . . . . . . . . . . . . .
140
8.3.3 INSTRUMENTAL RESOLUTION . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . 142
8.3.4 OTHER EXPERIMENTAL CONSIDERATIONS
AND POTENTIAL ARTIFACTS . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . 145
8.3.5 DATA ANALYSIS: EXTRACTING STRUCTURAL AND SHAPE
PARAMETERS FROM SANS DATA AND
P
(
R
) ANALYSIS..........146
8.4 SANS APPLICATION:
INVESTIGATING CONFORMATIONAL CHANGES
OFMYOSINLIGHTCHAINKINASE................................149
8.4.1 SOLVENT MATCHING OF A SPECIFICALLY DEUTERATED CAM
BOUND TO A SHORT PEPTIDE SEQUENCE . . . . . . . . . . . . . . . . . . .
. 149
8.4.2 CONTRAST VARIATION OF DEUTERATED CAM
BOUNDTOMLCKENZYME .............................150
8.4.3 MECHANISM OF THE CAM-ACTIVATION STEP:
SAXS/SANS STUDIES OF A (DEUTERATED) MUTANT CAM . . . . . 153
8.5 CONCLUSIONSANDOUTLOOK....................................155
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 157
CONTENTS XIII
9 SMALL ANGLE NEUTRON SCATTERING
FROM PROTEINS, NUCLEIC ACIDS, AND VIRUSES
S. KRUEGER, U.A. PEREZ-SALAS, S.K. GREGURICK, D. KUZMANOVIC
.........
161
9.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . 161
9.1.1 MODELING SANS DATA . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 162
9.1.2 CONTRAST VARIATION . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 164
9.1.3 EXPERIMENTAL EXAMPLES . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 165
9.2 NUCLEICACIDS:RNAFOLDING .................................165
9.2.1 COMPACTION OF A BACTERIAL GROUP I RIBOZYME . . . . . . . . . . . .
165
9.2.2 RNA COMPACTION AND HELICAL ASSEMBLY . . . . . . . . . . . . . . .
. . 170
9.3 PROTEIN COMPLEXES:
MULTISUBUNIT PROTEINS AND VIRUSES . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 172
9.3.1 CONFORMATION OF A POLYPEPTIDE SUBSTRATE
IN MODEL GROEL/GROES CHAPERONIN COMPLEXES . . . . . . . . . . 172
9.3.2 SPATIAL DISTRIBUTION AND MOLECULAR WEIGHT OF THE PROTEIN
AND RNA COMPONENTS OF BACTERIOPHAGE MS2 . . . . . . . . . . . . 178
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 184
10 STRUCTURE AND KINETICS OF PROTEINS OBSERVED
BY SMALL ANGLE NEUTRON SCATTERING
M.W. ROESSLE, R.P. MAY
..........................................
187
10.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 187
10.2 SOLUTION SCATTERING . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . 187
10.2.1 SPECIFIC ASPECTS OF NEUTRON SCATTERING . . . . . . . . . . . . .
. . . . . 189
10.3 TIME-RESOLVED EXPERIMENTS: DYNAMICS VS. STEADY STATE . . . . . . .
. . 189
10.3.1 PROTEIN MOTIONS AND KINETICS . . . . . . . . . . . . . . . . . .
. . . . . . . . 190
10.3.2 COOPERATIVE CONTROL OF PROTEIN ACTIVITY . . . . . . . . . . . . .
. . . . 191
10.4 PROTEIN KINETIC ANALYSIS
BY NEUTRON SCATTERING EXPERIMENTS . . . . . . . . . . . . . . . . . . .
. . . . . . . . 192
10.4.1 TRAPPING OF REACTION INTERMEDIATES:
THE (
**
)-THERMOSOME................................193
10.4.2 QUASI-STATIC ANALYSIS OF REACTION KINETICS*THE
SYMMETRIC GROES*GROEL*GROES COMPLEX . . . . . . . . . . . . . . 196
10.4.3 CHASING EXPERIMENTS (SLOW KINETICS) . . . . . . . . . . . . . . .
. . . . 199
10.4.4 TIME RESOLVED SMALL-ANGLE NEUTRON SCATTERING . . . . . . . . .
200
10.5 CONCLUSIONS AND OUTLOOK . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . 203
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 203
11 COMPLEX BIOLOGICAL STRUCTURES:
COLLAGEN AND BONE
P. FRATZL, O. PARIS
...............................................
205
11.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 205
11.2 COLLAGENOUS CONNECTIVE TISSUE . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 206
11.2.1 STRUCTURE AND DYNAMICS BY NEUTRON SCATTERING . . . . . . . . . .
206
XIV CONTENTS
11.2.2 ELASTIC AND VISCO-ELASTIC BEHAVIOR OF COLLAGEN
FROM IN SITU MECHANICAL EXPERIMENTS
WITH SYNCHROTRON RADIATION . . . . . . . . . . . . . . . . . . . . . . .
. . . . 208
11.3 BONE AND OTHER CALCIFIED TISSUE . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . 209
11.3.1 STRUCTURE OF MINERALIZED COLLAGEN * CONTRIBUTIONS FROM
NEUTRON SCATTERING . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . 209
11.3.2 INVESTIGATING THE HIERARCHICAL STRUCTURE OF BONE . . . . . . . .
. . 212
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 221
12 STRUCTURAL INVESTIGATIONS OF MEMBRANES
IN BIOLOGY BY NEUTRON REFLECTOMETRY
C.F. MAJKRZAK, N.F. BERK, S. KRUEGER, U.A. PEREZ*SALAS
.............
225
12.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 225
12.2 THEORY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . 227
12.2.1 THE EXACT (*DYNAMICAL*) SOLUTION . . . . . . . . . . . . . . . .
. . . . . 227
12.2.2 THE BORN APPROXIMATION . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . 232
12.2.3 MULTILAYERS . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . 233
12.2.4 SCALE OF SPATIAL RESOLUTION . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 235
12.3 BASIC EXPERIMENTAL METHODS . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . 236
12.3.1 INSTRUMENTAL CONFIGURATION . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 237
12.3.2 INSTRUMENTAL RESOLUTION
AND THE INTRINSIC COHERENCE LENGTHS OF THE NEUTRON . . . . . . 239
12.3.3 IN-PLANE AVERAGING . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . 243
12.3.4
Q
-RESOLUTION FOR SPECULAR REFLECTIVITY, ASSUMING
ANINCOHERENTBEAM ..................................244
12.3.5 MEASUREMENT OF THE REFLECTIVITY . . . . . . . . . . . . . . . . .
. . . . . . . 246
12.3.6 SAMPLE CELL DESIGNS . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 248
12.3.7 SOURCES OF BACKGROUND . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . 251
12.3.8 MULTILAYER SAMPLES: SECONDARY EXTINCTION AND MOSAIC . . . . 254
12.3.9 DATA COLLECTION STRATEGIES
FOR TIME-DEPENDENT PHENOMENA . . . . . . . . . . . . . . . . . . . . . .
. 254
12.4 PHASE DETERMINATION TECHNIQUES . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 255
12.4.1 REFERENCE FILMS . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . 255
12.4.2 SURROUND VARIATION . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . 257
12.4.3 REFINEMENT . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . 258
12.5 AN ILLUSTRATIVE EXAMPLE . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . 259
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 262
13 PROTEIN ADSORPTION AND INTERACTIONS AT INTERFACES
J.R. LU
.........................................................
265
13.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 265
13.2 NEUTRON REFLECTION AND CONCEPT
OF ISOTOPIC CONTRAST VARIATION . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 266
13.3 ADSORPTION OF OTHER PROTEINS AT THE AIR*WATER INTERFACE . . . . . .
. . 270
CONTENTS XV
13.4 ADSORPTION AT THE SOLID*WATER INTERFACE: THE EFFECT OF SURFACE
CHEMISTRY.................................................271
13.5 INTERACTION BETWEEN SURFACTANT AND PROTEIN . . . . . . . . . . . .
. . . . . . . . 277
13.6 FUTURE PROSPECTS . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . 280
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 280
14 COMPLEX BIOMIMETIC STRUCTURES AT FLUID SURFACES
AND SOLID*LIQUID INTERFACES
T. GUTBERLET, M. L¨OSCHE
..........................................
283
14.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 283
14.2 SURFACE-SENSITIVE SCATTERING . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . 284
14.2.1 SPECULAR REFLECTIVITY . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . 284
14.2.2 STRUCTURE-BASED MODEL REFINEMENT . . . . . . . . . . . . . . . .
. . . . . 287
14.3 FLOATING LIPID MONOLAYERS: STRUCTURAL INVESTIGATIONS AND THE
INTERACTION OF PEPTIDES AND PROTEINS WITH LIPID INTERFACES . . . . . . .
289
14.3.1 SINGLE PHOSPHOLIPID LMS . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 290
14.3.2 FUNCTIONALIZED PHOSPHOLIPID LMS . . . . . . . . . . . . . . . . .
. . . . . 291
14.4 LIPOPOLYMERS . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . 292
14.5 PROTEIN ADSORPTION AND STABILITY
AT FUNCTIONALIZED SOLID INTERFACES . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . 294
14.5.1 HYDROPHOBIC MODIFIED INTERFACES . . . . . . . . . . . . . . . . .
. . . . . . 294
14.5.2 HYDROPHILIC MODIFIED INTERFACES . . . . . . . . . . . . . . . . .
. . . . . . . 296
14.6 FUNCTIONALIZED LIPID INTERFACES
AND SUPPORTED LIPID BILAYERS . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . 297
14.6.1 SOLID-SUPPORTED PHOSPHOLIPID BILAYERS . . . . . . . . . . . . . .
. . . . 297
14.6.2 HYBRID BILAYER MEMBRANES . . . . . . . . . . . . . . . . . . . .
. . . . . . . . 299
14.6.3 POLYMER-SUPPORTED PHOSPHOLIPID BILAYERS . . . . . . . . . . . . .
. . 301
14.7 CONCLUSIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 302
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 302
PART II INELASTIC TECHNIQUES
15 QUASIELASTIC NEUTRON SCATTERING IN BIOLOGY, PART I:
METHODS
R.E. LECHNER, S. LONGEVILLE
.......................................
309
15.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 309
15.2 BASIC THEORY OF NEUTRON SCATTERING . . . . . . . . . . . . . . . .
. . . . . . . . . . . 311
15.2.1 VAN HOVE SCATTERING FUNCTIONS
AND CORRELATION FUNCTIONS . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . 313
15.2.2 THE ELASTIC INCOHERENT STRUCTURE FACTOR . . . . . . . . . . . . .
. . . . 316
15.2.3 EXPERIMENTAL ENERGY RESOLUTION . . . . . . . . . . . . . . . . .
. . . . . . 319
15.3 INSTRUMENTS FOR QENS SPECTROSCOPY IN (
Q
,*
)-SPACE . . . . . . . . . . . . 323
15.3.1 XTL*TOF SPECTROMETERS . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . 323
15.3.2 TOF*TOF SPECTROMETERS . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . 325
XVI CONTENTS
15.3.3 XTL*XTL SPECTROMETERS . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . 328
15.3.4 TOF*XTL SPECTROMETERS . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . 333
15.4 INSTRUMENTS FOR QENS SPECTROSCOPY IN (
Q
,T
)-SPACE . . . . . . . . . . . . . 335
15.4.1 NSE SPECTROMETERS . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 335
SPIN 1/2 AND LARMOR PRECESSION . . . . . . . . . . . . . . . . . . . . .
. . 336
THE NEUTRON SPIN-ECHO PRINCIPLE . . . . . . . . . . . . . . . . . . . .
. . 337
TRANSMISSION OF POLARIZERS AND ANALYZERS . . . . . . . . . . . . . . . .
339
GETTING A SPIN-ECHO, AS A MEASURE OF THE POLARIZATION . . . . 340
MEASURING QUASIELASTIC NEUTRON SCATTERING . . . . . . . . . . . . . .
342
15.4.2 NEUTRON RESONANCE SPIN-ECHO SPECTROMETRY . . . . . . . . . . . .
. 344
15.4.3 OBSERVATION FUNCTION, EFFECT OF WAVELENGTH DISTRIBUTION
ON SPIN-ECHO TIME . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . 346
15.5 MISCELLANEOUS TECHNICAL POINTS:
MSC, CALIBRATION, CONTRAST . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 348
15.6 CONCLUSIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 350
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 352
16 QUASIELASTIC NEUTRON SCATTERING IN BIOLOGY, PART II:
APPLICATIONS
R.E. LECHNER, S. LONGEVILLE
.......................................
355
16.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 355
16.2 DYNAMICAL MODELS . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . 356
16.2.1 DYNAMICAL-INDEPENDENCE APPROXIMATION . . . . . . . . . . . . . .
. . 356
16.3 THE GAUSSIAN APPROXIMATION . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . 357
16.3.1 SIMPLE TRANSLATIONAL DIFFUSION . . . . . . . . . . . . . . . . .
. . . . . . . . 358
16.3.2 THREE-DIMENSIONAL DIFFUSION OF PROTEIN MOLECULES
IN SOLUTION (CROWDED MEDIA) . . . . . . . . . . . . . . . . . . . . . .
. . . . 359
16.3.3 VIBRATIONAL MOTIONS, PHONON-EXPANSION AND
DEBYE*WALLER FACTOR (DWF), DYNAMIC SUSCEPTIBILITY . . . . . 361
16.3.4 VIBRATIONAL DENSITY OF STATES
OF THE LIGHT-HARVESTING COMPLEX II OF GREEN PLANTS . . . . . . 364
16.4 NON-GAUSSIAN MOTION . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . 367
16.4.1 ATOMIC JUMP MOTIONS DESCRIBED BY RATE EQUATIONS . . . . . . 368
16.4.2 CONFINED OR LOCALIZED DIFFUSIVE ATOMIC AND MOLECULAR
MOTIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . 370
16.4.3 ENVIRONMENT-DEPENDENCE
OF CONFINED DIFFUSIVE PROTEIN MOTIONS:
EXAMPLELYSOZYME...................................371
16.4.4 CHANGE OF PROTEIN DYNAMICS ON LIGAND BINDING:
EXAMPLE DIHYDROFOLATE REDUCTASE . . . . . . . . . . . . . . . . . . . .
. . 374
16.5 LOW-DIMENSIONAL SYSTEMS . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . 378
16.5.1 TWO-DIMENSIONAL LONG-RANGE DIFFUSION
OF ROTATING MOLECULES . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . 378
16.5.2 DYNAMICAL TRANSITION AND TEMPERATURE-DEPENDENT
HYDRATION: EXAMPLE PURPLE MEMBRANE . . . . . . . . . . . . . . . . . .
383
CONTENTS XVII
16.6 CONCLUSIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 389
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 392
17 CONFORMATIONAL DYNAMICS MEASURED
WITH PROTEINS IN SOLUTION
J. FITTER
........................................................
399
17.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 399
17.1.1 DYNAMICS IN PROTEINS:
TYPES OF MOTIONS AND THEIR BIOLOGICAL RELEVANCE . . . . . . . . . 400
17.2 SAMPLES IN NEUTRON SPECTROSCOPY:
SAMPLE PREPARATION, SAMPLE CHARACTERIZATION,
ANDSAMPLEENVIRONMENT....................................403
17.3 FROM SPECTRA TO RESULTS: DATA ACQUISITION, DATA ANALYSIS,
AND DATA INTERPRETATION . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . 405
17.4 APPLICATIONS AND EXAMPLES . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . 412
17.4.1 COMPARISON OF FOLDED AND UNFOLDED STATES . . . . . . . . . . . .
. . 412
17.4.2 CONFORMATIONAL ENTROPY CALCULATION FROM NEUTRON
SCATTERING DATA . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . 415
17.5 CONCLUSIONS AND OUTLOOK . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . 416
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 417
18 RELATING PROTEIN DYNAMICS TO FUNCTION AND STRUCTURE:
THE PURPLE MEMBRANE
U. LEHNERT, M. WEIK
.............................................
419
18.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 419
18.1.1 ELASTIC INCOHERENT NEUTRON SCATTERING . . . . . . . . . . . . . .
. . . . 420
18.2 METHODS OF INVESTIGATION . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . 421
18.2.1 ELASTIC INCOHERENT NEUTRON SCATTERING ON POWDER SAMPLES . 421
18.2.2 MODELS FOR DESCRIBING THERMAL PROTEIN DYNAMICS . . . . . . . .
421
18.2.3 H/D LABELING TECHNIQUES . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . 423
18.3 RELATING THERMAL MOTIONS IN PURPLE MEMBRANES
TO STRUCTURAL AND FUNCTIONAL CHARACTERISTICS
OFBACTERIORHODOPSIN........................................424
18.3.1 THERMAL MOTIONS IN BACTERIORHODOPSIN AND THE PURPLE
MEMBRANE ..........................................424
18.3.2 HYDRATION DEPENDENCE OF THERMAL MOTIONS . . . . . . . . . . . . .
. 426
18.3.3 LOCAL CORE MOTIONS . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 427
18.3.4 LIPID ENVIRONMENT . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 428
18.3.5 RELATION BETWEEN PM DYNAMICS
AND CRYSTALLOGRAPHIC B-FACTORS . . . . . . . . . . . . . . . . . . . . .
. . . . 429
18.3.6 COMPARISON OF FORCE CONSTANTS WITH FORCES MEASURED
BYAFM ............................................430
18.4 PROTEIN DYNAMICS AND FUNCTION IN SOME OTHER PROTEINS . . . . . . .
. . 431
18.5 CONCLUSIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 432
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 432
XVIII CONTENTS
19 BIOMOLECULAR SPECTROSCOPY
USING PULSED-SOURCE INSTRUMENTS
H.D. MIDDENDORF
.................................................
435
19.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 435
19.2 WHY PULSED SOURCES? . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . 435
19.3 PULSED SOURCE VS. REACTOR INSTRUMENTS . . . . . . . . . . . . . . .
. . . . . . . . . 437
19.4 BACKSCATTERING SPECTROMETERS . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . 439
19.4.1 HYDRATION DYNAMICS . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 440
19.4.2 LOW-TEMPERATURE DYNAMICS AND GLASS-LIKE TRANSITIONS . . . 441
19.4.3 ENZYME DYNAMICS AND FOLDING*UNFOLDING PROCESSES . . . . . . 443
19.5 INELASTIC SCATTERING
AT1MEV
*
1EV(8
*
8
,
000 CM
*
1
).................445
19.5.1 CHOPPER SPECTROMETERS . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 446
19.5.2 CRYSTAL-ANALYZER AND FILTER-DIFFERENCE SPECTROMETERS . . . . .
446
19.5.3 BUILDING BLOCKS AND MODEL COMPOUNDS . . . . . . . . . . . . . . .
. . 449
19.5.4 INTERPRETATIONAL ASPECTS . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . 451
19.5.5 PROTEINS AND BIOMATERIALS . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 451
19.5.6 BIOPOLYMERS . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . 453
19.5.7 NUCLEOTIDES AND NUCLEOSIDES . . . . . . . . . . . . . . . . . . .
. . . . . . . . 455
19.6 NEUTRON COMPTON SCATTERING (NCS) . . . . . . . . . . . . . . . . .
. . . . . . . . . 456
19.7 CONCLUSIONS AND OUTLOOK . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . 457
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 458
20 BROWNIAN OSCILLATOR ANALYSIS OF MOLECULAR
MOTIONS IN BIOMOLECULES
W. DOSTER
......................................................
461
20.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 461
20.2 DYNAMICS OF PROTEIN*SOLVENT INTERACTIONS . . . . . . . . . . . . .
. . . . . . . . 461
20.3 PROPERTIES OF THE INTERMEDIATE SCATTERING FUNCTION . . . . . . . .
. . . . . 463
20.4 RELEVANT TIME AND SPATIAL SCALES . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . 467
20.5 THE BROWNIAN OSCILLATOR AS A MODEL
OF PROTEIN-RESIDUE MOTION . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . 467
20.6 THE VISCO-ELASTIC BROWNIAN OSCILLATOR . . . . . . . . . . . . . . .
. . . . . . . . . 470
20.7 MOMENT ANALYSIS OF HYDRATION WATER DISPLACEMENTS . . . . . . . . .
. . . 474
20.8 ANALYSIS OF PROTEIN DISPLACEMENTS . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 476
20.9 DATA ANALYSIS . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . 479
20.10 CONCLUSIONS . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . 481
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 482
21 INTERNAL DYNAMICS OF PROTEINS AND DNA:
ANALOGY TO GLASS-FORMING SYSTEMS
A.P. SOKOLOV, R.B. GREGORY
.......................................
485
21.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 485
21.2 ANALYSIS OF RELAXATION SPECTRA:
SUSCEPTIBILITY PRESENTATION VS. DYNAMIC STRUCTURE FACTOR . . . . . . . .
486
CONTENTS XIX
21.3 SLOW RELAXATION PROCESS . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . 487
21.4 THE NATURE OF THE DYNAMICAL TRANSITION IN PROTEINS AND DNA . . .
492
21.5 FAST PICOSECOND RELAXATION . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . 496
21.6 CONCLUSIONS AND FUTURE PROSPECTS . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 498
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 500
22 STRUCTURE AND DYNAMICS OF MODEL MEMBRANE SYSTEMS
PROBED BY ELASTIC AND INELASTIC NEUTRON SCATTERING
T. SALDITT, M.C. RHEINST¨ADTER
......................................
503
22.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 503
22.2 SAMPLE PREPARATION AND SAMPLE ENVIRONMENT . . . . . . . . . . . . .
. . . . . 504
22.3 SPECULAR NEUTRON REFLECTIVITY . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . 506
22.4 NONSPECULAR NEUTRON REFLECTIVITY . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 510
22.4.1 MODELS OF BILAYER UNDULATIONS . . . . . . . . . . . . . . . . . .
. . . . . . . 512
22.4.2 MONOCHROMATIC NSNR EXPERIMENTS . . . . . . . . . . . . . . . . .
. . . 513
22.4.3 WHITE-BEAM NSNR EXPERIMENTS . . . . . . . . . . . . . . . . . . .
. . . . 514
22.4.4 CHANGE OF FLUCTUATIONS
BY ADDED ANTIMICROBIAL PEPTIDES . . . . . . . . . . . . . . . . . . . .
. . 516
22.5 ELASTIC AND INELASTIC STUDIES
OF THE ACYL CHAIN CORRELATION PEAK . . . . . . . . . . . . . . . . . . .
. . . . . . . . 518
22.5.1 INELASTIC NEUTRON SCATTERING . . . . . . . . . . . . . . . . . .
. . . . . . . . . 518
22.5.2 ELASTIC NEUTRON SCATTERING . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 521
22.5.3 COLLECTIVE DYNAMICS . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 523
22.6 CONCLUSIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 526
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 528
23 SUBNANOSECOND DYNAMICS OF PROTEINS IN SOLUTION:
MD SIMULATIONS AND INELASTIC NEUTRON SCATTERING
M. TAREK, D.J. TOBIAS
............................................
531
23.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 531
23.2 MD SIMULATIONS . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . 534
23.2.1 SYSTEMS SET-UP AND SIMULATIONS . . . . . . . . . . . . . . . . .
. . . . . . . 536
23.2.2 GENERATING NEUTRON SPECTRA . . . . . . . . . . . . . . . . . . .
. . . . . . . . 537
23.3 OVERALL PROTEIN STRUCTURE AND MOTION IN SOLUTION . . . . . . . . .
. . . . . 539
23.3.1 INTERNAL PROTEIN DYNAMICS . . . . . . . . . . . . . . . . . . . .
. . . . . . . . 543
23.3.2 DYNAMICS OF PROTEINS IN SOLUTION FROM MD SIMULATIONS . . . 544
23.4 CONCLUSIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 546
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 547
INDEX
..........................................................549
|
| adam_txt |
CONTENTS
1 NEUTRON SCATTERING FOR BIOLOGY
T.A. HARROUN, G.D. WIGNALL, J. KATSARAS
.
1
1.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . 1
1.2 PRODUCTION OF NEUTRONS . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . 2
1.3 ELEMENTS OF NEUTRON SCATTERING THEORY . . . . . . . . . . . . . . .
. . . . . . . . 5
1.3.1 PROPERTIES OF NEUTRONS . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . 5
1.3.2 ENERGY AND MOMENTUM TRANSFER . . . . . . . . . . . . . . . . . . .
. . . . 5
1.3.3 DIFFRACTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . 6
1.3.4 SCATTERING LENGTH AND CROSS-SECTION . . . . . . . . . . . . . . .
. . . . . 7
1.3.5 COHERENT AND INCOHERENT CROSS-SECTIONS . . . . . . . . . . . . . .
. . . 8
1.4 NEUTRON DIFFRACTION AND CONTRAST . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 10
1.4.1 CONTRAST AND STRUCTURE . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 11
1.4.2 CONTRAST AND DYNAMICS . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 13
1.4.3 CONTRAST AND BIOLOGY . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . 13
1.5 CONCLUSIONS. 16
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 17
PART I ELASTIC TECHNIQUES
2 SINGLE CRYSTAL NEUTRON DIFFRACTION
AND PROTEIN CRYSTALLOGRAPHY
C.C. WILSON, D.A. MYLES
.
21
2.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . 21
2.2 SINGLE CRYSTAL NEUTRON DIFFRACTOMETERS:
BASICPRINCIPLES. 22
2.2.1 DEVELOPMENT OF SINGLE CRYSTAL NEUTRON DIFFRACTOMETERS . . . 25
2.2.2 ACHIEVEMENTS OF NEUTRON MACROMOLECULAR
CRYSTALLOGRAPHY AT REACTOR SOURCES . . . . . . . . . . . . . . . . . . .
. . 25
2.2.3 DEVELOPMENTS AT SPALLATION SOURCES . . . . . . . . . . . . . . . .
. . . . 28
XC
O
N
T
E
N
T
S
2.2.4 FORWARD 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
2.3.3 SAMPLE AND DATA REQUIREMENTS
FOR SINGLE CRYSTAL NEUTRON DIFFRACTION . . . . . . . . . . . . . . . . .
. 34
2.4 BRIEF REVIEW OF THE USE OF NEUTRON DIFFRACTION
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
3.2.2 HYDROGEN ATOMS WHICH CANNOT BE PREDICTED
STEREOCHEMICALLY . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 45
3.3 HYDROGENBONDING . 50
3.3.1 WEAK AND STRONG HYDROGEN BONDING . . . . . . . . . . . . . . . . .
. . 50
3.3.2 BIFURCATED HYDROGEN BONDS . . . . . . . . . . . . . . . . . . . .
. . . . . . . 51
3.4 H/DEXCHANGE. 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 CONCLUSIONSANDFUTUREPROSPECTS . 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
CONTENTS XI
4.3 REALIZING A COMPLETE STRUCTURE:
THE COMPLEMENTARY ROLES OF X-RAY
AND NEUTRON PROTEIN CRYSTALLOGRAPHY . . . . . . . . . . . . . . . . . .
. . . . . . . 65
4.4 CRYO-NEUTRON PROTEIN CRYSTALLOGRAPHY . . . . . . . . . . . . . . . .
. . . . . . . . 66
4.5 CURRENT TECHNIQUE, SOURCE,
ANDAPPARATUSDEVELOPMENTS. 67
4.6 PLANSFORTHEESSANDNPX. 69
4.7 CONCLUSIONSANDFUTUREPROSPECTS . 69
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 72
5 DETERGENT BINDING IN MEMBRANE PROTEIN CRYSTALS
BY NEUTRON CRYSTALLOGRAPHY
P. TIMMINS
.
73
5.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . 73
5.2 ADVANTAGES OF NEUTRONS . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . 73
5.3 INSTRUMENTATION AND DATA REDUCTION . . . . . . . . . . . . . . . . .
. . . . . . . . 75
5.3.1 THE CRYSTALLOGRAPHIC PHASE PROBLEM . . . . . . . . . . . . . . . .
. . . 76
5.4 COMPARISON OF PROTEIN DETERGENT INTERACTIONS
IN SEVERAL MEMBRANE PROTEIN CRYSTALS . . . . . . . . . . . . . . . . . .
. . . . . . 78
5.4.1 REACTION CENTERS AND LIGHT HARVESTING COMPLEXES . . . . . . . 79
5.4.2 PORINS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . 80
5.5 CONCLUSIONS. 82
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 82
6 HIGH-ANGLE NEUTRON FIBER DIFFRACTION
IN THE STUDY OF BIOLOGICAL SYSTEMS
V.T. FORSYTH, I.M. PARROT
.
85
6.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . 85
6.2 FIBERS AND FIBER DIFFRACTION . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . 86
6.3 NEUTRON FIBER DIFFRACTION: GENERAL ISSUES . . . . . . . . . . . . .
. . . . . . . . . 87
6.4 FACILITIES FOR NEUTRON FIBER DIFFRACTION . . . . . . . . . . . . . .
. . . . . . . . . . 90
6.5 NUCLEICACIDS. 92
6.6 CELLULOSE . 98
6.7 CONCLUSIONSANDFUTUREPROSPECTS .100
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 103
7 NEUTRON SCATTERING FROM BIOMATERIALS
IN COMPLEX SAMPLE ENVIRONMENTS
J. KATSARAS, T.A. HARROUN, M.P. NIEH, M. CHAKRAPANI, M.J. WATSON,
V.A. RAGHUNATHAN
.
107
7.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . 107
7.2 ALIGNMENT IN A MAGNETIC FIELD . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . 107
7.2.1 MAGNETIC ALIGNMENT OF LIPID BILAYERS . . . . . . . . . . . . . . .
. . . . 108
7.2.2 NEUTRON SCATTERING IN A MAGNETIC FIELD: OTHER EXAMPLES . . 111
7.3 HIGHPRESSURESTUDIES.113
7.3.1 HYDROSTATIC PRESSURE AND ALIGNED LIPID BILAYERS . . . . . . . . .
114
XII CONTENTS
7.3.2 HIGH PRESSURE NEUTRON SCATTERING EXPERIMENTS:
OTHEREXAMPLES .117
7.4 SHEAR FLOW INDUCED STRUCTURES
IN BIOLOGICALLY RELEVANT MATERIALS . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 118
7.4.1 SHEAR CELLS SUITABLE FOR NEUTRON SCATTERING . . . . . . . . . . .
. . . 118
7.4.2 SHEAR STUDIES OF BIOLOGICALLY RELEVANT SYSTEMS . . . . . . . . . .
. 119
7.5 COMPARISON OF A NEUTRON AND X-RAY SAMPLE ENVIRONMENT . . . . . . .
120
7.5.1 100% RELATIVE HUMIDITY SAMPLE CELLS . . . . . . . . . . . . . . .
. . . 120
7.6 CONCLUSIONS.121
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 122
8 SMALL-ANGLE NEUTRON SCATTERING
FROM BIOLOGICAL MOLECULES
J.K. KRUEGER, G.D. WIGNALL
.
127
8.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . 127
8.1.1 WHY NEUTRON SCATTERING IS APPROPRIATE AND COMPARISON
WITH OTHER LOW-
Q
SCATTERING TECHNIQUES . . . . . . . . . . . . . . . . 127
8.1.2 COMPLEMENTARY ASPECTS OF LIGHT, SMALL-ANGLE NEUTRON
AND X-RAY SCATTERING FOR SOLUTION STUDIES . . . . . . . . . . . . . . .
130
8.2 ELEMENTS OF NEUTRON SCATTERING THEORY . . . . . . . . . . . . . . .
. . . . . . . . 131
8.2.1 COHERENT AND INCOHERENT CROSS-SECTIONS . . . . . . . . . . . . . .
. . . 131
8.2.2 SCATTERING LENGTH DENSITY . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 134
8.2.3 CONTRAST VARIATION . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 135
8.3 PRACTICAL ASPECTS OF SANS EXPERIMENTS AND DATA ANALYSIS . . . . . .
137
8.3.1 SANS INSTRUMENTATION . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 137
8.3.2 THE IMPORTANCE OF ABSOLUTE CALIBRATION
AND HAVING WELL-CHARACTERIZED SAMPLES . . . . . . . . . . . . . . . . .
140
8.3.3 INSTRUMENTAL RESOLUTION . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . 142
8.3.4 OTHER EXPERIMENTAL CONSIDERATIONS
AND POTENTIAL ARTIFACTS . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . 145
8.3.5 DATA ANALYSIS: EXTRACTING STRUCTURAL AND SHAPE
PARAMETERS FROM SANS DATA AND
P
(
R
) ANALYSIS.146
8.4 SANS APPLICATION:
INVESTIGATING CONFORMATIONAL CHANGES
OFMYOSINLIGHTCHAINKINASE.149
8.4.1 SOLVENT MATCHING OF A SPECIFICALLY DEUTERATED CAM
BOUND TO A SHORT PEPTIDE SEQUENCE . . . . . . . . . . . . . . . . . . .
. 149
8.4.2 CONTRAST VARIATION OF DEUTERATED CAM
BOUNDTOMLCKENZYME .150
8.4.3 MECHANISM OF THE CAM-ACTIVATION STEP:
SAXS/SANS STUDIES OF A (DEUTERATED) MUTANT CAM . . . . . 153
8.5 CONCLUSIONSANDOUTLOOK.155
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 157
CONTENTS XIII
9 SMALL ANGLE NEUTRON SCATTERING
FROM PROTEINS, NUCLEIC ACIDS, AND VIRUSES
S. KRUEGER, U.A. PEREZ-SALAS, S.K. GREGURICK, D. KUZMANOVIC
.
161
9.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . 161
9.1.1 MODELING SANS DATA . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 162
9.1.2 CONTRAST VARIATION . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 164
9.1.3 EXPERIMENTAL EXAMPLES . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 165
9.2 NUCLEICACIDS:RNAFOLDING .165
9.2.1 COMPACTION OF A BACTERIAL GROUP I RIBOZYME . . . . . . . . . . . .
165
9.2.2 RNA COMPACTION AND HELICAL ASSEMBLY . . . . . . . . . . . . . . .
. . 170
9.3 PROTEIN COMPLEXES:
MULTISUBUNIT PROTEINS AND VIRUSES . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 172
9.3.1 CONFORMATION OF A POLYPEPTIDE SUBSTRATE
IN MODEL GROEL/GROES CHAPERONIN COMPLEXES . . . . . . . . . . 172
9.3.2 SPATIAL DISTRIBUTION AND MOLECULAR WEIGHT OF THE PROTEIN
AND RNA COMPONENTS OF BACTERIOPHAGE MS2 . . . . . . . . . . . . 178
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 184
10 STRUCTURE AND KINETICS OF PROTEINS OBSERVED
BY SMALL ANGLE NEUTRON SCATTERING
M.W. ROESSLE, R.P. MAY
.
187
10.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 187
10.2 SOLUTION SCATTERING . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . 187
10.2.1 SPECIFIC ASPECTS OF NEUTRON SCATTERING . . . . . . . . . . . . .
. . . . . 189
10.3 TIME-RESOLVED EXPERIMENTS: DYNAMICS VS. STEADY STATE . . . . . . .
. . 189
10.3.1 PROTEIN MOTIONS AND KINETICS . . . . . . . . . . . . . . . . . .
. . . . . . . . 190
10.3.2 COOPERATIVE CONTROL OF PROTEIN ACTIVITY . . . . . . . . . . . . .
. . . . 191
10.4 PROTEIN KINETIC ANALYSIS
BY NEUTRON SCATTERING EXPERIMENTS . . . . . . . . . . . . . . . . . . .
. . . . . . . . 192
10.4.1 TRAPPING OF REACTION INTERMEDIATES:
THE (
**
)-THERMOSOME.193
10.4.2 QUASI-STATIC ANALYSIS OF REACTION KINETICS*THE
SYMMETRIC GROES*GROEL*GROES COMPLEX . . . . . . . . . . . . . . 196
10.4.3 CHASING EXPERIMENTS (SLOW KINETICS) . . . . . . . . . . . . . . .
. . . . 199
10.4.4 TIME RESOLVED SMALL-ANGLE NEUTRON SCATTERING . . . . . . . . .
200
10.5 CONCLUSIONS AND OUTLOOK . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . 203
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 203
11 COMPLEX BIOLOGICAL STRUCTURES:
COLLAGEN AND BONE
P. FRATZL, O. PARIS
.
205
11.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 205
11.2 COLLAGENOUS CONNECTIVE TISSUE . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 206
11.2.1 STRUCTURE AND DYNAMICS BY NEUTRON SCATTERING . . . . . . . . . .
206
XIV CONTENTS
11.2.2 ELASTIC AND VISCO-ELASTIC BEHAVIOR OF COLLAGEN
FROM IN SITU MECHANICAL EXPERIMENTS
WITH SYNCHROTRON RADIATION . . . . . . . . . . . . . . . . . . . . . . .
. . . . 208
11.3 BONE AND OTHER CALCIFIED TISSUE . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . 209
11.3.1 STRUCTURE OF MINERALIZED COLLAGEN * CONTRIBUTIONS FROM
NEUTRON SCATTERING . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . 209
11.3.2 INVESTIGATING THE HIERARCHICAL STRUCTURE OF BONE . . . . . . . .
. . 212
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 221
12 STRUCTURAL INVESTIGATIONS OF MEMBRANES
IN BIOLOGY BY NEUTRON REFLECTOMETRY
C.F. MAJKRZAK, N.F. BERK, S. KRUEGER, U.A. PEREZ*SALAS
.
225
12.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 225
12.2 THEORY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . 227
12.2.1 THE EXACT (*DYNAMICAL*) SOLUTION . . . . . . . . . . . . . . . .
. . . . . 227
12.2.2 THE BORN APPROXIMATION . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . 232
12.2.3 MULTILAYERS . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . 233
12.2.4 SCALE OF SPATIAL RESOLUTION . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 235
12.3 BASIC EXPERIMENTAL METHODS . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . 236
12.3.1 INSTRUMENTAL CONFIGURATION . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 237
12.3.2 INSTRUMENTAL RESOLUTION
AND THE INTRINSIC COHERENCE LENGTHS OF THE NEUTRON . . . . . . 239
12.3.3 IN-PLANE AVERAGING . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . 243
12.3.4
Q
-RESOLUTION FOR SPECULAR REFLECTIVITY, ASSUMING
ANINCOHERENTBEAM .244
12.3.5 MEASUREMENT OF THE REFLECTIVITY . . . . . . . . . . . . . . . . .
. . . . . . . 246
12.3.6 SAMPLE CELL DESIGNS . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 248
12.3.7 SOURCES OF BACKGROUND . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . 251
12.3.8 MULTILAYER SAMPLES: SECONDARY EXTINCTION AND MOSAIC . . . . 254
12.3.9 DATA COLLECTION STRATEGIES
FOR TIME-DEPENDENT PHENOMENA . . . . . . . . . . . . . . . . . . . . . .
. 254
12.4 PHASE DETERMINATION TECHNIQUES . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 255
12.4.1 REFERENCE FILMS . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . 255
12.4.2 SURROUND VARIATION . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . 257
12.4.3 REFINEMENT . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . 258
12.5 AN ILLUSTRATIVE EXAMPLE . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . 259
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 262
13 PROTEIN ADSORPTION AND INTERACTIONS AT INTERFACES
J.R. LU
.
265
13.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 265
13.2 NEUTRON REFLECTION AND CONCEPT
OF ISOTOPIC CONTRAST VARIATION . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 266
13.3 ADSORPTION OF OTHER PROTEINS AT THE AIR*WATER INTERFACE . . . . . .
. . 270
CONTENTS XV
13.4 ADSORPTION AT THE SOLID*WATER INTERFACE: THE EFFECT OF SURFACE
CHEMISTRY.271
13.5 INTERACTION BETWEEN SURFACTANT AND PROTEIN . . . . . . . . . . . .
. . . . . . . . 277
13.6 FUTURE PROSPECTS . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . 280
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 280
14 COMPLEX BIOMIMETIC STRUCTURES AT FLUID SURFACES
AND SOLID*LIQUID INTERFACES
T. GUTBERLET, M. L¨OSCHE
.
283
14.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 283
14.2 SURFACE-SENSITIVE SCATTERING . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . 284
14.2.1 SPECULAR REFLECTIVITY . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . 284
14.2.2 STRUCTURE-BASED MODEL REFINEMENT . . . . . . . . . . . . . . . .
. . . . . 287
14.3 FLOATING LIPID MONOLAYERS: STRUCTURAL INVESTIGATIONS AND THE
INTERACTION OF PEPTIDES AND PROTEINS WITH LIPID INTERFACES . . . . . . .
289
14.3.1 SINGLE PHOSPHOLIPID LMS . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 290
14.3.2 FUNCTIONALIZED PHOSPHOLIPID LMS . . . . . . . . . . . . . . . . .
. . . . . 291
14.4 LIPOPOLYMERS . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . 292
14.5 PROTEIN ADSORPTION AND STABILITY
AT FUNCTIONALIZED SOLID INTERFACES . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . 294
14.5.1 HYDROPHOBIC MODIFIED INTERFACES . . . . . . . . . . . . . . . . .
. . . . . . 294
14.5.2 HYDROPHILIC MODIFIED INTERFACES . . . . . . . . . . . . . . . . .
. . . . . . . 296
14.6 FUNCTIONALIZED LIPID INTERFACES
AND SUPPORTED LIPID BILAYERS . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . 297
14.6.1 SOLID-SUPPORTED PHOSPHOLIPID BILAYERS . . . . . . . . . . . . . .
. . . . 297
14.6.2 HYBRID BILAYER MEMBRANES . . . . . . . . . . . . . . . . . . . .
. . . . . . . . 299
14.6.3 POLYMER-SUPPORTED PHOSPHOLIPID BILAYERS . . . . . . . . . . . . .
. . 301
14.7 CONCLUSIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 302
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 302
PART II INELASTIC TECHNIQUES
15 QUASIELASTIC NEUTRON SCATTERING IN BIOLOGY, PART I:
METHODS
R.E. LECHNER, S. LONGEVILLE
.
309
15.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 309
15.2 BASIC THEORY OF NEUTRON SCATTERING . . . . . . . . . . . . . . . .
. . . . . . . . . . . 311
15.2.1 VAN HOVE SCATTERING FUNCTIONS
AND CORRELATION FUNCTIONS . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . 313
15.2.2 THE ELASTIC INCOHERENT STRUCTURE FACTOR . . . . . . . . . . . . .
. . . . 316
15.2.3 EXPERIMENTAL ENERGY RESOLUTION . . . . . . . . . . . . . . . . .
. . . . . . 319
15.3 INSTRUMENTS FOR QENS SPECTROSCOPY IN (
Q
,*
)-SPACE . . . . . . . . . . . . 323
15.3.1 XTL*TOF SPECTROMETERS . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . 323
15.3.2 TOF*TOF SPECTROMETERS . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . 325
XVI CONTENTS
15.3.3 XTL*XTL SPECTROMETERS . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . 328
15.3.4 TOF*XTL SPECTROMETERS . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . 333
15.4 INSTRUMENTS FOR QENS SPECTROSCOPY IN (
Q
,T
)-SPACE . . . . . . . . . . . . . 335
15.4.1 NSE SPECTROMETERS . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 335
SPIN 1/2 AND LARMOR PRECESSION . . . . . . . . . . . . . . . . . . . . .
. . 336
THE NEUTRON SPIN-ECHO PRINCIPLE . . . . . . . . . . . . . . . . . . . .
. . 337
TRANSMISSION OF POLARIZERS AND ANALYZERS . . . . . . . . . . . . . . . .
339
GETTING A SPIN-ECHO, AS A MEASURE OF THE POLARIZATION . . . . 340
MEASURING QUASIELASTIC NEUTRON SCATTERING . . . . . . . . . . . . . .
342
15.4.2 NEUTRON RESONANCE SPIN-ECHO SPECTROMETRY . . . . . . . . . . . .
. 344
15.4.3 OBSERVATION FUNCTION, EFFECT OF WAVELENGTH DISTRIBUTION
ON SPIN-ECHO TIME . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . 346
15.5 MISCELLANEOUS TECHNICAL POINTS:
MSC, CALIBRATION, CONTRAST . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 348
15.6 CONCLUSIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 350
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 352
16 QUASIELASTIC NEUTRON SCATTERING IN BIOLOGY, PART II:
APPLICATIONS
R.E. LECHNER, S. LONGEVILLE
.
355
16.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 355
16.2 DYNAMICAL MODELS . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . 356
16.2.1 DYNAMICAL-INDEPENDENCE APPROXIMATION . . . . . . . . . . . . . .
. . 356
16.3 THE GAUSSIAN APPROXIMATION . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . 357
16.3.1 SIMPLE TRANSLATIONAL DIFFUSION . . . . . . . . . . . . . . . . .
. . . . . . . . 358
16.3.2 THREE-DIMENSIONAL DIFFUSION OF PROTEIN MOLECULES
IN SOLUTION (CROWDED MEDIA) . . . . . . . . . . . . . . . . . . . . . .
. . . . 359
16.3.3 VIBRATIONAL MOTIONS, PHONON-EXPANSION AND
DEBYE*WALLER FACTOR (DWF), DYNAMIC SUSCEPTIBILITY . . . . . 361
16.3.4 VIBRATIONAL DENSITY OF STATES
OF THE LIGHT-HARVESTING COMPLEX II OF GREEN PLANTS . . . . . . 364
16.4 NON-GAUSSIAN MOTION . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . 367
16.4.1 ATOMIC JUMP MOTIONS DESCRIBED BY RATE EQUATIONS . . . . . . 368
16.4.2 CONFINED OR LOCALIZED DIFFUSIVE ATOMIC AND MOLECULAR
MOTIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . 370
16.4.3 ENVIRONMENT-DEPENDENCE
OF CONFINED DIFFUSIVE PROTEIN MOTIONS:
EXAMPLELYSOZYME.371
16.4.4 CHANGE OF PROTEIN DYNAMICS ON LIGAND BINDING:
EXAMPLE DIHYDROFOLATE REDUCTASE . . . . . . . . . . . . . . . . . . . .
. . 374
16.5 LOW-DIMENSIONAL SYSTEMS . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . 378
16.5.1 TWO-DIMENSIONAL LONG-RANGE DIFFUSION
OF ROTATING MOLECULES . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . 378
16.5.2 DYNAMICAL TRANSITION AND TEMPERATURE-DEPENDENT
HYDRATION: EXAMPLE PURPLE MEMBRANE . . . . . . . . . . . . . . . . . .
383
CONTENTS XVII
16.6 CONCLUSIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 389
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 392
17 CONFORMATIONAL DYNAMICS MEASURED
WITH PROTEINS IN SOLUTION
J. FITTER
.
399
17.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 399
17.1.1 DYNAMICS IN PROTEINS:
TYPES OF MOTIONS AND THEIR BIOLOGICAL RELEVANCE . . . . . . . . . 400
17.2 SAMPLES IN NEUTRON SPECTROSCOPY:
SAMPLE PREPARATION, SAMPLE CHARACTERIZATION,
ANDSAMPLEENVIRONMENT.403
17.3 FROM SPECTRA TO RESULTS: DATA ACQUISITION, DATA ANALYSIS,
AND DATA INTERPRETATION . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . 405
17.4 APPLICATIONS AND EXAMPLES . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . 412
17.4.1 COMPARISON OF FOLDED AND UNFOLDED STATES . . . . . . . . . . . .
. . 412
17.4.2 CONFORMATIONAL ENTROPY CALCULATION FROM NEUTRON
SCATTERING DATA . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . 415
17.5 CONCLUSIONS AND OUTLOOK . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . 416
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 417
18 RELATING PROTEIN DYNAMICS TO FUNCTION AND STRUCTURE:
THE PURPLE MEMBRANE
U. LEHNERT, M. WEIK
.
419
18.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 419
18.1.1 ELASTIC INCOHERENT NEUTRON SCATTERING . . . . . . . . . . . . . .
. . . . 420
18.2 METHODS OF INVESTIGATION . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . 421
18.2.1 ELASTIC INCOHERENT NEUTRON SCATTERING ON POWDER SAMPLES . 421
18.2.2 MODELS FOR DESCRIBING THERMAL PROTEIN DYNAMICS . . . . . . . .
421
18.2.3 H/D LABELING TECHNIQUES . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . 423
18.3 RELATING THERMAL MOTIONS IN PURPLE MEMBRANES
TO STRUCTURAL AND FUNCTIONAL CHARACTERISTICS
OFBACTERIORHODOPSIN.424
18.3.1 THERMAL MOTIONS IN BACTERIORHODOPSIN AND THE PURPLE
MEMBRANE .424
18.3.2 HYDRATION DEPENDENCE OF THERMAL MOTIONS . . . . . . . . . . . . .
. 426
18.3.3 LOCAL CORE MOTIONS . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 427
18.3.4 LIPID ENVIRONMENT . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 428
18.3.5 RELATION BETWEEN PM DYNAMICS
AND CRYSTALLOGRAPHIC B-FACTORS . . . . . . . . . . . . . . . . . . . . .
. . . . 429
18.3.6 COMPARISON OF FORCE CONSTANTS WITH FORCES MEASURED
BYAFM .430
18.4 PROTEIN DYNAMICS AND FUNCTION IN SOME OTHER PROTEINS . . . . . . .
. . 431
18.5 CONCLUSIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 432
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 432
XVIII CONTENTS
19 BIOMOLECULAR SPECTROSCOPY
USING PULSED-SOURCE INSTRUMENTS
H.D. MIDDENDORF
.
435
19.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 435
19.2 WHY PULSED SOURCES? . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . 435
19.3 PULSED SOURCE VS. REACTOR INSTRUMENTS . . . . . . . . . . . . . . .
. . . . . . . . . 437
19.4 BACKSCATTERING SPECTROMETERS . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . 439
19.4.1 HYDRATION DYNAMICS . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 440
19.4.2 LOW-TEMPERATURE DYNAMICS AND GLASS-LIKE TRANSITIONS . . . 441
19.4.3 ENZYME DYNAMICS AND FOLDING*UNFOLDING PROCESSES . . . . . . 443
19.5 INELASTIC SCATTERING
AT1MEV
*
1EV(8
*
8
,
000 CM
*
1
).445
19.5.1 CHOPPER SPECTROMETERS . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 446
19.5.2 CRYSTAL-ANALYZER AND FILTER-DIFFERENCE SPECTROMETERS . . . . .
446
19.5.3 BUILDING BLOCKS AND MODEL COMPOUNDS . . . . . . . . . . . . . . .
. . 449
19.5.4 INTERPRETATIONAL ASPECTS . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . 451
19.5.5 PROTEINS AND BIOMATERIALS . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 451
19.5.6 BIOPOLYMERS . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . 453
19.5.7 NUCLEOTIDES AND NUCLEOSIDES . . . . . . . . . . . . . . . . . . .
. . . . . . . . 455
19.6 NEUTRON COMPTON SCATTERING (NCS) . . . . . . . . . . . . . . . . .
. . . . . . . . . 456
19.7 CONCLUSIONS AND OUTLOOK . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . 457
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 458
20 BROWNIAN OSCILLATOR ANALYSIS OF MOLECULAR
MOTIONS IN BIOMOLECULES
W. DOSTER
.
461
20.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 461
20.2 DYNAMICS OF PROTEIN*SOLVENT INTERACTIONS . . . . . . . . . . . . .
. . . . . . . . 461
20.3 PROPERTIES OF THE INTERMEDIATE SCATTERING FUNCTION . . . . . . . .
. . . . . 463
20.4 RELEVANT TIME AND SPATIAL SCALES . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . 467
20.5 THE BROWNIAN OSCILLATOR AS A MODEL
OF PROTEIN-RESIDUE MOTION . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . 467
20.6 THE VISCO-ELASTIC BROWNIAN OSCILLATOR . . . . . . . . . . . . . . .
. . . . . . . . . 470
20.7 MOMENT ANALYSIS OF HYDRATION WATER DISPLACEMENTS . . . . . . . . .
. . . 474
20.8 ANALYSIS OF PROTEIN DISPLACEMENTS . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 476
20.9 DATA ANALYSIS . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . 479
20.10 CONCLUSIONS . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . 481
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 482
21 INTERNAL DYNAMICS OF PROTEINS AND DNA:
ANALOGY TO GLASS-FORMING SYSTEMS
A.P. SOKOLOV, R.B. GREGORY
.
485
21.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 485
21.2 ANALYSIS OF RELAXATION SPECTRA:
SUSCEPTIBILITY PRESENTATION VS. DYNAMIC STRUCTURE FACTOR . . . . . . . .
486
CONTENTS XIX
21.3 SLOW RELAXATION PROCESS . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . 487
21.4 THE NATURE OF THE DYNAMICAL TRANSITION IN PROTEINS AND DNA . . .
492
21.5 FAST PICOSECOND RELAXATION . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . 496
21.6 CONCLUSIONS AND FUTURE PROSPECTS . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 498
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 500
22 STRUCTURE AND DYNAMICS OF MODEL MEMBRANE SYSTEMS
PROBED BY ELASTIC AND INELASTIC NEUTRON SCATTERING
T. SALDITT, M.C. RHEINST¨ADTER
.
503
22.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 503
22.2 SAMPLE PREPARATION AND SAMPLE ENVIRONMENT . . . . . . . . . . . . .
. . . . . 504
22.3 SPECULAR NEUTRON REFLECTIVITY . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . 506
22.4 NONSPECULAR NEUTRON REFLECTIVITY . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 510
22.4.1 MODELS OF BILAYER UNDULATIONS . . . . . . . . . . . . . . . . . .
. . . . . . . 512
22.4.2 MONOCHROMATIC NSNR EXPERIMENTS . . . . . . . . . . . . . . . . .
. . . 513
22.4.3 WHITE-BEAM NSNR EXPERIMENTS . . . . . . . . . . . . . . . . . . .
. . . . 514
22.4.4 CHANGE OF FLUCTUATIONS
BY ADDED ANTIMICROBIAL PEPTIDES . . . . . . . . . . . . . . . . . . . .
. . 516
22.5 ELASTIC AND INELASTIC STUDIES
OF THE ACYL CHAIN CORRELATION PEAK . . . . . . . . . . . . . . . . . . .
. . . . . . . . 518
22.5.1 INELASTIC NEUTRON SCATTERING . . . . . . . . . . . . . . . . . .
. . . . . . . . . 518
22.5.2 ELASTIC NEUTRON SCATTERING . . . . . . . . . . . . . . . . . . .
. . . . . . . . . 521
22.5.3 COLLECTIVE DYNAMICS . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . 523
22.6 CONCLUSIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 526
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 528
23 SUBNANOSECOND DYNAMICS OF PROTEINS IN SOLUTION:
MD SIMULATIONS AND INELASTIC NEUTRON SCATTERING
M. TAREK, D.J. TOBIAS
.
531
23.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 531
23.2 MD SIMULATIONS . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . 534
23.2.1 SYSTEMS SET-UP AND SIMULATIONS . . . . . . . . . . . . . . . . .
. . . . . . . 536
23.2.2 GENERATING NEUTRON SPECTRA . . . . . . . . . . . . . . . . . . .
. . . . . . . . 537
23.3 OVERALL PROTEIN STRUCTURE AND MOTION IN SOLUTION . . . . . . . . .
. . . . . 539
23.3.1 INTERNAL PROTEIN DYNAMICS . . . . . . . . . . . . . . . . . . . .
. . . . . . . . 543
23.3.2 DYNAMICS OF PROTEINS IN SOLUTION FROM MD SIMULATIONS . . . 544
23.4 CONCLUSIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . 546
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . 547
INDEX
.549 |
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| index_date | 2024-07-02T13:59:29Z |
| indexdate | 2024-07-09T20:35:39Z |
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| language | English |
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| spelling | Neutron scattering in biology techniques and applications Jörg Fitter ... (eds.) Berlin [u.a.] Springer 2006 XXIV, 557 S. Ill., graph. Darst. 235 mm x 155 mm txt rdacontent n rdamedia nc rdacarrier Biological and medical physics, biomedical engineering Biophysique ram Neutrons - Diffusion Neutrons - Diffusion ram Spectroscopie moléculaire ram Neutron Diffraction methods Neutrons Scattering Biologie (DE-588)4006851-1 gnd rswk-swf Neutronenstreuung (DE-588)4041980-0 gnd rswk-swf Biochemie (DE-588)4006777-4 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Biologie (DE-588)4006851-1 s Neutronenstreuung (DE-588)4041980-0 s DE-604 Biochemie (DE-588)4006777-4 s Fitter, Jörg Sonstige oth text/html http://deposit.dnb.de/cgi-bin/dokserv?id=2687013&prov=M&dok_var=1&dok_ext=htm Inhaltstext DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014643382&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Neutron scattering in biology techniques and applications Biophysique ram Neutrons - Diffusion Neutrons - Diffusion ram Spectroscopie moléculaire ram Neutron Diffraction methods Neutrons Scattering Biologie (DE-588)4006851-1 gnd Neutronenstreuung (DE-588)4041980-0 gnd Biochemie (DE-588)4006777-4 gnd |
| subject_GND | (DE-588)4006851-1 (DE-588)4041980-0 (DE-588)4006777-4 (DE-588)4143413-4 |
| title | Neutron scattering in biology techniques and applications |
| title_auth | Neutron scattering in biology techniques and applications |
| title_exact_search | Neutron scattering in biology techniques and applications |
| title_exact_search_txtP | Neutron scattering in biology techniques and applications |
| title_full | Neutron scattering in biology techniques and applications Jörg Fitter ... (eds.) |
| title_fullStr | Neutron scattering in biology techniques and applications Jörg Fitter ... (eds.) |
| title_full_unstemmed | Neutron scattering in biology techniques and applications Jörg Fitter ... (eds.) |
| title_short | Neutron scattering in biology |
| title_sort | neutron scattering in biology techniques and applications |
| title_sub | techniques and applications |
| topic | Biophysique ram Neutrons - Diffusion Neutrons - Diffusion ram Spectroscopie moléculaire ram Neutron Diffraction methods Neutrons Scattering Biologie (DE-588)4006851-1 gnd Neutronenstreuung (DE-588)4041980-0 gnd Biochemie (DE-588)4006777-4 gnd |
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