406 Index
Protein unfolding, AFM studies (continued )
single-parameter model, 325–327
sorting data, 321
Protomers, bacterial pore unzipping, 287
Q
QPD, see Quadrant photodiode
Quadrant photodiode, PFM studies, 203–204
R
Recording mode photonic force microscopy
contact mode, 208–209
fast 3D single-particle tracking, 210
tapping mode, 209–210
Resolution, PFM studies, 207–208
RL cells, adhesion force measurements, 100–104
S
Salt, SFM of supercoiled DNA, 385–388
SATP, see
N-Succinnimidyl-3-(S-acetylthio)propionate
Scanning force microscopy
DNA
AC modes, 367
covalent, anchoring, 365–366
electron microscope legacy, 359
fragment ablation, 379
mobility modulation and solution dynamics,
371–374
molecular motion, 374–376
organic solvents, humidity issue, 366–367
protein interactions, 376–377
protein and ligand interactions, 368–369

secondary structure, 369–370
sharper probes, 367–368
single-molecule dissection, 377–379
single-molecule stretching, 388
solid-state sizing, 370
ss-DNA structure, 388
supercoiled, salt and surface effects, 385–388
water and buffers, 370–371
DNA curvature and flexibility
basic approaches, 380–384
ergodicity, 384–385
scanning forces, 54–56
Scanning nearfield optical microscopy, 4
Scanning tunneling microscopy
bacteriophage T5, 4–7
instrumentation and function, 2
liquid crystals, 6
Sensory cells, live, AFM studies, 38
SFM, see Scanning force microscopy
SGLT1, see Na
+
/D-glucose cotransporter
Silane, treatment of DNA on mica, 360–361
Single-molecule force, 292
Single-particle tracking, fast 3D, PFM studies, 210
Single-stranded DNA, SFM studies, 388
Small unilamellar vesicles, fusion, AFM studies,
232–234
SNOM, see Scanning nearfield optical microscopy
Soft samples, AFM force curves, 70

Solid-state sizing, SFM of DNA, 370
Solutions, DNA
adsorption, charged molecule role, 364
mica, dehydration, 360
SFM studies, 371–374
Spectrin, AFM studies, 313
Staphylococcal α-hemolysin, AFM studies, 270
Stereocilia, 144–146
STM, see Scanning tunneling microscopy
Strain, induced, AFM calculations, 181–182
Streptavidin–biotin unbinding, AFM studies,
306–307
Structural biology, cryo-AFM
individual molecules, 248–250
large assembly surface details, 250–252
Substrates, AFM studies, 215
N-Succinnimidyl-3-(S-acetylthio)propionate, AFM
tips, 119
Supported lipid bilayers, AFM studies
Langmuir trough, 234–235
Langmuir trough and small Teflon wells,
235–236
small vesicle fusion, 232–234
Surface chemistry, AFM studies
basic studies, 215
cleaning, 117–118
crosslinker binding, 119
esterification, 118
large assemblies, cryo-AFM studies, 250–252
ligand binding, 119

ligand density and functionality, 119–120
probe surfaces, 120–121
Surfaces
SFM of supercoiled DNA, 385–388
treatments for DNA adsorption, 365
SUVs, see Small unilamellar vesicles
T
Tapping mode atomic force microscopy
basic operation, 35
Index 407
benefits, 338–339
overview, 261–263
Tapping recording mode photonic force microscopy,
209–210
TDFM, see Transverse dynamic force microscopy
Teflon, small wells, AFM studies, 235–236
TEM, see Transmission electron microscopy
Thermodynamics
equilibrium, DNA on mica, 363–364
vascular endothelial cadherin, 129–130
Transduction channel, OHC, gating, 161–165
Transient fusion, depressions, AFM studies, 43–47
trans-interaction force, vascular endothelial
cadherin, 127–128
Transmission electron microscopy
bacteriophage T5, STM comparison, 6–7
transient fusions at depressions, 46
Transverse dynamic force microscopy
application, 353–354
overview, 352–353

Transverse dynamic force spectroscopy
application, 353–354
overview, 351–353
U
Unbinding force, ligand–receptor recognition
distribution, 123
dynamic force microscopy, 124–125
force–distance cycle, 121–123
V
Vascular endothelial cells, cadherin, dynamic force
microscopy
binding strength, 128–129
Ca
2+
dependence, 127–128
conformation, 126
overview, 125–126
thermodynamics and structural parameters,
129–130
trans association, 127–128
VE cells, see Vascular endothelial cells
VIP receptor, mapping on osteoclasts, 184
Viscosity, local, PFM studies, 28–29
Voltage-sensitive ion channels, AFM–path–clamp
combination, 12–13
W
Water, SFM of DNA, 370–371
WLC, see Worm-like chain model
Worm-like chain model, protein folding, 17
Y

Yeast cells, AFM studies, 38
Z
z-range scanner, AFM, 177
Zymogen granules, AFM studies, 39
This Page Intentionally Left Blank
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