Methods in nano cell biology /

Contributors p. xiii
Preface p. xvii
1 Extracellular Dynamics at nm Resolution in Live Cells Bhanu P. Jena
I Introduction p. 2
II Materials and Methods p. 3
III Conclusion p. 16
References p. 17
2 Intracellular Organelle Dynamics at nm Resolution Bhanu P. Jena
I Introduction p. 20
II Materials and Methods p. 20
III Discussion p. 24
References p. 36
3 Atomic Force Microscopy as a Tool to Study the Proteasome Assemblies Maria Gaczynska and Pawel A. Osmulski
I Introduction p. 40
II Rationale p. 44
III Methods p. 45
IV Discussion p. 56
V Summary p. 59
References p. 59
4 Biomineralization at the Nanoscale: Learning from Diatoms David P. Allison and Yves F. Dufrene and Mitchel J. Doktycz and Mark Hildebrand
I Introduction to Nanotechnology p. 62
II Introduction to Diatoms p. 65
III Investigating Diatom Mesoscale Silica Formation p. 67
IV Nanoscale Imaging of Living Diatoms p. 69
V Nanoscale Elasticity Measurements p. 71
VI Examination of Diatom Valves p. 75
VII Examination of Diatom Girdle Bands p. 78
VIII Examination of Diatom Setae p. 80
IX Future Directions p. 81
References p. 83
5 Quantitative Phase Imaging of Nanoscale Cell Structure and Dynamics Gabriel Popescu
I Introduction and Rationale p. 88
II Methods p. 88
III Applications of QPI p. 97
IV Summary and Outlook p. 108
References p. 110
6 Fourier Imaging Correlation Spectroscopy for Cellular Structure-Function Eric N. Senning and Geoffrey A. Lott and Andrew H. Marcus
I Introduction and Background p. 118
II Theoretical Descriptions of FICS p. 119
III FICS Optical Layout p. 127
IV Examples of FICS Applications p. 129
V Conclusions p. 136
References p. 136
7 Nanobiology of the Primary Cilium-Paradigm of a Multifunctional Nanomachine Complex Denys N. Wheatley
I Introduction p. 140
II Self-Assembly p. 141
III Ciliogenesis p. 141
IV Elucidating the Functional Role of Primary Cilia p. 151
V The Medical Consequences of Aciliogenesis-A Veritable Pandora's Box p. 153
VI Concluding Remarks p. 153
References p. 154
8 Assembly and Disassembly of SNAREs in Membrane Fusion Bhanu P. Jena
I Introduction p. 158
II Materials and Methods p. 161
III Discussion p. 164
References p. 181
9 Understanding Membrane Fusion: Combining Experimental and Simulation Studies Bhanu P. Jena
I Introduction p. 184
II Materials and Methods p. 185
III Discussion p. 186
References p. 197
10 Structure and Dynamics of Metalloproteins in Live Cells Jeremy D. Cook and James E. Penner-Hahn and Timothy L. Stemmler
I Introduction p. 200
II Rationale p. 201
III Methods p. 202
IV Materials p. 205
V Discussion p. 207
VI Summary p. 214
References p. 214
11 Light-Activated Ion Channels for Remote Control of Neural Activity James J. Chambers and Richard H. Kramer
I Introduction p. 218
II Discussion p. 221
III Methods p. 230
IV Conclusion p. 231
References p. 231
12 Molecular Modeling and Simulation Studies of Ion Channel Structures, Dynamics and Mechanisms Kaihsu Tai and Philip Fowler and Younes Mokrab and Phillip Stansfeld and Mark S.P. Sansom
I Introduction p. 234
II Homology-Based Structure Prediction of Transmembrane Proteins p. 234
III PB Profiles for the Energetics of an Ion in a Channel p. 241
IV MD Simulations p. 245
V Free Energy Methods p. 251
VI Summary p. 259
References p. 260
13 Nano-Scale Imaging and Dynamics of Amylin-Membrane Interactions and Its Implication in Type II Diabetes Mellitus Won-Jin Cho and Bhanu P. Jena and Aleksandar M. Jeremic
I Introduction p. 268
II Materials and Methods p. 270
III Results and Discussion p. 272
IV Summary p. 282
References p. 284
14 Real Time Investigation of Protein Folding, Structure, and Dynamics in Living Cells Qianqian Li and Yuefei Huang and Nan Xiao and Victoria Murray and Jianglei Chen and Jianjun Wang
I Introduction p. 288
II Rationale p. 294
III Methods and Materials p. 295
IV Summary p. 322
References p. 323
15 Structural Basis of Human High-density Lipoprotein Formation and Assembly at Sub nanometer Resolution Arun Sivashanmugam and Yunhuang Yang and Victoria Murray and Christopher McCullough and Bin Chen and Xuefeng Ren and Qianqian Li and Jianjun Wang
I Introduction p. 328
II Rationale p. 332
III Methods and Materials p. 333
IV Discussion p. 354
V Summary p. 359
References p. 360
16 Nano-scale Characterization of the Dynamics of the Chloroplast Toc Translocon L. Evan Reddick and Prakitchai Chotewutmontri and Will Crenshaw and Ashita Dave and Michael Vaughn and Barry D. Bruce
I Introduction p. 367
II In organeller Chloroplast Import and Binding Assays p. 370
III Toc Translocon Dynamics p. 377
IV Activity and Enzymology of Toc GTPases p. 384
V Molecular Modeling of Toc Proteins p. 391
VI Conclusions and Perspectives p. 392
References p. 396
17 A System Biology Approach to Understand Functional Activity of Cell Communication Systems Julio Vera and Olaf Wolkenhauer
I Introduction p. 400
II Methods p. 401
III Materials p. 404
IV Discussion p. 412
References p. 413
18 THz Investigations of Condensed Phase Biomolecular Systems Hailiang Zhang and Karen Siegrist and Kevin O. Douglas and Susan K. Gregurick and David F. Plusquellic
I Introduction p. 418
II Instrumentation p. 420
III Theory p. 422
IV Dipeptides Nanotubes p. 423
References p. 432
19 Combined Single-Molecule Electrical Recording and Single-Molecule Spectroscopy Studies of Ion Channel Conformational Dynamics H. Peter Lu
I Introduction p. 436
II Development of Simultaneous Single-Molecule Fluorescence Spectroscopy and Patch-Clamp Electrical Recordings p. 437
III Summary and Prospects p. 446
References p. 449
Index p. 453
Volumes in Series p. 465